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A

ABOUT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
ABOUT_DIALOG_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
ABOUT_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
AboutDialog - Class in ca.corefacility.gview.map.gui.dialog
Creates the about dialog.
AboutDialog(JFrame) - Constructor for class ca.corefacility.gview.map.gui.dialog.AboutDialog
Create the dialog.
AboutMenuItem - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating the "About" menu item.
AboutMenuItem(GViewGUIFrame) - Constructor for class ca.corefacility.gview.map.gui.menu.AboutMenuItem
 
AbstractAllEffectRenderer - Class in ca.corefacility.gview.map.effects
 
AbstractAllEffectRenderer() - Constructor for class ca.corefacility.gview.map.effects.AbstractAllEffectRenderer
 
AbstractArrowShapeRealizer - Class in ca.corefacility.gview.layout.feature
An abstract class containing common code for making arrow shapes.
AbstractArrowShapeRealizer(double) - Constructor for class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Constructs an arrow shape realizer with the arrow head taking up the passed length.
AbstractArrowShapeRealizer() - Constructor for class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Constructs an arrow shape realizer with the default arrow length.
AbstractBackbone - Class in ca.corefacility.gview.layout.sequence
 
AbstractBackbone(LocationConverter) - Constructor for class ca.corefacility.gview.layout.sequence.AbstractBackbone
 
AbstractBackboneShapeItem - Class in ca.corefacility.gview.map.items
 
AbstractBackboneShapeItem() - Constructor for class ca.corefacility.gview.map.items.AbstractBackboneShapeItem
 
AbstractBackboneTextItem - Class in ca.corefacility.gview.map.items
 
AbstractBackboneTextItem(Backbone, SequencePoint) - Constructor for class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
AbstractBackboneTextItem(String) - Constructor for class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
AbstractDescendentCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
AbstractDescendentCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.AbstractDescendentCoder
 
AbstractFileFormatReader - Class in ca.corefacility.gview.data.readers
 
AbstractFileFormatReader() - Constructor for class ca.corefacility.gview.data.readers.AbstractFileFormatReader
 
AbstractSequencePath - Class in ca.corefacility.gview.layout.sequence
 
AbstractSequencePath(Backbone) - Constructor for class ca.corefacility.gview.layout.sequence.AbstractSequencePath
Creates a new SequencePath around the passed data.
AbstractShapeItem - Class in ca.corefacility.gview.map.items
 
AbstractShapeItem() - Constructor for class ca.corefacility.gview.map.items.AbstractShapeItem
 
AbstractSlotRegion - Class in ca.corefacility.gview.layout.sequence
 
AbstractSlotRegion(Backbone, SlotTranslator) - Constructor for class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
accept(Feature) - Method in class ca.corefacility.gview.data.readers.cgview.CGViewSetFeatureFilter
 
accept(File) - Method in class ca.corefacility.gview.map.gui.open.GFFFilter
 
accept(File) - Method in class ca.corefacility.gview.map.gui.open.SequenceDataFilter
 
accept(File) - Method in class ca.corefacility.gview.map.gui.open.StyleDataFilter
 
accept(PNode) - Method in class ca.corefacility.gview.map.items.MapItemFilter
 
accept(Feature) - Method in class ca.corefacility.gview.utils.AndFilter
 
accept(Feature) - Method in class ca.corefacility.gview.utils.AnnotationValueContains
 
accept(Feature) - Method in class ca.corefacility.gview.utils.SequenceNameFilter
 
accept(File) - Method in class ca.corefacility.gview.writers.ImageWriterFilter
 
acceptChildrenOf(PNode) - Method in class ca.corefacility.gview.map.items.MapItemFilter
 
acceptsExtension(String) - Static method in class ca.corefacility.gview.writers.ImageWriterFactory
Determines if we can construct an ImageWriter with the passed extension.
acceptsFile(File) - Static method in class ca.corefacility.gview.writers.ImageWriterFactory
Checks if the passed file can be saved to (format is correct).
acceptsFileFormat(String) - Static method in class ca.corefacility.gview.writers.ImageWriterPNG
 
ACCESSION_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
Action - Class in ca.corefacility.gview.map.gui.action
The abstract action class.
Action() - Constructor for class ca.corefacility.gview.map.gui.action.Action
 
Action.ActionRunException - Exception in ca.corefacility.gview.map.gui.action
 
Action.ActionRunException(String) - Constructor for exception ca.corefacility.gview.map.gui.action.Action.ActionRunException
 
Action.ActionRunException(Throwable) - Constructor for exception ca.corefacility.gview.map.gui.action.Action.ActionRunException
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.AboutDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.MoveDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.ScaleDialog
Listens for the buttons.
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.SliderDialog
Listens for the buttons being pressed.
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.StyleDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.dialog.ZoomDialog
Listens for the buttons.
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.menu.FileMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.menu.HelpMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.menu.SelectionMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.menu.SlotDetailMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.menu.ViewMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.BackbonePanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.GlobalPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperChooserDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.RulerPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.TooltipPanel
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.SlotSelectionDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.StyleColoredButton
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorToolBar
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTreeComboBox
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.StyleMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.editor.TreeRightClickMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.GViewToolBar
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.AboutMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.BackboneStyleMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.BEVMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.ExitMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.ExportMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.FitMapToScreenMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.GlobalStyleMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.LayoutMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.MoveMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.OpenMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.QualityMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.RulerStyleMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.ScaleMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.StyleEditorMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.StyleMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.TooltipStyleMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.ViewerUsageMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.WebsiteMenuItem
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.menu.ZoomMenu
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.gui.open.OpenDialog
 
actionPerformed(ActionEvent) - Method in class ca.corefacility.gview.map.inputHandler.PopupInputEventHandler
 
add(MutableTreeNode) - Method in class ca.corefacility.gview.map.gui.editor.node.SlotsNode
 
add(MutableTreeNode) - Method in class ca.corefacility.gview.map.gui.editor.node.StyleEditorNode
 
add(MapComponent) - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
add(MapComponent) - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
add(MapComponent) - Method in class ca.corefacility.gview.map.items.FeatureItemsCache
 
add(MapComponent) - Method in class ca.corefacility.gview.map.items.Layer
 
add(MapComponent) - Method in interface ca.corefacility.gview.map.items.MapComponent
Adds a new MapComponent to this component.
add(MapComponent) - Method in class ca.corefacility.gview.map.items.OptimizedLayer
 
add(MapComponent) - Method in class ca.corefacility.gview.map.items.TextItemImp
 
add(FeatureFilter) - Method in class ca.corefacility.gview.utils.AndFilter
 
add(Collection<FeatureFilter>) - Method in class ca.corefacility.gview.utils.AndFilter
 
addAnnotation(String) - Method in class ca.corefacility.gview.map.gui.editor.AnnotationComboBox
Adds an annotation in sorted order.
addAnnotationValue(String, String, double) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Annotation
 
addEdit(UndoableEdit) - Method in class ca.corefacility.gview.map.gui.action.Action
 
addEffect(ShapeEffectRenderer) - Method in class ca.corefacility.gview.map.effects.CompositeEffect
 
addElement(PropertyMapperListItem) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperList
Adds the passed element to the list.
addElement(int, PropertyMapperListItem) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperList
Adds the passed element to the list.
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
Event Subject
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.layout.sequence.AbstractBackbone
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.managers.LayoutManager
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.managers.SectionManager
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.managers.StyleEventManager
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.managers.ZoomEventDistributor
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.map.controllers.GUIController
Adds a GViewEventListener to the GUI controller.
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.map.event.DisplayChangeListener
 
addEventListener(GViewEventListener) - Method in interface ca.corefacility.gview.map.event.GViewEventSubject
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.map.event.GViewEventSubjectImp
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.map.gui.GViewMapManager
Adds a GViewEventListener to the GViewMap.
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.map.GViewMapImp
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.map.inputHandler.PanEventHandler
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.style.datastyle.DataStyle
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.style.GlobalStyle
 
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.style.items.BackboneStyle
Event methods
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.style.items.RulerStyle
Event methods
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.style.items.TooltipStyle
Event methods
addEventListener(GViewEventListener) - Method in class ca.corefacility.gview.style.MapStyle
 
addFeature(Feature) - Method in class ca.corefacility.gview.data.readers.cgview.CGViewSetFeatureFilter
 
addFilterCoder(Class<? extends FeatureFilter>, FeatureFilterCoder) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoderMap
Adds a new FilterFeatureCoder to this list of coders.
addGUIEventBroadcaster(GUIEventBroadcaster) - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
Adds a GUIEvent broadcaster to this panel.
addInputEventListener(PInputEventListener) - Method in class ca.corefacility.gview.map.gui.GViewMapManager
Adds an InputEventListener to the GViewMap, specifically to the map's camera object.
addItem(Object) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTreeComboBox
 
addLabel(Label, LabelRank) - Method in class ca.corefacility.gview.managers.labels.LabelsStore
 
addLabelBoundsTo(SequenceLabelBounds, int) - Method in class ca.corefacility.gview.managers.labels.LabelSlotBounds
 
addLegendItem(LegendItemStyle) - Method in class ca.corefacility.gview.style.items.LegendStyle
 
addLegendStyle(LegendStyle) - Method in class ca.corefacility.gview.style.GlobalStyle
 
addLinkListener(LinkListener) - Method in class ca.corefacility.gview.map.controllers.link.LinkController
Adds a link listener.
addMapToPanel(JPanel) - Method in class ca.corefacility.gview.map.gui.GViewMapManager
Adds the GViewMap to the passed panel.
addNotifier(ProgressNotifier) - Static method in class ca.corefacility.gview.utils.ProgressHandler
Adds the passed notifier to the list of notifiers.
addPaint(Paint) - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
 
addPoint(int, double) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Points
 
addPropertyMapper(PropertyMapperListItem) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperPanel
Adds the list item property mapper to the list.
addRange(int, int, double) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
Adds a range to this plot.
addRange(int, int, double) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Range
Adds a range to this plot.
addStyle(Style) - Method in class ca.corefacility.gview.map.controllers.GUIController
Adds a new style and automatically makes it the active style.
addStyleItem(SlotItemStyle) - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
addToBucket(LabelPosition, int) - Method in class ca.corefacility.gview.managers.labels.LabelBuckets
Adds the passed LabelPosition to the bucket with the passed value.
alignLegend(Rectangle2D, boolean) - Method in class ca.corefacility.gview.map.items.LegendItem
Aligns this legend item within the display bounds.
ALIGNMENT_MAP_ALIGN_TO_STRINGS - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
ALIGNMENT_MAP_STRINGS_TO_ALIGN - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
AlignmentHandler - Class in ca.corefacility.gview.style.io.gss
 
AlignmentHandler() - Constructor for class ca.corefacility.gview.style.io.gss.AlignmentHandler
 
AllCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
 
AllCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.AllCoder
 
AllLabelRanker - Class in ca.corefacility.gview.managers.labels
 
AllLabelRanker() - Constructor for class ca.corefacility.gview.managers.labels.AllLabelRanker
 
allLabels - Variable in class ca.corefacility.gview.managers.labels.LabelsManager
 
AndCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
 
AndCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.AndCoder
 
AndFilter - Class in ca.corefacility.gview.utils
 
AndFilter() - Constructor for class ca.corefacility.gview.utils.AndFilter
 
AndFilter(FeatureFilter, FeatureFilter) - Constructor for class ca.corefacility.gview.utils.AndFilter
 
AndFilter(Collection<FeatureFilter>) - Constructor for class ca.corefacility.gview.utils.AndFilter
 
ANNOTATION - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
AnnotationComboBox - Class in ca.corefacility.gview.map.gui.editor
A customized combo box for displaying annotations.
AnnotationComboBox(GenomeDataController) - Constructor for class ca.corefacility.gview.map.gui.editor.AnnotationComboBox
 
AnnotationExtractor - Class in ca.corefacility.gview.textextractor
Extracts an arbitrary annotation from a feature.
AnnotationExtractor(String) - Constructor for class ca.corefacility.gview.textextractor.AnnotationExtractor
 
AnnotationMapper - Class in ca.corefacility.gview.style.datastyle.mapper
 
AnnotationMapper(String, String[]) - Constructor for class ca.corefacility.gview.style.datastyle.mapper.AnnotationMapper
 
AnnotationValueContains - Class in ca.corefacility.gview.utils
Used to filter features who's annotation's value contains a substring of the passed string TODO find another package for this
AnnotationValueContains(String, String) - Constructor for class ca.corefacility.gview.utils.AnnotationValueContains
 
AnnotationValueContainsCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
 
AnnotationValueContainsCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueContainsCoder
 
AnnotationValueContainsPanel - Class in ca.corefacility.gview.map.gui.editor.featureFilter
 
AnnotationValueContainsPanel(GenomeDataController) - Constructor for class ca.corefacility.gview.map.gui.editor.featureFilter.AnnotationValueContainsPanel
Create the panel.
AnnotationValueEqualsCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
 
AnnotationValueEqualsCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueEqualsCoder
 
AnnotationValueEqualsPanel - Class in ca.corefacility.gview.map.gui.editor.featureFilter
 
AnnotationValueEqualsPanel(GenomeDataController) - Constructor for class ca.corefacility.gview.map.gui.editor.featureFilter.AnnotationValueEqualsPanel
Create the panel.
appendFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
appendName(String) - Static method in class ca.corefacility.gview.map.gui.editor.StyleNameManager
Appends a suffix to the name (only if required) to ensure uniqueness.
appendSegment(StretchableSegment) - Method in class ca.corefacility.gview.layout.prototype.NonFragmentingStretchableShape
Appends the passed segment onto this shape prototype.
appendSegment(StretchableSegment) - Method in class ca.corefacility.gview.layout.prototype.StretchableShape
Appends the passed segment onto this shape prototype.
appendWithScale(Path2D, Backbone) - Method in class ca.corefacility.gview.layout.prototype.segments.StretchableSegment
Appends this StretchableSegment to the passed path.
apply() - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
Applies the panel's properties to the appropriate style.
APPLY_CHANGES - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
applyCurrentStyle() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorFrame
Applies the changes to the current style.
applyDefaults(LegendItemStyle) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
Applies the default styling attributes as appropriate.
applyDefaults(LegendStyle) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
Applies the default styling attributes as appropriate.
ApplyStyleAction - Class in ca.corefacility.gview.map.gui.action.style
 
ApplyStyleAction(GUIController) - Constructor for class ca.corefacility.gview.map.gui.action.style.ApplyStyleAction
 
Arc2DPrecision - Class in ca.corefacility.gview.utils.geom
Defines an Arc2D class which can adjust the precision of the curves used to approximate it.
Arc2DPrecision(int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision
This is an abstract class that cannot be instantiated directly.
Arc2DPrecision.Double - Class in ca.corefacility.gview.utils.geom
This class defines an arc specified in double precision.
Arc2DPrecision.Double() - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Constructs a new OPEN arc, initialized to location (0, 0), size (0, 0), angular extents (start = 0, extent = 0).
Arc2DPrecision.Double(int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Constructs a new arc, initialized to location (0, 0), size (0, 0), angular extents (start = 0, extent = 0), and the specified closure type.
Arc2DPrecision.Double(double, double, double, double, double, double, int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Constructs a new arc, initialized to the specified location, size, angular extents, and closure type.
Arc2DPrecision.Double(Rectangle2D, double, double, int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Constructs a new arc, initialized to the specified location, size, angular extents, and closure type.
Arc2DPrecision.Float - Class in ca.corefacility.gview.utils.geom
This class defines an arc specified in float precision.
Arc2DPrecision.Float() - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Constructs a new OPEN arc, initialized to location (0, 0), size (0, 0), angular extents (start = 0, extent = 0).
Arc2DPrecision.Float(int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Constructs a new arc, initialized to location (0, 0), size (0, 0), angular extents (start = 0, extent = 0), and the specified closure type.
Arc2DPrecision.Float(float, float, float, float, float, float, int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Constructs a new arc, initialized to the specified location, size, angular extents, and closure type.
Arc2DPrecision.Float(Rectangle2D, float, float, int) - Constructor for class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Constructs a new arc, initialized to the specified location, size, angular extents, and closure type.
ARROW_LENGTH - Variable in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
 
AUTHORS_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
AUTO_POPULATE_COG_CATEGORIES - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
autoPopulateCogsToColors() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperPanel
Automatically fills the list with any missing COG categories with default colours if possible.
autoScale() - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
Automatically sets scaling of points so that max point is at top of slot, min is at bottom of slot.
autoScale() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
Automatically sets scaling of points so that max point is at top of slot, min is at bottom of slot.
autoScale() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderPoints
 
autoScale() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
Automatically sets scaling of points so that max point is at top of slot, min is at bottom of slot.
autoscale - Variable in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
autoScale(boolean) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
Turns on/off autoscaling.
autoScaleCenter() - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
Automatically sets scaling of points so that the largest value on either side of the center point is the highest point above and below the line
autoScaleCenter() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
autoScaleCenter() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderPoints
 
autoScaleCenter() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
AverageCalculator - Class in ca.corefacility.gview.utils.content
 
AverageCalculator(GenomeData, Set<Symbol>, int, int) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator
Creates a new AverageCalculator around the passed genomic data, with the passed properties.
AverageCalculator(GenomeData, Set<Symbol>) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator
Creates a new AverageCalculator around the passed genomic data, with the passed properties.
AverageCalculator(GenomeData, boolean, Set<Symbol>, int, int) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator
Creates a new AverageCalculator around the passed genomic data, with the passed properties.
AverageCalculator(GenomeData, boolean, Set<Symbol>) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator
Creates a new AverageCalculator around the passed genomic data, with the passed properties.
AverageCalculator.GC - Class in ca.corefacility.gview.utils.content
Sets up AverageCalculator to perform GC content calculations.
AverageCalculator.GC(GenomeData, boolean, int, int) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator.GC
Creates a new GC calculator around the passed genomic data, with the passed properties.
AverageCalculator.GC(GenomeData, boolean) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator.GC
Creates a new GC calculator around the passed genomic data, with the passed properties.
AverageCalculator.GC(GenomeData, int, int) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator.GC
Creates a new GC calculator around the passed genomic data, with the passed properties.
AverageCalculator.GC(GenomeData) - Constructor for class ca.corefacility.gview.utils.content.AverageCalculator.GC
Creates a new GC calculator around the passed genomic data, with the passed properties.

B

BACKBONE - Static variable in class ca.corefacility.gview.data.Slot
The backbone slot number.
backbone - Variable in class ca.corefacility.gview.layout.prototype.BackboneShape
 
backbone - Variable in class ca.corefacility.gview.layout.sequence.AbstractSequencePath
 
backbone - Variable in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
Backbone - Interface in ca.corefacility.gview.layout.sequence
Backbone stores the actual shape of the backbone, and how items should "wrap" themselves around backbone.
BACKBONE - Static variable in interface ca.corefacility.gview.map.gui.editor.node.Slotable
 
backbone - Variable in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
Backbone.ShiftDirection - Enum in ca.corefacility.gview.layout.sequence
 
BACKBONE_IMAGE - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BACKBONE_SLOT_NUMBER - Static variable in class ca.corefacility.gview.map.controllers.SlotStyleController
 
BACKBONE_SLOT_NUMBER - Static variable in interface ca.corefacility.gview.map.gui.editor.node.Slotable
 
BACKBONE_STYLE - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
BACKBONE_STYLE_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
BACKBONE_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BackboneCircular - Class in ca.corefacility.gview.layout.sequence.circular
 
BackboneCircular(LocationConverter, double, double) - Constructor for class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
Creates a new circular backbone.
BackboneCircular.ClashShiftException - Exception in ca.corefacility.gview.layout.sequence.circular
 
BackboneCircular.ClashShiftException(String) - Constructor for exception ca.corefacility.gview.layout.sequence.circular.BackboneCircular.ClashShiftException
 
BackboneCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
BackboneCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.BackboneCoder
 
BackboneItem - Interface in ca.corefacility.gview.map.items
An item which has a particular location on the backbone.
BackboneLabelItem - Class in ca.corefacility.gview.map.items
 
BackboneLabelItem(Backbone, SequencePoint, FeatureItem) - Constructor for class ca.corefacility.gview.map.items.BackboneLabelItem
 
BackboneLabelItem(Backbone, FeatureItem) - Constructor for class ca.corefacility.gview.map.items.BackboneLabelItem
 
BackboneLinear - Class in ca.corefacility.gview.layout.sequence.linear
 
BackboneLinear(LocationConverter, double) - Constructor for class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
Creates a new circular backbone.
BackboneNode - Class in ca.corefacility.gview.map.gui.editor.node
The node class for the backbone panel.
BackboneNode(BackbonePanel) - Constructor for class ca.corefacility.gview.map.gui.editor.node.BackboneNode
 
BackbonePanel - Class in ca.corefacility.gview.map.gui.editor.panel
The backbone panel.
BackbonePanel(BackboneStyleController) - Constructor for class ca.corefacility.gview.map.gui.editor.panel.BackbonePanel
Create the panel.
BackbonePinnable - Interface in ca.corefacility.gview.layout.prototype
Describes something that can be "pinned" to a particular location on the backbone, so that it always stays there no matter the zoom level.
BackboneShape - Class in ca.corefacility.gview.layout.prototype
Describes a shape that is layed out along the Backbone and which can stretch/shrink on zoom levels.
BackboneShape(Backbone) - Constructor for class ca.corefacility.gview.layout.prototype.BackboneShape
Creates a new Backbone Shape about the passed backbone.
BackboneShapeItem - Interface in ca.corefacility.gview.map.items
Describes a shape which is bound to the backbone.
BackboneSlotNode - Class in ca.corefacility.gview.map.gui.editor.node
The node used to represent the backbone as it sits in GView's collection of slots.
BackboneSlotNode(BackbonePanel) - Constructor for class ca.corefacility.gview.map.gui.editor.node.BackboneSlotNode
 
BackboneSlotPanel - Class in ca.corefacility.gview.map.gui.editor.panel
 
BackboneSlotPanel() - Constructor for class ca.corefacility.gview.map.gui.editor.panel.BackboneSlotPanel
 
BackboneStyle - Class in ca.corefacility.gview.style.items
Style information for the backbone.
BackboneStyle() - Constructor for class ca.corefacility.gview.style.items.BackboneStyle
 
BackboneStyle(BackboneStyle) - Constructor for class ca.corefacility.gview.style.items.BackboneStyle
 
BackboneStyleController - Class in ca.corefacility.gview.map.controllers
This class is responsible for controlling access to the backbone style.
BackboneStyleController(StyleController, BackboneStyle) - Constructor for class ca.corefacility.gview.map.controllers.BackboneStyleController
 
BackboneStyleMenuItem - Class in ca.corefacility.gview.map.gui.menu
The backbone style menu item.
BackboneStyleMenuItem(GUIController) - Constructor for class ca.corefacility.gview.map.gui.menu.BackboneStyleMenuItem
 
BackboneTextItem - Interface in ca.corefacility.gview.map.items
Describes a Text item that is to be pinned to the backbone.
BackboneTextItemImp - Class in ca.corefacility.gview.map.items
 
BackboneTextItemImp(Backbone, SequencePoint) - Constructor for class ca.corefacility.gview.map.items.BackboneTextItemImp
 
BackboneZoomEvent - Class in ca.corefacility.gview.map.event
Defines a change in the scale of the backbone.
BackboneZoomEvent(Backbone) - Constructor for class ca.corefacility.gview.map.event.BackboneZoomEvent
 
BackgroundCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
BackgroundCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.BackgroundCoder
 
backgroundPaint - Variable in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
baseOnSequence(int) - Method in interface ca.corefacility.gview.data.GenomeData
Determines if the passed base is on the sequence.
baseOnSequence(int) - Method in class ca.corefacility.gview.data.GenomeDataImp
 
BaseRange - Class in ca.corefacility.gview.layout.sequence
 
BaseRange(double, double) - Constructor for class ca.corefacility.gview.layout.sequence.BaseRange
 
BASIC - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BASIC_RENDERER - Static variable in interface ca.corefacility.gview.map.effects.ShapeEffectRenderer
 
BasicBackboneItem - Class in ca.corefacility.gview.map.items
Stores the actual shape of the backbone.
BasicBackboneItem(Location, String) - Constructor for class ca.corefacility.gview.map.items.BasicBackboneItem
 
BasicBackboneItem(Location) - Constructor for class ca.corefacility.gview.map.items.BasicBackboneItem
 
BasicEffect - Class in ca.corefacility.gview.map.effects
 
BasicEffect() - Constructor for class ca.corefacility.gview.map.effects.BasicEffect
 
BasicItem - Class in ca.corefacility.gview.map.items
 
BasicItem(String) - Constructor for class ca.corefacility.gview.map.items.BasicItem
 
BasicItem() - Constructor for class ca.corefacility.gview.map.items.BasicItem
 
BEV - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
BEV_SHORTCUT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
BEV_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
BEVDialog - Class in ca.corefacility.gview.map.gui.dialog
The bird's eye view dialog box.
BEVDialog(GUIController) - Constructor for class ca.corefacility.gview.map.gui.dialog.BEVDialog
 
BEVDialogListener - Class in ca.corefacility.gview.map.gui.dialog
A custom listener class for the BEV Dialog.
BEVDialogListener(GUIController, BirdsEyeViewImp, JSlider) - Constructor for class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
BEVMenuItem - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating and managing the Bird's Eye View menu item.
BEVMenuItem(GViewGUIFrame) - Constructor for class ca.corefacility.gview.map.gui.menu.BEVMenuItem
Creates a new BEV menu item within the specified frame.
BirdsEyeView - Interface in ca.corefacility.gview.map
 
BirdsEyeViewImp - Class in ca.corefacility.gview.map
 
BirdsEyeViewImp() - Constructor for class ca.corefacility.gview.map.BirdsEyeViewImp
Creates a new instance of a BirdsEyeView
BirdsEyeViewImp(GUIController) - Constructor for class ca.corefacility.gview.map.BirdsEyeViewImp
Creates a new instance of a BirdsEyeView
BLANK - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BLANK - Static variable in interface ca.corefacility.gview.textextractor.FeatureTextExtractor
A FeatureTextExtractor which returns a blank string always.
BlankExtractor - Class in ca.corefacility.gview.textextractor
Text extractor which returns a blank string.
BlankExtractor() - Constructor for class ca.corefacility.gview.textextractor.BlankExtractor
 
BlankSymbolList - Class in ca.corefacility.gview.data
An implementation of Symbol list which has a length but no symbols.
BlankSymbolList(int) - Constructor for class ca.corefacility.gview.data.BlankSymbolList
Creates a new BlankSymbol list with the passed length.
BLOCK - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BOLD - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BOLD_ITALIC - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
BooleanHandler - Class in ca.corefacility.gview.style.io.gss
 
BooleanHandler() - Constructor for class ca.corefacility.gview.style.io.gss.BooleanHandler
 
BorderItem - Class in ca.corefacility.gview.map.items
 
BorderItem() - Constructor for class ca.corefacility.gview.map.items.BorderItem
 
BOTTOM - Static variable in interface ca.corefacility.gview.layout.sequence.SlotTranslator
The bottom of a slot.
breadthFirstEnumeration() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Checks to make sure that all children of the tree and style editor nodes and returns a breadth first enumeration of the nodes.
broadcastEvent(GUIEvent) - Method in interface ca.corefacility.gview.map.gui.editor.communication.GUIEventBroadcaster
 
broadcastEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.communication.LinkEventBroadcaster
 
broadcastEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.communication.SelectionEventBroadcaster
 
broadcastEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
Allows broadcasters to broadcast the event to their listeners.
build() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorFrame
Builds the style editor frame.
build(String, boolean) - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
 
buildAbove() - Method in enum ca.corefacility.gview.style.items.LabelLocation
Determines the state is such that we should place labels above backbone.
buildBelow() - Method in enum ca.corefacility.gview.style.items.LabelLocation
Determines the state is such that we should place labels below backbone.
buildGUIFrame(String, GViewMap) - Method in class ca.corefacility.gview.map.gui.GUIManager
 
buildGUIFrame(String, GViewMap, String) - Method in class ca.corefacility.gview.map.gui.GUIManager
 
buildGUIFrame(String, GViewMap, URI) - Method in class ca.corefacility.gview.map.gui.GUIManager
 
buildGViewGUIFrameFromInput(URI, URI, URI, LayoutFactory) - Method in class ca.corefacility.gview.map.gui.GUIManager
 
buildGViewGUIFrameFromInput(URI, URI, ArrayList<URI>, LayoutFactory) - Method in class ca.corefacility.gview.map.gui.GUIManager
 
BUILDING_FEATURES_STRING - Static variable in class ca.corefacility.gview.utils.ProgressHandler
 
buildLabel(LabelStyle, FeatureItem, boolean) - Method in class ca.corefacility.gview.managers.labels.LabelsManager
Adds a label item for the passed FeatureItem, using the passed label style.
buildLegend(LegendStyle) - Static method in class ca.corefacility.gview.map.items.LegendItem
 
buildNonContiguousShape(boolean, Location, SlotPath, double, double, int) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Creates a non-contiguous shape, with or without the reduced point arrow.
ByTypeCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
 
ByTypeCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.ByTypeCoder
 
ByTypePanel - Class in ca.corefacility.gview.map.gui.editor.featureFilter
 
ByTypePanel(GenomeDataController) - Constructor for class ca.corefacility.gview.map.gui.editor.featureFilter.ByTypePanel
Create the panel.

C

ca.corefacility.gview.data - package ca.corefacility.gview.data
Provides storage/access to the sequence data displayed by GView.
ca.corefacility.gview.data.readers - package ca.corefacility.gview.data.readers
Provides for classes used to read in the data to display on the GView map.
ca.corefacility.gview.data.readers.cgview - package ca.corefacility.gview.data.readers.cgview
Provides an implementation of FileFormatReader used to read CGView XML formatted data to display on the GView map.
ca.corefacility.gview.layout - package ca.corefacility.gview.layout
Provides for methods to be used to layout all of the items on the GView map.
ca.corefacility.gview.layout.feature - package ca.corefacility.gview.layout.feature
Provides for implementations to construct particular "shapes" for a feature.
ca.corefacility.gview.layout.plot - package ca.corefacility.gview.layout.plot
Provides necessary code to draw out different types of plots on a GView map.
ca.corefacility.gview.layout.prototype - package ca.corefacility.gview.layout.prototype
Provides implementations of different "prototype" shapes.
ca.corefacility.gview.layout.prototype.segments - package ca.corefacility.gview.layout.prototype.segments
Provides implementations of different segments used to construct a "prototype" shape.
ca.corefacility.gview.layout.sequence - package ca.corefacility.gview.layout.sequence
Provides for methods to use to layout and position any items along the sequence, and dividing up the map into different slots.
ca.corefacility.gview.layout.sequence.circular - package ca.corefacility.gview.layout.sequence.circular
Provides for layout implementations specific to the circular mode.
ca.corefacility.gview.layout.sequence.linear - package ca.corefacility.gview.layout.sequence.linear
Provides layout implementations specific to the linear mode.
ca.corefacility.gview.main - package ca.corefacility.gview.main
Provides the main class for the command line interface to GView.
ca.corefacility.gview.managers - package ca.corefacility.gview.managers
Provides for dynamic handling of different items on the map.
ca.corefacility.gview.managers.labels - package ca.corefacility.gview.managers.labels
Provides for classes to handle management of labels.
ca.corefacility.gview.managers.ruler - package ca.corefacility.gview.managers.ruler
Provides for classes to handle management of the items for the Ruler on the GView map.
ca.corefacility.gview.map - package ca.corefacility.gview.map
Provides for implementations of the main GView map, as well as some extras (Birds eye view, etc).
ca.corefacility.gview.map.controllers - package ca.corefacility.gview.map.controllers
Provides a controlled interface to the various styling objects.
ca.corefacility.gview.map.controllers.link - package ca.corefacility.gview.map.controllers.link
Package providing links between sets and legend items.
ca.corefacility.gview.map.controllers.selection - package ca.corefacility.gview.map.controllers.selection
Package providing classes for selecting items.
ca.corefacility.gview.map.effects - package ca.corefacility.gview.map.effects
Provides for different effects that can be used to render items on the GView map.
ca.corefacility.gview.map.event - package ca.corefacility.gview.map.event
Provides for implementations of different events in GView.
ca.corefacility.gview.map.event.style - package ca.corefacility.gview.map.event.style
Provides for implementations of Events specific to style information.
ca.corefacility.gview.map.gui - package ca.corefacility.gview.map.gui
Provides for implementations of a simple GUI for the GView map.
ca.corefacility.gview.map.gui.action - package ca.corefacility.gview.map.gui.action
Provides classes for defining different actions to perform on a GView map.
ca.corefacility.gview.map.gui.action.dialog.hide - package ca.corefacility.gview.map.gui.action.dialog.hide
Provides classes for actions to hide dialogs.
ca.corefacility.gview.map.gui.action.dialog.show - package ca.corefacility.gview.map.gui.action.dialog.show
Provides classes for actions to show dialogs.
ca.corefacility.gview.map.gui.action.map - package ca.corefacility.gview.map.gui.action.map
Provides classes for actions relating to resizing/exporting the map.
ca.corefacility.gview.map.gui.action.map.hide - package ca.corefacility.gview.map.gui.action.map.hide
Provides classes for actions to hide different elements on the GView map.
ca.corefacility.gview.map.gui.action.map.move - package ca.corefacility.gview.map.gui.action.map.move
Provides classes for actions to move on the GView map.
ca.corefacility.gview.map.gui.action.map.scale - package ca.corefacility.gview.map.gui.action.map.scale
Provides classes for actions to change the scale of the map.
ca.corefacility.gview.map.gui.action.map.show - package ca.corefacility.gview.map.gui.action.map.show
Provides classes for actions to show different elements on the map.
ca.corefacility.gview.map.gui.action.map.zoom - package ca.corefacility.gview.map.gui.action.map.zoom
Provides classes for actions to zoom in/out on the map.
ca.corefacility.gview.map.gui.action.style - package ca.corefacility.gview.map.gui.action.style
Provides classes for modifying the style of the GView map.
ca.corefacility.gview.map.gui.action.system - package ca.corefacility.gview.map.gui.action.system
Provides classes for actions performed on the overall GView application.
ca.corefacility.gview.map.gui.dialog - package ca.corefacility.gview.map.gui.dialog
Provides classes for different GView dialogs.
ca.corefacility.gview.map.gui.editor - package ca.corefacility.gview.map.gui.editor
Provides classes for the Style Editor.
ca.corefacility.gview.map.gui.editor.communication - package ca.corefacility.gview.map.gui.editor.communication
Package providing classes for communication between editor items.
ca.corefacility.gview.map.gui.editor.communication.labelEvent - package ca.corefacility.gview.map.gui.editor.communication.labelEvent
Package providing classes for communication of label events.
ca.corefacility.gview.map.gui.editor.communication.legendEvent - package ca.corefacility.gview.map.gui.editor.communication.legendEvent
Package providing classes for communication of legend events.
ca.corefacility.gview.map.gui.editor.communication.plotEvent - package ca.corefacility.gview.map.gui.editor.communication.plotEvent
Package providing classes for communication of plot events.
ca.corefacility.gview.map.gui.editor.communication.propertyMapperEvent - package ca.corefacility.gview.map.gui.editor.communication.propertyMapperEvent
Package providing classes for communication of property mapper events.
ca.corefacility.gview.map.gui.editor.communication.setEvent - package ca.corefacility.gview.map.gui.editor.communication.setEvent
Package providing classes for communication of set events.
ca.corefacility.gview.map.gui.editor.communication.slotEvent - package ca.corefacility.gview.map.gui.editor.communication.slotEvent
Package providing classes for communication of slot events.
ca.corefacility.gview.map.gui.editor.featureFilter - package ca.corefacility.gview.map.gui.editor.featureFilter
Provides classes for different Feature Filters in the style editor.
ca.corefacility.gview.map.gui.editor.icon - package ca.corefacility.gview.map.gui.editor.icon
This package provides various custom menus for the style editor.
ca.corefacility.gview.map.gui.editor.menu - package ca.corefacility.gview.map.gui.editor.menu
This package provides various custom icons.
ca.corefacility.gview.map.gui.editor.node - package ca.corefacility.gview.map.gui.editor.node
Provides for different nodes of the Style Editor tree.
ca.corefacility.gview.map.gui.editor.panel - package ca.corefacility.gview.map.gui.editor.panel
Provides classes for different style editor panels.
ca.corefacility.gview.map.gui.editor.panel.propertyMapper - package ca.corefacility.gview.map.gui.editor.panel.propertyMapper
Provides classes for the Property Mapper panel.
ca.corefacility.gview.map.gui.editor.panel.proxy - package ca.corefacility.gview.map.gui.editor.panel.proxy
Package providing classes for proxy panels.
ca.corefacility.gview.map.gui.editor.transfer - package ca.corefacility.gview.map.gui.editor.transfer
Provides classes for dragging and dropping different nodes in the style editor tree.
ca.corefacility.gview.map.gui.hint - package ca.corefacility.gview.map.gui.hint
Package providing classes for custom hints/tooltips.
ca.corefacility.gview.map.gui.menu - package ca.corefacility.gview.map.gui.menu
Provides classes different menus on the GView GUI.
ca.corefacility.gview.map.gui.open - package ca.corefacility.gview.map.gui.open
Defines classes related to the Open Dialog used to generate GView maps.
ca.corefacility.gview.map.inputHandler - package ca.corefacility.gview.map.inputHandler
Provides for classes to handle different aspects of user input.
ca.corefacility.gview.map.items - package ca.corefacility.gview.map.items
Provides for implementations of specific items to be displayed on the GView map.
ca.corefacility.gview.style - package ca.corefacility.gview.style
Provides for storage/manipulation of style information for GView.
ca.corefacility.gview.style.datastyle - package ca.corefacility.gview.style.datastyle
Provides for storage/manipulation of style information specific to the particular data we are displaying (such as the specific sequence/features).
ca.corefacility.gview.style.datastyle.mapper - package ca.corefacility.gview.style.datastyle.mapper
Defines classes which can be used to map certain properties of features to style properties used to display those features.
ca.corefacility.gview.style.io - package ca.corefacility.gview.style.io
Provides for classes to perform I/O on style information.
ca.corefacility.gview.style.io.gss - package ca.corefacility.gview.style.io.gss
Provides for GSS specific I/O implementations.
ca.corefacility.gview.style.io.gss.coders - package ca.corefacility.gview.style.io.gss.coders
Provides for coders used to encode/decode GSS style information.
ca.corefacility.gview.style.io.gss.exceptions - package ca.corefacility.gview.style.io.gss.exceptions
Provides exceptions for reading GSS information.
ca.corefacility.gview.style.io.gss.featureFilterCoder - package ca.corefacility.gview.style.io.gss.featureFilterCoder
Provides for methods to encode/decode FeatureFilters in GSS style information.
ca.corefacility.gview.style.items - package ca.corefacility.gview.style.items
Provides for storage/manipulation of style information for particular items on the GView map.
ca.corefacility.gview.textextractor - package ca.corefacility.gview.textextractor
Provides for classes used to extract text from Features.
ca.corefacility.gview.utils - package ca.corefacility.gview.utils
Provides for very basic utility classes used, but don't fit in anywhere else.
ca.corefacility.gview.utils.content - package ca.corefacility.gview.utils.content
Provides for classes to perform calculations on the symbols within the sequence.
ca.corefacility.gview.utils.geom - package ca.corefacility.gview.utils.geom
Provides for implementations of Arc2D which allows for more precision on the curves defining the shape.
ca.corefacility.gview.utils.thread - package ca.corefacility.gview.utils.thread
Package providing classes for handling multiple threads.
ca.corefacility.gview.writers - package ca.corefacility.gview.writers
Provides for classes to write the GView screen to an image file.
calculateClashShift(SequencePoint, double, double, double, Backbone.ShiftDirection) - Method in interface ca.corefacility.gview.layout.sequence.Backbone
Calculates the necessary shift needed for a rectangle centred at pinnedPoint so it is either just above or below (depending on passed direction) the height defined by heightLimitFromBackbone.
calculateClashShift(SequencePoint, double, double, double, Backbone.ShiftDirection) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
calculateClashShift(SequencePoint, double, double, double, Backbone.ShiftDirection) - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
calculateIntersectionScale(SequencePoint, Dimension2D, SequencePoint, Dimension2D) - Method in interface ca.corefacility.gview.layout.sequence.Backbone
Calculates the scale at which the rectangle R1 (defined by a pinned point, and a size) would not be overlapping rectangle R2 (defined by a pinned point and size) anymore.
calculateIntersectionScale(SequencePoint, Dimension2D, SequencePoint, Dimension2D) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
calculateIntersectionScale(SequencePoint, Dimension2D, SequencePoint, Dimension2D) - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
calculateMinSegments() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision
 
calculateScaleOverlap(Dimension2D, SequencePoint, double) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
Calculates the scale at which a rectangle with the given bounds and centre is just outside the overlap radius.
CALCULATING_GC_CONTENT_STRING - Static variable in class ca.corefacility.gview.utils.ProgressHandler
 
CALCULATING_GC_SKEW_STRING - Static variable in class ca.corefacility.gview.utils.ProgressHandler
 
call() - Method in class ca.corefacility.gview.utils.thread.PaintThread
 
call() - Method in class ca.corefacility.gview.utils.thread.ZoomEventThread
 
canAddSetNodeAsChild() - Method in class ca.corefacility.gview.map.gui.editor.node.FeatureContainerNode
 
canAddSetNodeAsChild() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
 
canAddSetNodeAsChild() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
 
CANCEL - Variable in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
CANCEL_BUTTON - Variable in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AllCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AndCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueContainsCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueEqualsCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.ByTypeCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoderMap
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.HasAnnotationCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.NotCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OrCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OverlapsLocationCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.SequenceNameCoder
 
canCode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.StrandedCoder
 
canImport(TransferHandler.TransferSupport) - Method in class ca.corefacility.gview.map.gui.editor.transfer.StyleTransferHandler
 
canProcess(String) - Static method in class ca.corefacility.gview.style.io.gss.PaintHandler
 
canProcess(String) - Static method in class ca.corefacility.gview.style.io.gss.PaintsHandler
 
canProcessSelector(Selector) - Method in class ca.corefacility.gview.style.io.gss.FilterConverter
 
canProcessSelector(Selector) - Method in class ca.corefacility.gview.style.io.gss.SelectorConverter
 
canProcessSelector(Selector) - Method in class ca.corefacility.gview.style.io.gss.StyleConverter
 
canProcessSelectors(SelectorList) - Method in class ca.corefacility.gview.style.io.gss.SelectorConverter
 
canRead(URI) - Method in class ca.corefacility.gview.data.readers.cgview.CGViewXMLReader
 
canRead(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.cgview.CGViewXMLReader
 
canRead(URI) - Method in class ca.corefacility.gview.data.readers.CGViewTabReader
 
canRead(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.CGViewTabReader
 
canRead(File) - Method in class ca.corefacility.gview.data.readers.EMBLFormatModified
A file is in EMBL format if its name contains the word eem or edat, or the first line matches the EMBL format for the ID line.
canRead(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.EMBLFormatModified
A stream is in EMBL format if its first line matches the EMBL format for the ID line.
canRead(URI) - Method in interface ca.corefacility.gview.data.readers.FileFormatReader
Determines if this reader can read the passed file.
canRead(BufferedInputStream) - Method in interface ca.corefacility.gview.data.readers.FileFormatReader
Determines if this reader can read the passed input stream.
canRead(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.GenbankFormatModified
A stream is in GenBank format if the first line of the stream starts with the word LOCUS
canRead(URI) - Method in class ca.corefacility.gview.data.readers.GFF3Reader
 
canRead(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.GFF3Reader
 
canRead(URL) - Static method in class ca.corefacility.gview.data.readers.GViewFileReader
Determines if GView can read the passed file.
canRead(URI) - Method in class ca.corefacility.gview.data.readers.StandardSequenceFormatReader
 
canRead(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.StandardSequenceFormatReader
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.Action
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.map.ExportAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.ExportStyleAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.ImportStyleAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.NewLegendAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.NewPlotAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.NewSetAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.NewSlotAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.NewStyleAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.style.RefineSetAction
 
canRedo() - Method in class ca.corefacility.gview.map.gui.action.system.SystemAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.Action
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.map.ExportAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.ExportStyleAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.ImportStyleAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.NewLegendAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.NewPlotAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.NewSetAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.NewSlotAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.NewStyleAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.style.RefineSetAction
 
canUndo() - Method in class ca.corefacility.gview.map.gui.action.system.SystemAction
 
CENTER - Static variable in interface ca.corefacility.gview.layout.sequence.SlotTranslator
The center of a slot.
centerMap() - Method in interface ca.corefacility.gview.map.GViewMap
Centres the GView map to the very middle of the sequence.
centerMap() - Method in class ca.corefacility.gview.map.GViewMapImp
 
CGViewSetFeatureFilter - Class in ca.corefacility.gview.data.readers.cgview
A class which simple stores a set of features to filter out Used by CGView so we don't have to waste so much time filtering out all the features of a particular style.
CGViewSetFeatureFilter() - Constructor for class ca.corefacility.gview.data.readers.cgview.CGViewSetFeatureFilter
 
CGViewTabReader - Class in ca.corefacility.gview.data.readers
FileFormatReader for reading in cgview tab delimited files.
CGViewTabReader() - Constructor for class ca.corefacility.gview.data.readers.CGViewTabReader
 
CGViewXMLReader - Class in ca.corefacility.gview.data.readers.cgview
A FileFormatReader for handling CGView xml file formats.
CGViewXMLReader() - Constructor for class ca.corefacility.gview.data.readers.cgview.CGViewXMLReader
Constructs an object to read in information from the CGView xml format.
changeBackboneLength(double) - Method in class ca.corefacility.gview.managers.ruler.TickMarkCalculator
Changes the backbone length we use to the passed value.
changedUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
changedUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
changedUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
changedUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
changedUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
changeGViewMapLayout(Style, GViewMapManager.Layout) - Method in class ca.corefacility.gview.map.gui.GViewMapManager
This is used to change the Style layout.
changeLabelTo() - Method in class ca.corefacility.gview.managers.labels.LabelPosition
 
changeLayout(LayoutFactory, ZoomSubject) - Method in class ca.corefacility.gview.managers.DisplayManager
 
changeStyleLayout(Style, GViewMapManager.Layout) - Static method in class ca.corefacility.gview.style.StyleFactory
 
charset(String) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
CHECKBOARD - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
children() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotsNode
 
CIRCULAR_LAYOUT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
CircularArcSegment - Class in ca.corefacility.gview.layout.prototype.segments
Stores a segment that is a circular arc.
CircularArcSegment(SequencePoint, SequencePoint, Direction, SequencePath.Orientation) - Constructor for class ca.corefacility.gview.layout.prototype.segments.CircularArcSegment
Creates a new CircularArcSegment.
CircularUtils - Class in ca.corefacility.gview.utils.geom
 
CircularUtils() - Constructor for class ca.corefacility.gview.utils.geom.CircularUtils
 
clear() - Method in class ca.corefacility.gview.layout.sequence.AbstractSequencePath
 
clear() - Method in class ca.corefacility.gview.layout.sequence.circular.SequencePathCircular
 
clear() - Method in class ca.corefacility.gview.layout.sequence.linear.SequencePathLinear
 
clear() - Method in interface ca.corefacility.gview.layout.sequence.SequencePath
Clears this SequencePath.
clear() - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
Clears SlotPath
clear() - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
clear() - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
Clear the popup.
clear() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
clear() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
clear() - Method in class ca.corefacility.gview.map.items.FeatureItemsCache
 
clear() - Method in class ca.corefacility.gview.map.items.Layer
 
clear() - Method in interface ca.corefacility.gview.map.items.MapComponent
Removes all children from this MapComponent
clear() - Method in class ca.corefacility.gview.map.items.TextItemImp
 
CLOCKWISE_ARROW - Static variable in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Draws features with the first type of arrow head, in the forward direction.
CLOCKWISE_ARROW - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
CLOCKWISE_ARROW2 - Static variable in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Draws features with another type of arrow head (looks more like a standard arrow) in the forward direction.
CLOCKWISE_ARROW_2 - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
clone() - Method in class ca.corefacility.gview.data.readers.cgview.FeaturePositionsTextExtractor
 
clone() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
clone() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderGCContent
 
clone() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderGCSkew
 
clone() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
clone() - Method in class ca.corefacility.gview.layout.prototype.SequenceOffset
 
clone() - Method in interface ca.corefacility.gview.layout.prototype.SequencePoint
 
clone() - Method in class ca.corefacility.gview.layout.prototype.SequencePointImp
 
clone() - Method in class ca.corefacility.gview.managers.labels.AllLabelRanker
 
clone() - Method in interface ca.corefacility.gview.managers.labels.FeatureLabelRanker
 
clone() - Method in class ca.corefacility.gview.managers.labels.GeneLabelRanker
 
clone() - Method in class ca.corefacility.gview.managers.labels.HiddenLabelRanker
 
clone() - Method in class ca.corefacility.gview.managers.labels.LocationLabelRanker
 
clone() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
clone() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyleFactory
 
clone() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
clone() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
clone() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
clone() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
clone() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
clone() - Method in class ca.corefacility.gview.textextractor.AnnotationExtractor
 
clone() - Method in class ca.corefacility.gview.textextractor.BlankExtractor
 
clone() - Method in interface ca.corefacility.gview.textextractor.FeatureTextExtractor
 
clone() - Method in class ca.corefacility.gview.textextractor.GeneTextExtractor
 
clone() - Method in class ca.corefacility.gview.textextractor.LocationExtractor
 
clone() - Method in class ca.corefacility.gview.textextractor.StringBuilder
 
clone() - Method in class ca.corefacility.gview.textextractor.StringExtractor
 
clone() - Method in class ca.corefacility.gview.textextractor.SymbolsExtractor
 
CLOSED_FOLDER - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
closePath() - Method in class ca.corefacility.gview.layout.sequence.AbstractSequencePath
 
closePath(SequencePath.Orientation) - Method in class ca.corefacility.gview.layout.sequence.circular.SequencePathCircular
 
closePath(SequencePath.Orientation) - Method in class ca.corefacility.gview.layout.sequence.linear.SequencePathLinear
 
closePath() - Method in interface ca.corefacility.gview.layout.sequence.SequencePath
Closes the path, draws line back to coords of last moveTo.
closePath(SequencePath.Orientation) - Method in interface ca.corefacility.gview.layout.sequence.SequencePath
Closes the path, draws line back to coords of last moveTo.
closePath(SequencePath.Orientation) - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
Closes the path, draws line back to coords of last moveTo.
closePath() - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
Closes the path, draws line back to coords of last moveTo.
closePath() - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
closePath(SequencePath.Orientation) - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
CloseSegment - Class in ca.corefacility.gview.layout.prototype.segments
 
CloseSegment(SequencePath.Orientation) - Constructor for class ca.corefacility.gview.layout.prototype.segments.CloseSegment
Creates a new CloseSegment type.
coderMap - Variable in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
 
COG_CATEGORIES - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
COG_COLORS - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
COG_TO_COLOR_MAPPER - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
COGMapper - Class in ca.corefacility.gview.style.datastyle.mapper
 
COGMapper(String[]) - Constructor for class ca.corefacility.gview.style.datastyle.mapper.COGMapper
 
COGToColorMapperListItem - Class in ca.corefacility.gview.map.gui.editor.panel.propertyMapper
This class represents a single COG category to color as a list item.
COGToColorMapperListItem(String, Paint) - Constructor for class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorMapperListItem
 
COGToColorPanel - Class in ca.corefacility.gview.map.gui.editor.panel.propertyMapper
The COG to color panel.
COGToColorPanel() - Constructor for class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorPanel
Creates a new COGToColorPanel.
collapse() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Collapses all the tree's nodes recursively.
comment(String) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
COMMENT_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
CommunicationEvent - Class in ca.corefacility.gview.map.gui.editor.communication
This class facilitates the communication between GUI objects.
CommunicationEvent(GUIEvent) - Constructor for class ca.corefacility.gview.map.gui.editor.communication.CommunicationEvent
 
compare(RangeLocation, RangeLocation) - Method in class ca.corefacility.gview.layout.RangeLocationComparator
 
compare(Object, Object) - Method in class ca.corefacility.gview.managers.labels.Label.BaseComparator
 
compare(Object, Object) - Method in class ca.corefacility.gview.managers.labels.Label.HeightComparator
 
compare(Label, Label) - Method in class ca.corefacility.gview.managers.labels.Label.PriorityComparatorDescending
 
compare(Label, Label) - Method in class ca.corefacility.gview.managers.labels.Label.ZoomScaleComparatorAscending
 
compare(Label, Label) - Method in class ca.corefacility.gview.managers.labels.Label.ZoomScaleComparatorDescending
 
compareTo(StyleEditorTree) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
componentHidden(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
componentHidden(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
componentMoved(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
componentMoved(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
componentResized(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
componentResized(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
componentShown(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
componentShown(ComponentEvent) - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
CompositeEffect - Class in ca.corefacility.gview.map.effects
 
CompositeEffect() - Constructor for class ca.corefacility.gview.map.effects.CompositeEffect
 
CompositeShape - Class in ca.corefacility.gview.layout.prototype
A Backbone shape that can be composed from two different backbone shapes, and controls switching between them at certain zoom levels.
CompositeShape(BackboneShape, BackboneShape, double, double) - Constructor for class ca.corefacility.gview.layout.prototype.CompositeShape
Creates a CompositeShape which may contain other shapes, and switches between them at the passed zoom level.
connect(GViewMap) - Method in interface ca.corefacility.gview.map.BirdsEyeView
 
connect(GViewMap) - Method in class ca.corefacility.gview.map.BirdsEyeViewImp
 
connectGViewMap(BirdsEyeViewImp) - Method in class ca.corefacility.gview.map.gui.GViewMapManager
Connects the Bird's Eye View object to the GViewMap object.
CONSORTIUM_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
constantBaseMoves - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
constrainWidthTo(float) - Method in class ca.corefacility.gview.map.items.TextItemImp
Constrains the width of this text item to the given width.
contains(double, double, double, double) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
Overridden methods for Shape
contains(double, double) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
contains(Point2D) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
contains(Rectangle2D) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
containsFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
containsFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
containsFeatureHolderStyle(FeatureFilter) - Method in interface ca.corefacility.gview.style.datastyle.StyleHolder
Determines if this style holder contains a feature holder style for the passed filter.
containsFilter(FeatureFilter) - Method in class ca.corefacility.gview.style.io.FeatureSetMap
 
containsItem(Object) - Method in class ca.corefacility.gview.map.gui.editor.AnnotationComboBox
 
containsLabelStyleNode() - Method in class ca.corefacility.gview.map.gui.editor.node.FeatureContainerNode
Whether or not node contains a label style node as a child.
containsPlotNode() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
Determines whether or not the slot node has a plot node child.
containsPropertyMapper() - Method in class ca.corefacility.gview.map.gui.editor.node.FeatureContainerNode
Determines whether or not the FeatureContainerNode has a property mapper node child.
containsSetNode() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
Determines whether or not the slot node has a set node child.
containsSlotStyle(int) - Method in class ca.corefacility.gview.style.datastyle.DataStyle
Determines if this DataStyle contains a SlotStyle object for the passed slot number.
containsSymbol(Symbol) - Method in class ca.corefacility.gview.utils.content.ContentCalculator
 
containsSymbol(Symbol) - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
CONTENT_PANEL - Variable in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
ContentCalculator - Class in ca.corefacility.gview.utils.content
Calculates the content frequencies of symbols within the sequence.
ContentCalculator(GenomeData, boolean, int, int) - Constructor for class ca.corefacility.gview.utils.content.ContentCalculator
Creates a new ContentCalculator around the passed genomic data, with the passed properties.
ContentCalculator(GenomeData, int, int) - Constructor for class ca.corefacility.gview.utils.content.ContentCalculator
Creates a new ContentCalculator around the passed genomic data, with the passed properties.
ContentCalculator(GenomeData) - Constructor for class ca.corefacility.gview.utils.content.ContentCalculator
Creates a new ContentCalculator around the passed genomic data, with the passed properties.
ContentCalculator(GenomeData, boolean) - Constructor for class ca.corefacility.gview.utils.content.ContentCalculator
Creates a new ContentCalculator around the passed genomic data, with the passed properties.
ContentCalculator.ContentIterator - Class in ca.corefacility.gview.utils.content
 
ContentCalculator.ContentIterator(Symbol[]) - Constructor for class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
ContentCalculator.RangeValue - Class in ca.corefacility.gview.utils.content
Class to tie together the location on the sequence and a value.
ContentCalculator.RangeValue() - Constructor for class ca.corefacility.gview.utils.content.ContentCalculator.RangeValue
 
contentIterator() - Method in class ca.corefacility.gview.utils.content.AverageCalculator
 
contentIterator() - Method in class ca.corefacility.gview.utils.content.ContentCalculator
Creates an iterator to iterate over the content and do the appropriate calculations.
contentIterator() - Method in class ca.corefacility.gview.utils.content.SkewCalculator
 
CONTIG_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
ContinuousMapperListItem - Class in ca.corefacility.gview.map.gui.editor.panel.propertyMapper
This class represents a continuous property style mapper list item.
ContinuousMapperListItem() - Constructor for class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.ContinuousMapperListItem
Default constructor.
ContinuousMapperListItem(ContinuousPropertyMapper, ContinuousStyleMapper) - Constructor for class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.ContinuousMapperListItem
 
ContinuousPropertyMapper - Interface in ca.corefacility.gview.style.datastyle.mapper
 
ContinuousStyleMapper - Interface in ca.corefacility.gview.style.datastyle.mapper
 
Controller - Class in ca.corefacility.gview.map.controllers
The abstract class for style controllers.
Controller() - Constructor for class ca.corefacility.gview.map.controllers.Controller
 
convertLocation(Location) - Method in class ca.corefacility.gview.layout.sequence.LocationConverter
Converts a constant location value (such as full) to a real location.
convertScaleToSlider(double) - Static method in class ca.corefacility.gview.map.gui.GUIUtility
Converts a scale value to a slider value.
convertSliderValueToScale(int) - Static method in class ca.corefacility.gview.map.gui.GUIUtility
Converts the value on the scale slider to an appropriate integer to scale the gViewMap.
COUNTERCLOCKWISE_ARROW - Static variable in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Draws features with the first type of arrow head, in the reverse direction.
COUNTERCLOCKWISE_ARROW - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
COUNTERCLOCKWISE_ARROW2 - Static variable in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Draws features with another type of arrow head (looks more like a standard arrow) in the reverse direction.
COUNTERCLOCKWISE_ARROW_2 - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
createAnyNodeSelector() - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createArcClockwise(double, double, double, int) - Static method in class ca.corefacility.gview.utils.geom.CircularUtils
 
createArcCounterClockwise(double, double, double, int) - Static method in class ca.corefacility.gview.utils.geom.CircularUtils
 
createArrowBlock(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Method to override to create the arrow block part of the shape.
createArrowBlock(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
 
createArrowBlock(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
 
createArrowBlock(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ReverseArrow2ShapeRealizer
 
createArrowBlock(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ReverseArrowShapeRealizer
 
createArrowHead(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Method to override to create the arrow head part of the shape.
createArrowHead(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
 
createArrowHead(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
 
createArrowHead(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ReverseArrow2ShapeRealizer
 
createArrowHead(SlotPath, int, float, int, double, double) - Method in class ca.corefacility.gview.layout.feature.ReverseArrowShapeRealizer
 
createBackboneNode(GlobalNode) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the backbone node.
createBackboneNode(GlobalNode, BackbonePanel) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the backbone node, when there already exists a backbone panel.
createBlankGenomeData(int) - Static method in class ca.corefacility.gview.data.GenomeDataFactory
Creates a blank GenomeData object which has a sequenceLength, but no associated symbols/features.
createCDataSectionSelector(String) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createChildSelector(Selector, SimpleSelector) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createCommentSelector(String) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createConditionalSelector(SimpleSelector, Condition) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createContext(ColorModel, Rectangle, Rectangle2D, AffineTransform, RenderingHints) - Method in class ca.corefacility.gview.utils.Gradient
 
createDefaultStyle() - Static method in class ca.corefacility.gview.style.StyleFactory
 
createDefaultStyle2() - Static method in class ca.corefacility.gview.style.StyleFactory
Alternative style!
createDescendantSelector(Selector, SimpleSelector) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createDirectAdjacentSelector(short, Selector, SimpleSelector) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createElementSelector(String, String) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
createFeatureHolderStyle(FeatureFilter, FeatureHolderStyle) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyleFactory
Creates a new FeatureHolderStyle with the passed information, sets the id properly
createFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
Creates a style in this slot with the passed filter.
createFeatureHolderStyle(FeatureFilter) - Method in interface ca.corefacility.gview.style.datastyle.StyleHolder
Creates a FeatureHolderStyle within this style holder.
createFeaturePrototype(LocationConverter, SlotPath, Location, double, double) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Creates a shape in the passed slot, at the passed location.
createFeaturePrototype(SlotPath, Location, double) - Method in class ca.corefacility.gview.layout.feature.HiddenShapeRealizer
 
createFirstBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Method to override to create the first block for non-contiguous regions.
createFirstBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
 
createFirstBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
 
createFirstBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ReverseArrow2ShapeRealizer
 
createFirstBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ReverseArrowShapeRealizer
 
createFont(String, String, String) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
This method is a utility to turn the font parameters into a Font object.
createFullBackboneShape(double, double, Location) - Method in class ca.corefacility.gview.layout.sequence.circular.SequencePathCircular
 
createFullBackboneShape(double, double, Location) - Method in class ca.corefacility.gview.layout.sequence.linear.SequencePathLinear
 
createFullBackboneShape(double, double, Location) - Method in interface ca.corefacility.gview.layout.sequence.SequencePath
Creates a shape that stretches the full length of the backbone with the passed top/bottom values.
createFullBackboneShape(double, double, Location) - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
Builds a shape which stretches all the way along the backbone.
createFullBackboneShape(double, double, Location) - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
createGenomeData(Sequence) - Static method in class ca.corefacility.gview.data.GenomeDataFactory
Creates a genome data object from the passed sequence.
createGenomeData(Sequence, boolean) - Static method in class ca.corefacility.gview.data.GenomeDataFactory
Creates a genome data object from the passed sequence.
createGlobalNode() - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a global node.
createImageCache(Dimension2D) - Method in class ca.corefacility.gview.map.items.FeatureItemsCache
 
createImageWriter(String) - Static method in class ca.corefacility.gview.writers.ImageWriterFactory
Create an ImageWriter for the passed file format.
createImageWriter(File) - Static method in class ca.corefacility.gview.writers.ImageWriterFactory
Creates an ImageWriter from the passed file, based on the file format.
createLabelsManager() - Method in class ca.corefacility.gview.layout.sequence.circular.LayoutFactoryCircular
 
createLabelsManager() - Method in class ca.corefacility.gview.layout.sequence.LayoutFactory
Builds the LabelsManager used to position labels.
createLabelsManager() - Method in class ca.corefacility.gview.layout.sequence.linear.LayoutFactoryLinear
 
createLabelStyleNode(FeatureContainerNode, LabelStyleToken, FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a label style node.
createLastBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Method to override to create last block for non-contiguous regions.
createLastBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
 
createLastBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
 
createLastBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ReverseArrow2ShapeRealizer
 
createLastBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ReverseArrowShapeRealizer
 
createLayout(LayoutFactory, MapStyle, ZoomSubject) - Method in class ca.corefacility.gview.managers.LayoutManager
 
createLegend() - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
Creates a new legend.
createLegendItem(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
Creates a new legend item.
createLegendItemNode(LegendStyleNode) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a default legend item style node and adds it under the passed parent node.
createLegendItemStyleNode(LegendStyleNode, LegendStyleToken, LegendItemStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a legend item style node.
createLegendItemStyleNodes(LegendStyleNode, LegendStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the legend item style nodes.
createLegendNode(GlobalNode) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the legend node.
createLegendNode() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a new default legend node and adds it to the tree under the legend node.
createLegendStyleNode(LegendNode, LegendStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a legend style node.
createLegendStyleNodes(LegendNode) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the legend style nodes.
createMap(GenomeData, MapStyle, LayoutFactory) - Static method in class ca.corefacility.gview.map.GViewMapFactory
Creates and sets up a new gViewMap from the passed data.
createMap(Sequence, MapStyle, LayoutFactory) - Static method in class ca.corefacility.gview.map.GViewMapFactory
Creates and sets up a new GView map from the passed sequence data.
createMap(URI, URI, ArrayList<URI>, LayoutFactory) - Static method in class ca.corefacility.gview.map.GViewMapFactory
Creates and sets up a new GViewMap from the parameters provided.
createMarks(double, double) - Method in class ca.corefacility.gview.managers.ruler.TickMarkCalculator
Creates tick mark objects for each tick mark to create in between the two passed bases.
createMiddleBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
Method to override to create middle block for non-contiguous regions.
createMiddleBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
 
createMiddleBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
 
createMiddleBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ReverseArrow2ShapeRealizer
 
createMiddleBlock(SlotPath, int, int, double, double, int) - Method in class ca.corefacility.gview.layout.feature.ReverseArrowShapeRealizer
 
createNegativeSelector(SimpleSelector) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createNewBlankStyle(GenomeData) - Static method in class ca.corefacility.gview.style.StyleFactory
Creates a new, blank style.
createNewDefaultStyle(GenomeData) - Static method in class ca.corefacility.gview.style.StyleFactory
Creates a new, default style.
createPlot(GenomeData, SlotPath, PlotDrawer) - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
Builds the plot defined by this builder within the passed path
createPlot(GenomeData, SlotPath, PlotDrawer) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
createPlot(GenomeData, SlotPath, PlotDrawer) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderGCContent
 
createPlot(GenomeData, SlotPath, PlotDrawer) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderGCSkew
 
createPlot(GenomeData, SlotPath, PlotDrawer) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderPoints
 
createPlot(GenomeData, SlotPath, PlotDrawer) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
createPlot(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
createPlotBuilder() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Annotation
 
createPlotBuilder() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
createPlotBuilder() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.GCContent
 
createPlotBuilder() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.GCSkew
 
createPlotBuilder() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Points
 
createPlotBuilder() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Range
 
createPlotDrawer() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Bar
 
createPlotDrawer() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Center
 
createPlotDrawer() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType
 
createPlotDrawer() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Line
 
createPlotDrawer() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Solid
 
createPlotNode(PlotStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a plot node.
createPlotNode(Integer) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a plot node, if possible, at the passed slot number.
createPlotNode(SlotNode) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a new default plot node and adds it to the passed slot node.
createPointBlock(SlotPath, int, double, double) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
 
createPolar(Point2D) - Static method in class ca.corefacility.gview.layout.sequence.circular.Polar
Creates a polar point from the passed cartesian point.
createPolar(double, double) - Static method in class ca.corefacility.gview.layout.sequence.circular.Polar
Creates a polar point from the passed cartesian coords.
createPopup() - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
createPopup() - Method in class ca.corefacility.gview.map.gui.hint.WarningLabel
 
createProcessingInstructionSelector(String, String) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createPropertyMapper(FeatureContainerNode) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a property mapper.
createPropertyMapperNode(FeatureContainerNode, FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a property mapper node.
createPropertyMapperNode(FeatureContainerNode, SlotStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a property mapper node.
createPropertyMapperNode(FeatureContainerNode, PropertyMappableToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a property mapper node.
createProxy() - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
createProxy() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
createProxy() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendPanel
 
createProxy() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
createProxy() - Method in interface ca.corefacility.gview.map.gui.editor.panel.proxy.ProxiablePanel
 
createProxy() - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
createProxy() - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
createPseudoElementSelector(String, String) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createRecursiveSetNodes(StyleEditorNode, ArrayList<SlotItemStyleToken>) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Recursively creates all set nodes for the passed list of sets and their children.
createResolutionSwitchEvent(Backbone) - Method in class ca.corefacility.gview.managers.ResolutionManager
 
createRootNodeSelector() - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createRulerNode(GlobalNode) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the ruler node.
createSet(SlotStyleToken, FeatureFilter) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
createSet(FeatureHolderStyleToken, FeatureFilter) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
createSetNode(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a set node.
createSetNode(Integer) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
createSetNode(FeatureContainerNode) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a set node under the passed parent node.
createSetNodeFromFeatureFilter(FeatureContainerNode, FeatureFilter) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a set node from the passed feature filter and adds it under the passed parent node.
createSlot(int) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
Attempts to create a slot at the specified slot location.
createSlotNode(SlotStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates a single slot node under the slots node.
createSlotNode() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Creates a new, default and empty slot node and adds it to the root node.
createSlotNodes() - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the slots node.
createSlotRegion(MapStyle, LocationConverter, double) - Method in class ca.corefacility.gview.layout.sequence.circular.LayoutFactoryCircular
 
createSlotRegion(MapStyle, LocationConverter, double) - Method in class ca.corefacility.gview.layout.sequence.LayoutFactory
Builds the SlotRegion for this layout.
createSlotRegion(MapStyle, LocationConverter, double) - Method in class ca.corefacility.gview.layout.sequence.linear.LayoutFactoryLinear
 
createSlotStyle(int) - Method in class ca.corefacility.gview.style.datastyle.DataStyle
Creates a new slot style with the passed slot.
createSpinner(double, double, double, double, int) - Static method in class ca.corefacility.gview.map.gui.editor.ProxiableDoubleSpinner
 
createStandardBlock(SlotPath, int, int, double, double, double) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
A convience method used to create a standard (no arrow heads etc) block.
createStandardBlock(SlotPath, int, int, double, double) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
This creates a standard block (no decoration) in the slot.
createStrokedShape(Stroke) - Method in class ca.corefacility.gview.layout.sequence.AbstractSequencePath
 
createStrokedShape(Stroke) - Method in interface ca.corefacility.gview.layout.sequence.SequencePath
Returns the created shape with the passed stroke applied to it.
createStrokedShape(Stroke) - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
Creates a shape by stroking the path defined with the passed stroke.
createStrokedShape(Stroke) - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
createStyle(GenomeDataImp) - Method in class ca.corefacility.gview.map.gui.action.style.NewBlankStyleAction
 
createStyle(GenomeDataImp) - Method in class ca.corefacility.gview.map.gui.action.style.NewDefaultStyleAction
 
createStyle(GenomeDataImp) - Method in class ca.corefacility.gview.map.gui.action.style.NewStyleAction
Creates the actual style.
createTextNodeSelector(String) - Method in class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
createTooltipNode(GlobalNode) - Method in class ca.corefacility.gview.map.gui.editor.node.NodeBuilder
Creates the tool tip node.
createTransferable(JComponent) - Method in class ca.corefacility.gview.map.gui.editor.transfer.StyleTransferHandler
Creates the transferable object.
CREATING_LAYOUT_STRING - Static variable in class ca.corefacility.gview.utils.ProgressHandler
 
CREATING_PLOTS_STRING - Static variable in class ca.corefacility.gview.utils.ProgressHandler
 
CubicSegment - Class in ca.corefacility.gview.layout.prototype.segments
 
CubicSegment(SequencePoint, SequencePoint, SequencePoint, SequencePath.Orientation) - Constructor for class ca.corefacility.gview.layout.prototype.segments.CubicSegment
Creates a new CubicSegment which can be stretched.
currentStartBase() - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
currentStopBase() - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
CUSTOM_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 

D

DATABASE_XREF_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
DataStyle - Class in ca.corefacility.gview.style.datastyle
DataStyle controls any style information directly related to the specific genome data to use.
DataStyle() - Constructor for class ca.corefacility.gview.style.datastyle.DataStyle
Creates a new data style.
DataStyleCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
DataStyleCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.DataStyleCoder
 
DATE_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
dbxp - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.AlignmentHandler
 
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.BooleanHandler
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AllCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AndCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueContainsCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueEqualsCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.ByTypeCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
Decodes the passed FeatureFilter corresponding to the passed LexicalUnit value.
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoderMap
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.HasAnnotationCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.NotCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OrCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OverlapsLocationCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.SequenceNameCoder
 
decode(LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.StrandedCoder
 
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.FeatureFilterHandler
 
decode(MapStyle, Selector, String, LexicalUnit, boolean) - Method in class ca.corefacility.gview.style.io.gss.FilterConverter
 
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.FontHandler
 
decode(Reader, URI) - Method in class ca.corefacility.gview.style.io.gss.GeneralStyleConverter
Decodes the style information read from the passed reader into a new MapStyle.
decode(MapStyle, Reader) - Method in class ca.corefacility.gview.style.io.gss.GeneralStyleConverter
 
decode(MapStyle, Reader, URI) - Method in class ca.corefacility.gview.style.io.gss.GeneralStyleConverter
Decodes the style information read from the passed reader into the passed MapStyle.
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.LabelLocationHandler
 
decode(String, LinkMapper) - Static method in class ca.corefacility.gview.style.io.gss.LinkHandler
Decodes to a link.
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.PaintHandler
 
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.PaintsHandler
 
decode(URI, LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.PlotDataHandler
Decodes the passed LexicalUnit into a plot builder.
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.PlotTypeHandler
Attempts to decode the given unit into a PlotDrawerType.
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.PropertyMapperHandler
 
decode(MapStyle, Selector, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.StyleConverter
Decodes the passed "name" and "value" within the passed selector, and writes the appropriate style information to the passed MapStyle.
decode(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.TextExtractorHandler
 
decodeFeatureTextExtractor(String) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
Extracts the feature text extractor from the passed string.
decodeProperty(Selector, MapStyle, String, LexicalUnit, boolean) - Method in class ca.corefacility.gview.style.io.gss.coders.DataStyleCoder
 
decodeProperty(DescendantSelector, MapStyle, FeatureSetMap, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.coders.DescendentCoder
 
decodeProperty(FeatureHolderStyle, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.coders.FeatureSetCoder
 
decodeProperty(FeatureSetMap, String, LexicalUnit) - Method in class ca.corefacility.gview.style.io.gss.coders.FilterCoder
Decoes the passed property (name/value) into the passed filtersMap
decodeProperty(Selector, MapStyle, FeatureSetMap, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSCoder
 
decodeProperty(LabelStyle, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.coders.LabelCoder
Decodes the passed LexicalUnit value into the passed LabelStyle
decodeProperty(String, LegendStyle, ConditionalSelector, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.coders.LegendItemCoder
Decodes the passed LexicalUnit value representing the legendItemStyle under the passed legendStyle.
decodeProperty(PlotStyle, String, LexicalUnit, URI) - Method in class ca.corefacility.gview.style.io.gss.coders.PlotCoder
Decodes the passed name, value into the passed PlotStyle.
decodeShape(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.ShapeHandler
 
decodeShapeEffect(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.ShapeEffectHandler
 
decodeTextAlignment(LexicalUnit) - Static method in class ca.corefacility.gview.style.io.gss.AlignmentHandler
 
DEFAULT - Static variable in interface ca.corefacility.gview.managers.labels.FeatureLabelRanker
 
DEFAULT_AUTOSCALE - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_BACKBONE_COLOR - Static variable in class ca.corefacility.gview.map.controllers.BackboneStyleController
 
DEFAULT_BACKGROUND_COLOR - Static variable in class ca.corefacility.gview.map.controllers.GlobalStyleController
 
DEFAULT_BACKGROUND_COLOR - Static variable in class ca.corefacility.gview.map.controllers.LabelStyleController
 
DEFAULT_BACKGROUND_COLOR - Static variable in class ca.corefacility.gview.map.controllers.LegendStyleController
 
DEFAULT_BACKGROUND_COLOR - Static variable in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
DEFAULT_BUILDER_TYPE - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_COLOR - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
DEFAULT_DRAWER_TYPE - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_EXTRACTOR - Static variable in class ca.corefacility.gview.map.controllers.SetStyleController
 
DEFAULT_EXTRACTOR - Static variable in class ca.corefacility.gview.map.controllers.SlotStyleController
 
DEFAULT_FONT - Static variable in class ca.corefacility.gview.map.controllers.LabelStyleController
 
DEFAULT_FONT - Static variable in class ca.corefacility.gview.map.controllers.LegendStyleController
 
DEFAULT_FONT - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_FONT - Static variable in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
DEFAULT_FONT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
DEFAULT_FONT_COLOR - Static variable in class ca.corefacility.gview.map.controllers.LabelStyleController
 
DEFAULT_FONT_COLOR - Static variable in class ca.corefacility.gview.map.controllers.LegendStyleController
 
DEFAULT_FONT_COLOR - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
DEFAULT_GRID_COLOR - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_LAYOUT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
DEFAULT_LEGEND_ALIGNMENT - Static variable in class ca.corefacility.gview.map.controllers.LegendStyleController
 
DEFAULT_LOWER_COLOR - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_MAJOR_TICK_COLOR - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_MAXIMUM - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_MINIMUM - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_MINOR_TICK_COLOR - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_NUM_GRID_LINES - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_OUTLINE_COLOR - Static variable in class ca.corefacility.gview.map.controllers.LegendStyleController
 
DEFAULT_OUTLINE_COLOR - Static variable in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
DEFAULT_PAINT - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFAULT_REALIZER - Static variable in class ca.corefacility.gview.map.controllers.SetStyleController
 
DEFAULT_REALIZER - Static variable in class ca.corefacility.gview.map.controllers.SlotStyleController
 
DEFAULT_RENDERER - Static variable in class ca.corefacility.gview.map.controllers.SetStyleController
 
DEFAULT_RENDERER - Static variable in class ca.corefacility.gview.map.controllers.SlotStyleController
 
DEFAULT_RULER_LABEL_LOCATION - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_SET_COLOR - Static variable in class ca.corefacility.gview.map.controllers.SetStyleController
 
DEFAULT_SHAPE_EFFECT_RENDERER - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_SLOT_COLOR - Static variable in class ca.corefacility.gview.map.controllers.SlotStyleController
 
DEFAULT_SLOT_SPACING - Static variable in class ca.corefacility.gview.map.controllers.GlobalStyleController
 
DEFAULT_STYLE_NAME - Static variable in class ca.corefacility.gview.map.gui.editor.StyleNameManager
 
DEFAULT_STYLE_NODE_NAME - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
DEFAULT_SWATCH_COLOR - Static variable in class ca.corefacility.gview.map.controllers.LegendStyleController
 
DEFAULT_TEXT_BACKGROUND_COLOR - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_TEXT_COLOR - Static variable in class ca.corefacility.gview.map.controllers.RulerStyleController
 
DEFAULT_TEXT_COLOR - Static variable in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
DEFAULT_THICKNESS - Static variable in class ca.corefacility.gview.map.controllers.BackboneStyleController
 
DEFAULT_THICKNESS - Static variable in class ca.corefacility.gview.map.controllers.SlotStyleController
 
DEFAULT_UPPER_COLOR - Static variable in class ca.corefacility.gview.map.controllers.PlotStyleController
 
DEFINITION_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
delete() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Attempts to "delete" the tree by removing all of its nodes appropriately.
DELIMITER_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
DescendentCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
DescendentCoder(LinkMapper) - Constructor for class ca.corefacility.gview.style.io.gss.coders.DescendentCoder
 
destroyLink(Link, StyleEditorTree) - Static method in class ca.corefacility.gview.map.controllers.link.LinkController
Destroys the link by enumerating over the entire tree and setting all link references that match the passed link to NULL.
determineAlignment(Point2D, Rectangle2D, boolean) - Method in class ca.corefacility.gview.map.items.LegendItem
 
determineSizeOf(RulerStyle, String) - Static method in class ca.corefacility.gview.managers.ruler.RulerManager
Determines the size of a constructed label with the given ruler style and text.
DIALOG_MESSAGE - Variable in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
die() - Method in class ca.corefacility.gview.map.gui.action.Action
 
Dimension2DDouble - Class in ca.corefacility.gview.utils
A class storing a dimension in double precision.
Dimension2DDouble(double, double) - Constructor for class ca.corefacility.gview.utils.Dimension2DDouble
 
Direction - Enum in ca.corefacility.gview.layout
Defines a direction along the path.
DiscreteMapperListItem - Class in ca.corefacility.gview.map.gui.editor.panel.propertyMapper
This class represents a discrete property style mapper list item.
DiscreteMapperListItem() - Constructor for class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.DiscreteMapperListItem
Default constructor.
DiscreteMapperListItem(DiscretePropertyMapper, DiscreteStyleMapper) - Constructor for class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.DiscreteMapperListItem
 
DiscretePaintMapper - Class in ca.corefacility.gview.style.datastyle.mapper
 
DiscretePaintMapper(Paint[]) - Constructor for class ca.corefacility.gview.style.datastyle.mapper.DiscretePaintMapper
 
DiscretePropertyMapper - Interface in ca.corefacility.gview.style.datastyle.mapper
 
DiscreteStyleMapper - Interface in ca.corefacility.gview.style.datastyle.mapper
 
DisplacementSolution - Class in ca.corefacility.gview.layout.sequence.circular
Used so we can return the 2,1,or 0 solutions of findDisplacementToIntersection.
DisplacementSolution(double, double) - Constructor for class ca.corefacility.gview.layout.sequence.circular.DisplacementSolution
 
displayAddDialog() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperChooserDialog
Displays the add dialog.
DisplayChangeListener - Class in ca.corefacility.gview.map.event
Listens/handles any events which signal a change in the display.
DisplayChangeListener(PCamera) - Constructor for class ca.corefacility.gview.map.event.DisplayChangeListener
Pass the camera so we can obtain the view bounds on any change.
displayedState - Variable in class ca.corefacility.gview.managers.labels.LabelsManager
 
DisplayManager - Class in ca.corefacility.gview.managers
 
DisplayManager(PCamera, GenomeData, MapStyle, LayoutFactory, ZoomSubject, DisplayChangeListener, ToolTipHandler) - Constructor for class ca.corefacility.gview.managers.DisplayManager
Creates a new manager which handles the display/layout of items on the map.
displayModifyDialog(PropertyMapperListItem) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperChooserDialog
Displays the modify dialog to for modifying the passed list item.
displayNode(StyleEditorNode) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorFrame
Sets the selection to be only the passed node, displays the associated panel in the contextual area and scrolls the JTree so that the selected node is visible.
displayProgressWhileRebuilding(Runnable) - Method in class ca.corefacility.gview.map.controllers.GUIController
This method displays the progress notification dialog while working on rebuilding the GViewMap.
DisplayUpdated - Class in ca.corefacility.gview.map.event
 
DisplayUpdated(Object, Rectangle2D, Rectangle2D, boolean) - Constructor for class ca.corefacility.gview.map.event.DisplayUpdated
An event summarising information about the current display bounds.
displayXMLNotification(Component) - Static method in class ca.corefacility.gview.map.gui.GUIUtility
Displays a pop-up notification about the limitations of using an XML file.
disposeGUI() - Method in class ca.corefacility.gview.map.controllers.GUIController
Disposes of the controller's GUI components.
disposeGUI(GUIController) - Method in class ca.corefacility.gview.map.gui.GUIManager
Disposes of the GUIController and it's related GUIComponents.
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.BackbonePanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.BackboneSlotPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.GlobalPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendsPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxyLabelPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxyLegendItemPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxyLegendPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxyPlotPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxyPropertyMapperPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxySetPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.proxy.ProxySlotPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.RootPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.RulerPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotsPanel
 
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
Applies changes.
doApply() - Method in class ca.corefacility.gview.map.gui.editor.panel.TooltipPanel
 
downstreamLength() - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
dp - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
draw(Graphics2D) - Method in interface ca.corefacility.gview.map.GViewMap
Draws out this map onto the passed graphics context.
draw(Graphics2D) - Method in class ca.corefacility.gview.map.GViewMapImp
 
draw(Shape) - Method in class ca.corefacility.gview.utils.SVGGraphics2DCustom
 
drawLegend(Graphics2D) - Method in interface ca.corefacility.gview.map.GViewMap
Draws out the legend onto the passed graphics context.
drawLegend(Graphics2D) - Method in class ca.corefacility.gview.map.GViewMapImp
 
drawPoint(int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawer
Draws out the next point on this plot.
drawPoint(int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerBar
 
drawPoint(int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerCenter
 
drawPoint(int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerLine
 
drawPoint(int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerSolid
 
drawRange(int, int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawer
Draws out a point in a given range.
drawRange(int, int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerBar
 
drawRange(int, int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerCenter
 
drawRange(int, int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerLine
 
drawRange(int, int, double, SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerSolid
 

E

edit(Edit) - Method in class ca.corefacility.gview.data.BlankSymbolList
 
ElementControl - Class in ca.corefacility.gview.map
Allows for controlling of which elements are to be displayed on the map.
ElementControl(DisplayManager) - Constructor for class ca.corefacility.gview.map.ElementControl
 
EMBL_FORMAT - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
The name of the current format
EMBL_PRE87_FORMAT - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
The name of the Pre-87 format
EMBLFormatModified - Class in ca.corefacility.gview.data.readers
Code from biojava 1.7.1 org.biojavax.bio.seq.io.EMBLFormat Fixes a bug with parsing EMBL files where an 'XX' line does not separate an 'FT' line from the rest of the sequence
EMBLFormatModified() - Constructor for class ca.corefacility.gview.data.readers.EMBLFormatModified
 
EMBLFormatModified.Terms - Class in ca.corefacility.gview.data.readers
Implements some EMBL-specific terms.
EMBLFormatModified.Terms() - Constructor for class ca.corefacility.gview.data.readers.EMBLFormatModified.Terms
 
encode(LegendAlignment) - Static method in class ca.corefacility.gview.style.io.gss.AlignmentHandler
 
encode(boolean) - Static method in class ca.corefacility.gview.style.io.gss.BooleanHandler
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AllCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AndCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueContainsCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueEqualsCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.ByTypeCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
Encodes the passed FeatureFilter into a string, using this FeatureFilterCoder.
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoderMap
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.HasAnnotationCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.NotCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OrCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OverlapsLocationCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.SequenceNameCoder
 
encode(FeatureFilter) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.StrandedCoder
 
encode(FeatureFilter) - Static method in class ca.corefacility.gview.style.io.gss.FeatureFilterHandler
 
encode(Font) - Static method in class ca.corefacility.gview.style.io.gss.FontHandler
 
encode(MapStyle, Writer) - Method in class ca.corefacility.gview.style.io.gss.GeneralStyleConverter
Encodes the passed style and writes to the passed writer.
encode(MapStyle, String) - Method in class ca.corefacility.gview.style.io.gss.GeneralStyleConverter
 
encode(LabelLocation) - Static method in class ca.corefacility.gview.style.io.gss.LabelLocationHandler
 
encode(Link, LinkMapper) - Static method in class ca.corefacility.gview.style.io.gss.LinkHandler
Encodes the link.
encode(Paint) - Static method in class ca.corefacility.gview.style.io.gss.PaintHandler
Encodes the passed paint into a String (only handled paint type of Color for now).
encode(PlotBuilderType) - Static method in class ca.corefacility.gview.style.io.gss.PlotDataHandler
 
encode(PlotDrawerType) - Static method in class ca.corefacility.gview.style.io.gss.PlotTypeHandler
Encodes the given plot drawer type to a GSS string.
encode(PropertyStyleMapper) - Static method in class ca.corefacility.gview.style.io.gss.PropertyMapperHandler
 
encode(FeatureTextExtractor) - Static method in class ca.corefacility.gview.style.io.gss.TextExtractorHandler
 
encodeLegendItemStyle(LegendItemStyle, GSSWriter, String, int) - Method in class ca.corefacility.gview.style.io.gss.coders.LegendItemCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.BackboneCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.BackgroundCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.DataStyleCoder
Performs the actual encoding of the properties of the selector.
encodeProperties(FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.FilterCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSCoder
Performs the actual encoding of the properties of the selector.
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.LegendCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.RulerCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.SlotCoder
 
encodeProperties(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.TooltipCoder
 
encodeSelector(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.DataStyleCoder
Encodes the appropriate information from the style object and writes it to the passed PrintWriter.
encodeSelector(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSCoder
 
encodeSelector(MapStyle, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.StyleConverter
 
encodeShape(FeatureShapeRealizer) - Static method in class ca.corefacility.gview.style.io.gss.ShapeHandler
 
encodeShapeEffect(ShapeEffectRenderer) - Static method in class ca.corefacility.gview.style.io.gss.ShapeEffectHandler
 
encodeStyle(FeatureHolderStyle, String, FeatureSetMap, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.FeatureSetCoder
 
encodeStyle(LabelStyle, String, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.LabelCoder
Encodes the passed LabelStyle into the passed GSSWriter
encodeStyle(PlotStyle, String, GSSWriter) - Method in class ca.corefacility.gview.style.io.gss.coders.PlotCoder
Encodes the passed style into the passed writer
END - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
END_SEQUENCE_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
endDocument(InputSource) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
endFontFace() - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
endMedia(SACMediaList) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
endPage(String, String) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
endSelector(Selector) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSCoder
 
endSelector() - Method in class ca.corefacility.gview.style.io.gss.coders.GSSWriter
 
endSelector(SelectorList) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
equals(Object) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.FeatureFilterMappable
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderGCContent
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderGCSkew
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerBar
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerCenter
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerLine
 
equals(Object) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerSolid
 
equals(Object) - Method in class ca.corefacility.gview.managers.labels.AllLabelRanker
 
equals(Object) - Method in class ca.corefacility.gview.managers.LegendManager
 
equals(Object) - Method in class ca.corefacility.gview.managers.SectionID
 
equals(Object) - Method in class ca.corefacility.gview.map.controllers.FeatureHolderStyleToken
 
equals(Object) - Method in class ca.corefacility.gview.map.controllers.LabelStyleToken
 
equals(Object) - Method in class ca.corefacility.gview.map.controllers.LegendItemStyleToken
 
equals(Object) - Method in class ca.corefacility.gview.map.controllers.LegendStyleToken
 
equals(Object) - Method in class ca.corefacility.gview.map.controllers.link.Link
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.BasicEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.CompositeEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.HighlightEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.LabelLineRenderer
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.OutlineEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.OutsideEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.RaisedShadedEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.ShadingEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.ShadowEffect
 
equals(Object) - Method in interface ca.corefacility.gview.map.effects.ShapeEffectRenderer
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.StandardEffect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.StandardEffectMouseOverSelect
 
equals(Object) - Method in class ca.corefacility.gview.map.effects.StandardEffectSelect
 
equals(Object) - Method in class ca.corefacility.gview.map.event.GViewEventSubjectImp
 
equals(Object) - Method in class ca.corefacility.gview.map.gui.Style
 
equals(Object) - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
equals(Object) - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyleFactory
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.AnnotationMapper
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.COGMapper
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.DiscretePaintMapper
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.OpacityFeatureStyleMapper
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyMapperScore
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleContinuous
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleDiscrete
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Annotation
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.GCContent
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.GCSkew
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Points
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Range
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Bar
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Center
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Line
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Solid
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.GlobalStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
 
equals(Object) - Method in class ca.corefacility.gview.style.items.BackboneStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.items.LegendStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.items.RulerStyle
 
equals(Object) - Method in class ca.corefacility.gview.style.items.TooltipStyle
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.AnnotationExtractor
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.BlankExtractor
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.GeneTextExtractor
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.LocationExtractor
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.StringBuilder
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.StringExtractor
 
equals(Object) - Method in class ca.corefacility.gview.textextractor.SymbolsExtractor
 
equals(Object) - Method in class ca.corefacility.gview.utils.AndFilter
 
equals(Object) - Method in class ca.corefacility.gview.utils.Gradient
 
equals(Object) - Method in class ca.corefacility.gview.utils.SequenceNameFilter
 
error(CSSParseException) - Method in class ca.corefacility.gview.style.io.gss.GSSErrorHandler
 
error(ParseException) - Method in class ca.corefacility.gview.style.io.gss.GSSErrorHandler
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.layout.prototype.CompositeShape
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.layout.prototype.StrokedBackboneShape
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.layout.sequence.AbstractBackbone
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.DisplayManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.FeaturesManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.labels.Label
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.labels.LabelsManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.labels.LabelsManagerSingle
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.labels.LabelsManagerSlots
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.LayoutManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.LegendManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.PlotsManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.ruler.RulerManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.SectionManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.StyleEventManager
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.managers.ZoomEventDistributor
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.controllers.GUIController
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.event.DisplayChangeListener
 
eventOccured(GViewEvent) - Method in interface ca.corefacility.gview.map.event.GViewEventListener
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.gui.dialog.BEVDialogListener
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.gui.dialog.ScaleDialog
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.gui.dialog.ZoomDialog
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.gui.GViewToolBar
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.gui.menu.ZoomMenu
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.GViewMapImp
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.inputHandler.ZoomSubject
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.map.items.TextItemImp
 
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.style.datastyle.DataStyle
Event methods
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.style.GlobalStyle
Event methods: These were to be used so that we can send messages if any information from the style changes.
eventOccured(GViewEvent) - Method in class ca.corefacility.gview.style.MapStyle
Event methods
eventSubject - Variable in class ca.corefacility.gview.layout.sequence.AbstractBackbone
 
EXCLAMATION - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
executeGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
Executes the event.
executeOnEDT(Runnable) - Static method in class ca.corefacility.gview.utils.thread.ThreadService
This class will execute the passed runnable on the Swing Event Dispatch Thread or the current thread if the current thread is the Swing Event Dispatch Thread.
EXIT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
EXIT_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
EXIT_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
ExitMenuItem - Class in ca.corefacility.gview.map.gui.menu
Creates the Exit menu item.
ExitMenuItem() - Constructor for class ca.corefacility.gview.map.gui.menu.ExitMenuItem
 
expanedForLegends(Rectangle2D, boolean) - Method in class ca.corefacility.gview.managers.DisplayManager
 
expanedForLegends(Rectangle2D, boolean) - Method in class ca.corefacility.gview.managers.LegendManager
 
EXPORT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
EXPORT_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
ExportAction - Class in ca.corefacility.gview.map.gui.action.map
The export action class.
ExportAction(GViewMapManager) - Constructor for class ca.corefacility.gview.map.gui.action.map.ExportAction
 
exportDone(JComponent, Transferable, int) - Method in class ca.corefacility.gview.map.gui.editor.transfer.StyleTransferHandler
Finalizes the export.
exportImage() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
Attempts to export the image to file.
ExportImage - Class in ca.corefacility.gview.map.inputHandler
A class used to export the current view of the map to an image.
ExportImage() - Constructor for class ca.corefacility.gview.map.inputHandler.ExportImage
 
ExportMenuItem - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating the Export menu item.
ExportMenuItem(GUIController) - Constructor for class ca.corefacility.gview.map.gui.menu.ExportMenuItem
 
ExportStyleAction - Class in ca.corefacility.gview.map.gui.action.style
 
ExportStyleAction(GUIController) - Constructor for class ca.corefacility.gview.map.gui.action.style.ExportStyleAction
 
exportView(GViewMap) - Method in class ca.corefacility.gview.map.inputHandler.ExportImage
 
extent - Variable in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
The angular extent of the arc in degrees.
extent - Variable in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
The angular extent of the arc in degrees.
extractExtension(String) - Static method in class ca.corefacility.gview.utils.Util
Extracts the extension from the file name.
extractExtension(String) - Static method in class ca.corefacility.gview.writers.ImageWriterFactory
Extracts the extension from the passed file name.
extractExtension(File) - Static method in class ca.corefacility.gview.writers.ImageWriterFilter
 
extractExtension(String) - Static method in class ca.corefacility.gview.writers.ImageWriterFilter
 
extractFeatureFilter(ConditionalSelector, FeatureSetMap) - Static method in class ca.corefacility.gview.style.io.gss.coders.FeatureSetCoder
Extracts a FeatureFilter from the passed FeatureSet#set selector.
extractMinMaxLength(Location, int) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Returns the length of a location, this may overlap the 0 base (circular)
extractSelectorId(ConditionalSelector) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSCoder
 
extractSlotStyle(ConditionalSelector, DataStyle) - Static method in class ca.corefacility.gview.style.io.gss.coders.SlotCoder
 
extractStart(Location) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Returns the very start of this location
extractStop(Location) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Returns the very stop of this location
extractText(Feature) - Method in class ca.corefacility.gview.data.readers.cgview.FeaturePositionsTextExtractor
 
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.AnnotationExtractor
 
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.BlankExtractor
 
extractText(Feature) - Method in interface ca.corefacility.gview.textextractor.FeatureTextExtractor
Extracts information from the passed feature.
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.GeneTextExtractor
 
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.LocationExtractor
 
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.StringBuilder
 
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.StringExtractor
 
extractText(Feature) - Method in class ca.corefacility.gview.textextractor.SymbolsExtractor
 

F

fatalError(CSSParseException) - Method in class ca.corefacility.gview.style.io.gss.GSSErrorHandler
 
fatalError(ParseException) - Method in class ca.corefacility.gview.style.io.gss.GSSErrorHandler
 
FEATURE_ALL - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_AND - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_ANNOTATION_VALUE_CONTAINS - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_ANNOTATION_VALUE_EQUALS - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_BY_TYPE - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_FILTERS - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_GSS_STRING - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_HAS_ANNOTATION - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_HEADER_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
FEATURE_NOT - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_OR - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_OVERLAPS_LOCATION - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_SEQUENCE_NAME - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_STRANDED - Static variable in class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FEATURE_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
FeatureContainerNode - Class in ca.corefacility.gview.map.gui.editor.node
This node class is an abstract representation of nodes that are intended to represent styles that contain features, such as slots and sets.
FeatureContainerNode(StylePanel, String) - Constructor for class ca.corefacility.gview.map.gui.editor.node.FeatureContainerNode
 
FeatureContainerStyle - Interface in ca.corefacility.gview.style.datastyle
This allows for (data) styles that contain features, such as sets and slots, to interface more easily.
featureEffects - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
FeatureFilterChooserDialog - Class in ca.corefacility.gview.map.gui.editor.featureFilter
A subclass of JDialog, used for returning a new FeatureFilter.
FeatureFilterChooserDialog(StyleEditorTree, GenomeDataController, FeatureContainerNode, FeatureFilterChooserDialog.DIALOG_TYPE) - Constructor for class ca.corefacility.gview.map.gui.editor.featureFilter.FeatureFilterChooserDialog
 
FeatureFilterChooserDialog.DIALOG_TYPE - Enum in ca.corefacility.gview.map.gui.editor.featureFilter
 
FeatureFilterCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
Defines a class used to encode/decode feature filters.
FeatureFilterCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
 
FeatureFilterCoderMap - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
An implementation of FeatureFilterCoder used to detect/encode any general FeatureFilter.
FeatureFilterCoderMap() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoderMap
 
FeatureFilterHandler - Class in ca.corefacility.gview.style.io.gss
 
FeatureFilterHandler() - Constructor for class ca.corefacility.gview.style.io.gss.FeatureFilterHandler
 
FeatureFilterMappable - Class in ca.corefacility.gview.layout.plot
Wrapper around FeatureFilter.ByAnnotation which can be stored in a hash map.
FeatureFilterMappable(String, String) - Constructor for class ca.corefacility.gview.layout.plot.FeatureFilterMappable
 
FeatureHolderStyle - Class in ca.corefacility.gview.style.datastyle
Stores the style information for a particular set of features.
FeatureHolderStyle(FeatureHolderStyleFactory, FeatureHolderStyle, FeatureFilter, int) - Constructor for class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
Constructs a FeatureHolderStyle with the passed information.
FeatureHolderStyle(FeatureHolderStyle) - Constructor for class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
FeatureHolderStyleFactory - Class in ca.corefacility.gview.style.datastyle
Used to assign unique id's to each featureHolderStyle.
FeatureHolderStyleFactory() - Constructor for class ca.corefacility.gview.style.datastyle.FeatureHolderStyleFactory
 
FeatureHolderStyleToken - Class in ca.corefacility.gview.map.controllers
This class is responsible for providing access to it's associated style to ONLY the controllers, which is achieved by using "protected final" method specifiers and by having the controllers and tokens in the same package.
FeatureHolderStyleToken(FeatureHolderStyle) - Constructor for class ca.corefacility.gview.map.controllers.FeatureHolderStyleToken
 
FeatureItem - Interface in ca.corefacility.gview.map.items
 
FeatureItemImp - Class in ca.corefacility.gview.map.items
 
FeatureItemImp(FeatureHolderStyle, Feature) - Constructor for class ca.corefacility.gview.map.items.FeatureItemImp
 
FeatureItemsCache - Class in ca.corefacility.gview.map.items
 
FeatureItemsCache() - Constructor for class ca.corefacility.gview.map.items.FeatureItemsCache
 
FeatureLabelRanker - Interface in ca.corefacility.gview.managers.labels
Defines how to assign rankings to the labels of Features.
FeaturePositionsTextExtractor - Class in ca.corefacility.gview.data.readers.cgview
A text extractor used to add feature positions to cgview labels.
FeaturePositionsTextExtractor() - Constructor for class ca.corefacility.gview.data.readers.cgview.FeaturePositionsTextExtractor
 
FeatureSelectEvent - Class in ca.corefacility.gview.map.event
Describes a event where the used clicked on a FeatureItem.
FeatureSelectEvent(Object, Collection<FeatureItem>) - Constructor for class ca.corefacility.gview.map.event.FeatureSelectEvent
 
FeatureSetCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
FeatureSetCoder(LinkMapper) - Constructor for class ca.corefacility.gview.style.io.gss.coders.FeatureSetCoder
 
FeatureSetMap - Class in ca.corefacility.gview.style.io
Ties together the names of Feature sets, and the corresponding FeatureFilters.
FeatureSetMap() - Constructor for class ca.corefacility.gview.style.io.FeatureSetMap
 
FeatureShapeRealizer - Class in ca.corefacility.gview.layout.feature
Deals with defining the actual shape representing a feature.
FeatureShapeRealizer() - Constructor for class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
 
featureShapes - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
FeaturesLayer - Class in ca.corefacility.gview.map.items
This class is a custom implementation of the Layer class.
FeaturesLayer() - Constructor for class ca.corefacility.gview.map.items.FeaturesLayer
 
FeaturesManager - Class in ca.corefacility.gview.managers
Handles layout/building up of features within the slots.
FeaturesManager(GenomeData, MapStyle, LabelsManager) - Constructor for class ca.corefacility.gview.managers.FeaturesManager
 
FeatureTextExtractor - Interface in ca.corefacility.gview.textextractor
Extracts text from a feature to be displayed in a tooltip or label.
FILE_EXTENSION_DELIM - Static variable in class ca.corefacility.gview.map.gui.editor.StyleNameManager
 
FILE_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
FILE_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
FileFormatReader - Interface in ca.corefacility.gview.data.readers
Defines an interface for reading in/extracting data and style for specific file formats.
FileLocationHandler - Class in ca.corefacility.gview.utils
A class which helps in locating files to read in for GView
FileLocationHandler() - Constructor for class ca.corefacility.gview.utils.FileLocationHandler
 
FileMenu - Class in ca.corefacility.gview.map.gui.editor.menu
The file menu class.
FileMenu(GUIController) - Constructor for class ca.corefacility.gview.map.gui.editor.menu.FileMenu
 
FileMenu - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating the File menu.
FileMenu(GUIController) - Constructor for class ca.corefacility.gview.map.gui.menu.FileMenu
 
FileWriterManager - Class in ca.corefacility.gview.map.controllers
This class is responsible for controlling access to file writing.
FileWriterManager(MapStyle) - Constructor for class ca.corefacility.gview.map.controllers.FileWriterManager
 
fill(Shape) - Method in class ca.corefacility.gview.utils.SVGGraphics2DCustom
 
fillCountsForCurrentWindow(int[]) - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
Fills in symbol counts for the current window.
filter(LinkedList<Label>) - Method in class ca.corefacility.gview.managers.labels.LabelsFilterer
 
FilterCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
FilterCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.FilterCoder
 
FilterConverter - Class in ca.corefacility.gview.style.io.gss
 
FilterConverter() - Constructor for class ca.corefacility.gview.style.io.gss.FilterConverter
 
FINALIZING_STRING - Static variable in class ca.corefacility.gview.utils.ProgressHandler
 
findCenterBase(int, int, int) - Method in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
 
findClosestOnLine(double, double, double, double, double, double) - Static method in class ca.corefacility.gview.layout.sequence.circular.Geometry
Finds the point on the line defined from (x1,y1) to (x2,y2) that is closest to the point defined by (tx, ty).
findClosestOnRectangle(double, double, double, double, double, double) - Static method in class ca.corefacility.gview.layout.sequence.circular.Geometry
Finds closest point on rectangle defined by top-left = (topLeftX, topLeftY) and width/height to the point (tx, ty).
findDisplacementToIntersection(Point2D, Point2D, Point2D, double) - Static method in class ca.corefacility.gview.layout.sequence.circular.Geometry
Find displacement from "point" to intersection of circle of radius r (centered at circleCenter), along vector "direction".
findFeatureItems(Feature) - Method in class ca.corefacility.gview.managers.DisplayManager
Searches for the FeatureItems associated with the passed feature.
findFeatureItems(Feature) - Method in class ca.corefacility.gview.managers.FeaturesManager
Searches for the FeatureItem associated with the passed feature.
findFurthestOnRectangle(double, double, double, double, double, double) - Static method in class ca.corefacility.gview.layout.sequence.circular.Geometry
 
findLegendNode(LegendItemStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Finds the legend item node that shares the target style in the tree, if it exists.
findSetNode(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Finds the set node that shares the target style in the tree, if it exists.
findZoomForLength(double, double) - Method in interface ca.corefacility.gview.layout.sequence.Backbone
Determines the zoom level where the on screen length for the base range deltaBase is equal to length.
findZoomForLength(double, double) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
findZoomForLength(double, double) - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
finish(ProgressHandler.Stage) - Static method in class ca.corefacility.gview.utils.ProgressHandler
Finishes the passed stage.
finishPlotPoint(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawer
Adds finishing touches to this plot.
finishPlotPoint(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerBar
 
finishPlotPoint(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerCenter
 
finishPlotPoint(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerLine
 
finishPlotPoint(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerSolid
 
finishPlotRange(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawer
 
finishPlotRange(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerBar
 
finishPlotRange(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerCenter
 
finishPlotRange(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerLine
 
finishPlotRange(SlotPath) - Method in class ca.corefacility.gview.layout.plot.PlotDrawerSolid
 
fireEvent(LinkEvent) - Method in class ca.corefacility.gview.map.controllers.link.LinkController
Fires the link event to all link listeners.
fireEvent(SelectionEvent) - Method in class ca.corefacility.gview.map.controllers.selection.SelectionController
Fires a selection event to all the selected objects.
fireEvent(GViewEvent) - Method in class ca.corefacility.gview.map.event.GViewEventSubjectImp
 
FIRST_LOWER - Static variable in class ca.corefacility.gview.data.Slot
The first lower slot on the map.
FIRST_UPPER - Static variable in class ca.corefacility.gview.data.Slot
The first upper slot on the map.
FITMAction - Class in ca.corefacility.gview.map.gui.action.map
The Fit Image to Map / Fit Map to Screen action.
FITMAction(GViewMapManager) - Constructor for class ca.corefacility.gview.map.gui.action.map.FITMAction
 
FitMapToScreenMenuItem - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating the "Fit Image to Map" menu item.
FitMapToScreenMenuItem(GUIController) - Constructor for class ca.corefacility.gview.map.gui.menu.FitMapToScreenMenuItem
 
FMTS - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
FMTS_SHORTCUT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
FMTS_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
FONT_NAMES - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
FONT_STYLES - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
FontHandler - Class in ca.corefacility.gview.style.io.gss
 
FontHandler() - Constructor for class ca.corefacility.gview.style.io.gss.FontHandler
 
FontHandler.MalformedFontStringException - Exception in ca.corefacility.gview.style.io.gss
 
FontHandler.MalformedFontStringException() - Constructor for exception ca.corefacility.gview.style.io.gss.FontHandler.MalformedFontStringException
 
FontHandler.MalformedFontStringException(String, Throwable) - Constructor for exception ca.corefacility.gview.style.io.gss.FontHandler.MalformedFontStringException
 
FontHandler.MalformedFontStringException(String) - Constructor for exception ca.corefacility.gview.style.io.gss.FontHandler.MalformedFontStringException
 
FontHandler.MalformedFontStringException(Throwable) - Constructor for exception ca.corefacility.gview.style.io.gss.FontHandler.MalformedFontStringException
 
ForwardArrow2ShapeRealizer - Class in ca.corefacility.gview.layout.feature
FeatureShapeRealizer used to draw an arrow which looks like ---->
ForwardArrow2ShapeRealizer(double, double) - Constructor for class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
Constructs a ForwardArrow2ShapeRealizer to draw alternate arrow shapes with the passed arrow length and height decrease.
ForwardArrow2ShapeRealizer() - Constructor for class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
Constructs a ForwardArrow2ShapeRealizer to draw arrow shapes with the default settings
ForwardArrowShapeRealizer - Class in ca.corefacility.gview.layout.feature
FeatureShapeRealizer used to draw an arrow which looks like ===>
ForwardArrowShapeRealizer(double) - Constructor for class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
Constructs a ForwardArrowShapeRealizer to draw arrow shapes with the passed arrow length.
ForwardArrowShapeRealizer() - Constructor for class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
Constructs a ForwardArrowShapeRealizer to draw arrow shapes with the default arrow lenth.
FULL_SCREEN - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
FULL_SCREEN_SHORTCUT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
FULL_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
FullBackboneShapeRealizer - Class in ca.corefacility.gview.layout.feature
Used to build a shape that extends the full backbone width.
FullBackboneShapeRealizer() - Constructor for class ca.corefacility.gview.layout.feature.FullBackboneShapeRealizer
 
FullCircularArcSegment - Class in ca.corefacility.gview.layout.prototype.segments
 
FullCircularArcSegment(SequencePoint, Direction, SequencePath.Orientation) - Constructor for class ca.corefacility.gview.layout.prototype.segments.FullCircularArcSegment
 
fullPaint(PPaintContext) - Method in class ca.corefacility.gview.map.items.OptimizedLayer
 
FullScreenAction - Class in ca.corefacility.gview.map.gui.action.map
The full screen action class.
FullScreenAction(JFrame) - Constructor for class ca.corefacility.gview.map.gui.action.map.FullScreenAction
 
FullScreenMenuItem - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating the "Full Screen" menu item.
FullScreenMenuItem(GViewGUIFrame) - Constructor for class ca.corefacility.gview.map.gui.menu.FullScreenMenuItem
Creates a new menu item for Full Screen within the specified frame.
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AllCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AndCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueContainsCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.AnnotationValueEqualsCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.ByTypeCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoderMap
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.HasAnnotationCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.NotCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OrCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.OverlapsLocationCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.SequenceNameCoder
 
functionName() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.StrandedCoder
 

G

gc - Static variable in class ca.corefacility.gview.utils.content.ContentCalculator
 
GenbankFormatModified - Class in ca.corefacility.gview.data.readers
Code from biojava 1.7.1 org.biojavax.bio.seq.io.GenbankFormat Enables parsing of genbank files which have no sequence data into a sequence object.
GenbankFormatModified() - Constructor for class ca.corefacility.gview.data.readers.GenbankFormatModified
 
GeneLabelRanker - Class in ca.corefacility.gview.managers.labels
 
GeneLabelRanker() - Constructor for class ca.corefacility.gview.managers.labels.GeneLabelRanker
 
GeneralStyleConverter - Class in ca.corefacility.gview.style.io.gss
 
GeneralStyleConverter() - Constructor for class ca.corefacility.gview.style.io.gss.GeneralStyleConverter
 
generateDefaultName(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
Generates a default name for the set.
generateShortName(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
Generates a short name for the set.
GeneTextExtractor - Class in ca.corefacility.gview.textextractor
 
GeneTextExtractor() - Constructor for class ca.corefacility.gview.textextractor.GeneTextExtractor
 
GenomeData - Interface in ca.corefacility.gview.data
Manages the data of the genome sequence.
genomeData - Variable in class ca.corefacility.gview.utils.content.ContentCalculator
 
GenomeDataController - Class in ca.corefacility.gview.map.controllers
This class controls access to the GenomeData object and provides methods for operating on that data.
GenomeDataController(GenomeData) - Constructor for class ca.corefacility.gview.map.controllers.GenomeDataController
 
GenomeDataFactory - Class in ca.corefacility.gview.data
A factory used to create a genome data object from the passed sequence.
GenomeDataFactory() - Constructor for class ca.corefacility.gview.data.GenomeDataFactory
 
GenomeDataImp - Class in ca.corefacility.gview.data
An implementation of GenomeData.
GenomeDataImp(Sequence) - Constructor for class ca.corefacility.gview.data.GenomeDataImp
Creates a new structure to store the sequence data.
GenomeDataImp(Sequence, boolean) - Constructor for class ca.corefacility.gview.data.GenomeDataImp
Creates a new structure to store the sequence data.
Geometry - Class in ca.corefacility.gview.layout.sequence.circular
Class of utilities for doing geometry-related operations.
Geometry() - Constructor for class ca.corefacility.gview.layout.sequence.circular.Geometry
 
get(int) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperList
Returns the PropertyMapperListItem at the specific index.
get(String) - Method in class ca.corefacility.gview.style.io.FeatureSetMap
 
get(FeatureFilter) - Method in class ca.corefacility.gview.style.io.FeatureSetMap
 
getAboutDialog() - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
 
getAcceptedExtensions() - Static method in class ca.corefacility.gview.writers.ImageWriterFactory
Gets a copy of the string array of accepted extensions.
getAcceptedImageFormats() - Method in class ca.corefacility.gview.writers.ImageWriter
Gets the image formats accepted by this ImageWriter.
getAcceptedImageFormats() - Method in class ca.corefacility.gview.writers.ImageWriterJPG
 
getAcceptedImageFormats() - Method in class ca.corefacility.gview.writers.ImageWriterPNG
 
getAcceptedImageFormats() - Method in class ca.corefacility.gview.writers.ImageWriterSVG
 
getAlignment(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getAlignment() - Method in class ca.corefacility.gview.map.items.LegendEntryItem
 
getAlignment() - Method in class ca.corefacility.gview.map.items.LegendItem
 
getAlignment() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
getAllDisplayed() - Method in class ca.corefacility.gview.map.ElementControl
 
getAllFeatures(FeatureHolderStyle) - Method in interface ca.corefacility.gview.data.GenomeData
Obtains a FeatureHolder from an associated FeatureHolderStyle.
getAllFeatures(FeatureHolderStyle) - Method in class ca.corefacility.gview.data.GenomeDataImp
 
getAlphabet() - Method in class ca.corefacility.gview.data.BlankSymbolList
 
getAncestorSelectors(DescendantSelector) - Static method in class ca.corefacility.gview.style.io.gss.coders.AbstractDescendentCoder
 
getAngle(double) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
Returns the angle of the circle given the difference of base pairs.
getAngleExtent() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
getAngleExtent() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
getAngleStart() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
getAngleStart() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
getAnnotation() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.AnnotationValueContainsPanel
 
getAnnotation() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.AnnotationValueEqualsPanel
 
getAnnotation() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.HasAnnotationPanel
 
getAnnotation() - Method in class ca.corefacility.gview.textextractor.AnnotationExtractor
 
getAnnotations() - Method in class ca.corefacility.gview.map.controllers.GenomeDataController
 
getAnnotationsAsStrings() - Method in class ca.corefacility.gview.map.controllers.GenomeDataController
 
getArrowLocation(Location) - Method in class ca.corefacility.gview.layout.feature.AbstractArrowShapeRealizer
A method used to determine which location would have the arrow.
getArrowLocation(Location) - Method in class ca.corefacility.gview.layout.feature.ForwardArrow2ShapeRealizer
 
getArrowLocation(Location) - Method in class ca.corefacility.gview.layout.feature.ForwardArrowShapeRealizer
 
getArrowLocation(Location) - Method in class ca.corefacility.gview.layout.feature.ReverseArrow2ShapeRealizer
 
getArrowLocation(Location) - Method in class ca.corefacility.gview.layout.feature.ReverseArrowShapeRealizer
 
getArrowState(InputEventHandler.ARROW) - Method in class ca.corefacility.gview.map.inputHandler.InputEventHandler
 
getAutoScale(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getAutoScale() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
getBackbone() - Method in class ca.corefacility.gview.layout.sequence.AbstractSequencePath
 
getBackbone() - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
getBackbone() - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
 
getBackbone() - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
getBackbone() - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
 
getBackbone() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getBackbone() - Method in class ca.corefacility.gview.managers.LayoutManager
 
getBackbone() - Method in class ca.corefacility.gview.map.event.BackboneZoomEvent
 
getBackbone() - Method in class ca.corefacility.gview.map.event.ResolutionSwitchEvent
 
getBackboneLength() - Method in interface ca.corefacility.gview.layout.sequence.Backbone
 
getBackboneLength() - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
getBackboneLength() - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
getBackboneLength() - Method in interface ca.corefacility.gview.map.GViewMap
 
getBackboneLength() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getBackboneLengthAt(double) - Method in interface ca.corefacility.gview.layout.sequence.Backbone
Gets the apparent length of the backbone at the passed scale.
getBackboneLengthAt(double) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
getBackboneLengthAt(double) - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
getBackboneNode() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotsNode
 
getBackboneStyle() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getBackboneStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getBackboneStyleController() - Method in class ca.corefacility.gview.map.gui.editor.panel.BackbonePanel
 
getBackgroundColor() - Method in class ca.corefacility.gview.map.controllers.GlobalStyleController
 
getBackgroundColor(LabelStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getBackgroundColor(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getBackgroundColor() - Method in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
getBackgroundPaint() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getBackgroundPaint() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getBackgroundPaint() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
getBackgroundPaint() - Method in class ca.corefacility.gview.style.items.TooltipStyle
 
getBase() - Method in class ca.corefacility.gview.layout.prototype.SequenceOffset
 
getBase() - Method in interface ca.corefacility.gview.layout.prototype.SequencePoint
 
getBase() - Method in class ca.corefacility.gview.layout.prototype.SequencePointImp
 
getBase() - Method in class ca.corefacility.gview.managers.ruler.TickMark
 
getBaseCoordinate(int) - Method in interface ca.corefacility.gview.map.GViewMap
Given a base on the current map, determines the current coordinates.
getBaseCoordinate(int) - Method in class ca.corefacility.gview.map.GViewMapImp
 
getBaseRange() - Method in class ca.corefacility.gview.layout.sequence.SequenceRectangle
 
getBaseResolutionScale() - Method in class ca.corefacility.gview.managers.ResolutionManager
 
getBaseResolutionScale() - Method in class ca.corefacility.gview.map.event.ResolutionSwitchEvent
 
getBEVDialog() - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
Returns the current Bird's Eye View dialog.
getBottomMostHeight() - Method in interface ca.corefacility.gview.layout.sequence.SlotTranslator
 
getBottomMostHeight() - Method in class ca.corefacility.gview.layout.sequence.SlotTranslatorImp
 
getBottomSlot() - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getBottomTickThickness() - Method in interface ca.corefacility.gview.layout.sequence.SlotTranslator
 
getBottomTickThickness() - Method in class ca.corefacility.gview.layout.sequence.SlotTranslatorImp
 
getBounds() - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
getBounds() - Method in class ca.corefacility.gview.managers.labels.Label
 
getBounds2D() - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
getBoundsList(int) - Method in class ca.corefacility.gview.managers.labels.LabelSlotBounds
 
getBucketToAddTo(double) - Method in class ca.corefacility.gview.managers.labels.LabelBuckets
Gives us the bucket value the passed zoomValue would be added to.
getBuildDate() - Method in class ca.corefacility.gview.utils.GViewInformation
 
getBuildRevision() - Method in class ca.corefacility.gview.utils.GViewInformation
 
getCameraBounds() - Method in class ca.corefacility.gview.map.event.DisplayUpdated
 
getCategories() - Method in class ca.corefacility.gview.style.datastyle.mapper.AnnotationMapper
 
getCategories() - Method in class ca.corefacility.gview.style.datastyle.mapper.COGMapper
 
getCategories() - Method in interface ca.corefacility.gview.style.datastyle.mapper.DiscretePropertyMapper
 
getCenter() - Method in class ca.corefacility.gview.layout.sequence.circular.SlotRegionCircular
 
getCenter() - Method in class ca.corefacility.gview.layout.sequence.linear.SlotRegionLinear
 
getCenter() - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
 
getCenterBaseValue() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getCenterBaseValue() - Method in interface ca.corefacility.gview.map.GViewMap
 
getCenterBaseValue() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getCenterPoint() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getCenterPoint() - Method in class ca.corefacility.gview.managers.LayoutManager
 
getCleanInput() - Method in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
getClosestBottomHeight() - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getClosestTopHeight() - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getCOGCategory() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorMapperListItem
 
getCOGCategory() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorPanel
 
getColor() - Method in class ca.corefacility.gview.map.controllers.BackboneStyleController
 
getColor(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getColor(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getColor() - Method in class ca.corefacility.gview.map.gui.editor.icon.SimpleIcon
 
getColor1() - Method in class ca.corefacility.gview.utils.Gradient
 
getColor2() - Method in class ca.corefacility.gview.utils.Gradient
 
getColors() - Method in class ca.corefacility.gview.style.datastyle.mapper.DiscretePaintMapper
 
getComboBox() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorToolBar
 
getComponent() - Method in class ca.corefacility.gview.map.event.PopUpEvent
 
getConsensusColor(PlotStyleToken) - Static method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getConsensusColor(SlotStyleToken) - Static method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getConsensusColor() - Method in class ca.corefacility.gview.map.items.OptimizedLayer
 
getConsensusColor() - Method in class ca.corefacility.gview.map.items.PlotLayer
 
getConsensusColor() - Method in class ca.corefacility.gview.map.items.SlotLayer
 
getController() - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
getCurrentBounds() - Method in class ca.corefacility.gview.layout.sequence.circular.SlotRegionCircular
 
getCurrentBounds() - Method in class ca.corefacility.gview.layout.sequence.linear.SlotRegionLinear
 
getCurrentBounds() - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
Gives the bounding box around this slot region, depending on the zoom level.
getCurrentDirectory() - Method in class ca.corefacility.gview.map.controllers.GUIController
Returns the current directory.
getCurrentDirectory() - Method in class ca.corefacility.gview.map.gui.GUIManager
 
getCurrentDisplayedSections() - Method in class ca.corefacility.gview.map.event.SectionChangedEvent
Gets the list of currently displayed sections.
getCurrentResolutionLevel() - Method in class ca.corefacility.gview.managers.ResolutionManager
 
getCurrentShape() - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
getCurrentShape() - Method in class ca.corefacility.gview.layout.prototype.CompositeShape
 
getCurrentShape() - Method in class ca.corefacility.gview.layout.prototype.NonFragmentingStretchableShape
 
getCurrentShape() - Method in class ca.corefacility.gview.layout.prototype.PinnableShape
 
getCurrentShape() - Method in class ca.corefacility.gview.layout.prototype.StrokedBackboneShape
 
getCurrentStyle() - Method in class ca.corefacility.gview.map.controllers.GUIController
 
getCurrentStyleMapManager() - Method in class ca.corefacility.gview.map.controllers.GUIController
 
getCurrentStyleTree() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorFrame
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.GUIEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelBackgroundColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelFontFamilyEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelFontSizeEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelFontStyleEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelLockColorsEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelTextColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelTextEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelVisibleEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendAlignmentEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendBackgroundColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendBorderColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemFontFamilyEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemFontSizeEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemFontStyleEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemShowSwatchEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemSwatchColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemTextColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.legendEvent.LegendItemTextEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotAutoScaleEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotDataEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotDataFileTextEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotGridLinesColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotGridLinesEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotLowerColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotRangeMaximumEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotRangeMinimumEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotTypeEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.plotEvent.PlotUpperColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.propertyMapperEvent.PropertyMapperStyleMapperEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.setEvent.SetColorEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.setEvent.SetFeatureEffectEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.setEvent.SetFeatureShapeEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.setEvent.SetThicknessEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.setEvent.SetTooltipEvent
 
getData() - Method in class ca.corefacility.gview.map.gui.editor.communication.slotEvent.SlotThicknessEvent
 
getDataClassTerm() - Static method in class ca.corefacility.gview.data.readers.EMBLFormatModified.Terms
Getter for the Ensembl-specific 'dataClass' term
getDataStyle() - Method in class ca.corefacility.gview.style.MapStyle
 
getDefaultExtension() - Method in class ca.corefacility.gview.writers.ImageWriterFilter
 
getDefaultExtension() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.JPG
 
getDefaultExtension() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.PNG
 
getDefaultExtension() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.SVG
 
getDefaultExtension() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.SVGZ
 
getDefaultFont() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
getDefaultFontPaint() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
getDefaultFormat() - Method in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
getDefaultHeight() - Method in class ca.corefacility.gview.style.GlobalStyle
Gets the default height of the map (in pixels).
getDefaultWidth() - Method in class ca.corefacility.gview.style.GlobalStyle
Gets the default width of the map (in pixels).
getDeltaBase() - Method in class ca.corefacility.gview.layout.sequence.BaseRange
 
getDeltaHeight() - Method in class ca.corefacility.gview.layout.sequence.HeightRange
 
getDescendantName(String, String) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSWriter
Returns the selector name for the passed "base" selector name, and the passed "descendant" selector name
getDescription() - Method in class ca.corefacility.gview.map.gui.open.GFFFilter
 
getDescription() - Method in class ca.corefacility.gview.map.gui.open.SequenceDataFilter
 
getDescription() - Method in class ca.corefacility.gview.map.gui.open.StyleDataFilter
 
getDescription() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.JPG
 
getDescription() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.PNG
 
getDescription() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.SVG
 
getDescription() - Method in class ca.corefacility.gview.writers.ImageWriterFilter.SVGZ
 
getDimension() - Method in class ca.corefacility.gview.managers.labels.Label
 
getDimension() - Method in class ca.corefacility.gview.managers.labels.SequenceLabelBounds
 
getDimension() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
getDimension() - Method in interface ca.corefacility.gview.map.items.BackboneTextItem
 
getDirection() - Method in class ca.corefacility.gview.map.event.ResolutionSwitchEvent
 
getDisplayed() - Method in class ca.corefacility.gview.managers.labels.LabelsManager
 
getDisplayed() - Method in class ca.corefacility.gview.managers.LegendManager
 
getDisplayed() - Method in class ca.corefacility.gview.managers.ruler.RulerManager
 
getDisplayQuality() - Static method in class ca.corefacility.gview.map.gui.GUISettings
The quality of the PPaintContext.
getDisplayText() - Method in class ca.corefacility.gview.textextractor.StringExtractor
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.BasicEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.CompositeEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.HighlightEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.LabelLineRenderer
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.OutlineEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.OutsideEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.RaisedShadedEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.ShadingEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.ShadowEffect
 
getDrawnShape(Shape, MapItemState) - Method in interface ca.corefacility.gview.map.effects.ShapeEffectRenderer
Obtains the shape to draw, given a state and the original shape.
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.StandardEffect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.StandardEffectMouseOverSelect
 
getDrawnShape(Shape, MapItemState) - Method in class ca.corefacility.gview.map.effects.StandardEffectSelect
 
getElementControl() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getElementControl() - Method in interface ca.corefacility.gview.map.GViewMap
Provides access to an ElementControl object to control display of elements on the map.
getElementControl() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getEMBLTerm() - Static method in class ca.corefacility.gview.data.readers.EMBLFormatModified.Terms
Getter for the EMBL term
getEnd() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.OverlapsLocationPanel
 
getEnd() - Method in class ca.corefacility.gview.utils.thread.ThreadRange
 
getEndBase() - Method in class ca.corefacility.gview.layout.sequence.BaseRange
 
getEndBase() - Method in class ca.corefacility.gview.layout.sequence.SequenceRectangle
 
getEndHeight() - Method in class ca.corefacility.gview.layout.sequence.HeightRange
 
getEndHeight() - Method in class ca.corefacility.gview.layout.sequence.SequenceRectangle
 
getExpandedDescendantNodes(TreePath) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getFeature() - Method in interface ca.corefacility.gview.map.items.FeatureItem
 
getFeature() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getFeatureEffectRenderer(String) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
Converts the string to the associated ShapeEffectRender object.
getFeatureEffectRenderer(ShapeEffectRenderer) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
Converts the shape effect renderer to a string.
getFeatureFilters(MapStyle) - Method in class ca.corefacility.gview.style.io.gss.coders.FilterCoder
 
getFeatureHolderStyle() - Method in interface ca.corefacility.gview.map.items.FeatureItem
 
getFeatureHolderStyle() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
Searches for a sub-FeatureHolderStyle with the passed FeatureFilter
getFeatureHolderStyle(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getFeatureHolderStyle(FeatureFilter) - Method in interface ca.corefacility.gview.style.datastyle.StyleHolder
Gets a FeatureHolderStyle within this style holder.
getFeatureItem(Feature) - Method in interface ca.corefacility.gview.map.GViewMap
Searches for and returns the FeatureItem on the map representing the passed feature.
getFeatureItem(Feature) - Method in class ca.corefacility.gview.map.GViewMapImp
 
getFeatures(FeatureFilter) - Method in interface ca.corefacility.gview.data.GenomeData
Gives all features filtered out by the passed filter.
getFeatures(FeatureFilter) - Method in class ca.corefacility.gview.data.GenomeDataImp
 
getFeatures() - Method in class ca.corefacility.gview.data.readers.cgview.CGViewSetFeatureFilter
 
getFeatureSetMap() - Method in class ca.corefacility.gview.style.io.gss.FilterConverter
 
getFeatureShapeRealizer(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getFeatureShapeRealizer(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getFeatureShapeRealizer() - Method in interface ca.corefacility.gview.map.items.FeatureItem
Obtains the FeatureShapeRealizer which is used to draw out the feature's shape.
getFeatureShapeRealizer() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getFeatureShapeRealizer() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getFeatureShapeRealizer() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getFeaturesLayer() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getFeaturesLayer() - Method in class ca.corefacility.gview.managers.FeaturesManager
Provides access to layer storing all features, builds features if necessary.
getFeatureTextExtractors() - Method in class ca.corefacility.gview.textextractor.StringBuilder
 
getFileName(URI) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getFileWriterController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getFilter() - Method in class ca.corefacility.gview.layout.plot.FeatureFilterMappable
 
getFilter() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getFilters() - Method in class ca.corefacility.gview.utils.AndFilter
 
getFont(LabelStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getFont(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getFont(LegendItemStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getFont() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getFont() - Method in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
getFont() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getFont() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getFont() - Method in class ca.corefacility.gview.style.items.TooltipStyle
 
getFontColor(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getFontColor(LegendItemStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getFormat() - Method in class ca.corefacility.gview.textextractor.StringBuilder
 
getGenomeData() - Method in class ca.corefacility.gview.data.readers.GViewFileData
 
getGenomeData() - Method in class ca.corefacility.gview.map.gui.Style
 
getGenomeData() - Method in interface ca.corefacility.gview.map.GViewMap
Provides access to the GenomeData this map is viewing.
getGenomeData() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getGenomeDataController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getGenomicTerm() - Static method in class ca.corefacility.gview.data.readers.EMBLFormatModified.Terms
Getter for the Ensembl-specific 'genomic' term
getGlobalStyle() - Method in class ca.corefacility.gview.style.MapStyle
 
getGlobalStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getGradientPaint(Shape) - Method in class ca.corefacility.gview.utils.Gradient
 
getGridColor(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getGridLines(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getGridLines() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getGridLineThickness() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getGridPaint() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getGSS() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.GSSStringPanel
 
getGUIController() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorFrame
 
getGUIEvent() - Method in class ca.corefacility.gview.map.gui.editor.communication.CommunicationEvent
 
getGViewGUIFrame() - Method in class ca.corefacility.gview.map.controllers.GUIController
 
getGViewMapManager() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getHeight() - Method in class ca.corefacility.gview.utils.Dimension2DDouble
 
getHeight() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getHeight() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getHeightAdjust() - Method in interface ca.corefacility.gview.map.items.FeatureItem
 
getHeightAdjust() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getHeightAdjust() - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
Gets the heightAdjust in the slot.
getHeightFromBackbone() - Method in class ca.corefacility.gview.layout.prototype.SequenceOffset
 
getHeightFromBackbone() - Method in interface ca.corefacility.gview.layout.prototype.SequencePoint
 
getHeightFromBackbone() - Method in class ca.corefacility.gview.layout.prototype.SequencePointImp
 
getHeightFromBackbone(int, double) - Method in interface ca.corefacility.gview.layout.sequence.SlotTranslator
Gives the point on the actual screen from the passed parameters.
getHeightFromBackbone(int, double) - Method in class ca.corefacility.gview.layout.sequence.SlotTranslatorImp
 
getHeightRange() - Method in class ca.corefacility.gview.layout.sequence.SequenceRectangle
 
getHyperlink() - Method in interface ca.corefacility.gview.map.items.FeatureItem
 
getHyperlink() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getHyperlinkExtractor() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getHyperlinkExtractor() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getIconHeight() - Method in class ca.corefacility.gview.map.gui.editor.icon.SolidIcon
 
getIconHeight() - Method in class ca.corefacility.gview.map.gui.editor.icon.TreeIcon
 
getIconWidth() - Method in class ca.corefacility.gview.map.gui.editor.icon.SolidIcon
 
getIconWidth() - Method in class ca.corefacility.gview.map.gui.editor.icon.TreeIcon
 
getID() - Method in class ca.corefacility.gview.map.gui.editor.node.StyleEditorNode
 
getId() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getID() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getIdentifier(Link) - Method in class ca.corefacility.gview.style.io.gss.LinkMapper
This always returns the same identifier for the same link.
getImage() - Method in interface ca.corefacility.gview.map.GViewMap
Gets the current view as a BufferedImage (of type INT_ARGB).
getImage(int) - Method in interface ca.corefacility.gview.map.GViewMap
Gets the current view as a BufferedImage of the specific type
getImage() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getImage(int) - Method in class ca.corefacility.gview.map.GViewMapImp
 
getInitialBackboneLength() - Method in class ca.corefacility.gview.style.items.BackboneStyle
 
getInitialBase() - Method in interface ca.corefacility.gview.data.GenomeData
 
getInitialBase() - Method in class ca.corefacility.gview.data.GenomeDataImp
 
getInitialLineLength() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getInputStream(String) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getInputStream(URL) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getInstance() - Static method in class ca.corefacility.gview.map.gui.GUIManager
 
getInstance() - Static method in class ca.corefacility.gview.map.gui.open.OpenDialog
 
getInstance() - Static method in class ca.corefacility.gview.map.inputHandler.ImageExportHandler
 
getIteratorFor(LabelRank) - Method in class ca.corefacility.gview.managers.labels.LabelsStore
 
getKey() - Method in class ca.corefacility.gview.utils.AnnotationValueContains
 
getLabel() - Method in class ca.corefacility.gview.managers.labels.LabelPosition
 
getLabel() - Method in class ca.corefacility.gview.managers.ruler.TickMark
 
getLabeledFeature() - Method in class ca.corefacility.gview.managers.labels.Label
 
getLabeledFeature() - Method in class ca.corefacility.gview.map.items.BackboneLabelItem
 
getLabelExtractor(LabelStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getLabelExtractor() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getLabelLineLayer() - Method in class ca.corefacility.gview.managers.labels.Label
 
getLabelLinePaint() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
Gets the paint used to color the label line.
getLabelRanker() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getLabelsDisplayed() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getLabelsDisplayed() - Method in class ca.corefacility.gview.map.ElementControl
 
getLabelsLayer() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getLabelsLayer() - Method in class ca.corefacility.gview.managers.labels.LabelsManager
Creates the layer and stores all the labels added with addLabel into it.
getLabelsLayer() - Method in class ca.corefacility.gview.managers.labels.LabelsManagerSingle
Creates the layer and stores all the labels added with addLabel into it.
getLabelsLayer() - Method in class ca.corefacility.gview.managers.labels.LabelsManagerSlots
 
getLabelStyle() - Method in class ca.corefacility.gview.managers.labels.Label
 
getLabelStyle() - Method in interface ca.corefacility.gview.style.datastyle.FeatureContainerStyle
 
getLabelStyle() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getLabelStyle() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getLabelStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getLabelStyleToken(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getLabelStyleToken(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getLabelsVisible(LabelStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getLabelTextItem() - Method in class ca.corefacility.gview.managers.labels.Label
 
getLabelTextLayer() - Method in class ca.corefacility.gview.managers.labels.Label
 
getLayout() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getLayoutFactory() - Method in interface ca.corefacility.gview.map.GViewMap
Provides access to the layout for this map.
getLayoutFactory() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getLegendBounds() - Method in class ca.corefacility.gview.managers.LegendManager
 
getLegendDisplayed() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getLegendDisplayed() - Method in class ca.corefacility.gview.map.ElementControl
 
getLegendFlavor() - Static method in class ca.corefacility.gview.map.gui.editor.transfer.LegendTransferable
 
getLegendImage() - Method in interface ca.corefacility.gview.map.GViewMap
Gets the current Legend of this map as a BufferedImage (of type INT_ARGB)
getLegendImage(int) - Method in interface ca.corefacility.gview.map.GViewMap
Gets the current Legend of this map as a BufferedImage of the specific type.
getLegendImage() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getLegendImage(int) - Method in class ca.corefacility.gview.map.GViewMapImp
 
getLegendItems(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getLegendItemStyle() - Method in class ca.corefacility.gview.map.items.LegendEntryItem
 
getLegendItemStyle(int) - Method in class ca.corefacility.gview.style.items.LegendStyle
Returns the appropriate legend item style given its index.
getLegendItemStyleIndex() - Method in class ca.corefacility.gview.map.gui.editor.transfer.LegendTransferableData
 
getLegendItemSyle() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendItemNode
 
getLegendItemSyle() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
getLegendLayer() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getLegendLayer() - Method in class ca.corefacility.gview.managers.LegendManager
 
getLegends() - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getLegendStyle() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendStyleNode
 
getLegendStyle() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendPanel
 
getLegendStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getLegendStyleController() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
getLegendStyleController() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendPanel
 
getLegendStyleIndex() - Method in class ca.corefacility.gview.map.gui.editor.transfer.LegendTransferableData
 
getLegendText() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
getLengthFromBase() - Method in class ca.corefacility.gview.layout.prototype.SequenceOffset
 
getlengthProportion() - Method in class ca.corefacility.gview.managers.ruler.TickMark
 
getLine() - Method in class ca.corefacility.gview.managers.labels.Label
 
getLineThickness() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getLink(LegendItemStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getLink() - Method in interface ca.corefacility.gview.map.controllers.link.Linkable
 
getLink(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getLink() - Method in class ca.corefacility.gview.map.gui.editor.communication.LinkEvent
 
getLink() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendItemNode
 
getLink() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
 
getLink() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
 
getLink() - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
getLink() - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
getLink() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getLink(String) - Method in class ca.corefacility.gview.style.io.gss.LinkMapper
This always returns the same link for the same identifier.
getLink() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
getLinkController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getLinks() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
 
getListConsistency(Class<?>) - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperList
Determines whether or not this list is consistent.
getListSize() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperList
 
getLocation() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
getLocation() - Method in interface ca.corefacility.gview.map.items.BackboneItem
 
getLocation() - Method in class ca.corefacility.gview.map.items.BasicBackboneItem
 
getLocation() - Method in class ca.corefacility.gview.map.items.BorderItem
 
getLocation() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getLocation() - Method in class ca.corefacility.gview.map.items.PlotItem
 
getLocationConverter() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getLockedLabelColors(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getLockedLabelColors() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getLongestTickLabel(int) - Static method in class ca.corefacility.gview.managers.ruler.TickMarkCalculator
Determines the longest (in terms of characters) tick mark label possible for the given sequence length.
getLowerColor(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getLowerScale() - Method in class ca.corefacility.gview.managers.labels.SequenceLabelBounds
 
getLowerSlot() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getLowerSlot() - Method in class ca.corefacility.gview.style.datastyle.DataStyle
 
getLowerSlotNumber() - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getMajorLengthProportion() - Method in class ca.corefacility.gview.managers.ruler.TickMarkCalculator
 
getMajorTickColor() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getMajorTickLength() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getMajorTickLength() - Method in class ca.corefacility.gview.style.items.RulerStyle
Gets the length of the major tick marks.
getMajorTickPaint() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getMapItems() - Method in class ca.corefacility.gview.map.items.FeaturesLayer
 
getMapStyle() - Method in class ca.corefacility.gview.data.readers.GViewFileData
 
getMapStyle() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getMapStyle() - Method in interface ca.corefacility.gview.map.GViewMap
 
getMapStyle() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getMatchSymbols() - Method in class ca.corefacility.gview.utils.content.ContentCalculator
 
getMax() - Method in class ca.corefacility.gview.map.gui.editor.ScoreToOpacityMapperListItem
 
getMax() - Method in class ca.corefacility.gview.map.gui.editor.ScoreToOpacityPanel
 
getMaxBottomThickness() - Method in class ca.corefacility.gview.layout.sequence.RulerLabelThicknessCalculator
 
getMaxBucketValue() - Method in class ca.corefacility.gview.managers.labels.LabelBuckets
Gets the maximum allowable bucket value.
getMaximum(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getMaximum() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
getMaximum() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
getMaximumText() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
getMaxLabelsInSlot(int) - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getMaxMinValues() - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
 
getMaxMinValues() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
getMaxMinValues() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderPoints
 
getMaxMinValues() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
getMaxResolutionLevels(double) - Method in class ca.corefacility.gview.managers.ResolutionManager
Gets the maximum number of resolution levels.
getMaxScale() - Method in interface ca.corefacility.gview.layout.sequence.Backbone
 
getMaxScale() - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
getMaxScale() - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
getMaxScore() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyMapperScore
 
getMaxSequenceLength() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getMaxSequenceLength() - Method in interface ca.corefacility.gview.map.GViewMap
 
getMaxSequenceLength() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getMaxSlot() - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
getMaxSlots() - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getMaxTopThickness() - Method in class ca.corefacility.gview.layout.sequence.RulerLabelThicknessCalculator
 
getMaxZoomFactor() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
return The maximum zoom factor.
getMaxZoomFactor() - Method in interface ca.corefacility.gview.map.GViewMap
 
getMaxZoomFactor() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getMin() - Method in class ca.corefacility.gview.map.gui.editor.ScoreToOpacityMapperListItem
 
getMin() - Method in class ca.corefacility.gview.map.gui.editor.ScoreToOpacityPanel
 
getMinimum(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getMinimum() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
getMinimum() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
getMinimumText() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
getMinorLengthProportion() - Method in class ca.corefacility.gview.managers.ruler.TickMarkCalculator
 
getMinorTickColor() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getMinorTickLength() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getMinorTickLength() - Method in class ca.corefacility.gview.style.items.RulerStyle
Gets the length of the minor tick marks.
getMinorTickPaint() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getMinorTickThickness() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getMinScale() - Method in interface ca.corefacility.gview.layout.sequence.Backbone
 
getMinScale() - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
getMinScale() - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
getMinScore() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyMapperScore
 
getMinSlot() - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
getMinZoomFactor() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getMinZoomFactor() - Method in interface ca.corefacility.gview.map.GViewMap
 
getMinZoomFactor() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getMoveDialog() - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
 
getName() - Method in class ca.corefacility.gview.map.controllers.link.Link
 
getName() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperListItem
Returns the list item name.
getName() - Method in class ca.corefacility.gview.map.gui.Style
 
getNewStyleName() - Static method in class ca.corefacility.gview.map.gui.editor.StyleNameManager
 
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.BackboneNode
 
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.BackboneSlotNode
 
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendItemNode
 
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendStyleNode
 
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.PlotNode
 
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
This returns the color of the node.
getNodeColor() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
This returns the color of the node.
getNodeName() - Method in class ca.corefacility.gview.map.gui.editor.node.StyleEditorNode
Returns the name of the node.
getNumberOfCategories() - Method in class ca.corefacility.gview.style.datastyle.mapper.AnnotationMapper
 
getNumberOfCategories() - Method in class ca.corefacility.gview.style.datastyle.mapper.COGMapper
 
getNumberOfCategories() - Method in class ca.corefacility.gview.style.datastyle.mapper.DiscretePaintMapper
 
getNumberOfCategories() - Method in interface ca.corefacility.gview.style.datastyle.mapper.DiscretePropertyMapper
 
getNumberOfCategories() - Method in interface ca.corefacility.gview.style.datastyle.mapper.DiscreteStyleMapper
 
getNumGUIInstances() - Method in class ca.corefacility.gview.map.gui.GUIManager
 
getNumLegendItems(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getNumLegends() - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getNumPoints() - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
 
getNumPoints() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
getNumPoints() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderPoints
 
getNumPoints() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
getNumSlots() - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getOnlyFeatures(FeatureHolderStyle) - Method in interface ca.corefacility.gview.data.GenomeData
Obtains the set of all features which are styled according to the passed style.
getOnlyFeatures(FeatureHolderStyle) - Method in class ca.corefacility.gview.data.GenomeDataImp
 
getOrientation() - Method in class ca.corefacility.gview.layout.prototype.segments.StretchableSegment
 
getOutlineColor(LegendStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getOutlineColor() - Method in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
getOutlineColor(Paint) - Method in class ca.corefacility.gview.map.effects.AbstractAllEffectRenderer
 
getOutlinePaint() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
getOutlinePaint() - Method in class ca.corefacility.gview.style.items.TooltipStyle
 
getPadding() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getPaint() - Method in class ca.corefacility.gview.map.gui.editor.icon.SimpleIcon
 
getPaint() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorMapperListItem
 
getPaint() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.COGToColorPanel
 
getPaint() - Method in class ca.corefacility.gview.map.gui.editor.StyleColoredButton
 
getPaint() - Method in interface ca.corefacility.gview.map.items.FeatureItem
 
getPaint() - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
Gets the paint associated with this feature holder.
getPaint() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getPaint() - Method in class ca.corefacility.gview.style.items.BackboneStyle
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.BackboneNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.BackboneSlotNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.GlobalNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.LabelNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendItemNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendStyleNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.PlotNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.PropertyMapperNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.RootNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.RulerNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotsNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.StyleEditorNode
 
getPanel() - Method in class ca.corefacility.gview.map.gui.editor.node.TooltipNode
 
getParent() - Method in class ca.corefacility.gview.map.gui.editor.node.LegendItemNode
 
getParent() - Method in class ca.corefacility.gview.map.gui.editor.node.PlotNode
 
getParent() - Method in class ca.corefacility.gview.map.gui.editor.node.PropertyMapperNode
 
getParent() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
 
getParent() - Method in class ca.corefacility.gview.map.gui.editor.node.StyleEditorNode
 
getParent() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getPath(TreeNode) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getPathIterator(AffineTransform, double) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
getPathIterator(AffineTransform) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
getPathIterator(AffineTransform) - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision
Returns an iteration object that defines the boundary of the arc.
getPinnedPoint() - Method in interface ca.corefacility.gview.layout.prototype.BackbonePinnable
 
getPinnedPoint() - Method in class ca.corefacility.gview.layout.prototype.PinnableShape
 
getPinnedPoint() - Method in class ca.corefacility.gview.managers.labels.Label
 
getPinnedPoint() - Method in class ca.corefacility.gview.managers.labels.SequenceLabelBounds
 
getPinnedPoint() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
getPlotBuilderType(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getPlotBuilderType() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getPlotController() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
getPlotDrawerType(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getPlotDrawerType() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getPlotsLayer() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getPlotsLayer() - Method in class ca.corefacility.gview.managers.PlotsManager
 
getPlotStyle() - Method in class ca.corefacility.gview.map.controllers.PlotStyleToken
 
getPlotStyle() - Method in class ca.corefacility.gview.map.gui.editor.node.PlotNode
 
getPlotStyle() - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
getPlotStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getPopup() - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
getPopupLocation() - Method in class ca.corefacility.gview.map.gui.hint.HintLabel
 
getPopupLocation() - Method in class ca.corefacility.gview.map.gui.hint.WarningLabel
 
getPresentationName() - Method in class ca.corefacility.gview.map.gui.action.Action
 
getPriority() - Method in class ca.corefacility.gview.managers.labels.Label
 
getProperFileName(File) - Method in class ca.corefacility.gview.writers.ImageWriterFilter
Given a File, determines if the extension matches the specific instance of this file filter.
getPropertyMappable() - Method in class ca.corefacility.gview.map.controllers.PropertyMappableToken
 
getPropertyMappable(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PropertyMapperController
 
getPropertyMappable(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.PropertyMapperController
 
getPropertyMapper() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleContinuous
 
getPropertyMapper() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleDiscrete
 
getPropertyMapperController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getPropertyStyleMapper(PropertyMappableToken) - Method in class ca.corefacility.gview.map.controllers.PropertyMapperController
 
getPropertyStyleMapper() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getPropertyStyleMapper() - Method in interface ca.corefacility.gview.style.datastyle.mapper.PropertyMappable
 
getPropertyStyleMapper() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getRadius() - Method in class ca.corefacility.gview.layout.sequence.circular.Polar
 
getRadiusFromHeight(double) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
Appends the radius of the backbone to the passed height from the backbone.
getRanges(int) - Static method in class ca.corefacility.gview.utils.thread.ThreadService
This method will return a list of equal ranges, determined by the passed count parameter and the number of active threads.
getRangesFor(GenomeData) - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
getReader(URI) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getReader(String) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getReader(URL) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getRedoPresentationName() - Method in class ca.corefacility.gview.map.gui.action.Action
 
getRegion(SequencePath.Orientation) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
getRegion(SequencePath.Orientation) - Method in class ca.corefacility.gview.layout.prototype.CompositeShape
 
getRegion(SequencePath.Orientation) - Method in class ca.corefacility.gview.layout.prototype.NonFragmentingStretchableShape
 
getRegion(SequencePath.Orientation) - Method in interface ca.corefacility.gview.layout.prototype.OrientableShape
Gets the sub region of this shape with the given orientation.
getRelUpdatedRecordVersionTerm() - Static method in class ca.corefacility.gview.data.readers.EMBLFormatModified.Terms
Getter for the RelUpdatedRecordVersion term
getRenderingQuality() - Static method in class ca.corefacility.gview.map.gui.GUISettings
 
getResolutionLevel(double) - Method in class ca.corefacility.gview.managers.ResolutionManager
Determines the particular resolution level that the passed scale would lie within.
getResolutionLevel() - Method in class ca.corefacility.gview.map.event.ResolutionSwitchEvent
 
getResolutionManager() - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
getResolutionManager() - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
 
getRoot() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getRulerDisplayed() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getRulerDisplayed() - Method in class ca.corefacility.gview.map.ElementControl
 
getRulerLabelLocation() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getRulerLabelsLocation() - Method in class ca.corefacility.gview.style.items.RulerStyle
Gets the location of the labels for the ruler.
getRulerLayer() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getRulerLayer() - Method in class ca.corefacility.gview.managers.ruler.RulerManager
 
getRulerStyle() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getRulerStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getScale() - Method in class ca.corefacility.gview.layout.sequence.AbstractBackbone
 
getScale() - Method in interface ca.corefacility.gview.layout.sequence.Backbone
 
getScale() - Method in class ca.corefacility.gview.map.event.ZoomEvent
Gets the new scale of the map.
getScale() - Method in class ca.corefacility.gview.map.event.ZoomNormalEvent
 
getScaledHeight(double) - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
Returns the heightInSlot corresponding to the passed height, scaled to be between [-1, 1]
getScaleDialog() - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
 
getSectionLevel() - Method in class ca.corefacility.gview.managers.SectionID
 
getSectionLevel() - Method in class ca.corefacility.gview.managers.SectionManager
 
getSectionManager() - Method in class ca.corefacility.gview.map.event.SectionChangedEvent
Gets the current section manager.
getSectionNumber() - Method in class ca.corefacility.gview.managers.SectionID
 
getSelectedItems() - Method in class ca.corefacility.gview.map.event.FeatureSelectEvent
 
getSelectedNode() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getSelectedString() - Method in class ca.corefacility.gview.map.gui.editor.AnnotationComboBox
 
getSelection() - Method in interface ca.corefacility.gview.map.controllers.selection.Selectable
 
getSelection() - Method in class ca.corefacility.gview.map.controllers.selection.SelectionController
 
getSelection() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getSelectionController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.BackboneCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.BackgroundCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.DataStyleCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.FeatureSetCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.FilterCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.GSSCoder
 
getSelectorName(String, String) - Method in class ca.corefacility.gview.style.io.gss.coders.GSSWriter
Gives the selector name for the passed "element" name, with the passed id
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.LabelCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.LegendCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.LegendItemCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.PlotCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.RulerCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.SlotCoder
 
getSelectorName() - Method in class ca.corefacility.gview.style.io.gss.coders.TooltipCoder
 
getSelectorType(DescendantSelector) - Method in class ca.corefacility.gview.style.io.gss.coders.AbstractDescendentCoder
Returns the type of selector, given the base selector.
getSequence() - Method in interface ca.corefacility.gview.data.GenomeData
 
getSequence() - Method in class ca.corefacility.gview.data.GenomeDataImp
 
getSequenceLength() - Method in interface ca.corefacility.gview.data.GenomeData
 
getSequenceLength() - Method in class ca.corefacility.gview.data.GenomeDataImp
 
getSequenceLength() - Method in class ca.corefacility.gview.layout.sequence.LocationConverter
 
getSequenceName() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.SequenceNamePanel
 
getSequenceName() - Method in class ca.corefacility.gview.utils.SequenceNameFilter
 
getSequencePath() - Method in class ca.corefacility.gview.layout.sequence.circular.SlotRegionCircular
 
getSequencePath() - Method in class ca.corefacility.gview.layout.sequence.linear.SlotRegionLinear
 
getSequencePath() - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
 
getSetStyle() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
 
getSetStyle() - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
getSetStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getShape() - Method in class ca.corefacility.gview.layout.sequence.AbstractSequencePath
 
getShape() - Method in interface ca.corefacility.gview.layout.sequence.SequencePath
Gets the shape described by this SequencePath.
getShape() - Method in interface ca.corefacility.gview.layout.sequence.SlotPath
 
getShape() - Method in class ca.corefacility.gview.layout.sequence.SlotPathImp
 
getShape() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
getShape() - Method in interface ca.corefacility.gview.map.items.ShapeItem
 
getShapeEffectRenderer() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getShapeEffectRenderer(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getShapeEffectRenderer(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getShapeEffectRenderer() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getShapeEffectRenderer() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
getShapeEffectRenderer() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getShapeEffectRenderer() - Method in class ca.corefacility.gview.style.items.BackboneStyle
 
getShapeEffectRenderer() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getShapeRealizer(String) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
Converts the string to an associated feature shape realizer.
getShortNodeName() - Method in class ca.corefacility.gview.map.gui.editor.node.SetNode
 
getSlot() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getSlotFlavor() - Static method in class ca.corefacility.gview.map.gui.editor.transfer.SlotableTransferable
 
getSlotHeight(int) - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getSlotItems(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getSlotItems(SlotItemStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getSlotNodeDetail() - Static method in class ca.corefacility.gview.map.gui.GUISettings
 
getSlotNumber(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getSlotNumber() - Method in class ca.corefacility.gview.map.gui.editor.node.BackboneSlotNode
 
getSlotNumber() - Method in interface ca.corefacility.gview.map.gui.editor.node.Slotable
Returns the slot number.
getSlotNumber() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
 
getSlotNumber() - Method in class ca.corefacility.gview.map.gui.editor.SlotSelectionDialog
 
getSlotPath(int) - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
getSlotPath(int) - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
 
getSlotRegion() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getSlotRegion() - Method in class ca.corefacility.gview.managers.LayoutManager
 
getSlotRegion() - Method in class ca.corefacility.gview.map.event.LayoutChangedEvent
 
getSlots() - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getSlotsComparator() - Static method in class ca.corefacility.gview.map.gui.editor.transfer.StyleTransferHandler
 
getSlotSpacing() - Method in class ca.corefacility.gview.map.controllers.GlobalStyleController
 
getSlotSpacing() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getSlotStyle() - Method in class ca.corefacility.gview.map.gui.editor.node.SlotNode
 
getSlotStyle() - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
getSlotStyle(int) - Method in class ca.corefacility.gview.style.datastyle.DataStyle
Obtains a style for a feature slot with the passed name (creating it if necessary).
getSlotStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getSlotStyleController() - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
getSlotTranslator() - Method in class ca.corefacility.gview.layout.sequence.AbstractSlotRegion
 
getSlotTranslator() - Method in interface ca.corefacility.gview.layout.sequence.SlotRegion
 
getSolution1() - Method in class ca.corefacility.gview.layout.sequence.circular.DisplacementSolution
 
getSolution2() - Method in class ca.corefacility.gview.layout.sequence.circular.DisplacementSolution
 
getSourceActions(JComponent) - Method in class ca.corefacility.gview.map.gui.editor.transfer.StyleTransferHandler
 
getSpannedBases(double) - Method in interface ca.corefacility.gview.layout.sequence.Backbone
Converts from a given length along the backbone to the spanned base pairs this length covers at the current scale.
getSpannedBases(double) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
getSpannedBases(double) - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
getSpannedBases(int) - Method in interface ca.corefacility.gview.map.GViewMap
 
getSpannedBases(int) - Method in class ca.corefacility.gview.map.GViewMapImp
 
getSpannedRectangle(Rectangle2D) - Method in interface ca.corefacility.gview.layout.sequence.Backbone
Obtains the spanned SequenceRectangle on the Backbone of the passed rectangle.
getSpannedRectangle(Rectangle2D) - Method in class ca.corefacility.gview.layout.sequence.circular.BackboneCircular
 
getSpannedRectangle(Rectangle2D) - Method in class ca.corefacility.gview.layout.sequence.linear.BackboneLinear
 
getSplashScreen() - Method in class ca.corefacility.gview.map.gui.GUIManager
 
getStage() - Static method in class ca.corefacility.gview.utils.ProgressHandler
 
getStart() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.OverlapsLocationPanel
 
getStart() - Method in class ca.corefacility.gview.utils.thread.ThreadRange
 
getStartBase() - Method in class ca.corefacility.gview.layout.sequence.BaseRange
 
getStartBase() - Method in class ca.corefacility.gview.layout.sequence.SequenceRectangle
 
getStartHeight() - Method in class ca.corefacility.gview.layout.sequence.HeightRange
 
getStartHeight() - Method in class ca.corefacility.gview.layout.sequence.SequenceRectangle
 
getState() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
getState() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
getState() - Method in interface ca.corefacility.gview.map.items.MapItem
 
getState() - Method in class ca.corefacility.gview.map.items.TextItemImp
 
getStranded() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.StrandedPanel
 
getStretchZoomFactor() - Method in class ca.corefacility.gview.map.inputHandler.ZoomSubject
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.FeatureHolderStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.LabelStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.LegendItemStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.LegendStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.PlotStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.SlotItemStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.controllers.SlotStyleToken
 
getStyle() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getStyleController() - Method in class ca.corefacility.gview.map.gui.Style
 
getStyleEditor() - Method in class ca.corefacility.gview.map.controllers.GUIController
 
getStyleMapper() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleContinuous
 
getStyleMapper() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleDiscrete
 
getStyleName() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Returns the name of the tree.
getStyleNameFromFile(URI) - Static method in class ca.corefacility.gview.map.gui.editor.StyleNameManager
Derives the name of the style based on the passed file.
getStyles() - Method in class ca.corefacility.gview.map.controllers.GUIController
 
getStyleTrees() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorFrame
 
getSwatchColor(LegendItemStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getSwatchPaint() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
getSwatchVisible(LegendItemStyleToken) - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getSwitchScale() - Method in class ca.corefacility.gview.managers.ResolutionManager
The Scale switch value defines the value which is multiplied by the previous zoom level we switched at to get the next zoom level to switch.
getText(LegendItemStyleToken) - Static method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
getText() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
getTextAlignment() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
getTextBackgroundColor() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getTextBackgroundPaint() - Method in class ca.corefacility.gview.style.items.RulerStyle
Gets the text background paint for the ruler labels.
getTextBounds() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
getTextBounds() - Method in interface ca.corefacility.gview.map.items.BackboneTextItem
 
getTextColor(LabelStyleToken) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
 
getTextColor() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getTextColor() - Method in class ca.corefacility.gview.map.controllers.TooltipStyleController
 
getTextExtractor(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getTextExtractor(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getTextFont() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
getTextPaint() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
getTextPaint() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
getTextPaint() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getTextPaint() - Method in class ca.corefacility.gview.style.items.TooltipStyle
The paint used for the text.
getTheta() - Method in class ca.corefacility.gview.layout.sequence.circular.Polar
 
getThetaDegree() - Method in class ca.corefacility.gview.layout.sequence.circular.Polar
 
getThickness() - Method in class ca.corefacility.gview.map.controllers.BackboneStyleController
 
getThickness(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
getThickness(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getThickness() - Method in interface ca.corefacility.gview.map.items.FeatureItem
 
getThickness() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getThickness() - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
Gets the thickness of the features in this holder (in range [0,1])
getThickness() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
Gets the thickness of this slot.
getThickness() - Method in class ca.corefacility.gview.style.items.BackboneStyle
 
getTickDensity() - Method in class ca.corefacility.gview.managers.ruler.TickMarkCalculator
 
getTickDensity() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getTickDensity() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
getTickThickness() - Method in class ca.corefacility.gview.map.controllers.RulerStyleController
 
getTickThickness() - Method in class ca.corefacility.gview.style.items.RulerStyle
The thickness of the tick marks.
getTitle() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getTitleFont() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getTitlePaint() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getToolTip() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
getToolTip() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
getToolTip() - Method in class ca.corefacility.gview.map.items.BasicBackboneItem
 
getToolTip() - Method in class ca.corefacility.gview.map.items.BasicItem
 
getToolTip() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
getToolTip() - Method in class ca.corefacility.gview.map.items.LabelLineItem
 
getToolTip() - Method in interface ca.corefacility.gview.map.items.MapItem
 
getToolTip() - Method in class ca.corefacility.gview.map.items.TextItemImp
 
getToolTipExtractor() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
getToolTipExtractor() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getToolTipItem() - Method in class ca.corefacility.gview.managers.DisplayManager
 
getToolTipItem() - Method in class ca.corefacility.gview.map.inputHandler.ToolTipHandler
 
getTooltipStyle() - Method in class ca.corefacility.gview.style.GlobalStyle
Used to access the tool tip style for the viewer.
getTooltipStyleController() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
getTopMostHeight() - Method in interface ca.corefacility.gview.layout.sequence.SlotTranslator
 
getTopMostHeight() - Method in class ca.corefacility.gview.layout.sequence.SlotTranslatorImp
 
getTopSlot() - Method in class ca.corefacility.gview.managers.labels.LabelSlots
 
getTopTickThickness() - Method in interface ca.corefacility.gview.layout.sequence.SlotTranslator
 
getTopTickThickness() - Method in class ca.corefacility.gview.layout.sequence.SlotTranslatorImp
 
getTotalAverageContent() - Method in class ca.corefacility.gview.utils.content.AverageCalculator
Calculates the average symbol content from the registered symbols.
getTotalAverageContent() - Method in class ca.corefacility.gview.utils.content.SkewCalculator
Calculates average skew for the whole sequence.
getTotalSections() - Method in class ca.corefacility.gview.managers.SectionManager
 
getTransferData(DataFlavor) - Method in class ca.corefacility.gview.map.gui.editor.transfer.LegendTransferable
 
getTransferData(DataFlavor) - Method in class ca.corefacility.gview.map.gui.editor.transfer.SlotableTransferable
 
getTransferDataFlavors() - Method in class ca.corefacility.gview.map.gui.editor.transfer.LegendTransferable
 
getTransferDataFlavors() - Method in class ca.corefacility.gview.map.gui.editor.transfer.SlotableTransferable
 
getTransparency() - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
Opacity defining how the features in this holder will be drawn.
getTransparency() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
getTransparency() - Method in class ca.corefacility.gview.utils.Gradient
 
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTreeRenderer
 
getTreeModel() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
Returns the tree model.
getType() - Method in class ca.corefacility.gview.managers.ruler.TickMark
 
getType() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.ByTypePanel
 
getTypes() - Method in class ca.corefacility.gview.map.controllers.GenomeDataController
 
getUndoPresentationName() - Method in class ca.corefacility.gview.map.gui.action.Action
 
getUpperColor(PlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.PlotStyleController
 
getUpperScale() - Method in class ca.corefacility.gview.managers.labels.SequenceLabelBounds
 
getUpperSlot() - Method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
getUpperSlot() - Method in class ca.corefacility.gview.style.datastyle.DataStyle
 
getUpperSlotNumber() - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
getURI() - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
 
getURI() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
getURI() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderPoints
 
getURI() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
getURI() - Method in class ca.corefacility.gview.map.gui.Style
 
getURI() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
Gets the URI where this plot builder got its data.
getURI(String) - Static method in class ca.corefacility.gview.utils.FileLocationHandler
 
getValue() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.AnnotationValueContainsPanel
 
getValue() - Method in class ca.corefacility.gview.map.gui.editor.featureFilter.AnnotationValueEqualsPanel
 
getValue() - Method in class ca.corefacility.gview.utils.AnnotationValueContains
 
getVersion() - Method in class ca.corefacility.gview.utils.GViewInformation
 
getVersionLineTerm() - Static method in class ca.corefacility.gview.data.readers.EMBLFormatModified.Terms
Getter for the Ensembl-specific 'versionLine' term
getViewBounds() - Method in class ca.corefacility.gview.map.event.DisplayUpdated
 
getViewHeight() - Method in interface ca.corefacility.gview.map.GViewMap
Gets the height of the current view
getViewHeight() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getViewWidth() - Method in interface ca.corefacility.gview.map.GViewMap
Gets the width of the current view
getViewWidth() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getWarningFont() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getWarningPaint() - Method in class ca.corefacility.gview.style.GlobalStyle
 
getWidth() - Method in class ca.corefacility.gview.utils.Dimension2DDouble
 
getWidth() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getWidth() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getWindowPanel() - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
 
getX() - Method in class ca.corefacility.gview.map.event.PopUpEvent
 
getX() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getX() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getY() - Method in class ca.corefacility.gview.map.event.PopUpEvent
 
getY() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getY() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
Note that the arc partially inscribes the framing rectangle of this RectangularShape.
getZoomDialog() - Method in class ca.corefacility.gview.map.gui.GViewGUIFrame
 
getZoomFactor() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getZoomFactor() - Method in interface ca.corefacility.gview.map.GViewMap
 
getZoomFactor() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getZoomFactorForDistance(double, double) - Method in interface ca.corefacility.gview.map.GViewMap
 
getZoomFactorForDistance(double, double) - Method in class ca.corefacility.gview.map.GViewMapImp
 
getZoomNormalFactor() - Method in class ca.corefacility.gview.map.gui.GViewMapManager
 
getZoomNormalFactor() - Method in interface ca.corefacility.gview.map.GViewMap
 
getZoomNormalFactor() - Method in class ca.corefacility.gview.map.GViewMapImp
 
getZoomPoint() - Method in class ca.corefacility.gview.map.event.ZoomEvent
Gets the point the zoom event occured on.
getZoomToDisplay() - Method in class ca.corefacility.gview.managers.labels.Label
 
GFF3Reader - Class in ca.corefacility.gview.data.readers
 
GFF3Reader() - Constructor for class ca.corefacility.gview.data.readers.GFF3Reader
 
GFFFilter - Class in ca.corefacility.gview.map.gui.open
 
GFFFilter() - Constructor for class ca.corefacility.gview.map.gui.open.GFFFilter
 
giveLegendItemStyleID() - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
giveLegendStyleID() - Method in class ca.corefacility.gview.map.controllers.LegendStyleController
 
GLOBAL_STYLE - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
GLOBAL_STYLE_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
GLOBAL_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
GlobalNode - Class in ca.corefacility.gview.map.gui.editor.node
The node class for the global style.
GlobalNode(GlobalPanel) - Constructor for class ca.corefacility.gview.map.gui.editor.node.GlobalNode
 
GlobalPanel - Class in ca.corefacility.gview.map.gui.editor.panel
The panel for the global properties.
GlobalPanel(GlobalStyleController) - Constructor for class ca.corefacility.gview.map.gui.editor.panel.GlobalPanel
Create the panel.
GlobalStyle - Class in ca.corefacility.gview.style
Stores all the information would effect the appearance of the map independent of the data.
GlobalStyle() - Constructor for class ca.corefacility.gview.style.GlobalStyle
Creates a new object used to define global styles.
GlobalStyle(GlobalStyle) - Constructor for class ca.corefacility.gview.style.GlobalStyle
 
GlobalStyleController - Class in ca.corefacility.gview.map.controllers
This class is responsible for controlling access to the global style.
GlobalStyleController(StyleController, GlobalStyle) - Constructor for class ca.corefacility.gview.map.controllers.GlobalStyleController
 
GlobalStyleMenuItem - Class in ca.corefacility.gview.map.gui.menu
The global style menu item.
GlobalStyleMenuItem(GUIController) - Constructor for class ca.corefacility.gview.map.gui.menu.GlobalStyleMenuItem
 
GLOBE_IMAGE - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
Gradient - Class in ca.corefacility.gview.utils
 
Gradient(Color, Color) - Constructor for class ca.corefacility.gview.utils.Gradient
 
GSSCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
GSSCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.GSSCoder
 
GSSErrorHandler - Class in ca.corefacility.gview.style.io.gss
 
GSSErrorHandler() - Constructor for class ca.corefacility.gview.style.io.gss.GSSErrorHandler
 
GSSSelectorFactory - Class in ca.corefacility.gview.style.io.gss
 
GSSSelectorFactory() - Constructor for class ca.corefacility.gview.style.io.gss.GSSSelectorFactory
 
GSSStringPanel - Class in ca.corefacility.gview.map.gui.editor.featureFilter
 
GSSStringPanel() - Constructor for class ca.corefacility.gview.map.gui.editor.featureFilter.GSSStringPanel
Create the panel.
GSSWriter - Class in ca.corefacility.gview.style.io.gss.coders
 
GSSWriter(PrintWriter) - Constructor for class ca.corefacility.gview.style.io.gss.coders.GSSWriter
 
GSSWriter(Writer) - Constructor for class ca.corefacility.gview.style.io.gss.coders.GSSWriter
 
guessSymbolTokenization(File) - Method in class ca.corefacility.gview.data.readers.EMBLFormatModified
Always returns a DNA tokenizer.
guessSymbolTokenization(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.EMBLFormatModified
Always returns a DNA tokenizer.
guessSymbolTokenization(File) - Method in class ca.corefacility.gview.data.readers.GenbankFormatModified
Returns an dna parser if the letters DNA or RNA appear in the first line of the file.
guessSymbolTokenization(BufferedInputStream) - Method in class ca.corefacility.gview.data.readers.GenbankFormatModified
 
GUIController - Class in ca.corefacility.gview.map.controllers
The GUI controller is responsible for maintaining a single instance of the GUI in it's entirety.
GUIController() - Constructor for class ca.corefacility.gview.map.controllers.GUIController
 
guiController - Variable in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
GUIEvent - Class in ca.corefacility.gview.map.gui.editor.communication
This class represents a GUI event.
GUIEvent() - Constructor for class ca.corefacility.gview.map.gui.editor.communication.GUIEvent
 
GUIEventBroadcaster - Interface in ca.corefacility.gview.map.gui.editor.communication
This class represents a GUI event broadcaster.
GUIManager - Class in ca.corefacility.gview.map.gui
 
GUISettings - Class in ca.corefacility.gview.map.gui
 
GUISettings() - Constructor for class ca.corefacility.gview.map.gui.GUISettings
 
GUISettings.RenderingQuality - Enum in ca.corefacility.gview.map.gui
 
GUISettings.SlotNodeDetail - Enum in ca.corefacility.gview.map.gui
 
GUIUtility - Class in ca.corefacility.gview.map.gui
Provides utility for the GUI.
GUIUtility() - Constructor for class ca.corefacility.gview.map.gui.GUIUtility
 
GViewDataParseException - Exception in ca.corefacility.gview.data.readers
An exception thrown when there is a parsing error for the genome data.
GViewDataParseException() - Constructor for exception ca.corefacility.gview.data.readers.GViewDataParseException
 
GViewDataParseException(String, Throwable) - Constructor for exception ca.corefacility.gview.data.readers.GViewDataParseException
 
GViewDataParseException(String) - Constructor for exception ca.corefacility.gview.data.readers.GViewDataParseException
 
GViewDataParseException(Throwable) - Constructor for exception ca.corefacility.gview.data.readers.GViewDataParseException
 
GViewEvent - Class in ca.corefacility.gview.map.event
The root class for all GView events.
GViewEvent(Object) - Constructor for class ca.corefacility.gview.map.event.GViewEvent
Constructs an event object.
GViewEventListener - Interface in ca.corefacility.gview.map.event
 
GViewEventSubject - Interface in ca.corefacility.gview.map.event
Interface defining an observer for GView events.
GViewEventSubjectImp - Class in ca.corefacility.gview.map.event
A standalone implementation of the GViewEventSubject interface
GViewEventSubjectImp() - Constructor for class ca.corefacility.gview.map.event.GViewEventSubjectImp
 
GViewEventSubjectImp(GViewEventSubjectImp) - Constructor for class ca.corefacility.gview.map.event.GViewEventSubjectImp
 
GViewFileData - Class in ca.corefacility.gview.data.readers
Defines a class which can store the GView data that is extracted from a file.
GViewFileData(GenomeData, MapStyle) - Constructor for class ca.corefacility.gview.data.readers.GViewFileData
Constructs a new GViewFileData object storing the passed information.
GViewFileReader - Class in ca.corefacility.gview.data.readers
A factory to create GViewFileReaders from the passed input file.
GViewFileReader() - Constructor for class ca.corefacility.gview.data.readers.GViewFileReader
 
GViewGUIFrame - Class in ca.corefacility.gview.map.gui
The GUI frame for GView.
GViewGUIFrame(GUIController) - Constructor for class ca.corefacility.gview.map.gui.GViewGUIFrame
 
GViewInformation - Class in ca.corefacility.gview.utils
Extracts GView version information from the GView jar.
GViewMain - Class in ca.corefacility.gview.main
The main class for the GView jar file.
GViewMain() - Constructor for class ca.corefacility.gview.main.GViewMain
 
GViewMap - Interface in ca.corefacility.gview.map
gview.main viewing area, handles display of items
GViewMapFactory - Class in ca.corefacility.gview.map
Responsible for creating a new gViewMap with the appropriate info.
GViewMapFactory() - Constructor for class ca.corefacility.gview.map.GViewMapFactory
 
GViewMapImp - Class in ca.corefacility.gview.map
 
GViewMapImp(GenomeData, MapStyle, LayoutFactory) - Constructor for class ca.corefacility.gview.map.GViewMapImp
Creates a new map from the passed data.
GViewMapManager - Class in ca.corefacility.gview.map.gui
 
GViewMapManager(Style, GViewMap) - Constructor for class ca.corefacility.gview.map.gui.GViewMapManager
 
GViewMapManager.Layout - Enum in ca.corefacility.gview.map.gui
 
GViewToolBar - Class in ca.corefacility.gview.map.gui
The default tool bar for the GUI frame.
GViewToolBar(GUIController) - Constructor for class ca.corefacility.gview.map.gui.GViewToolBar
 
gViewWebsite - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 

H

HALF - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
handleGUIEvent(GUIEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
Appropriately handles the event.
handlesType(String) - Method in class ca.corefacility.gview.writers.ImageWriterFilter
Determines the file type (by extension) this filter handles.
handlesType(String) - Method in class ca.corefacility.gview.writers.ImageWriterFilter.JPG
 
handlesType(String) - Method in class ca.corefacility.gview.writers.ImageWriterFilter.PNG
 
handlesType(String) - Method in class ca.corefacility.gview.writers.ImageWriterFilter.SVG
 
handlesType(String) - Method in class ca.corefacility.gview.writers.ImageWriterFilter.SVGZ
 
HasAnnotationCoder - Class in ca.corefacility.gview.style.io.gss.featureFilterCoder
 
HasAnnotationCoder() - Constructor for class ca.corefacility.gview.style.io.gss.featureFilterCoder.HasAnnotationCoder
 
HasAnnotationPanel - Class in ca.corefacility.gview.map.gui.editor.featureFilter
 
HasAnnotationPanel(GenomeDataController) - Constructor for class ca.corefacility.gview.map.gui.editor.featureFilter.HasAnnotationPanel
Create the panel.
hasElement(JComboBox, Object) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
Determines whether a JComboBox contains the passed object.
hasFeatureFilter(FeatureFilter) - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
Determines if this holder style is using the passed FeatureFilter.
hashCode() - Method in class ca.corefacility.gview.layout.plot.FeatureFilterMappable
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotBuilder
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderAnnotation
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotBuilderRange
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotDrawerBar
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotDrawerCenter
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotDrawerLine
 
hashCode() - Method in class ca.corefacility.gview.layout.plot.PlotDrawerSolid
 
hashCode() - Method in class ca.corefacility.gview.managers.LegendManager
 
hashCode() - Method in class ca.corefacility.gview.managers.SectionID
 
hashCode() - Method in class ca.corefacility.gview.map.effects.CompositeEffect
 
hashCode() - Method in class ca.corefacility.gview.map.effects.OutsideEffect
 
hashCode() - Method in class ca.corefacility.gview.map.effects.RaisedShadedEffect
 
hashCode() - Method in class ca.corefacility.gview.map.effects.ShadowEffect
 
hashCode() - Method in class ca.corefacility.gview.map.effects.StandardEffect
 
hashCode() - Method in class ca.corefacility.gview.map.event.GViewEventSubjectImp
 
hashCode() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
hashCode() - Method in class ca.corefacility.gview.map.items.FeatureItemImp
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyleFactory
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.AnnotationMapper
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.COGMapper
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.DiscretePaintMapper
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.OpacityFeatureStyleMapper
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyMapperScore
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleContinuous
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.mapper.PropertyStyleDiscrete
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Annotation
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.GCContent
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.GCSkew
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Points
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotBuilderType.Range
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Bar
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Center
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Line
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotDrawerType.Solid
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.PlotStyle
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.SlotItemStyle
 
hashCode() - Method in class ca.corefacility.gview.style.datastyle.SlotStyle
 
hashCode() - Method in class ca.corefacility.gview.style.GlobalStyle
 
hashCode() - Method in class ca.corefacility.gview.style.io.gss.featureFilterCoder.FeatureFilterCoder
 
hashCode() - Method in class ca.corefacility.gview.style.items.BackboneStyle
 
hashCode() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
hashCode() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
hashCode() - Method in class ca.corefacility.gview.style.items.RulerStyle
 
hashCode() - Method in class ca.corefacility.gview.style.items.TooltipStyle
 
hashCode() - Method in class ca.corefacility.gview.textextractor.AnnotationExtractor
 
hashCode() - Method in class ca.corefacility.gview.textextractor.StringBuilder
 
hashCode() - Method in class ca.corefacility.gview.textextractor.StringExtractor
 
hashCode() - Method in class ca.corefacility.gview.utils.AndFilter
 
hashCode() - Method in class ca.corefacility.gview.utils.Gradient
 
hashCode() - Method in class ca.corefacility.gview.utils.SequenceNameFilter
 
hasLink(TreePath[]) - Static method in class ca.corefacility.gview.map.gui.editor.StyleEditorTree
 
hasNext() - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
hasPropertyMapper(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.SetStyleController
 
hasPropertyMapper(SlotStyleToken) - Method in class ca.corefacility.gview.map.controllers.SlotStyleController
 
hasSameStyleReference(FeatureHolderStyleToken) - Method in class ca.corefacility.gview.map.controllers.FeatureHolderStyleToken
Determines whether or not the feature holder style objects within the tokens are both pointing to the same object.
headerLine - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 
height - Variable in class ca.corefacility.gview.map.gui.editor.icon.TreeIcon
 
height - Variable in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
The overall height of the full ellipse of which this arc is a partial section (not considering the angular extents).
height - Variable in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
The overall height of the full ellipse of which this arc is a partial section (not considering the angular extents).
heightAdjust - Variable in class ca.corefacility.gview.style.datastyle.SlotItemStyle
Defines the adjusted height of the center of this item in the slot.
HeightRange - Class in ca.corefacility.gview.layout.sequence
Defines a range in terms of height coordinates on the sequence.
HeightRange(double, double) - Constructor for class ca.corefacility.gview.layout.sequence.HeightRange
 
HELP_PAGE_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
HELP_SHORTCUT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
HELP_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
HELP_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
HelpMenu - Class in ca.corefacility.gview.map.gui.editor.menu
The help menu for the style editor.
HelpMenu() - Constructor for class ca.corefacility.gview.map.gui.editor.menu.HelpMenu
 
HelpMenu - Class in ca.corefacility.gview.map.gui.menu
Responsible for creating the help menu.
HelpMenu(GViewGUIFrame) - Constructor for class ca.corefacility.gview.map.gui.menu.HelpMenu
Creates the help menu.
HIDDEN - Static variable in class ca.corefacility.gview.layout.feature.FeatureShapeRealizer
Does not create any shape for a feature, so that it is hidden.
HiddenLabelRanker - Class in ca.corefacility.gview.managers.labels
 
HiddenLabelRanker() - Constructor for class ca.corefacility.gview.managers.labels.HiddenLabelRanker
 
HiddenShapeRealizer - Class in ca.corefacility.gview.layout.feature
Draws no shape for the feature.
HiddenShapeRealizer() - Constructor for class ca.corefacility.gview.layout.feature.HiddenShapeRealizer
 
HideAllAction - Class in ca.corefacility.gview.map.gui.action.map.hide
Hide all action class.
HideAllAction(ElementControl) - Constructor for class ca.corefacility.gview.map.gui.action.map.hide.HideAllAction
 
HideBEVDialogAction - Class in ca.corefacility.gview.map.gui.action.dialog.hide
Hide bird's eye view dialog action class.
HideBEVDialogAction(BEVDialog) - Constructor for class ca.corefacility.gview.map.gui.action.dialog.hide.HideBEVDialogAction
 
HideDialogAction - Class in ca.corefacility.gview.map.gui.action.dialog.hide
Hide dialog action class.
HideItemAction - Class in ca.corefacility.gview.map.gui.action.map.hide
Hide item action class.
HideItemAction() - Constructor for class ca.corefacility.gview.map.gui.action.map.hide.HideItemAction
 
HideLabelsAction - Class in ca.corefacility.gview.map.gui.action.map.hide
Hide labels action class.
HideLabelsAction(ElementControl) - Constructor for class ca.corefacility.gview.map.gui.action.map.hide.HideLabelsAction
 
HideLegendAction - Class in ca.corefacility.gview.map.gui.action.map.hide
Hide legend action class.
HideLegendAction(ElementControl) - Constructor for class ca.corefacility.gview.map.gui.action.map.hide.HideLegendAction
 
hideOpenDialog() - Static method in class ca.corefacility.gview.map.gui.open.OpenDialog
 
HideRulerAction - Class in ca.corefacility.gview.map.gui.action.map.hide
Hide ruler action class.
HideRulerAction(ElementControl) - Constructor for class ca.corefacility.gview.map.gui.action.map.hide.HideRulerAction
 
HideStyleEditorAction - Class in ca.corefacility.gview.map.gui.action.map.hide
Hide style editor action class.
HideStyleEditorAction(StyleEditorFrame) - Constructor for class ca.corefacility.gview.map.gui.action.map.hide.HideStyleEditorAction
 
hideToolTip() - Method in class ca.corefacility.gview.map.inputHandler.ToolTipHandler
Hides the tool tip item if necessary.
HIGH_QUALITY_TEXT - Static variable in class ca.corefacility.gview.map.gui.GUIUtility
 
HighlightEffect - Class in ca.corefacility.gview.map.effects
 
HighlightEffect() - Constructor for class ca.corefacility.gview.map.effects.HighlightEffect
 
HintLabel - Class in ca.corefacility.gview.map.gui.hint
A label designed to show tooltip help information on mouse-over.
HintLabel(String) - Constructor for class ca.corefacility.gview.map.gui.hint.HintLabel
 
HintLabel(String, ImageIcon) - Constructor for class ca.corefacility.gview.map.gui.hint.HintLabel
 
HintPopup - Class in ca.corefacility.gview.map.gui.hint
The custom implementation of the tooltip as a window.
HintPopup(HintLabel) - Constructor for class ca.corefacility.gview.map.gui.hint.HintPopup
 
HueFeatureStyleMapper - Class in ca.corefacility.gview.style.datastyle.mapper
 
HueFeatureStyleMapper() - Constructor for class ca.corefacility.gview.style.datastyle.mapper.HueFeatureStyleMapper
 
HueFeatureStyleMapper(float, float) - Constructor for class ca.corefacility.gview.style.datastyle.mapper.HueFeatureStyleMapper
 
hyperlinkUpdate(HyperlinkEvent) - Method in class ca.corefacility.gview.map.gui.dialog.AboutDialog
 

I

ignorableAtRule(String) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
ImageExportHandler - Class in ca.corefacility.gview.map.inputHandler
 
ImageWriter - Class in ca.corefacility.gview.writers
Writes the map to an image.
ImageWriter() - Constructor for class ca.corefacility.gview.writers.ImageWriter
 
ImageWriterFactory - Class in ca.corefacility.gview.writers
Provides methods to build an ImageWriter to be used to write GView-generated images to a specific file format.
ImageWriterFactory() - Constructor for class ca.corefacility.gview.writers.ImageWriterFactory
 
ImageWriterFilter - Class in ca.corefacility.gview.writers
 
ImageWriterFilter() - Constructor for class ca.corefacility.gview.writers.ImageWriterFilter
 
ImageWriterFilter.JPG - Class in ca.corefacility.gview.writers
 
ImageWriterFilter.JPG() - Constructor for class ca.corefacility.gview.writers.ImageWriterFilter.JPG
 
ImageWriterFilter.PNG - Class in ca.corefacility.gview.writers
 
ImageWriterFilter.PNG() - Constructor for class ca.corefacility.gview.writers.ImageWriterFilter.PNG
 
ImageWriterFilter.SVG - Class in ca.corefacility.gview.writers
 
ImageWriterFilter.SVG() - Constructor for class ca.corefacility.gview.writers.ImageWriterFilter.SVG
 
ImageWriterFilter.SVGZ - Class in ca.corefacility.gview.writers
 
ImageWriterFilter.SVGZ() - Constructor for class ca.corefacility.gview.writers.ImageWriterFilter.SVGZ
 
ImageWriterJPG - Class in ca.corefacility.gview.writers
 
ImageWriterJPG() - Constructor for class ca.corefacility.gview.writers.ImageWriterJPG
 
ImageWriterPNG - Class in ca.corefacility.gview.writers
 
ImageWriterPNG() - Constructor for class ca.corefacility.gview.writers.ImageWriterPNG
 
ImageWriterSVG - Class in ca.corefacility.gview.writers
 
ImageWriterSVG(String) - Constructor for class ca.corefacility.gview.writers.ImageWriterSVG
Creates a new SVG image writer
importData(TransferHandler.TransferSupport) - Method in class ca.corefacility.gview.map.gui.editor.transfer.StyleTransferHandler
 
importStyle(String, SACMediaList, String) - Method in class ca.corefacility.gview.style.io.gss.StyleHandler
 
ImportStyleAction - Class in ca.corefacility.gview.map.gui.action.style
 
ImportStyleAction(GUIController) - Constructor for class ca.corefacility.gview.map.gui.action.style.ImportStyleAction
 
initialize() - Static method in class ca.corefacility.gview.utils.ProgressHandler
Initialize without a splash screen.
initialize(SplashScreen) - Static method in class ca.corefacility.gview.utils.ProgressHandler
Initialize with a splash screen.
initializeGUI() - Method in class ca.corefacility.gview.map.controllers.GUIController
Initializes the GUI.
initializeLabelLocks(Iterator<SlotStyle>) - Method in class ca.corefacility.gview.map.controllers.LabelStyleController
Determines whether or not to set ALL the label locks.
initializeLocks(LabelStyleController) - Method in class ca.corefacility.gview.map.gui.GViewMapManager
Initalizes the set-label locks.
injectGFFFeatures(GenomeData, String) - Method in class ca.corefacility.gview.data.readers.GFF3Reader
 
InputEventHandler - Class in ca.corefacility.gview.map.inputHandler
Handles keyboard and mouse events on the GView map.
InputEventHandler(PCamera, GViewMap, ZoomSubject, SelectHandler, ToolTipHandler) - Constructor for class ca.corefacility.gview.map.inputHandler.InputEventHandler
Handles all keyboard/mouse input events.
inRange(double) - Method in class ca.corefacility.gview.managers.labels.SequenceLabelBounds
 
insertLegendItem(LegendItemStyle, int) - Method in class ca.corefacility.gview.style.items.LegendStyle
Inserts the legend item style at the index.
insertUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
insertUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LegendItemPanel
 
insertUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
insertUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SetPanel
 
insertUpdate(DocumentEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.SlotPanel
 
inSlotRange(int) - Static method in class ca.corefacility.gview.data.Slot
Determines if the passed slot is within the defined max/min real slot numbers.
instance - Static variable in class ca.corefacility.gview.layout.feature.FullBackboneShapeRealizer
 
instance() - Static method in class ca.corefacility.gview.utils.GViewInformation
 
intersects(double, double, double, double) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
intersects(Rectangle2D) - Method in class ca.corefacility.gview.layout.prototype.BackboneShape
 
intersects(Rectangle2D) - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
intersectsAtScale(Label, SlotRegion) - Method in class ca.corefacility.gview.layout.sequence.circular.ScaleCalculatorCircular
 
intersectsAtScale(Label, SlotRegion) - Method in class ca.corefacility.gview.layout.sequence.ScaleCalculator
 
INVALID - Static variable in class ca.corefacility.gview.data.Slot
An invalid slot number.
INVALID - Variable in class ca.corefacility.gview.map.gui.dialog.SliderDialog
 
INVALID - Static variable in interface ca.corefacility.gview.style.datastyle.mapper.ContinuousPropertyMapper
 
INVALID - Static variable in interface ca.corefacility.gview.style.datastyle.mapper.DiscretePropertyMapper
 
invokeAll(List<Callable<Object>>) - Static method in class ca.corefacility.gview.utils.thread.ThreadService
Invokes all the callables and returns a list of their Future objects or NULL list if there was an exception.
isAboveBackbone() - Method in class ca.corefacility.gview.managers.labels.Label
 
isAutoLabelLinePaint() - Method in class ca.corefacility.gview.style.datastyle.LabelStyle
Checks if the label style is such that label lines should automatically be colored (using the same paint as the label text).
isCircular() - Method in interface ca.corefacility.gview.data.GenomeData
Determines if the sequence data is circular.
isCircular() - Method in class ca.corefacility.gview.data.GenomeDataImp
 
isCircular() - Method in class ca.corefacility.gview.utils.content.ContentCalculator.ContentIterator
 
isDataFlavorSupported(DataFlavor) - Method in class ca.corefacility.gview.map.gui.editor.transfer.LegendTransferable
 
isDataFlavorSupported(DataFlavor) - Method in class ca.corefacility.gview.map.gui.editor.transfer.SlotableTransferable
 
isDisplayBoundsChanged() - Method in class ca.corefacility.gview.map.event.DisplayUpdated
 
isDisplayed() - Method in class ca.corefacility.gview.managers.labels.Label
 
isDisplayedAt(double) - Method in class ca.corefacility.gview.managers.labels.Label
Determines whether or not we should display this label, given the passed zoom level.
isDisplayLegend() - Method in class ca.corefacility.gview.style.items.LegendStyle
 
isDouble(String) - Static method in class ca.corefacility.gview.utils.Util
 
isEmpty() - Method in class ca.corefacility.gview.map.gui.editor.panel.propertyMapper.PropertyMapperList
Determines whether or not the list is empty.
isEmpty() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Double
isEmpty() - Method in class ca.corefacility.gview.utils.geom.Arc2DPrecision.Float
isEqual(Link, Link) - Static method in class ca.corefacility.gview.map.controllers.link.Link
 
isEqual(double, double) - Static method in class ca.corefacility.gview.utils.Util
 
isEqual(float, float) - Static method in class ca.corefacility.gview.utils.Util
 
isEqual(Object, Object) - Static method in class ca.corefacility.gview.utils.Util
 
isFullRebuildRequired() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
isInteger(String) - Static method in class ca.corefacility.gview.utils.Util
 
isLast() - Method in class ca.corefacility.gview.managers.SectionID
 
isLinkable(TreePath[]) - Static method in class ca.corefacility.gview.map.controllers.link.LinkController
Determines whether or not the selection is linkable.
isLinkableEvent(Class<?>) - Method in class ca.corefacility.gview.map.controllers.link.LinkController
 
isLinkConsistent() - Method in class ca.corefacility.gview.map.controllers.selection.SelectionController
 
isMinResolutionLevel(double) - Method in class ca.corefacility.gview.managers.ResolutionManager
Determines if the passed zoom value is at the minimum resolution level.
isMouseOver() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
isMouseOver() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
isMouseOver() - Method in interface ca.corefacility.gview.map.items.MapItem
 
isMouseOver() - Method in enum ca.corefacility.gview.map.items.MapItemState
 
isMouseOver() - Method in class ca.corefacility.gview.map.items.TextItemImp
 
isNewResolutionLevel(double) - Method in class ca.corefacility.gview.managers.ResolutionManager
Determines if the passed scale would cause a switch to a new resolution.
isRebuildRequired() - Method in class ca.corefacility.gview.map.controllers.Controller
 
isRebuildRequired() - Method in class ca.corefacility.gview.map.controllers.StyleController
 
isSelected() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
isSelected() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
isSelected() - Method in interface ca.corefacility.gview.map.items.MapItem
 
isSelected() - Method in enum ca.corefacility.gview.map.items.MapItemState
 
isSelected() - Method in class ca.corefacility.gview.map.items.TextItemImp
 
isSelectionConsistent() - Method in class ca.corefacility.gview.map.controllers.selection.SelectionController
 
isShowSwatch() - Method in class ca.corefacility.gview.style.items.LegendItemStyle
 
isSignificant() - Method in class ca.corefacility.gview.map.gui.action.Action
 
isSignificant() - Method in class ca.corefacility.gview.map.gui.action.dialog.hide.HideDialogAction
 
isSignificant() - Method in class ca.corefacility.gview.map.gui.action.dialog.show.ShowDialogAction
 
isSignificant() - Method in class ca.corefacility.gview.map.gui.action.map.ExportAction
 
isStyled() - Method in enum ca.corefacility.gview.map.items.MapItemState
 
isUpdating() - Method in class ca.corefacility.gview.map.gui.editor.panel.StylePanel
 
isValid() - Method in class ca.corefacility.gview.style.datastyle.FeatureHolderStyle
 
isValidFileFormat(String) - Method in class ca.corefacility.gview.writers.ImageWriter
Determines if this ImageWriter accepts the passed file format.
isVisible() - Method in class ca.corefacility.gview.main.SplashScreen
 
isXML() - Method in interface ca.corefacility.gview.data.GenomeData
 
isXML() - Method in class ca.corefacility.gview.data.GenomeDataImp
 
isXML(URI) - Static method in class ca.corefacility.gview.data.readers.cgview.CGViewXMLReader
 
isXML() - Method in class ca.corefacility.gview.map.gui.Style
 
ITALIC - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
itemsIterator() - Method in class ca.corefacility.gview.map.items.AbstractBackboneTextItem
 
itemsIterator() - Method in class ca.corefacility.gview.map.items.AbstractShapeItem
 
itemsIterator() - Method in class ca.corefacility.gview.map.items.FeatureItemsCache
 
itemsIterator() - Method in class ca.corefacility.gview.map.items.Layer
 
itemsIterator() - Method in interface ca.corefacility.gview.map.items.MapComponent
 
itemsIterator() - Method in class ca.corefacility.gview.map.items.TextItemImp
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.LabelPanel
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.editor.panel.PlotPanel
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.editor.TriStateCheckBox
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.menu.FullScreenMenuItem
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.menu.ShowAllMenuItem
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.menu.ShowLabelsMenuItem
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.menu.ShowLegendMenuItem
 
itemStateChanged(ItemEvent) - Method in class ca.corefacility.gview.map.gui.menu.ShowRulerMenuItem
 
iterator() - Method in class ca.corefacility.gview.data.BlankSymbolList
 
iterator() - Method in class ca.corefacility.gview.managers.labels.LabelsStore
 

K

keyboardFocusGained(PInputEvent) - Method in class ca.corefacility.gview.map.inputHandler.InputEventHandler
 
keyboardFocusLost(PInputEvent) - Method in class ca.corefacility.gview.map.inputHandler.InputEventHandler
 
keyPressed(PInputEvent) - Method in class ca.corefacility.gview.map.inputHandler.InputEventHandler
 
keyReleased(PInputEvent) - Method in class ca.corefacility.gview.map.inputHandler.InputEventHandler
 
KEYWORDS_TAG - Static variable in class ca.corefacility.gview.data.readers.EMBLFormatModified
 

L

Label - Class in ca.corefacility.gview.managers.labels
 
Label(LabelStyle, FeatureItem, boolean) - Constructor for class ca.corefacility.gview.managers.labels.Label
 
Label.BaseComparator - Class in ca.corefacility.gview.managers.labels
 
Label.BaseComparator() - Constructor for class ca.corefacility.gview.managers.labels.Label.BaseComparator
 
Label.HeightComparator - Class in ca.corefacility.gview.managers.labels
 
Label.HeightComparator() - Constructor for class ca.corefacility.gview.managers.labels.Label.HeightComparator
 
Label.PriorityComparatorDescending - Class in ca.corefacility.gview.managers.labels
 
Label.PriorityComparatorDescending() - Constructor for class ca.corefacility.gview.managers.labels.Label.PriorityComparatorDescending
 
Label.ZoomScaleComparatorAscending - Class in ca.corefacility.gview.managers.labels
 
Label.ZoomScaleComparatorAscending() - Constructor for class ca.corefacility.gview.managers.labels.Label.ZoomScaleComparatorAscending
 
Label.ZoomScaleComparatorDescending - Class in ca.corefacility.gview.managers.labels
 
Label.ZoomScaleComparatorDescending() - Constructor for class ca.corefacility.gview.managers.labels.Label.ZoomScaleComparatorDescending
 
LABEL_IMAGE - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
LABEL_TEXT - Static variable in class ca.corefacility.gview.map.gui.editor.StyleEditorUtility
 
LabelBackgroundColorEvent - Class in ca.corefacility.gview.map.gui.editor.communication.labelEvent
An action for modifying the label's background color.
LabelBackgroundColorEvent(Color) - Constructor for class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelBackgroundColorEvent
 
LabelBuckets - Class in ca.corefacility.gview.managers.labels
 
LabelBuckets(ResolutionManager, double) - Constructor for class ca.corefacility.gview.managers.labels.LabelBuckets
 
LabelCoder - Class in ca.corefacility.gview.style.io.gss.coders
 
LabelCoder() - Constructor for class ca.corefacility.gview.style.io.gss.coders.LabelCoder
 
LabelEvent - Class in ca.corefacility.gview.map.event
 
LabelEvent(Object) - Constructor for class ca.corefacility.gview.map.event.LabelEvent
 
LabelEvent - Class in ca.corefacility.gview.map.gui.editor.communication.labelEvent
A label event.
LabelEvent() - Constructor for class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelEvent
 
LabelFontFamilyEvent - Class in ca.corefacility.gview.map.gui.editor.communication.labelEvent
An action for modifying the label font family.
LabelFontFamilyEvent(String) - Constructor for class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelFontFamilyEvent
 
LabelFontSizeEvent - Class in ca.corefacility.gview.map.gui.editor.communication.labelEvent
An action for modifying the label font size.
LabelFontSizeEvent(int) - Constructor for class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelFontSizeEvent
 
LabelFontStyleEvent - Class in ca.corefacility.gview.map.gui.editor.communication.labelEvent
An action for modifying the label font style.
LabelFontStyleEvent(String) - Constructor for class ca.corefacility.gview.map.gui.editor.communication.labelEvent.LabelFontStyleEvent
 
LabelLineItem - Class in ca.corefacility.gview.map.items
 
LabelLineItem(BackboneLabelItem) - Constructor for class ca.corefacility.gview.map.items.LabelLineItem
 
LabelLineRenderer - Class in ca.corefacility.gview.map.effects
 
LabelLineRenderer() - Constructor for class ca.corefacility.gview.map.effects.LabelLineRenderer
 
labelLinesLayer - Variable in class ca.corefacility.gview.managers.labels.LabelsManager
 
LabelLocation - Enum in ca.corefacility.gview.style.items
Defines the location of labels on the ruler.