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Functions2,432 in github.com/rambaut/figtree

↓ 5 callersMethodgetSelectedFont
Returns a Font object representing the selection in the panel. @return the font.
src/figtree/ui/FontChooserPanel.java:118
↓ 5 callersMethodgetSingleInstance
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:388
↓ 5 callersMethodgetTaxa
@return the set of taxa associated with the external nodes of this tree. The size of this set should be the same as the size of the ex
src/figtree/treeviewer/ReRootedTree.java:300
↓ 5 callersMethodhasOption
Does an argument with label exist?
src/figtree/application/Arguments.java:418
↓ 5 callersMethodisOrderBranchesOn
()
src/figtree/treeviewer/TreePane.java:467
↓ 5 callersMethodisRootingOn
()
src/figtree/treeviewer/TreePane.java:485
↓ 5 callersMethodisTransformBranchesOn
()
src/figtree/treeviewer/TreePane.java:449
↓ 5 callersMethodload
(File f)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:125
↓ 5 callersFunctionloadInt
packaging_tools/windows/launch4j/head_src/head.c:247
↓ 5 callersMethodmaintainAspectRatio
Return whether the two axis scales should be maintained relative to each other @return a boolean
src/figtree/treeviewer/treelayouts/TreeLayout.java:101
↓ 5 callersMethodparseColor
(String value)
src/figtree/treeviewer/decorators/InterpolatingColourDecorator.java:182
↓ 5 callersMethodselectNodes
(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive)
src/figtree/treeviewer/TreeViewer.java:81
↓ 5 callersMethodsetBranchStroke
(BasicStroke stroke)
src/figtree/treeviewer/TreePane.java:422
↓ 5 callersMethodsetCrosshairShown
(boolean crosshairShown)
src/figtree/treeviewer/TreePane.java:182
↓ 5 callersMethodsetDecoratorForAttribute
(String attribute, ColourDecorator decorator)
src/figtree/treeviewer/AttributeColourController.java:192
↓ 5 callersMethodsetPaintAttributeName
(String paintAttributeName)
src/figtree/treeviewer/decorators/AttributableDecorator.java:139
↓ 5 callersMethodsetSelectionColor
(Color selectionColor)
src/figtree/treeviewer/TreePane.java:441
↓ 5 callersMethodsetSelectionMode
(TreePaneSelector.SelectionMode selectionMode)
src/figtree/treeviewer/TreeViewer.java:104
↓ 5 callersMethodsetTipLabelPainter
(LabelPainter<Node> tipLabelPainter)
src/figtree/treeviewer/TreePane.java:985
↓ 5 callersMethodsetTreeLayout
(TreeLayoutType layoutType)
src/figtree/treeviewer/TreeViewerController.java:299
↓ 5 callersMethodsetupControls
( final JComboBox colourAttributeCombo, final JButton colourSetupButton)
src/figtree/treeviewer/AttributeColourController.java:57
↓ 5 callersMethodshowTree
(int index)
src/figtree/treeviewer/DefaultTreeViewer.java:172
↓ 5 callersMethodsignalLengthViolation
(String property, String name, int maxLength)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:242
↓ 5 callersMethodunwrap
(List<StringWrapper> wrappers)
packaging_tools/windows/launch4j/src/net/sf/launch4j/ant/StringWrapper.java:48
↓ 4 callersMethodaddAbsFile
(File file)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:183
↓ 4 callersMethodaddDecorator
(Decorator decorator)
src/figtree/treeviewer/decorators/CompoundDecorator.java:42
↓ 4 callersMethodaddWindowsPath
Stores path in Windows format with '\' separators.
packaging_tools/windows/launch4j/src/net/sf/launch4j/RcBuilder.java:331
↓ 4 callersFunctionappendAppClasspath
packaging_tools/windows/launch4j/head_src/head.c:568
↓ 4 callersMethodcheckIn
(String s, String[] strings, String property, String name)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:189
↓ 4 callersMethodcheckOptStrings
(List<String> strings, int maxLength, int totalMaxLength, String property, String name)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:84
↓ 4 callersMethodconvertMouseEvent
(WMouseEvent event, int type)
src/figtree/webui/TreeWidget.java:76
↓ 4 callersMethodcreateInternalNode
Once a SimpleRootedTree has been created, the node stucture can be created by calling createExternalNode and createInternalNode. First of all createEx
src/figtree/treeviewer/ReRootedTree.java:152
↓ 4 callersMethoddelete
(File f)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Util.java:217
↓ 4 callersMethoddoExportGraphic
(GraphicFormat format)
src/figtree/application/FigTreeFrame.java:1208
↓ 4 callersFunctionexpandVars
* Expand environment %variables% */
packaging_tools/windows/launch4j/head_src/head.c:577
↓ 4 callersMethodfireAnnotationsChanged
()
src/figtree/treeviewer/ExtendedTreeViewer.java:220
↓ 4 callersMethodgetAge
(double height, RootedTree tree)
src/figtree/treeviewer/TimeScale.java:58
↓ 4 callersMethodgetAttributeNames
(Collection<? extends Attributable> items)
src/figtree/panel/TreeColouringController.java:132
↓ 4 callersMethodgetBranchOrdering
()
src/figtree/treeviewer/TreePane.java:476
↓ 4 callersMethodgetCollapsedShape
(Node node)
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:66
↓ 4 callersMethodgetColor
(Object value)
src/figtree/treeviewer/decorators/DiscreteColourDecorator.java:149
↓ 4 callersMethodgetDecoratorForAttribute
(String attribute)
src/figtree/treeviewer/AttributeColourController.java:148
↓ 4 callersMethodgetFile
(String key)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:271
↓ 4 callersMethodgetIconHeight
()
src/figtree/ui/components/ColorWellButton.java:110
↓ 4 callersMethodgetInteger
Convert 0 to null
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Jre.java:289
↓ 4 callersMethodgetLength
@param node the node whose branch length (to its parent) is being requested. @return the length of the branch to the parent node (0.0 if the node is t
src/figtree/treeviewer/ReRootedTree.java:243
↓ 4 callersMethodgetMajorTickValue
getMajorTick Returns the value of the majorTickIndex'th major tick
src/figtree/treeviewer/ScaleAxis.java:684
↓ 4 callersMethodgetMaxValue
()
src/figtree/treeviewer/decorators/ContinuousScale.java:232
↓ 4 callersMethodgetMaximumFractionDigits
Returns the maximum number of digits allowed in the fraction portion of a number. @see #setMaximumFractionDigits
src/figtree/ui/PercentFormat.java:54
↓ 4 callersMethodgetMinValue
()
src/figtree/treeviewer/decorators/ContinuousScale.java:224
↓ 4 callersMethodgetNodeAt
(Graphics2D g2, Point point)
src/figtree/treeviewer/TreePane.java:1166
↓ 4 callersMethodgetNodeShapePath
(Node node)
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:110
↓ 4 callersMethodgetRootLength
()
src/figtree/treeviewer/treelayouts/TreeLayout.java:81
↓ 4 callersMethodgetRootingType
()
src/figtree/treeviewer/TreePane.java:489
↓ 4 callersMethodgetScaleBarStroke
()
src/figtree/treeviewer/painters/ScaleAxisPainter.java:286
↓ 4 callersMethodgetTreeLayoutCache
()
src/figtree/treeviewer/TreePane.java:143
↓ 4 callersMethodhasLengths
@return Whether this tree has branch lengths available
src/figtree/treeviewer/ReRootedTree.java:235
↓ 4 callersMethodisAxisReversed
()
src/figtree/treeviewer/TreePane.java:350
↓ 4 callersMethodisDiscrete
(String attributeName, Set<? extends Attributable> items)
src/figtree/treeviewer/decorators/ColourDecorator.java:165
↓ 4 callersMethodisDontWrapJar
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:335
↓ 4 callersMethodlog10
A static method that uses the natural log to obtain log to base10. This is required for the linear autoCalibrate but will also be used by a derived cl
src/figtree/treeviewer/ScaleAxis.java:277
↓ 4 callersMethodpaintMinorLine
(Graphics2D g2, Rectangle2D axisBounds, double value)
src/figtree/treeviewer/painters/ScaleGridPainter.java:147
↓ 4 callersMethodpaintMinorTick
(Graphics2D g2, Rectangle2D axisBounds, double value)
src/figtree/treeviewer/painters/ScaleAxisPainter.java:262
↓ 4 callersMethodprintTitle
()
src/figtree/application/FigTreeApplication.java:201
↓ 4 callersFunctionregSearchWow
packaging_tools/windows/launch4j/head_src/head.c:438
↓ 4 callersMethodscaleOnAxis
Transform a chart co-ordinates into a drawing co-ordinates
src/figtree/treeviewer/TreePane.java:305
↓ 4 callersMethodsetBranchLabelPainter
(LabelPainter<Node> branchLabelPainter)
src/figtree/treeviewer/TreePane.java:1019
↓ 4 callersMethodsetBranchTransform
(TransformedRootedTree.Transform branchTransform)
src/figtree/treeviewer/TreePane.java:462
↓ 4 callersMethodsetColourMap
(Collection<Object> values, Color[] colours)
src/figtree/treeviewer/decorators/DiscreteColourDecorator.java:153
↓ 4 callersMethodsetDecorator
(ContinuousColourDecorator decorator)
src/figtree/treeviewer/ContinuousColourScaleDialog.java:228
↓ 4 callersMethodsetExpansion
()
src/figtree/treeviewer/TreeViewerController.java:334
↓ 4 callersMethodsetHeight
@param node the node whose height is being set @param height the height
src/figtree/treeviewer/ReRootedTree.java:173
↓ 4 callersMethodsetLength
@param node the node whose branch length (to its parent) is being set @param length the length
src/figtree/treeviewer/ReRootedTree.java:191
↓ 4 callersMethodsetNodeLabelPainter
(LabelPainter<Node> nodeLabelPainter)
src/figtree/treeviewer/TreePane.java:1002
↓ 4 callersMethodsetRange
Set the range of the data
src/figtree/treeviewer/ScaleAxis.java:243
↓ 4 callersMethodsetSettings
(Map<String,Object> settings)
src/figtree/panel/TreesController.java:161
↓ 4 callersMethodsetStatusText
(String statusText)
src/figtree/panel/SimpleTreeViewer.java:115
↓ 4 callersMethodsetTreeLayout
(TreeLayout treeLayout)
src/figtree/treeviewer/TreePane.java:147
↓ 4 callersMethodsetTrees
(Collection<? extends Tree> trees)
src/figtree/treeviewer/TreeViewer.java:49
↓ 4 callersMethodsetVisible
Sets the glass pane as visible or invisible. The mouse cursor will be set accordingly.
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/GlassPane.java:57
↓ 4 callersMethodsetup
(String settings)
src/figtree/treeviewer/decorators/ColourDecorator.java:57
↓ 4 callersMethodshowConfigName
(File config)
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:228
↓ 4 callersMethodtrigger
(String path)
src/figtree/webui/FigTreeWebApplication.java:57
↓ 4 callersMethodvalueChanged
(ListSelectionEvent evt)
src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java:70
↓ 3 callersMethodadd
(Binding b)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Bindings.java:205
↓ 3 callersMethodaddFillComponents
Adds fill components to empty cells in the first row and first column of the grid. This ensures that the grid spacing will be the same as shown in the
packaging_tools/windows/launch4j/src/net/sf/launch4j/form/JreForm.java:61
↓ 3 callersMethodaddLabelCombo
(WVBoxLayout column, final SimpleLabelPainter labelPainter, String title)
src/figtree/webui/FigTreeWebApplication.java:223
↓ 3 callersMethodaddScalePainter
(ScalePainter scalePainter)
src/figtree/treeviewer/TreePane.java:1087
↓ 3 callersMethodaddTree
(Tree tree)
src/figtree/treeviewer/DefaultTreeViewer.java:106
↓ 3 callersMethodaddTree
(Tree tree)
src/figtree/treeviewer/MultiPaneTreeViewer.java:86
↓ 3 callersMethodbuild
@return Output file path.
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:71
↓ 3 callersMethodcalculateScaleRange
()
src/figtree/treeviewer/painters/ScaleBarPainter.java:193
↓ 3 callersMethodcanDiscardChanges
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:197
↓ 3 callersMethodcanSelectNode
(Node selectedNode)
src/figtree/treeviewer/TreePane.java:541
↓ 3 callersMethodcheckFile
(File f, String property, String fileDescription)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:216
↓ 3 callersMethodcheckRange
(int value, int min, int max, String property, String name)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:164
↓ 3 callersFunctioncloseProcessHandles
packaging_tools/windows/launch4j/head_src/head.c:1128
↓ 3 callersMethoderrorMsg
()
src/figtree/ui/components/WholeNumberField.java:89
↓ 3 callersMethoderrorMsg
()
src/figtree/ui/components/RealNumberField.java:98
↓ 3 callersMethodexec
(String[] cmd, Log log)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Util.java:120
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