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github.com/rambaut/figtree
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Functions
2,432 in github.com/rambaut/figtree
⨍
Functions
2,432
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Types & classes
285
↓ 3 callers
Method
fireChanged
()
src/figtree/ui/components/WholeNumberField.java:190
↓ 3 callers
Method
fireChanged
()
src/figtree/ui/components/RealNumberField.java:222
↓ 3 callers
Method
fireSettingsChanged
()
src/figtree/treeviewer/TreePane.java:1358
↓ 3 callers
Method
getAttributeMap
()
src/figtree/treeviewer/ReRootedTree.java:596
↓ 3 callers
Method
getAxisLine
Return a line that defines a particular height. Some layouts won't be able to produce this and may throw an UnsupportedOperationException. @param hei
src/figtree/treeviewer/treelayouts/TreeLayout.java:112
↓ 3 callers
Method
getBranchPathMap
()
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:54
↓ 3 callers
Method
getBranchTransform
()
src/figtree/treeviewer/TreePane.java:458
↓ 3 callers
Method
getCollapsedShapeMap
()
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:70
↓ 3 callers
Method
getDecorator
()
src/figtree/treeviewer/DiscreteColourScaleDialog.java:416
↓ 3 callers
Method
getDefinition
()
src/figtree/treeviewer/annotations/AnnotationDialog.java:201
↓ 3 callers
Method
getErrLine
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/ExecException.java:63
↓ 3 callers
Method
getFillPaint
(Paint paint)
src/figtree/treeviewer/decorators/Decorator.java:58
↓ 3 callers
Method
getFormatter
@return a DecimalFormat for formating the axis labels
src/figtree/treeviewer/ScaleAxis.java:617
↓ 3 callers
Method
getJar
Jar to wrap.
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:258
↓ 3 callers
Method
getLabelFirst
return show label for first tick flag
src/figtree/treeviewer/ScaleAxis.java:163
↓ 3 callers
Method
getLabelLast
return show label for last tick flag
src/figtree/treeviewer/ScaleAxis.java:173
↓ 3 callers
Method
getLighterColour
(Color color)
src/figtree/treeviewer/decorators/ColourDecorator.java:236
↓ 3 callers
Method
getMajorTickCount
Returns the number of major tick marks along the axis
src/figtree/treeviewer/ScaleAxis.java:654
↓ 3 callers
Method
getManifest
Wrapper's manifest for User Account Control.
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:240
↓ 3 callers
Method
getMaxHeight
()
src/figtree/treeviewer/painters/NodeBarPainter.java:188
↓ 3 callers
Method
getName
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/Main.java:74
↓ 3 callers
Method
getOptions
JVM options
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Jre.java:165
↓ 3 callers
Method
getScaleAxis
()
src/figtree/treeviewer/TreePane.java:329
↓ 3 callers
Method
getString
(String key)
packaging_tools/windows/launch4j/src/net/sf/launch4j/ant/Messages.java:48
↓ 3 callers
Method
getTipLabelPath
(Node node)
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:86
↓ 3 callers
Method
getTreeBounds
()
src/figtree/treeviewer/TreePane.java:288
↓ 3 callers
Method
getTreeCount
()
src/figtree/treeviewer/TreeViewer.java:57
↓ 3 callers
Method
getTreeLayout
()
src/figtree/treeviewer/TreePane.java:139
↓ 3 callers
Method
getValue
()
src/figtree/treeviewer/annotations/AnnotationDialog.java:208
↓ 3 callers
Method
getVariables
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:266
↓ 3 callers
Method
loadImage
Helper method to load an image file from the CLASSPATH @param imageName the package and name of the file to load relative to the CLASSPATH @return an
packaging_tools/windows/launch4j/src/net/sf/launch4j/form/SplashForm.java:84
↓ 3 callers
Method
octprint
(int b)
packaging_tools/windows/launch4j/src/net/sf/launch4j/KanjiEscapeOutputStream.java:79
↓ 3 callers
Method
paintMajorLine
(Graphics2D g2, Rectangle2D axisBounds, ScaleAxis axis, double value)
src/figtree/treeviewer/painters/ScaleGridPainter.java:141
↓ 3 callers
Method
paintMajorTick
(Graphics2D g2, Rectangle2D axisBounds, ScaleAxis axis, double value)
src/figtree/treeviewer/painters/ScaleAxisPainter.java:245
↓ 3 callers
Method
parseFigTreeBlock
Parses a 'FigTree' block.
src/figtree/application/FigTreeNexusImporter.java:52
↓ 3 callers
Method
printUsage
(Arguments arguments)
src/figtree/application/FigTreeApplication.java:225
↓ 3 callers
Method
readData
(Reader reader, boolean isNexus)
src/figtree/application/FigTreeFrame.java:727
↓ 3 callers
Method
refreshZoom
()
src/figtree/treeviewer/DefaultTreeViewer.java:235
↓ 3 callers
Method
refreshZoom
()
src/figtree/treeviewer/MultiPaneTreeViewer.java:220
↓ 3 callers
Method
selectTaxa
(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive)
src/figtree/treeviewer/TreeViewer.java:79
↓ 3 callers
Method
setAttributableItem
(Attributable item)
src/figtree/treeviewer/decorators/AttributableDecorator.java:152
↓ 3 callers
Method
setAttributes
(String attributeName, Set<? extends Attributable> items)
src/figtree/treeviewer/decorators/ColourDecorator.java:64
↓ 3 callers
Method
setAutomaticScale
(boolean automaticScale)
src/figtree/treeviewer/painters/ScaleBarPainter.java:183
↓ 3 callers
Method
setBounds
(int x, int y, int width, int height)
src/figtree/treeviewer/TreePane.java:2328
↓ 3 callers
Method
setColourDecorator
(ColourDecorator colourDecorator)
src/figtree/treeviewer/painters/LegendPainter.java:227
↓ 3 callers
Method
setComponentLook
(JComponent comp)
src/figtree/treeviewer/ControllerOptionsPanel.java:53
↓ 3 callers
Method
setConfigPath
(File configFile)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:231
↓ 3 callers
Method
setCursorPosition
(Point point)
src/figtree/treeviewer/TreePane.java:186
↓ 3 callers
Method
setFishEye
(double fishEye)
src/figtree/treeviewer/treelayouts/TreeLayout.java:91
↓ 3 callers
Method
setFontAttributeName
(String fontAttributeName)
src/figtree/treeviewer/decorators/AttributableDecorator.java:131
↓ 3 callers
Method
setJre
(Jre jre)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:287
↓ 3 callers
Method
setNodeType
(boolean external, boolean internal)
src/figtree/treeviewer/painters/NodeShapePainter.java:120
↓ 3 callers
Method
setSplash
(Splash splash)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:305
↓ 3 callers
Method
setStrokeAttributeName
(String strokeAttributeName)
src/figtree/treeviewer/decorators/AttributableDecorator.java:147
↓ 3 callers
Method
setTree
(Tree tree)
src/figtree/treeviewer/MultiPaneTreeViewer.java:72
↓ 3 callers
Method
setupComboBox
(String title, final SimpleLabelPainter labelPainter, final TreeViewer treeViewer)
src/figtree/panel/LabelPainterController.java:71
↓ 3 callers
Method
setupControls
()
src/figtree/panel/SimpleControlPalette.java:97
↓ 3 callers
Method
setupCursor
()
src/figtree/treeviewer/TreePaneSelector.java:101
↓ 3 callers
Method
showDialog
(List<AnnotationDefinition> annotations)
src/figtree/treeviewer/FindDialog.java:90
↓ 3 callers
Method
showNextTree
()
src/figtree/treeviewer/DefaultTreeViewer.java:192
↓ 3 callers
Method
sizeOf
(boolean[] s1)
src/figtree/treeviewer/Parsimony.java:263
↓ 3 callers
Method
toString
()
src/figtree/treeviewer/annotations/AnnotationDefinition.java:65
↓ 3 callers
Method
treeChanged
()
src/figtree/treeviewer/TreeViewerListener.java:34
↓ 3 callers
Method
updateComponents
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/OptComponentBinding.java:119
↓ 2 callers
Method
AppendCommandLine
(StringBuffer sb, String[] cmd)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Util.java:167
↓ 2 callers
Method
addExe
(String pathname)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:193
↓ 2 callers
Method
addFiles
(List<String> files)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:202
↓ 2 callers
Method
addSelectedChildTips
(Node selectedNode, boolean toggle)
src/figtree/treeviewer/TreePane.java:648
↓ 2 callers
Method
amendNodeSelection
(Node selectedNode, boolean toggle, boolean extend)
src/figtree/treeviewer/TreePane.java:582
↓ 2 callers
Method
annotateSelected
()
src/figtree/application/FigTreeFrame.java:567
↓ 2 callers
Method
annotationsChanged
()
src/figtree/treeviewer/AnnotationsListener.java:34
↓ 2 callers
Method
appendAttributes
(Attributable item, StringBuilder builder, int indent)
src/figtree/application/JSONTreeExporter.java:257
↓ 2 callers
Function
appendHeapSize
packaging_tools/windows/launch4j/head_src/head.c:654
↓ 2 callers
Function
appendLauncher
packaging_tools/windows/launch4j/head_src/head.c:556
↓ 2 callers
Function
bundledJreSearch
packaging_tools/windows/launch4j/head_src/head.c:775
↓ 2 callers
Method
calibrate
(Graphics2D g2, double width, double height)
src/figtree/treeviewer/TreePane.java:1755
↓ 2 callers
Method
checkOptFile
(File f, String property, String fileDescription)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:226
↓ 2 callers
Method
checkRelativeWinPath
(String path, String property, String msg)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:232
↓ 2 callers
Method
clear
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/Log.java:49
↓ 2 callers
Method
clearConfig
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:240
↓ 2 callers
Method
clearRotation
(Node node)
src/figtree/treeviewer/TreePane.java:247
↓ 2 callers
Method
clearSelectedNodeAnnotation
(String name)
src/figtree/treeviewer/TreePane.java:960
↓ 2 callers
Method
clearSelectedTaxa
()
src/figtree/treeviewer/TreeViewer.java:97
↓ 2 callers
Method
clearSelectedTipAnnotation
(String name)
src/figtree/treeviewer/TreePane.java:967
↓ 2 callers
Method
confirm
(String text)
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:190
↓ 2 callers
Method
constructTransformedTree
(RootedTree sourceTree)
src/figtree/treeviewer/TreePane.java:107
↓ 2 callers
Method
createBlank
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:114
↓ 2 callers
Method
createExternalNode
Creates a new external node with the given taxon. See createInternalNode for a description of how to use these methods. @param source the source node
src/figtree/treeviewer/ReRootedTree.java:135
↓ 2 callers
Method
createGraphic
(String graphicFormat, int width, int height, String treeFileName, String graphicFileName)
src/figtree/application/FigTreeApplication.java:99
↓ 2 callers
Method
createNodeShape
(Node node, double x, double y)
src/figtree/treeviewer/painters/NodeShapePainter.java:209
↓ 2 callers
Method
createNodes
Clones the entire tree structure from the given (unrooted) Tree. @param tree the unrooted tree @param parent the parent node @param child the child no
src/figtree/treeviewer/ReRootedTree.java:85
↓ 2 callers
Method
createTempFile
(String suffix)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Util.java:72
↓ 2 callers
Method
createThumbShape
Returns a Shape representing a thumb.
src/figtree/ui/components/RangeSliderUI.java:334
↓ 2 callers
Method
createUpload
()
src/figtree/webui/FileUploadWidget.java:28
↓ 2 callers
Method
dist
(Tree tree, Node root, Node node, Map<HashPair<Node>, Double> dists)
src/figtree/treeviewer/ReRootedTree.java:662
↓ 2 callers
Method
doDefineAnnotation
(AnnotationDefinition definition)
src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java:138
↓ 2 callers
Method
drawTree
(Graphics2D g2, double width, double height)
src/figtree/treeviewer/TreePane.java:1465
↓ 2 callers
Method
escape
(String text)
packaging_tools/windows/launch4j/src/net/sf/launch4j/RcBuilder.java:403
↓ 2 callers
Method
exec
(Log log)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:210
↓ 2 callers
Function
execute
packaging_tools/windows/launch4j/head_src/head.c:1134
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