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Functions
2,432 in github.com/rambaut/figtree
⨍
Functions
2,432
◇
Types & classes
285
↓ 5 callers
Method
getSelectedFont
Returns a Font object representing the selection in the panel. @return the font.
src/figtree/ui/FontChooserPanel.java:118
↓ 5 callers
Method
getSingleInstance
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:388
↓ 5 callers
Method
getTaxa
@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 callers
Method
hasOption
Does an argument with label exist?
src/figtree/application/Arguments.java:418
↓ 5 callers
Method
isOrderBranchesOn
()
src/figtree/treeviewer/TreePane.java:467
↓ 5 callers
Method
isRootingOn
()
src/figtree/treeviewer/TreePane.java:485
↓ 5 callers
Method
isTransformBranchesOn
()
src/figtree/treeviewer/TreePane.java:449
↓ 5 callers
Method
load
(File f)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:125
↓ 5 callers
Function
loadInt
packaging_tools/windows/launch4j/head_src/head.c:247
↓ 5 callers
Method
maintainAspectRatio
Return whether the two axis scales should be maintained relative to each other @return a boolean
src/figtree/treeviewer/treelayouts/TreeLayout.java:101
↓ 5 callers
Method
parseColor
(String value)
src/figtree/treeviewer/decorators/InterpolatingColourDecorator.java:182
↓ 5 callers
Method
selectNodes
(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive)
src/figtree/treeviewer/TreeViewer.java:81
↓ 5 callers
Method
setBranchStroke
(BasicStroke stroke)
src/figtree/treeviewer/TreePane.java:422
↓ 5 callers
Method
setCrosshairShown
(boolean crosshairShown)
src/figtree/treeviewer/TreePane.java:182
↓ 5 callers
Method
setDecoratorForAttribute
(String attribute, ColourDecorator decorator)
src/figtree/treeviewer/AttributeColourController.java:192
↓ 5 callers
Method
setPaintAttributeName
(String paintAttributeName)
src/figtree/treeviewer/decorators/AttributableDecorator.java:139
↓ 5 callers
Method
setSelectionColor
(Color selectionColor)
src/figtree/treeviewer/TreePane.java:441
↓ 5 callers
Method
setSelectionMode
(TreePaneSelector.SelectionMode selectionMode)
src/figtree/treeviewer/TreeViewer.java:104
↓ 5 callers
Method
setTipLabelPainter
(LabelPainter<Node> tipLabelPainter)
src/figtree/treeviewer/TreePane.java:985
↓ 5 callers
Method
setTreeLayout
(TreeLayoutType layoutType)
src/figtree/treeviewer/TreeViewerController.java:299
↓ 5 callers
Method
setupControls
( final JComboBox colourAttributeCombo, final JButton colourSetupButton)
src/figtree/treeviewer/AttributeColourController.java:57
↓ 5 callers
Method
showTree
(int index)
src/figtree/treeviewer/DefaultTreeViewer.java:172
↓ 5 callers
Method
signalLengthViolation
(String property, String name, int maxLength)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:242
↓ 5 callers
Method
unwrap
(List<StringWrapper> wrappers)
packaging_tools/windows/launch4j/src/net/sf/launch4j/ant/StringWrapper.java:48
↓ 4 callers
Method
addAbsFile
(File file)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:183
↓ 4 callers
Method
addDecorator
(Decorator decorator)
src/figtree/treeviewer/decorators/CompoundDecorator.java:42
↓ 4 callers
Method
addWindowsPath
Stores path in Windows format with '\' separators.
packaging_tools/windows/launch4j/src/net/sf/launch4j/RcBuilder.java:331
↓ 4 callers
Function
appendAppClasspath
packaging_tools/windows/launch4j/head_src/head.c:568
↓ 4 callers
Method
checkIn
(String s, String[] strings, String property, String name)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:189
↓ 4 callers
Method
checkOptStrings
(List<String> strings, int maxLength, int totalMaxLength, String property, String name)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:84
↓ 4 callers
Method
convertMouseEvent
(WMouseEvent event, int type)
src/figtree/webui/TreeWidget.java:76
↓ 4 callers
Method
createInternalNode
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 callers
Method
delete
(File f)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Util.java:217
↓ 4 callers
Method
doExportGraphic
(GraphicFormat format)
src/figtree/application/FigTreeFrame.java:1208
↓ 4 callers
Function
expandVars
* Expand environment %variables% */
packaging_tools/windows/launch4j/head_src/head.c:577
↓ 4 callers
Method
fireAnnotationsChanged
()
src/figtree/treeviewer/ExtendedTreeViewer.java:220
↓ 4 callers
Method
getAge
(double height, RootedTree tree)
src/figtree/treeviewer/TimeScale.java:58
↓ 4 callers
Method
getAttributeNames
(Collection<? extends Attributable> items)
src/figtree/panel/TreeColouringController.java:132
↓ 4 callers
Method
getBranchOrdering
()
src/figtree/treeviewer/TreePane.java:476
↓ 4 callers
Method
getCollapsedShape
(Node node)
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:66
↓ 4 callers
Method
getColor
(Object value)
src/figtree/treeviewer/decorators/DiscreteColourDecorator.java:149
↓ 4 callers
Method
getDecoratorForAttribute
(String attribute)
src/figtree/treeviewer/AttributeColourController.java:148
↓ 4 callers
Method
getFile
(String key)
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:271
↓ 4 callers
Method
getIconHeight
()
src/figtree/ui/components/ColorWellButton.java:110
↓ 4 callers
Method
getInteger
Convert 0 to null
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Jre.java:289
↓ 4 callers
Method
getLength
@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 callers
Method
getMajorTickValue
getMajorTick Returns the value of the majorTickIndex'th major tick
src/figtree/treeviewer/ScaleAxis.java:684
↓ 4 callers
Method
getMaxValue
()
src/figtree/treeviewer/decorators/ContinuousScale.java:232
↓ 4 callers
Method
getMaximumFractionDigits
Returns the maximum number of digits allowed in the fraction portion of a number. @see #setMaximumFractionDigits
src/figtree/ui/PercentFormat.java:54
↓ 4 callers
Method
getMinValue
()
src/figtree/treeviewer/decorators/ContinuousScale.java:224
↓ 4 callers
Method
getNodeAt
(Graphics2D g2, Point point)
src/figtree/treeviewer/TreePane.java:1166
↓ 4 callers
Method
getNodeShapePath
(Node node)
src/figtree/treeviewer/treelayouts/TreeLayoutCache.java:110
↓ 4 callers
Method
getRootLength
()
src/figtree/treeviewer/treelayouts/TreeLayout.java:81
↓ 4 callers
Method
getRootingType
()
src/figtree/treeviewer/TreePane.java:489
↓ 4 callers
Method
getScaleBarStroke
()
src/figtree/treeviewer/painters/ScaleAxisPainter.java:286
↓ 4 callers
Method
getTreeLayoutCache
()
src/figtree/treeviewer/TreePane.java:143
↓ 4 callers
Method
hasLengths
@return Whether this tree has branch lengths available
src/figtree/treeviewer/ReRootedTree.java:235
↓ 4 callers
Method
isAxisReversed
()
src/figtree/treeviewer/TreePane.java:350
↓ 4 callers
Method
isDiscrete
(String attributeName, Set<? extends Attributable> items)
src/figtree/treeviewer/decorators/ColourDecorator.java:165
↓ 4 callers
Method
isDontWrapJar
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:335
↓ 4 callers
Method
log10
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 callers
Method
paintMinorLine
(Graphics2D g2, Rectangle2D axisBounds, double value)
src/figtree/treeviewer/painters/ScaleGridPainter.java:147
↓ 4 callers
Method
paintMinorTick
(Graphics2D g2, Rectangle2D axisBounds, double value)
src/figtree/treeviewer/painters/ScaleAxisPainter.java:262
↓ 4 callers
Method
printTitle
()
src/figtree/application/FigTreeApplication.java:201
↓ 4 callers
Function
regSearchWow
packaging_tools/windows/launch4j/head_src/head.c:438
↓ 4 callers
Method
scaleOnAxis
Transform a chart co-ordinates into a drawing co-ordinates
src/figtree/treeviewer/TreePane.java:305
↓ 4 callers
Method
setBranchLabelPainter
(LabelPainter<Node> branchLabelPainter)
src/figtree/treeviewer/TreePane.java:1019
↓ 4 callers
Method
setBranchTransform
(TransformedRootedTree.Transform branchTransform)
src/figtree/treeviewer/TreePane.java:462
↓ 4 callers
Method
setColourMap
(Collection<Object> values, Color[] colours)
src/figtree/treeviewer/decorators/DiscreteColourDecorator.java:153
↓ 4 callers
Method
setDecorator
(ContinuousColourDecorator decorator)
src/figtree/treeviewer/ContinuousColourScaleDialog.java:228
↓ 4 callers
Method
setExpansion
()
src/figtree/treeviewer/TreeViewerController.java:334
↓ 4 callers
Method
setHeight
@param node the node whose height is being set @param height the height
src/figtree/treeviewer/ReRootedTree.java:173
↓ 4 callers
Method
setLength
@param node the node whose branch length (to its parent) is being set @param length the length
src/figtree/treeviewer/ReRootedTree.java:191
↓ 4 callers
Method
setNodeLabelPainter
(LabelPainter<Node> nodeLabelPainter)
src/figtree/treeviewer/TreePane.java:1002
↓ 4 callers
Method
setRange
Set the range of the data
src/figtree/treeviewer/ScaleAxis.java:243
↓ 4 callers
Method
setSettings
(Map<String,Object> settings)
src/figtree/panel/TreesController.java:161
↓ 4 callers
Method
setStatusText
(String statusText)
src/figtree/panel/SimpleTreeViewer.java:115
↓ 4 callers
Method
setTreeLayout
(TreeLayout treeLayout)
src/figtree/treeviewer/TreePane.java:147
↓ 4 callers
Method
setTrees
(Collection<? extends Tree> trees)
src/figtree/treeviewer/TreeViewer.java:49
↓ 4 callers
Method
setVisible
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 callers
Method
setup
(String settings)
src/figtree/treeviewer/decorators/ColourDecorator.java:57
↓ 4 callers
Method
showConfigName
(File config)
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:228
↓ 4 callers
Method
trigger
(String path)
src/figtree/webui/FigTreeWebApplication.java:57
↓ 4 callers
Method
valueChanged
(ListSelectionEvent evt)
src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java:70
↓ 3 callers
Method
add
(Binding b)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Bindings.java:205
↓ 3 callers
Method
addFillComponents
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 callers
Method
addLabelCombo
(WVBoxLayout column, final SimpleLabelPainter labelPainter, String title)
src/figtree/webui/FigTreeWebApplication.java:223
↓ 3 callers
Method
addScalePainter
(ScalePainter scalePainter)
src/figtree/treeviewer/TreePane.java:1087
↓ 3 callers
Method
addTree
(Tree tree)
src/figtree/treeviewer/DefaultTreeViewer.java:106
↓ 3 callers
Method
addTree
(Tree tree)
src/figtree/treeviewer/MultiPaneTreeViewer.java:86
↓ 3 callers
Method
build
@return Output file path.
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:71
↓ 3 callers
Method
calculateScaleRange
()
src/figtree/treeviewer/painters/ScaleBarPainter.java:193
↓ 3 callers
Method
canDiscardChanges
()
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:197
↓ 3 callers
Method
canSelectNode
(Node selectedNode)
src/figtree/treeviewer/TreePane.java:541
↓ 3 callers
Method
checkFile
(File f, String property, String fileDescription)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:216
↓ 3 callers
Method
checkRange
(int value, int min, int max, String property, String name)
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Validator.java:164
↓ 3 callers
Function
closeProcessHandles
packaging_tools/windows/launch4j/head_src/head.c:1128
↓ 3 callers
Method
errorMsg
()
src/figtree/ui/components/WholeNumberField.java:89
↓ 3 callers
Method
errorMsg
()
src/figtree/ui/components/RealNumberField.java:98
↓ 3 callers
Method
exec
(String[] cmd, Log log)
packaging_tools/windows/launch4j/src/net/sf/launch4j/Util.java:120
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