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| Packages that use Branch | |
|---|---|
| info.bioinfweb.treegraph.document |
Contains the classes that represent the data structure of TreeGraph 2 (document elements and
formats) as well as all edit operations in the undo-package to manipulate the data
structure and classes to read and write a document from and to different formats (io-
subpackage). |
| info.bioinfweb.treegraph.document.io.xtg | Contains classes implementing reading and writing of TreeGraph 2 documents. |
| info.bioinfweb.treegraph.document.nodebranchdata |
Contains classes that implement the access to different data fields of the document elements over the common
interface NodeBranchDataAdapter. |
| info.bioinfweb.treegraph.document.undo | Contains all document edits to manipulate the TreeGraph 2 data structure. |
| info.bioinfweb.treegraph.document.undo.edit | |
| info.bioinfweb.treegraph.document.undo.format | |
| info.bioinfweb.treegraph.graphics.positionpaint |
The classes in this package implement the output of an TreeGraph 2 document with Graphics2D. |
| Uses of Branch in info.bioinfweb.treegraph.document |
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| Fields in info.bioinfweb.treegraph.document declared as Branch | |
|---|---|
private Branch |
Node.afferentBranch
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private Branch |
Labels.holdingBranch
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| Methods in info.bioinfweb.treegraph.document that return Branch | |
|---|---|
Branch |
Branch.clone()
Clones this Branch including its Labels-object with the
included Labels. |
Branch |
Node.getAfferentBranch()
|
Branch |
Labels.getHoldingBranch()
|
Branch |
Label.getHoldingBranch()
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| Methods in info.bioinfweb.treegraph.document with parameters of type Branch | |
|---|---|
void |
Node.setAfferentBranch(Branch afferentBranch)
Sets the specified branch as the afferent branch of this node and additionally sets this node as the target node of the specified branch. |
void |
Labels.setHoldingBranch(Branch holdingBranch)
|
| Constructors in info.bioinfweb.treegraph.document with parameters of type Branch | |
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Labels(Branch holdingBranch)
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| Uses of Branch in info.bioinfweb.treegraph.document.io.xtg |
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| Methods in info.bioinfweb.treegraph.document.io.xtg with parameters of type Branch | |
|---|---|
private void |
XTGReader.readBranch(StartElement rootElement,
Branch b)
|
| Uses of Branch in info.bioinfweb.treegraph.document.nodebranchdata |
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| Methods in info.bioinfweb.treegraph.document.nodebranchdata that return Branch | |
|---|---|
Branch |
HiddenBranchDataAdapter.getDataElement(Node node)
|
Branch |
BranchLengthAdapter.getDataElement(Node node)
|
| Uses of Branch in info.bioinfweb.treegraph.document.undo |
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| Methods in info.bioinfweb.treegraph.document.undo that return Branch | |
|---|---|
protected Branch |
ComplexDocumentEdit.findEquivilant(Branch old)
Returns the branch in the new tree (copy of the old) with the equivilant position to old. |
| Methods in info.bioinfweb.treegraph.document.undo with parameters of type Branch | |
|---|---|
protected Branch |
ComplexDocumentEdit.findEquivilant(Branch old)
Returns the branch in the new tree (copy of the old) with the equivilant position to old. |
| Uses of Branch in info.bioinfweb.treegraph.document.undo.edit |
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| Fields in info.bioinfweb.treegraph.document.undo.edit declared as Branch | |
|---|---|
private Branch |
SeparateBranchEdit.branch
|
private Branch |
PasteLabelEdit.branch
|
private Branch |
PasteAllLabelsEdit.branch
|
private Branch |
BranchLengthEdit.branch
|
private Branch |
RerootEdit.rootingPoint
|
| Methods in info.bioinfweb.treegraph.document.undo.edit with parameters of type Branch | |
|---|---|
private void |
RerootEdit.copyBranchData(Branch source,
Branch target)
|
private void |
RerootEdit.reroot(Branch position)
|
| Constructors in info.bioinfweb.treegraph.document.undo.edit with parameters of type Branch | |
|---|---|
BranchLengthEdit(Document document,
Branch branch,
double newLength)
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InsertLabelsEdit(Document document,
Label label,
Branch[] branches)
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PasteAllLabelsEdit(Document document,
Branch branch,
Label[] labelList)
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PasteLabelEdit(Document document,
Branch branch,
Label label)
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RerootEdit(Document document,
Branch rootingPoint)
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SeparateBranchEdit(Document document,
Branch branch)
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|
| Uses of Branch in info.bioinfweb.treegraph.document.undo.format |
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| Fields in info.bioinfweb.treegraph.document.undo.format declared as Branch | |
|---|---|
private Branch[] |
AutoPositionLabelsEdit.branches
|
| Methods in info.bioinfweb.treegraph.document.undo.format with parameters of type Branch | |
|---|---|
private static void |
AutoPositionLabelsEdit.position(Branch branch,
String[] ids)
|
| Constructors in info.bioinfweb.treegraph.document.undo.format with parameters of type Branch | |
|---|---|
AutoPositionLabelsEdit(Document document,
Branch[] branches)
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|
| Uses of Branch in info.bioinfweb.treegraph.graphics.positionpaint |
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| Methods in info.bioinfweb.treegraph.graphics.positionpaint with parameters of type Branch | |
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private void |
RectangularCladogramPainter.paintBranch(Branch b)
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private void |
RectangularCladogramPositioner.positionLabelBlockX(Branch branch,
boolean above)
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private void |
RectangularCladogramPositioner.positionLabelBlockY(Branch branch)
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protected float |
RectangularCladogramPositioner.rescaleBranchWidth(Branch branch,
float width)
This methode can be overwritten by extending classes to define a different rescaling process. |
protected float |
PhylogramPositioner.rescaleBranchWidth(Branch branch,
float width)
This method is overwritten to regard the stored branch lengths. |
private ConcretePaintableElement |
RectangularCladogramPositioner.searchLabelBlock(Branch branch,
float x,
float y,
float margin)
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