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## Uses of Class
info.bioinfweb.treegraph.document.Branch

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`.
info.bioinfweb.treegraph.gui.treeframe | Contains all classes that make up a document window.

Uses of Branch in info.bioinfweb.treegraph.document

Fields in info.bioinfweb.treegraph.document declared as Branch
`private Branch` | `Node.afferentBranch`
`private Branch` | `Labels.holdingBranch`

Methods in info.bioinfweb.treegraph.document that return Branch
`Branch` | `Branch.clone()` Clones this `Branch` including its `Labels`-object with the included `Label`s.
`Branch` | `Node.getAfferentBranch()`
`static Branch[]` | `TreeSerializer.getBranches(Node root)`
`Branch` | `Labels.getHoldingBranch()`
`Branch` | `Label.getHoldingBranch()`

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
`Labels(Branch holdingBranch)`

Uses of Branch in info.bioinfweb.treegraph.document.io.xtg

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

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

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

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)`
`InsertLabelsEdit(Document document, Label label, Branch[] branches)`
`PasteAllLabelsEdit(Document document, Branch branch, Label[] labelList)`
`PasteLabelEdit(Document document, Branch branch, Label label)`
`RerootEdit(Document document, Branch rootingPoint)`
`SeparateBranchEdit(Document document, Branch branch)`

Uses of Branch in info.bioinfweb.treegraph.document.undo.format

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)`

Uses of Branch in info.bioinfweb.treegraph.graphics.positionpaint

Methods in info.bioinfweb.treegraph.graphics.positionpaint with parameters of type Branch
`private void` | `RectangularCladogramPainter.paintBranch(Branch b)`
`private void` | `RectangularCladogramPositioner.positionLabelBlockX(Branch branch, boolean above)`
`private void` | `RectangularCladogramPositioner.positionLabelBlockY(Branch branch)`
`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)`

Uses of Branch in info.bioinfweb.treegraph.gui.treeframe

Methods in info.bioinfweb.treegraph.gui.treeframe that return Branch
`Branch` | `TreeSelection.getFirstBranch()`

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