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info.bioinfweb.treegraph.graphics.positionpaint
Class RectangularCladogramPositioner

java.lang.Object
  info.bioinfweb.treegraph.graphics.positionpaint.RectangularCladogramPositioner

All Implemented Interfaces:

TreePositioner

Direct Known Subclasses:

PhylogramPositioner

public class RectangularCladogramPositioner
extends Object
implements TreePositioner

Field Summary

protected Document	document
private static RectangularCladogramPositioner	firstInstance
private float	maxLeafWidth
protected float	rescalingFactorX
protected PositionPaintType	type

Constructor Summary

protected

RectangularCladogramPositioner()

Method Summary

private float	alignToOtherLegends(Legends legends, int start, int end, float minLeft, float top, float bottom)
protected float	calculateCornerRadiusShift(Node node, float y) Returns the space between the right of the node and the real position of the node line dependant of the y position.
private void	calculateLabelBlockDimensions(Labels labels, boolean above)
protected void	calculatePaintDimension(float overallWidth, float overallHeight)
private DistanceDimension	calculateTaxonDimension(Node taxon)
private DistanceDimension	calculateTextDimension(TextElement textElement) Calculates the Dimensions of this text element.
private float	calculateWidthsHeights(Node root)
ConcretePaintableElement	elementToPosition(Document document, float x, float y, float margin) Determines the element to a position defined by x- and y-coordinates (e.g. to select an element by mouse).
static RectangularCladogramPositioner	getInstance()
private float	getLegendBottom(LegendFormats f)
private float	getLegendStartX(LegendFormats f, float treeRight)
private float	getLegendTop(LegendFormats f)
private float	labelBlockHeight(Labels labels, boolean above) Returns the overall height of all rows of labels above or below the branch.
private float	labelBlockWidth(Labels labels) Returns the maximum width of all lines of labels above and below the branch.
private float	labelLineHeight(Labels labels, boolean above, int lineNo)
private float	labelLineWidth(Labels labels, boolean above, int lineNo)
private void	moveAll(float dX, float dY)
private float	moveForLegends() Moves the tree down by the legends overlay on the top and calculates the new document height including the possible overlay of the legends.
private void	moveLabels(Labels labels, boolean above, float dX, float dY)
private void	movePosition(PositionData pd, float dX, float dY)
private void	moveSubtree(Node root, float dX, float dY)
void	positionAll(Document document, float rescalingFactorX)
private float	positionElements(Node root, float overallWidth, float y0) Positions the subtree under root.
private void	positionLabelBlockX(Branch branch, boolean above)
private void	positionLabelBlockY(Branch branch)
private float	positionLegends(float startX) Positions all legends rigths if startX.
private float	positionScaleBar(float treeWidth, float maxTreeY) Positions the scale bar.
protected float	rescaleBranchWidth(Branch branch, float width) This methode can be overwritten by extending classes to define a different rescaling process.
protected float	rescaleNodeWidth(Node node, float width) This methode can be overwritten by extending classes to define a different rescaling process.
private float	rescaleSubtree(Node root, float shift) Rescales the subtree under root.
private ConcretePaintableElement	searchElementToPosition(Node root, float x, float y, float margin)
private ConcretePaintableElement	searchLabelBlock(Branch branch, float x, float y, float margin)
protected boolean	xToHigh(float x, PositionData pd)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

firstInstance

private static RectangularCladogramPositioner firstInstance

type

protected PositionPaintType type

document

protected Document document

maxLeafWidth

private float maxLeafWidth

rescalingFactorX

protected float rescalingFactorX

Constructor Detail

RectangularCladogramPositioner

protected RectangularCladogramPositioner()

Method Detail

getInstance

public static RectangularCladogramPositioner getInstance()

calculateTextDimension

private DistanceDimension calculateTextDimension(TextElement textElement)

Calculates the Dimensions of this text element. The height is already defined in by the provided formats and the width will calculated from the the text length scaled with the provided height.

Parameters:

text - the text of the element which dimensions shall be calculated

formats - the text formats of the element

Returns:

the dimensions of the element not including optional margins

calculateTaxonDimension

private DistanceDimension calculateTaxonDimension(Node taxon)

calculateLabelBlockDimensions

private void calculateLabelBlockDimensions(Labels labels,
                                           boolean above)

labelLineHeight

private float labelLineHeight(Labels labels,
                              boolean above,
                              int lineNo)

labelBlockHeight

private float labelBlockHeight(Labels labels,
                               boolean above)

Returns the overall height of all rows of labels above or below the branch.

Returns:

the width in in millimeters

labelLineWidth

private float labelLineWidth(Labels labels,
                             boolean above,
                             int lineNo)

labelBlockWidth

private float labelBlockWidth(Labels labels)

Returns the maximum width of all lines of labels above and below the branch.

calculateWidthsHeights

private float calculateWidthsHeights(Node root)

positionLabelBlockX

private void positionLabelBlockX(Branch branch,
                                 boolean above)

positionLabelBlockY

private void positionLabelBlockY(Branch branch)

calculateCornerRadiusShift

protected float calculateCornerRadiusShift(Node node,
                                           float y)

Returns the space between the right of the node and the real position of the node line dependant of the y position.

Parameters:

node -

y - the absolute y position (not relative to the top of the node)

Returns:

the length in x (between 0 and cornerRadius)

positionElements

private float positionElements(Node root,
                               float overallWidth,
                               float y0)

Positions the subtree under root. (Widths ans heights must have been calculated already.)

Parameters:

root - the root of the subtree to position

overallWidth -

y0 - the start of the subtree on y

Returns:

the y coodinates untl which the positiones subtree reaches

calculatePaintDimension

protected void calculatePaintDimension(float overallWidth,
                                       float overallHeight)

rescaleNodeWidth

protected float rescaleNodeWidth(Node node,
                                 float width)

This methode can be overwritten by extending classes to define a different rescaling process. It could e.g. be used to reduce the corner radius of a node

Parameters:

node - the node to be rescaled

width - the old width of the node in millimeters

Returns:

the new width of the node in millimeters

rescaleBranchWidth

protected float rescaleBranchWidth(Branch branch,
                                   float width)

This methode can be overwritten by extending classes to define a different rescaling process.

Parameters:

branch - the branch to be rescaled

width - the old width of the branch in millimeters

Returns:

the new width of the branch in millimeters

rescaleSubtree

private float rescaleSubtree(Node root,
                             float shift)

Rescales the subtree under root.

Parameters:

root -

shift -

Returns:

the maximal y cooronate for the end of a branch

getLegendStartX

private float getLegendStartX(LegendFormats f,
                              float treeRight)

alignToOtherLegends

private float alignToOtherLegends(Legends legends,
                                  int start,
                                  int end,
                                  float minLeft,
                                  float top,
                                  float bottom)

getLegendTop

private float getLegendTop(LegendFormats f)

getLegendBottom

private float getLegendBottom(LegendFormats f)

positionLegends

private float positionLegends(float startX)

Positions all legends rigths if startX.

Parameters:

startX - the left border of the legends sector in the document

Returns:

the right border of the legends sector (= new width of the document without margin)

positionScaleBar

private float positionScaleBar(float treeWidth,
                               float maxTreeY)

Positions the scale bar.

Parameters:

treeWidth - the width of the tree positioned above

maxTreeY - the end of the tree positioned above on y

Returns:

the end of the scale bar on y

movePosition

private void movePosition(PositionData pd,
                          float dX,
                          float dY)

moveLabels

private void moveLabels(Labels labels,
                        boolean above,
                        float dX,
                        float dY)

moveSubtree

private void moveSubtree(Node root,
                         float dX,
                         float dY)

moveAll

private void moveAll(float dX,
                     float dY)

moveForLegends

private float moveForLegends()

Moves the tree down by the legends overlay on the top and calculates the new document height including the possible overlay of the legends. Additionaly the tree is moves to the left according to the document margin.

Returns:

the new overall height of the document (without document margin)

positionAll

public void positionAll(Document document,
                        float rescalingFactorX)

Specified by:

positionAll in interface TreePositioner

searchLabelBlock

private ConcretePaintableElement searchLabelBlock(Branch branch,
                                                  float x,
                                                  float y,
                                                  float margin)

xToHigh

protected boolean xToHigh(float x,
                          PositionData pd)

searchElementToPosition

private ConcretePaintableElement searchElementToPosition(Node root,
                                                         float x,
                                                         float y,
                                                         float margin)

elementToPosition

public ConcretePaintableElement elementToPosition(Document document,
                                                  float x,
                                                  float y,
                                                  float margin)

Determines the element to a position defined by x- and y-coordinates (e.g. to select an element by mouse).

Specified by:

elementToPosition in interface TreePositioner

Parameters:

document - the document where the position should be dertermined.

x - the x-position in mm

y - the y-position in mm

Returns:

The element or null if the given koordinates are located araound the elements.