org.biojava.bio.gui.sequence.SubPairwiseRenderContext

All Implemented Interfaces:: SwingConstants, PairwiseRenderContext, SequenceRenderContext

public class SubPairwiseRenderContext extends Object implements PairwiseRenderContext

SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own. If any of the SymbolList, FeatureHolder or RangeLocation arguments are not null, their values are returned. Otherwise the delegate's method is called and its return value is returned instead.

Since:: 1.2
Author:: Keith James, Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext
SequenceRenderContext.Border
Field Summary

Fields inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext
LAYOUT, REPAINT

Fields inherited from interface javax.swing.SwingConstants
BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST
Constructor Summary

Constructors

Constructor

Description

SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)

Creates a new SubPairwiseRenderContext.
Method Summary

Modifier and Type

Method

Description

int

getDirection()

Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.

FeatureHolder

getFeatures()

The features to render.

Font

getFont()

Gets the Font attribute of the SequenceRenderContext object

SequenceRenderContext.Border

getLeadingBorder()

Gets the LeadingBorder attribute of the SequenceRenderContext object.

RangeLocation

getRange()

The range of the SymbolList to render.

double

getScale()

Gets the scale as pixels per Symbol

int

getSecondaryDirection()

getSecondaryDirection returns the direction in which the secondary sequence is rendered.

FeatureHolder

getSecondaryFeatures()

getSecondaryFeatures returns the features on the secondary sequence.

RangeLocation

getSecondaryRange()

getSecondaryRange returns the range of the secondary sequence currently rendered.

SymbolList

getSecondarySymbols()

getSecondarySymbols returns the symbols of the secondary sequence.

SymbolList

getSymbols()

The SymbolList that is currently rendered by this SequenceRenderContext.

SequenceRenderContext.Border

getTrailingBorder()

Gets the TrailingBorder attribute of the SequenceRenderContext object.

int

graphicsToSecondarySequence(double graphicsPos)

graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence.

int

graphicsToSecondarySequence(Point point)

graphicsToSecondarySequence converts a graphical position to a secondary sequence index.

int

graphicsToSequence(double graphicsPos)

Converts a graphical position into a sequence coordinate.

int

graphicsToSequence(Point2D point)

Converts a graphical position into a sequence coordinate.

double

secondarySequenceToGraphics(int sequencePos)

secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.

double

sequenceToGraphics(int sequencePos)

Converts a sequence index into a graphical coordinate.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SubPairwiseRenderContext
  
  public SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)
  
  Creates a new SubPairwiseRenderContext.
  
  Parameters:
  
  context - a PairwiseRenderContext to wrap. This should not be null.
  
  symbols - a SymbolList to use instead of the delegate's. May be null.
  
  secondarySymbols - a SymbolList to use instead of the delegate's. May be null.
  
  features - a FeatureHolder to use instead of the delegate's. May be null.
  
  secondaryFeatures - a FeatureHolder to use instead of the delegate's. May be null.
  
  range - a RangeLocation to use instead of the delegate's. May be null.
  
  secondaryRange - a RangeLocation to use instead of the delegate's. May be null.
Method Details
- getSymbols
  
  public SymbolList getSymbols()
  
  Description copied from interface: SequenceRenderContext
  
  The SymbolList that is currently rendered by this SequenceRenderContext.
  
  Specified by:
  
  getSymbols in interface SequenceRenderContext
  
  Returns:
  
  The Sequence value
- getSecondarySymbols
  
  public SymbolList getSecondarySymbols()
  
  Description copied from interface: PairwiseRenderContext
  
  getSecondarySymbols returns the symbols of the secondary sequence.
  
  Specified by:
  
  getSecondarySymbols in interface PairwiseRenderContext
  
  Returns:
  
  a SymbolList.
- getFeatures
  
  public FeatureHolder getFeatures()
  
  Description copied from interface: SequenceRenderContext
  
  The features to render.
  
  Specified by:
  
  getFeatures in interface SequenceRenderContext
  
  Returns:
  
  a FeatureHolder with the Features to render
- getSecondaryFeatures
  
  public FeatureHolder getSecondaryFeatures()
  
  Description copied from interface: PairwiseRenderContext
  
  getSecondaryFeatures returns the features on the secondary sequence.
  
  Specified by:
  
  getSecondaryFeatures in interface PairwiseRenderContext
  
  Returns:
  
  a FeatureHolder.
- getRange
  
  public RangeLocation getRange()
  
  Description copied from interface: SequenceRenderContext
  
  The range of the SymbolList to render.
  
  Specified by:
  
  getRange in interface SequenceRenderContext
  
  Returns:
  
  the RangeLocation specifying which indices (inclusive) to render
- getSecondaryRange
  
  public RangeLocation getSecondaryRange()
  
  Description copied from interface: PairwiseRenderContext
  
  getSecondaryRange returns the range of the secondary sequence currently rendered.
  
  Specified by:
  
  getSecondaryRange in interface PairwiseRenderContext
  
  Returns:
  
  a RangeLocation.
- getDirection
  
  public int getDirection()
  
  Description copied from interface: SequenceRenderContext
  
  Gets the direction in which this context expects sequences to be rendered - HORIZONTAL or VERTICAL.
  
  Specified by:
  
  getDirection in interface SequenceRenderContext
  
  Returns:
  
  The Direction value
- getSecondaryDirection
  
  public int getSecondaryDirection()
  
  Description copied from interface: PairwiseRenderContext
  
  getSecondaryDirection returns the direction in which the secondary sequence is rendered. This may be either HORIZONTAL or VERTICAL.
  
  Specified by:
  
  getSecondaryDirection in interface PairwiseRenderContext
  
  Returns:
  
  an int.
- getScale
  
  public double getScale()
  
  Description copied from interface: SequenceRenderContext
  
  Gets the scale as pixels per Symbol
  
  Specified by:
  
  getScale in interface SequenceRenderContext
  
  Returns:
  
  The scale value
- getLeadingBorder
  
  public SequenceRenderContext.Border getLeadingBorder()
  
  Description copied from interface: SequenceRenderContext
  
  Gets the LeadingBorder attribute of the SequenceRenderContext object. This represents the space between the beginning of the rendering area and the beginning of the sequence.
  
  Specified by:
  
  getLeadingBorder in interface SequenceRenderContext
  
  Returns:
  
  The LeadingBorder value
- getTrailingBorder
  
  public SequenceRenderContext.Border getTrailingBorder()
  
  Description copied from interface: SequenceRenderContext
  
  Gets the TrailingBorder attribute of the SequenceRenderContext object. This represents the space between the end of the sequence and the end of the rendering area.
  
  Specified by:
  
  getTrailingBorder in interface SequenceRenderContext
  
  Returns:
  
  The TrailingBorder value
- sequenceToGraphics
  
  public double sequenceToGraphics(int sequencePos)
  
  Description copied from interface: SequenceRenderContext
  
  Converts a sequence index into a graphical coordinate. You will need to use this in conjunction with getDirection to correctly lay graphics out.
  
  Specified by:
  
  sequenceToGraphics in interface SequenceRenderContext
  
  Parameters:
  
  sequencePos - Index within the sequence
  
  Returns:
  
  Equivalent graphical position in pixels
- secondarySequenceToGraphics
  
  public double secondarySequenceToGraphics(int sequencePos)
  
  Description copied from interface: PairwiseRenderContext
  
  secondarySequenceToGraphics converts a sequence coordinate on the secondary sequence to a graphical position.
  
  Specified by:
  
  secondarySequenceToGraphics in interface PairwiseRenderContext
  
  Parameters:
  
  sequencePos - an int.
  
  Returns:
  
  a double.
- graphicsToSequence
  
  public int graphicsToSequence(double graphicsPos)
  
  Description copied from interface: SequenceRenderContext
  
  Converts a graphical position into a sequence coordinate. You will need to have used getDirection to decide whether to use the x or y coordinate.
  
  Specified by:
  
  graphicsToSequence in interface SequenceRenderContext
  
  Parameters:
  
  graphicsPos - A pixel position
  
  Returns:
  
  The corresponding sequence index
- graphicsToSequence
  
  public int graphicsToSequence(Point2D point)
  
  Description copied from interface: SequenceRenderContext
  
  Converts a graphical position into a sequence coordinate. This will use getDirection to decide whether to use the x or y coordinate.
  
  Specified by:
  
  graphicsToSequence in interface SequenceRenderContext
  
  Parameters:
  
  point - a point representing the position
  
  Returns:
  
  the corresponding sequence index
- graphicsToSecondarySequence
  
  public int graphicsToSecondarySequence(double graphicsPos)
  
  Description copied from interface: PairwiseRenderContext
  
  graphicsToSecondarySequence converts a graphical position to a sequence coordinate on the secondary sequence.
  
  Specified by:
  
  graphicsToSecondarySequence in interface PairwiseRenderContext
  
  Parameters:
  
  graphicsPos - a double.
  
  Returns:
  
  an int.
- graphicsToSecondarySequence
  
  public int graphicsToSecondarySequence(Point point)
  
  Description copied from interface: PairwiseRenderContext
  
  graphicsToSecondarySequence converts a graphical position to a secondary sequence index.
  
  Specified by:
  
  graphicsToSecondarySequence in interface PairwiseRenderContext
  
  Parameters:
  
  point - a Point.
  
  Returns:
  
  an int.
- getFont
  
  public Font getFont()
  
  Description copied from interface: SequenceRenderContext
  
  Gets the Font attribute of the SequenceRenderContext object
  
  Specified by:
  
  getFont in interface SequenceRenderContext
  
  Returns:
  
  The Font value

Class SubPairwiseRenderContext

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext

Field Summary

Fields inherited from interface org.biojava.bio.gui.sequence.SequenceRenderContext

Fields inherited from interface javax.swing.SwingConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

SubPairwiseRenderContext

Method Details

getSymbols

getSecondarySymbols

getFeatures

getSecondaryFeatures

getRange

getSecondaryRange

getDirection

getSecondaryDirection

getScale

getLeadingBorder

getTrailingBorder

sequenceToGraphics

secondarySequenceToGraphics

graphicsToSequence

graphicsToSequence

graphicsToSecondarySequence

graphicsToSecondarySequence

getFont