Class ColorAnnotationsColorScheme

All Implemented Interfaces:

public class ColorAnnotationsColorScheme
extends java.lang.Object
implements ResidueColorScheme,

Colors residues according to the sequence annotations. When no annotations are available, the choice of the colors defaults to another ResidueColorScheme.

See Also:
Serialized Form

Constructor Summary
ColorAnnotationsColorScheme(ResidueColorScheme defaultCS)
Method Summary
 void addResidues(int[] positions, java.awt.Color color)
          Cache the specified residue positions and color.
 java.awt.Color findColor(int position)
 java.awt.Color getBackgroundColor(char label, int position)
          Returns the background color.
 java.awt.Color getForegroundColor(char label, int position)
          Returns the foreground color.
 java.lang.String getInformation()
          Returns a descriptive text about this ColorScheme.
 java.lang.String getShortName()
          Returns a shortname for this ColorScheme.
 void parseAnnotations(BiologicalAnnotations annotations)
          Compiles the coloring from the annotations.
 void removeAllResidues()
          Cleans the residue/color association cache.
 void setDefaultScheme(ResidueColorScheme defaultCS)
          Sets the default color scheme.
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail


public ColorAnnotationsColorScheme(ResidueColorScheme defaultCS)
Method Detail


public void setDefaultScheme(ResidueColorScheme defaultCS)
Sets the default color scheme.


public java.awt.Color getForegroundColor(char label,
                                         int position)
Returns the foreground color. When a color annotation is associated with this residue, this color is returned. Otherwise, the choice is delegated to the background scheme.

Specified by:
getForegroundColor in interface ResidueColorScheme


public java.awt.Color getBackgroundColor(char label,
                                         int position)
Returns the background color. The residue position is ignored for that purpose.

Specified by:
getBackgroundColor in interface ResidueColorScheme


public java.lang.String getShortName()
Description copied from interface: ResidueColorScheme
Returns a shortname for this ColorScheme. This string is typically less than 10 characters and can be presented to the user to let him choose between several colorscheme.

Specified by:
getShortName in interface ResidueColorScheme


public java.lang.String getInformation()
Description copied from interface: ResidueColorScheme
Returns a descriptive text about this ColorScheme. This text should explain the choice and attribution of the colors to the residues of the sequences.

Specified by:
getInformation in interface ResidueColorScheme


public void parseAnnotations(BiologicalAnnotations annotations)
Compiles the coloring from the annotations. This method must be called after color annotations have been added to the sequence. It builds a summary of color annotations that speeds up the color lookup for each residue.


public void addResidues(int[] positions,
                        java.awt.Color color)
Cache the specified residue positions and color.


public void removeAllResidues()
Cleans the residue/color association cache.


public java.awt.Color findColor(int position)

Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.