org.biojava.bio.program.blast2html
Class AbstractAlignmentStyler

java.lang.Object
  extended byorg.biojava.bio.program.blast2html.AbstractAlignmentStyler
All Implemented Interfaces:
org.biojava.bio.program.blast2html.AlignmentStyler
Direct Known Subclasses:
SimpleAlignmentStyler

public abstract class AbstractAlignmentStyler
extends java.lang.Object
implements org.biojava.bio.program.blast2html.AlignmentStyler

Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.

Thus getAlignmentStyles() is implemented and all that remains to be implemented is the getStyle method.

 Primary author -
                 Colin Hardman      (CAT)
 Other authors  -
                 Tim Dilks          (CAT)
                 Simon Brocklehurst (CAT)
                 Stuart Johnston    (CAT)
                 Lawerence Bower    (CAT)
                 Derek Crockford    (CAT)
                 Neil Benn          (CAT)

 Copyright 2001 Cambridge Antibody Technology Group plc.
 All Rights Reserved.
 

This code released to the biojava project, May 2001 under the LGPL license.

Version:
1.0
Author:
Cambridge Antibody Technology Group plc, Greg Cox

Field Summary
protected  int iNumberOfColours
          The number of unique colours.
protected  java.util.HashMap oColourClassMap
           Stores mapping from a Colour to a FONT Class.
protected  java.util.HashMap oColourMap
           Map between Char and the Colour class.
protected  java.util.HashSet oColourSet
          Store the unique colours for markup.
 
Constructor Summary
AbstractAlignmentStyler()
           
 
Method Summary
 void addStyle(java.lang.String poChar, java.lang.String poColour)
          Add a colour style to this Styler.
 java.lang.String getAlignmentStyles()
           Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.
protected  java.lang.String getColourClass(java.lang.String poColour)
          Returns the colour class for the specified colour (in hex).
abstract  void getStyle(java.lang.String poFirst, java.lang.String poSecond, java.lang.String[] poStyleHolder)
           Return the styles for the two aligned characters.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

oColourSet

protected java.util.HashSet oColourSet
Store the unique colours for markup.


oColourClassMap

protected java.util.HashMap oColourClassMap

Stores mapping from a Colour to a FONT Class.

For example:


 Key      Value
 ---      -----
 #000000  C1-S

 


iNumberOfColours

protected int iNumberOfColours
The number of unique colours.


oColourMap

protected java.util.HashMap oColourMap

Map between Char and the Colour class.

Eg.


 Key      Value
 ---      -----
 A        C1-S

 

Constructor Detail

AbstractAlignmentStyler

public AbstractAlignmentStyler()
Method Detail

getAlignmentStyles

public java.lang.String getAlignmentStyles()

Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.

For example:

 FONT.C2-S{background-color:#FFFC50;color:#000000}
 FONT.C4-S{background-color:#FC50FF;color:#000000}
 FONT.C3-S{background-color:#FF7272;color:#000000}
 FONT.C0-S{background-color:#50FF78;color:#000000}
 FONT.C1-S{background-color:#FFCA50;color:#000000}
 FONT.C5-S{background-color:#A5A5FF;color:#000000}
 

Specified by:
getAlignmentStyles in interface org.biojava.bio.program.blast2html.AlignmentStyler
Returns:
String - the HTML

getStyle

public abstract void getStyle(java.lang.String poFirst,
                              java.lang.String poSecond,
                              java.lang.String[] poStyleHolder)

Return the styles for the two aligned characters. (in the form of predefined font classes).

Null is acceptable value for no style.

Specified by:
getStyle in interface org.biojava.bio.program.blast2html.AlignmentStyler
Parameters:
poFirst - - the first char in the alignment
poSecond - - the second char in the alignment
poStyleHolder - - an array to hold the styles, [0] = first etc

addStyle

public void addStyle(java.lang.String poChar,
                     java.lang.String poColour)
Add a colour style to this Styler.

Parameters:
poChar - the char for which this colour applies.
poColour - the color in hex eg 'FFA2A2' for a nice red ( R = FF, G = A2 and B = A2 )

getColourClass

protected java.lang.String getColourClass(java.lang.String poColour)

Returns the colour class for the specified colour (in hex). If one is not already defined for that colour then a new class is created and returned.

Colour specification is R G B in hex ie FF00FF is r = 255, g = 0, b = 255.

Parameters:
poColour - - a colour, eg 'C8FFC8'
Returns:
String - the colour class, eg 'C1-S'