Class AbstractAlignmentStyler

java.lang.Object
org.biojava.bio.program.blast2html.AbstractAlignmentStyler
Direct Known Subclasses:
SimpleAlignmentStyler

public abstract class AbstractAlignmentStyler extends Object

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.
 

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 Details

    • oColourSet

      protected HashSet oColourSet
      Store the unique colours for markup.
    • 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 HashMap oColourMap

      Map between Char and the Colour class.

      Eg.

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

  • Constructor Details

  • Method Details

    • 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}
       

      Returns:
      String - the HTML
    • getStyle

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

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

      Null is acceptable value for no style.

      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(String poChar, 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 String getColourClass(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'