Class AlignmentMarker

  • public class AlignmentMarker
    extends Object

    Class to do simple HTML colouring of sequence alignments.

    For any particular alignment position, the colouring depends only on the two characters at that position. The decision is made in two stages:-

    1. Whether to colour or not in the ColourCommand.isColoured() method
    2. what the colours are in the AlignmentStyler.getStyle() method

    This allows simple choices to highlight the mismatches, the identities or simply colour up everything.

    The current implemention of step 2. is a simple colour lookup.


    As the FONT styles need to be defined before being used in the HTML, it means the all colours to be used have to calculated up front.

    The position in the alignment is not passed in so position dependent colouring ( say against a HMM profile ) would be involve either changing the interfaces or implementing them such that they knew the required information via another route.

     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.

    Cambridge Antibody Technology Group plc, Greg Cox
    • Constructor Detail

      • AlignmentMarker

        public AlignmentMarker​(ColourCommand poColourCommand,
        Creates a new AlignmentMarker instance.
        poColourCommand - - controls whether a particular alignment pair should be coloured
        poStyler - - specifies all possible styles and where each style is used