Package org.biojava.bio.program.blast2html

Class SimpleAlignmentStyler

  • public class SimpleAlignmentStyler
extends AbstractAlignmentStyler
    Simple implementation for specifying markup styles. Has 3 modes of operation: SHOW_ALL, SHOW_SAME & SHOW_DIFF.

    SHOW_ALL - returns the default style for all given residues. SHOW_SAME - only returns a markup style if the styles for both characters are the same. SHOW_DIFF - only returns a markup style if the styles for both are different. Styles can be easily defined in two ways.
    1. Add each style by calling addStyle( poChar, poColour ) For example, String oRed = "FFA2A2"; oStyler.addStyle( "-", oRed ); oStyler.addStyle( "N", oRed ); oStyler.addStyle( "A", oRed ); oStyler.addStyle( "T", oRed ); oStyler.addStyle( "C", oRed ); oStyler.addStyle( "G", oRed );

    2. Alternatively the styles could be specified in a java properties file and loaded by calling readColourMapFromProperties( poFilename ), or readColourMap() and setting the system property 'colourMap' to the correct filename.
    This file should be in java properties format, mapping characters to colours, specified in HEX RGB. For example: 

     # set everything red
 - = FFA2A2
 N = FFA2A2
 A = FFA2A2
 T = FFA2A2
 C = FFA2A2
 G = FFA2A2
    Note this is simply character based, so if you want to colour gaps then you need to specify a colour for the gap character.

    If no colour is specified for a character then it is uncoloured. 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

    • Field Detail

      • SHOW_ALL

        public static int SHOW_ALL
        Return default styles

      • SHOW_SAME

        public static int SHOW_SAME
        Only return if the two colour classes for query and subject are the same

      • SHOW_DIFF

        public static int SHOW_DIFF
        As NORMAL except only return if the two colour classes for query and subject are the different

    • Constructor Detail

      • SimpleAlignmentStyler

        public SimpleAlignmentStyler​(int piStyle)
        Creates a new SimpleAlignmentStyler instance.

        The int flag should be one of SimpleAlignmentStyler.SHOW_ALL, SimpleAlignmentStyler.SHOW_SAME or SimpleAlignmentStyler.SHOW_DIFF.

        Parameters:
        piStyle - (one of SimpleAlignmentStyler.SHOW_SAME or SimpleAlignmentStyler.SHOW_DIFF).
        Throws:
        IllegalArgumentException - - if style not one of allowed values

    • Method Detail

      • readColourMapFromProperties

        protected void readColourMapFromProperties​(String poFileName)
        Setup styles from java property file.
        Parameters:
        poFileName - - the file name of the property file.

      • readColourMap

        protected void readColourMap()
        Read the the properties file that specifies the character/colour mapping. The location of the property file is specified by the system property 'colourMap'.

      • getStyle

        public void getStyle​(String poFirst,
                     String poSecond,
                     String[] poStyleHolder)
        Returns 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 class AbstractAlignmentStyler
        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