org.biojava.bio.program.blast2html

Class SimpleAlignmentStyler

java.lang.Object

org.biojava.bio.program.blast2html.AbstractAlignmentStyler

org.biojava.bio.program.blast2html.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 Summary

Fields

Modifier and Type	Field and Description
static int	SHOW_ALL Return default styles
static int	SHOW_DIFF As NORMAL except only return if the two colour classes for query and subject are the different
static int	SHOW_SAME Only return if the two colour classes for query and subject are the same

Fields inherited from class org.biojava.bio.program.blast2html.AbstractAlignmentStyler

iNumberOfColours, oColourClassMap, oColourMap, oColourSet

Constructor Summary

Constructors

Constructor and Description
SimpleAlignmentStyler(int piStyle) Creates a new SimpleAlignmentStyler instance.

Method Summary

Methods

Modifier and Type	Method and Description
void	getStyle(String poFirst, String poSecond, String[] poStyleHolder) Returns the styles for the two aligned characters in the form of predefined font classes.
protected void	readColourMap() Read the the properties file that specifies the character/colour mapping.
protected void	readColourMapFromProperties(String poFileName) Setup styles from java property file.

Methods inherited from class org.biojava.bio.program.blast2html.AbstractAlignmentStyler

addStyle, getAlignmentStyles, getColourClass

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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