Package org.biojava.bio.program.blast2html

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 Summary

Fields

Modifier and Type	Field	Description
protected int	iNumberOfColours	The number of unique colours.
protected HashMap	oColourClassMap	Stores mapping from a Colour to a FONT Class.
protected HashMap	oColourMap	Map between Char and the Colour class.
protected HashSet	oColourSet	Store the unique colours for markup.

Constructor Summary

Constructors

Constructor	Description
AbstractAlignmentStyler()

Method Summary

Modifier and Type	Method	Description
void	addStyle(String poChar, String poColour)	Add a colour style to this Styler.
String	getAlignmentStyles()	Returns a fragment of HTML that defines the FONT styles to be used in the alignment markup.
protected String	getColourClass(String poColour)	Returns the colour class for the specified colour (in hex).
abstract void	getStyle(String poFirst, String poSecond, 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 HashSet oColourSet

Store the unique colours for markup.

oColourClassMap

protected 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 HashMap oColourMap

Map between Char and the Colour class.

Eg.

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

 

Constructor Detail

AbstractAlignmentStyler

public AbstractAlignmentStyler()

Method Detail

getAlignmentStyles

public 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}
 

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'