/* * BioJava development code * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. If you do not have a copy, * see: * * http://www.gnu.org/copyleft/lesser.html * * Copyright for this code is held jointly by the individual * authors. These should be listed in @author doc comments. * * For more information on the BioJava project and its aims, * or to join the biojava-l mailing list, visit the home page * at: * * http://www.biojava.org/ * */ package org.biojava.bio.program.blast2html; /** *
* Interface for specifying both the overall set of possible * markup styles and the particular style for any pair * of residues/bases. *
* *
* This can be independent of the choice of whether to apply a style
* to a pair, by using the ColourCommand
interface.
*
* 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. *
* * @author Cambridge Antibody Technology Group plc * @version 1.0 * */ interface AlignmentStyler { /** ** 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} ** * @return String - the HTML */ String getAlignmentStyles(); /** *
* Modifies in place the styles for the two aligned characters and * the consensus ( in the form of predefined font classes ). *
* ** Null is acceptable value for no style. *
* * @param poFirst - the first char in the alignment * @param poSecond - the second char in the alignment * @param poStyleHolder - an array to hold the styles, * [0] = first, * [1] = second, * [2] = markup * */ void getStyle( String poFirst, String poSecond, String[] poStyleHolder ); }