/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.schemes;
-import java.awt.*;
+import java.awt.Color;
/**
* ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
* intelligently with mapping unknown names to user defined colourschemes (that
* exist or can be created from the string representation of the colourscheme
- * name - either a hex RGB triplet or a named colour under java.awt.color )
+ * name - either a hex RGB triplet or a named colour under java.awt.color ). The
+ * values of the colourscheme constants is important for callers of
+ * getColourName(int i), since it can be used to enumerate the set of built in
+ * colours. The FIRST_COLOUR and LAST_COLOUR symbols are provided for this.
*
* @author $author$
* @version $Revision$
*/
public class ColourSchemeProperty
{
- /** DOCUMENT ME!! */
- public static final int CLUSTAL = 0;
+ /** Undefined Colourscheme Index */
+ public static final int UNDEFINED = -1;
+
+ /** for schemes defined on the fly */
+ public static final int USER_DEFINED = 0;
+
+ /** No Colourscheme Index */
+ public static final int NONE = 1;
/** DOCUMENT ME!! */
- public static final int BLOSUM = 1;
+ public static final int CLUSTAL = 2;
/** DOCUMENT ME!! */
- public static final int PID = 2;
+ public static final int BLOSUM = 3;
/** DOCUMENT ME!! */
- public static final int ZAPPO = 3;
+ public static final int PID = 4;
/** DOCUMENT ME!! */
- public static final int TAYLOR = 4;
+ public static final int ZAPPO = 5;
/** DOCUMENT ME!! */
- public static final int HYDROPHOBIC = 5;
+ public static final int TAYLOR = 6;
/** DOCUMENT ME!! */
- public static final int HELIX = 6;
+ public static final int HYDROPHOBIC = 7;
/** DOCUMENT ME!! */
- public static final int STRAND = 7;
+ public static final int HELIX = 8;
/** DOCUMENT ME!! */
- public static final int TURN = 8;
+ public static final int STRAND = 9;
/** DOCUMENT ME!! */
- public static final int BURIED = 9;
+ public static final int TURN = 10;
/** DOCUMENT ME!! */
- public static final int NUCLEOTIDE = 10;
+ public static final int BURIED = 11;
/** DOCUMENT ME!! */
- public static final int USER_DEFINED = 11;
+ public static final int NUCLEOTIDE = 12;
- /** No Colourscheme Index */
- public static final int NONE = 12;
+ /**
+ * purine/pyrimidine
+ */
+ public static final int PURINEPYRIMIDINE = 13;
- /** Undefined Colourscheme Index */
- public static final int UNDEFINED = 13;
+ public static final int COVARIATION = 14;
+
+ public static final int TCOFFEE = 15;
+
+
+ /**
+ * index of first colourscheme (includes 'None')
+ */
+ public static final int FIRST_COLOUR = NONE;
+
+ public static final int LAST_COLOUR = NUCLEOTIDE;
/**
* DOCUMENT ME!
{
ret = NUCLEOTIDE;
}
+ else if (name.equalsIgnoreCase("T-Coffee scores"))
+ {
+ ret = TCOFFEE;
+ }
+
else if (name.equalsIgnoreCase("User Defined"))
{
ret = USER_DEFINED;
}
/**
- * DOCUMENT ME!
+ * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
*
* @param seqs
- * DOCUMENT ME!
+ * sequences to be coloured by colourscheme
* @param width
- * DOCUMENT ME!
+ * geometry of alignment
* @param index
- * DOCUMENT ME!
+ * colourscheme number
*
- * @return DOCUMENT ME!
+ * @return null or an instance of the colourscheme configured to colour given sequence set
*/
public static ColourSchemeI getColour(java.util.Vector seqs, int width,
int index)
{
+ // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
ColourSchemeI cs = null;
switch (index)
git://source.jalview.org / jalview.git / blobdiff