/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * 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.
- *
- * 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
+ *
+ * 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 jalview.datamodel.AnnotatedCollectionI;
+
+import java.awt.Color;
/**
- * ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
+ * 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!
- *
+ *
* @param name
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static int getColourIndexFromName(String name)
{
ret = NUCLEOTIDE;
}
+ else if (name.equalsIgnoreCase("T-Coffee Scores"))
+ {
+ ret = TCOFFEE;
+ }
+
else if (name.equalsIgnoreCase("User Defined"))
{
ret = USER_DEFINED;
{
ret = NONE;
}
+ else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
+ {
+ ret = PURINEPYRIMIDINE;
+ }
+ // else if (name.equalsIgnoreCase("Covariation"))
+ // {
+ // ret = COVARIATION;
+ // }
return ret;
}
/**
* DOCUMENT ME!
- *
+ *
* @param cs
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static String getColourName(ColourSchemeI cs)
{
index = NUCLEOTIDE;
}
+ else if (cs instanceof PurinePyrimidineColourScheme)
+ {
+ index = PURINEPYRIMIDINE;
+ }
+ else if (cs instanceof TCoffeeColourScheme)
+ {
+ index = TCOFFEE;
+ }
+ /*
+ * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
+ */
else if (cs instanceof UserColourScheme)
{
if ((((UserColourScheme) cs).getName() != null)
/**
* DOCUMENT ME!
- *
+ *
* @param index
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static String getColourName(int index)
break;
+ case PURINEPYRIMIDINE:
+ ret = "Purine/Pyrimidine";
+
+ break;
+
+ case TCOFFEE:
+ ret = "T-Coffee Scores";
+
+ break;
+ /*
+ * case COVARIATION: ret = "Covariation";
+ *
+ * break;
+ */
case USER_DEFINED:
ret = "User Defined";
return ret;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param al
- * DOCUMENT ME!
- * @param name
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
- String name)
- {
- return getColour(al.getSequences(), al.getWidth(), name);
- }
-
/**
* retrieve or create colourscheme associated with name
- *
+ *
* @param seqs
* sequences to colour
* @param width
* string to parse as colour for new coloursheme
* @return Valid Colourscheme
*/
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+ public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
String name)
{
int colindex = getColourIndexFromName(name);
}
}
}
- return getColour(seqs, width, getColourIndexFromName(name));
+ return getColour(alignment, getColourIndexFromName(name));
}
/**
- * 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!
- *
- * @return DOCUMENT ME!
+ * colourscheme number
+ *
+ * @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)
+ public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, 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)
{
case CLUSTAL:
- cs = new ClustalxColourScheme(seqs, width);
+ cs = new ClustalxColourScheme(coll, null);
break;
break;
+ case PURINEPYRIMIDINE:
+ cs = new PurinePyrimidineColourScheme();
+
+ break;
+
+ case TCOFFEE:
+ cs = new TCoffeeColourScheme(coll);
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+
+ // break;
+
case USER_DEFINED:
Color[] col = new Color[24];
for (int i = 0; i < 24; i++)
git://source.jalview.org / jalview.git / blobdiff