+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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
+ * 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
+ * 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.*;
+
+/**
+ * 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 ). 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
{
- public static final int CLUSTAL = 0;
- public static final int BLOSUM = 1;
- public static final int PID = 2;
- public static final int ZAPPO = 3;
- public static final int HYDROPHOBIC=4;
- public static final int HELIX=5;
- public static final int STRAND=6;
- public static final int TURN = 7;
- public static final int BURIED = 8;
- public static final int NUCLEOTIDE = 9;
- public static final int USER_DEFINED = 10;
- public static final int NONE = 11;
+ /** 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 CLUSTAL = 2;
+
+ /** DOCUMENT ME!! */
+ public static final int BLOSUM = 3;
+
+ /** DOCUMENT ME!! */
+ public static final int PID = 4;
+
+ /** DOCUMENT ME!! */
+ public static final int ZAPPO = 5;
+
+ /** DOCUMENT ME!! */
+ public static final int TAYLOR = 6;
+
+ /** DOCUMENT ME!! */
+ public static final int HYDROPHOBIC = 7;
+
+ /** DOCUMENT ME!! */
+ public static final int HELIX = 8;
+
+ /** DOCUMENT ME!! */
+ public static final int STRAND = 9;
+ /** DOCUMENT ME!! */
+ public static final int TURN = 10;
+
+ /** DOCUMENT ME!! */
+ public static final int BURIED = 11;
+
+ /** DOCUMENT ME!! */
+ public static final int NUCLEOTIDE = 12;
+
+ /**
+ * purine/pyrimidine
+ */
+ public static final int PURINEPYRIMIDINE = 13;
+
+ public static final int COVARIATION = 14;
+
+ /**
+ * 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)
{
- int ret=11;
- if(name.equals("Clustal"))
+ int ret = UNDEFINED;
+
+ if (name.equalsIgnoreCase("Clustal"))
+ {
ret = CLUSTAL;
- else if(name.equals("Blosum62"))
+ }
+ else if (name.equalsIgnoreCase("Blosum62"))
+ {
ret = BLOSUM;
- else if(name.equals("% Identity"))
+ }
+ else if (name.equalsIgnoreCase("% Identity"))
+ {
ret = PID;
- else if(name.equals("Zappo"))
+ }
+ else if (name.equalsIgnoreCase("Zappo"))
+ {
ret = ZAPPO;
- else if(name.equals("Hydrophobic"))
+ }
+ else if (name.equalsIgnoreCase("Taylor"))
+ {
+ ret = TAYLOR;
+ }
+ else if (name.equalsIgnoreCase("Hydrophobic"))
+ {
ret = HYDROPHOBIC;
- else if(name.equals("Helix Propensity"))
+ }
+ else if (name.equalsIgnoreCase("Helix Propensity"))
+ {
ret = HELIX;
- else if(name.equals("Strand Propensity"))
+ }
+ else if (name.equalsIgnoreCase("Strand Propensity"))
+ {
ret = STRAND;
- else if(name.equals("Turn Propensity"))
+ }
+ else if (name.equalsIgnoreCase("Turn Propensity"))
+ {
ret = TURN;
- else if(name.equals("Buried Index"))
+ }
+ else if (name.equalsIgnoreCase("Buried Index"))
+ {
ret = BURIED;
- else if(name.equals("Nucleotide"))
+ }
+ else if (name.equalsIgnoreCase("Nucleotide"))
+ {
ret = NUCLEOTIDE;
- else if(name.equals("User Defined"))
- ret = USER_DEFINED;
+ }
+ else if (name.equalsIgnoreCase("User Defined"))
+ {
+ ret = USER_DEFINED;
+ }
+ else if (name.equalsIgnoreCase("None"))
+ {
+ ret = NONE;
+ }
return ret;
}
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static String getColourName(ColourSchemeI cs)
+ {
+
+ int index = NONE;
+
+ if (cs instanceof ClustalxColourScheme)
+ {
+ index = CLUSTAL;
+ }
+ else if (cs instanceof Blosum62ColourScheme)
+ {
+ index = BLOSUM;
+ }
+ else if (cs instanceof PIDColourScheme)
+ {
+ index = PID;
+ }
+ else if (cs instanceof ZappoColourScheme)
+ {
+ index = ZAPPO;
+ }
+ else if (cs instanceof TaylorColourScheme)
+ {
+ index = TAYLOR;
+ }
+ else if (cs instanceof HydrophobicColourScheme)
+ {
+ index = HYDROPHOBIC;
+ }
+ else if (cs instanceof HelixColourScheme)
+ {
+ index = HELIX;
+ }
+ else if (cs instanceof StrandColourScheme)
+ {
+ index = STRAND;
+ }
+ else if (cs instanceof TurnColourScheme)
+ {
+ index = TURN;
+ }
+ else if (cs instanceof BuriedColourScheme)
+ {
+ index = BURIED;
+ }
+ else if (cs instanceof NucleotideColourScheme)
+ {
+ index = NUCLEOTIDE;
+ }
+ else if (cs instanceof UserColourScheme)
+ {
+ if ((((UserColourScheme) cs).getName() != null)
+ && (((UserColourScheme) cs).getName().length() > 0))
+ {
+ return ((UserColourScheme) cs).getName();
+ }
+ // get default colourscheme name
+ index = USER_DEFINED;
+ }
+
+ return getColourName(index);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param index
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
public static String getColourName(int index)
{
- String ret=null;
- switch(index)
- {
- case CLUSTAL: ret = "Clustal"; break;
- case BLOSUM: ret = "Blosum62"; break;
- case PID: ret = "% Identity"; break;
- case ZAPPO: ret = "Zappo"; break;
- case HYDROPHOBIC: ret="Hydrophobic";break;
- case HELIX: ret="Helix Propensity";break;
- case STRAND: ret="Strand Propensity";break;
- case TURN: ret="Turn Propensity";break;
- case BURIED: ret="Buried Index";break;
- case NUCLEOTIDE:ret="Nucleotide"; break;
- case USER_DEFINED:ret="User Defined";break;
- default: ret = "None"; break;
+ String ret = null;
+
+ switch (index)
+ {
+ case CLUSTAL:
+ ret = "Clustal";
+
+ break;
+
+ case BLOSUM:
+ ret = "Blosum62";
+
+ break;
+
+ case PID:
+ ret = "% Identity";
+
+ break;
+
+ case ZAPPO:
+ ret = "Zappo";
+
+ break;
+
+ case TAYLOR:
+ ret = "Taylor";
+ break;
+
+ case HYDROPHOBIC:
+ ret = "Hydrophobic";
+
+ break;
+
+ case HELIX:
+ ret = "Helix Propensity";
+
+ break;
+
+ case STRAND:
+ ret = "Strand Propensity";
+
+ break;
+
+ case TURN:
+ ret = "Turn Propensity";
+
+ break;
+
+ case BURIED:
+ ret = "Buried Index";
+
+ break;
+
+ case NUCLEOTIDE:
+ ret = "Nucleotide";
+
+ break;
+
+ case USER_DEFINED:
+ ret = "User Defined";
+
+ break;
+
+ default:
+ ret = "None";
+
+ break;
}
+
return ret;
}
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
+ /**
+ * 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, getColourIndexFromName(name));
+ return getColour(al.getSequences(), al.getWidth(), name);
}
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
+ /**
+ * retrieve or create colourscheme associated with name
+ *
+ * @param seqs
+ * sequences to colour
+ * @param width
+ * range of sequences to colour
+ * @param name
+ * colourscheme name, applet colour parameter specification, or
+ * string to parse as colour for new coloursheme
+ * @return Valid Colourscheme
+ */
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+ String name)
{
- ColourSchemeI cs = null;
- switch(index)
- {
- case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
- case BLOSUM: cs = new Blosum62ColourScheme(); break;
- case PID: cs = new PIDColourScheme(); break;
- case ZAPPO: cs = new ZappoColourScheme(); break;
- case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
- case HELIX: cs = new HelixColourScheme(); break;
- case STRAND: cs = new StrandColourScheme(); break;
- case TURN: cs = new TurnColourScheme(); break;
- case BURIED: cs = new BuriedColourScheme(); break;
- case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
- case USER_DEFINED:
- if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
+ int colindex = getColourIndexFromName(name);
+ if (colindex == UNDEFINED)
+ {
+ if (name.indexOf('=') == -1)
+ {
+ // try to build a colour from the string directly
+ try
+ {
+ return new UserColourScheme(name);
+ } catch (Exception e)
{
- cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
+ // System.err.println("Ignoring unknown colourscheme name");
}
- break;
+ }
+ else
+ {
+ // try to parse the string as a residue colourscheme
+ try
+ {
+ // fix the launchApp user defined coloursheme transfer bug
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ "white");
+ ucs.parseAppletParameter(name);
- default: break;
+ } catch (Exception e)
+ {
+ // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
+ }
+ }
+ }
+ return getColour(seqs, width, getColourIndexFromName(name));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seqs
+ * DOCUMENT ME!
+ * @param width
+ * DOCUMENT ME!
+ * @param index
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+ int index)
+ {
+ ColourSchemeI cs = null;
+
+ switch (index)
+ {
+ case CLUSTAL:
+ cs = new ClustalxColourScheme(seqs, width);
+
+ break;
+
+ case BLOSUM:
+ cs = new Blosum62ColourScheme();
+
+ break;
+
+ case PID:
+ cs = new PIDColourScheme();
+
+ break;
+
+ case ZAPPO:
+ cs = new ZappoColourScheme();
+
+ break;
+
+ case TAYLOR:
+ cs = new TaylorColourScheme();
+ break;
+
+ case HYDROPHOBIC:
+ cs = new HydrophobicColourScheme();
+
+ break;
+
+ case HELIX:
+ cs = new HelixColourScheme();
+
+ break;
+
+ case STRAND:
+ cs = new StrandColourScheme();
+
+ break;
+
+ case TURN:
+ cs = new TurnColourScheme();
+
+ break;
+
+ case BURIED:
+ cs = new BuriedColourScheme();
+
+ break;
+
+ case NUCLEOTIDE:
+ cs = new NucleotideColourScheme();
+
+ break;
+
+ case USER_DEFINED:
+ Color[] col = new Color[24];
+ for (int i = 0; i < 24; i++)
+ {
+ col[i] = Color.white;
+ }
+ cs = new UserColourScheme(col);
+ break;
+
+ default:
+ break;
}
return cs;
}
+
+ public static Color getAWTColorFromName(String name)
+ {
+ Color col = null;
+ name = name.toLowerCase();
+ if (name.equals("black"))
+ {
+ col = Color.black;
+ }
+ else if (name.equals("blue"))
+ {
+ col = Color.blue;
+ }
+ else if (name.equals("cyan"))
+ {
+ col = Color.cyan;
+ }
+ else if (name.equals("darkGray"))
+ {
+ col = Color.darkGray;
+ }
+ else if (name.equals("gray"))
+ {
+ col = Color.gray;
+ }
+ else if (name.equals("green"))
+ {
+ col = Color.green;
+ }
+ else if (name.equals("lightGray"))
+ {
+ col = Color.lightGray;
+ }
+ else if (name.equals("magenta"))
+ {
+ col = Color.magenta;
+ }
+ else if (name.equals("orange"))
+ {
+ col = Color.orange;
+ }
+ else if (name.equals("pink"))
+ {
+ col = Color.pink;
+ }
+ else if (name.equals("red"))
+ {
+ col = Color.red;
+ }
+ else if (name.equals("white"))
+ {
+ col = Color.white;
+ }
+ else if (name.equals("yellow"))
+ {
+ col = Color.yellow;
+ }
+
+ return col;
+ }
}