+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
+
+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 ). 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;
- public static int getColourIndexFromName(String name)
+ /**
+ * Returns a colour scheme for the given name, with which the given data may
+ * be coloured. The name is not case-sensitive, and may be one of
+ * <ul>
+ * <li>any currently registered colour scheme; Jalview by default
+ * provides</li>
+ * <ul>
+ * <li>Clustal</li>
+ * <li>Blosum62</li>
+ * <li>% Identity</li>
+ * <li>Hydrophobic</li>
+ * <li>Zappo</li>
+ * <li>Taylor</li>
+ * <li>Helix Propensity</li>
+ * <li>Strand Propensity</li>
+ * <li>Turn Propensity</li>
+ * <li>Buried Index</li>
+ * <li>Nucleotide</li>
+ * <li>Purine/Pyrimidine</li>
+ * <li>T-Coffee Scores</li>
+ * <li>RNA Helices</li>
+ * </ul>
+ * <li>the name of a programmatically added colour scheme</li>
+ * <li>an AWT colour name e.g. red</li>
+ * <li>an AWT hex rgb colour e.g. ff2288</li>
+ * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+ * </ul>
+ *
+ * If none of these formats is matched, the string is converted to a colour
+ * using a hashing algorithm. For name "None", returns null.
+ *
+ * @param forData
+ * @param name
+ * @return
+ */
+ public static ColourSchemeI getColourScheme(AnnotatedCollectionI forData,
+ String name)
{
- int ret=11;
- if(name.equals("Clustal"))
- ret = CLUSTAL;
- else if(name.equals("Blosum62"))
- ret = BLOSUM;
- else if(name.equals("% Identity"))
- ret = PID;
- else if(name.equals("Zappo"))
- ret = ZAPPO;
- else if(name.equals("Hydrophobic"))
- ret = HYDROPHOBIC;
- else if(name.equals("Helix Propensity"))
- ret = HELIX;
- else if(name.equals("Strand Propensity"))
- ret = STRAND;
- else if(name.equals("Turn Propensity"))
- ret = TURN;
- else if(name.equals("Buried Index"))
- ret = BURIED;
- else if(name.equals("Nucleotide"))
- ret = NUCLEOTIDE;
- else if(name.equals("User Defined"))
- ret = USER_DEFINED;
+ if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
+ {
+ return null;
+
+ }
- return ret;
+ /*
+ * if this is the name of a registered colour scheme, just
+ * create a new instance of it
+ */
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ forData, null);
+ if (scheme != null)
+ {
+ return scheme;
+ }
+
+ /*
+ * try to parse the string as a residues colour scheme
+ * e.g. A=red;T,G=blue etc
+ * else parse the name as a colour specification
+ * e.g. "red" or "ff00ed",
+ * or failing that hash the name to a colour
+ */
+ UserColourScheme ucs = new UserColourScheme(name);
+ return ucs;
}
- public static String getColourName(int index)
+ public static Color rnaHelices[] = null;
+
+ public static void initRnaHelicesShading(int n)
{
- String ret=null;
- switch(index)
+ int j = 0;
+ if (rnaHelices == null)
+ {
+ rnaHelices = new Color[n + 1];
+ }
+ else if (rnaHelices != null && rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+ j = rnaHelices.length;
+ rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; j <= n; j++)
{
- 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;
+ rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
}
- return ret;
}
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
+ /**
+ * delete the existing cached RNA helices colours
+ */
+ public static void resetRnaHelicesShading()
{
- return getColour(al, getColourIndexFromName(name));
+ rnaHelices = null;
}
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
+ /**
+ * Returns the name of the colour scheme (or "None" if it is null)
+ *
+ * @param cs
+ * @return
+ */
+ public static String getColourName(ColourSchemeI cs)
{
- 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)
- {
- cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
- }
- break;
-
- default: break;
- }
-
- return cs;
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
}
+
}
git://source.jalview.org / jalview.git / blobdiff