/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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/>.
+ * 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 java.awt.*;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
+
+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 ). The
*/
public class ColourSchemeProperty
{
- /** 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!
+ * 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>
*
- * @param name
- * DOCUMENT ME!
+ * If none of these formats is matched, the string is converted to a colour
+ * using a hashing algorithm. For name "None", returns null.
*
- * @return DOCUMENT ME!
+ * @param forData
+ * @param name
+ * @return
*/
- public static int getColourIndexFromName(String name)
+ public static ColourSchemeI getColourScheme(AlignViewportI view,
+ AnnotatedCollectionI forData, String name)
{
- int ret = UNDEFINED;
-
- if (name.equalsIgnoreCase("Clustal"))
- {
- ret = CLUSTAL;
- }
- else if (name.equalsIgnoreCase("Blosum62"))
- {
- ret = BLOSUM;
- }
- else if (name.equalsIgnoreCase("% Identity"))
- {
- ret = PID;
- }
- else if (name.equalsIgnoreCase("Zappo"))
- {
- ret = ZAPPO;
- }
- else if (name.equalsIgnoreCase("Taylor"))
- {
- ret = TAYLOR;
- }
- else if (name.equalsIgnoreCase("Hydrophobic"))
- {
- ret = HYDROPHOBIC;
- }
- else if (name.equalsIgnoreCase("Helix Propensity"))
- {
- ret = HELIX;
- }
- else if (name.equalsIgnoreCase("Strand Propensity"))
- {
- ret = STRAND;
- }
- else if (name.equalsIgnoreCase("Turn Propensity"))
- {
- ret = TURN;
- }
- else if (name.equalsIgnoreCase("Buried Index"))
- {
- ret = BURIED;
- }
- else if (name.equalsIgnoreCase("Nucleotide"))
+ if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
{
- ret = NUCLEOTIDE;
- }
- else if (name.equalsIgnoreCase("User Defined"))
- {
- ret = USER_DEFINED;
+ return null;
+
}
- else if (name.equalsIgnoreCase("None"))
+
+ /*
+ * if this is the name of a registered colour scheme, just
+ * create a new instance of it
+ */
+ ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
+ view, forData, null);
+ if (scheme != null)
{
- ret = NONE;
+ return scheme;
}
- return ret;
+ /*
+ * 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;
}
- /**
- * DOCUMENT ME!
- *
- * @param cs
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String getColourName(ColourSchemeI cs)
- {
-
- int index = NONE;
+ public static Color rnaHelices[] = null;
- 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)
+ public static void initRnaHelicesShading(int n)
+ {
+ int j = 0;
+ if (rnaHelices == null)
{
- index = BURIED;
+ rnaHelices = new Color[n + 1];
}
- else if (cs instanceof NucleotideColourScheme)
+ else if (rnaHelices != null && rnaHelices.length <= n)
{
- index = NUCLEOTIDE;
+ Color[] t = new Color[n + 1];
+ System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+ j = rnaHelices.length;
+ rnaHelices = t;
}
- else if (cs instanceof UserColourScheme)
+ else
{
- if ((((UserColourScheme) cs).getName() != null)
- && (((UserColourScheme) cs).getName().length() > 0))
- {
- return ((UserColourScheme) cs).getName();
- }
- // get default colourscheme name
- index = USER_DEFINED;
+ return;
}
-
- return getColourName(index);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param index
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String getColourName(int index)
- {
- String ret = null;
-
- switch (index)
+ // 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 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;
+ rnaHelices[j] = ColorUtils.generateRandomColor(Color.white);
}
-
- return ret;
}
/**
- * DOCUMENT ME!
- *
- * @param al
- * DOCUMENT ME!
- * @param name
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * delete the existing cached RNA helices colours
*/
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
- String name)
+ public static void resetRnaHelicesShading()
{
- return getColour(al.getSequences(), al.getWidth(), name);
+ rnaHelices = null;
}
/**
- * retrieve or create colourscheme associated with name
+ * Returns the name of the colour scheme (or "None" if it is null)
*
- * @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
+ * @param cs
+ * @return
*/
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
- String name)
+ public static String getColourName(ColourSchemeI cs)
{
- 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)
- {
- // System.err.println("Ignoring unknown colourscheme name");
- }
- }
- 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);
-
- } catch (Exception e)
- {
- // System.err.println("Ignoring exception when parsing colourscheme as applet-parameter");
- }
- }
- }
- return getColour(seqs, width, getColourIndexFromName(name));
+ return cs == null ? ResidueColourScheme.NONE : cs.getSchemeName();
}
- /**
- * 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;
- }
}
git://source.jalview.org / jalview.git / blobdiff