-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.schemes;\r
-\r
-public class ColourSchemeProperty\r
-{\r
- public static final int CLUSTAL = 0;\r
- public static final int BLOSUM = 1;\r
- public static final int PID = 2;\r
- public static final int ZAPPO = 3;\r
- public static final int HYDROPHOBIC=4;\r
- public static final int HELIX=5;\r
- public static final int STRAND=6;\r
- public static final int TURN = 7;\r
- public static final int BURIED = 8;\r
- public static final int NUCLEOTIDE = 9;\r
- public static final int USER_DEFINED = 10;\r
- public static final int NONE = 11;\r
-\r
- public static int getColourIndexFromName(String name)\r
- {\r
- int ret=11;\r
- if(name.equalsIgnoreCase("Clustal"))\r
- ret = CLUSTAL;\r
- else if(name.equalsIgnoreCase("Blosum62"))\r
- ret = BLOSUM;\r
- else if(name.equalsIgnoreCase("% Identity"))\r
- ret = PID;\r
- else if(name.equalsIgnoreCase("Zappo"))\r
- ret = ZAPPO;\r
- else if(name.equalsIgnoreCase("Hydrophobic"))\r
- ret = HYDROPHOBIC;\r
- else if(name.equalsIgnoreCase("Helix Propensity"))\r
- ret = HELIX;\r
- else if(name.equalsIgnoreCase("Strand Propensity"))\r
- ret = STRAND;\r
- else if(name.equalsIgnoreCase("Turn Propensity"))\r
- ret = TURN;\r
- else if(name.equalsIgnoreCase("Buried Index"))\r
- ret = BURIED;\r
- else if(name.equalsIgnoreCase("Nucleotide"))\r
- ret = NUCLEOTIDE;\r
- else if(name.equalsIgnoreCase("User Defined"))\r
- ret = USER_DEFINED;\r
-\r
- return ret;\r
- }\r
-\r
- public static String getColourName(ColourSchemeI cs)\r
- {\r
- if(cs instanceof ConservationColourScheme)\r
- cs = ((ConservationColourScheme)cs).cs;\r
-\r
-\r
- int index = 11;\r
- if(cs instanceof ClustalxColourScheme)\r
- index = CLUSTAL;\r
- else if(cs instanceof Blosum62ColourScheme)\r
- index = BLOSUM;\r
- else if(cs instanceof PIDColourScheme)\r
- index = PID;\r
- else if(cs instanceof ZappoColourScheme)\r
- index = ZAPPO;\r
- else if(cs instanceof HydrophobicColourScheme)\r
- index = HYDROPHOBIC;\r
- else if(cs instanceof HelixColourScheme)\r
- index = HELIX;\r
- else if(cs instanceof StrandColourScheme)\r
- index = STRAND;\r
- else if(cs instanceof TurnColourScheme)\r
- index = TURN;\r
- else if(cs instanceof BuriedColourScheme)\r
- index = BURIED;\r
- else if(cs instanceof NucleotideColourScheme)\r
- index = NUCLEOTIDE;\r
- else if(cs instanceof UserColourScheme)\r
- index = USER_DEFINED;\r
-\r
- return getColourName(index);\r
- }\r
-\r
- public static String getColourName(int index)\r
- {\r
- String ret=null;\r
- switch(index)\r
- {\r
- case CLUSTAL: ret = "Clustal"; break;\r
- case BLOSUM: ret = "Blosum62"; break;\r
- case PID: ret = "% Identity"; break;\r
- case ZAPPO: ret = "Zappo"; break;\r
- case HYDROPHOBIC: ret="Hydrophobic";break;\r
- case HELIX: ret="Helix Propensity";break;\r
- case STRAND: ret="Strand Propensity";break;\r
- case TURN: ret="Turn Propensity";break;\r
- case BURIED: ret="Buried Index";break;\r
- case NUCLEOTIDE:ret="Nucleotide"; break;\r
- case USER_DEFINED:ret="User Defined";break;\r
- default: ret = "None"; break;\r
- }\r
- return ret;\r
- }\r
-\r
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)\r
- {\r
- return getColour(al, getColourIndexFromName(name));\r
- }\r
-\r
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)\r
- {\r
- ColourSchemeI cs = null;\r
- switch(index)\r
- {\r
- case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;\r
- case BLOSUM: cs = new Blosum62ColourScheme(); break;\r
- case PID: cs = new PIDColourScheme(); break;\r
- case ZAPPO: cs = new ZappoColourScheme(); break;\r
- case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;\r
- case HELIX: cs = new HelixColourScheme(); break;\r
- case STRAND: cs = new StrandColourScheme(); break;\r
- case TURN: cs = new TurnColourScheme(); break;\r
- case BURIED: cs = new BuriedColourScheme(); break;\r
- case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;\r
- case USER_DEFINED: cs = new UserColourScheme(null);\r
- break;\r
-\r
- default: break;\r
- }\r
-\r
- return cs;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 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
+{
+ /** 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;
+
+ public static final int TCOFFEE = 15;
+
+ public static final int RNAHELIX = 16;
+
+ public static final int RNAINTERACTION = 17;
+
+ /**
+ * index of first colourscheme (includes 'None')
+ */
+ public static final int FIRST_COLOUR = NONE;
+
+ public static final int LAST_COLOUR = RNAINTERACTION;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int getColourIndexFromName(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"))
+ {
+ ret = NUCLEOTIDE;
+ }
+ else if (name.equalsIgnoreCase("T-Coffee Scores"))
+ {
+ ret = TCOFFEE;
+ }
+
+ else if (name.equalsIgnoreCase("User Defined"))
+ {
+ ret = USER_DEFINED;
+ }
+ else if (name.equalsIgnoreCase("None"))
+ {
+ ret = NONE;
+ }
+ else if (name.equalsIgnoreCase("Purine/Pyrimidine"))
+ {
+ ret = PURINEPYRIMIDINE;
+ }
+ else if (name.equalsIgnoreCase("RNA Interaction type"))
+ {
+ ret = RNAINTERACTION;
+ }
+ else if (name.equalsIgnoreCase("RNA Helices"))
+ {
+ ret = RNAHELIX;
+ }
+ // else if (name.equalsIgnoreCase("Covariation"))
+ // {
+ // ret = COVARIATION;
+ // }
+
+ 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 PurinePyrimidineColourScheme)
+ {
+ index = PURINEPYRIMIDINE;
+ }
+ else if (cs instanceof TCoffeeColourScheme)
+ {
+ index = TCOFFEE;
+ }
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
+ /*
+ * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
+ */
+ 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 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 PURINEPYRIMIDINE:
+ ret = "Purine/Pyrimidine";
+
+ break;
+
+ case TCOFFEE:
+ ret = "T-Coffee Scores";
+
+ break;
+
+ case RNAINTERACTION:
+ ret = "RNA Interaction type";
+
+ break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
+ /*
+ * case COVARIATION: ret = "Covariation";
+ *
+ * break;
+ */
+ case USER_DEFINED:
+ ret = "User Defined";
+
+ break;
+
+ default:
+ ret = "None";
+
+ break;
+ }
+
+ return ret;
+ }
+
+ /**
+ * 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(AnnotatedCollectionI alignment,
+ String name)
+ {
+ 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(alignment, getColourIndexFromName(name));
+ }
+
+ /**
+ * Construct an instance of ColourSchemeI corresponding to the given
+ * colourscheme index
+ *
+ * @param seqs
+ * sequences to be coloured by colourscheme
+ * @param width
+ * geometry of alignment
+ * @param index
+ * colourscheme number
+ *
+ * @return null or an instance of the colourscheme configured to colour given
+ * sequence set
+ */
+ 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(coll, null);
+
+ 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 PURINEPYRIMIDINE:
+ cs = new PurinePyrimidineColourScheme();
+
+ break;
+
+ case TCOFFEE:
+ cs = new TCoffeeColourScheme(coll);
+ break;
+
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
+
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+ // 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;
+ }
+
+ public static Color rnaHelices[] = null;
+
+ public static void initRnaHelicesShading(int n)
+ {
+ 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++)
+ {
+ rnaHelices[j] = jalview.util.ColorUtils
+ .generateRandomColor(Color.white);
+ }
+ }
+
+ /**
+ * delete the existing cached RNA helces colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ rnaHelices = null;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff