X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=fc92cd96b2f400fcb0cc4739d640f6b28df25877;hb=36067eda8f713ab855b839fd4cc9af5cf36854a4;hp=012c3a9b8fa503fc3b0eddf43e79d52cdda5f65d;hpb=ef3333028b291ce92bdae34bd2f8487d35d0a0d3;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 012c3a9..fc92cd9 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,426 +1,155 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-package jalview.schemes;
-
-import java.awt.*;
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class ColourSchemeProperty
-{
- /** DOCUMENT ME!! */
- public static final int CLUSTAL = 0;
-
- /** DOCUMENT ME!! */
- public static final int BLOSUM = 1;
-
- /** DOCUMENT ME!! */
- public static final int PID = 2;
-
- /** DOCUMENT ME!! */
- public static final int ZAPPO = 3;
-
- /** DOCUMENT ME!! */
- public static final int TAYLOR = 4;
-
- /** DOCUMENT ME!! */
- public static final int HYDROPHOBIC = 5;
-
- /** DOCUMENT ME!! */
- public static final int HELIX = 6;
-
- /** DOCUMENT ME!! */
- public static final int STRAND = 7;
-
- /** DOCUMENT ME!! */
- public static final int TURN = 8;
-
- /** DOCUMENT ME!! */
- public static final int BURIED = 9;
-
- /** DOCUMENT ME!! */
- public static final int NUCLEOTIDE = 10;
-
- /** DOCUMENT ME!! */
- public static final int USER_DEFINED = 11;
-
-
- /** DOCUMENT ME!! */
- public static final int NONE = 12;
-
- /**
- * DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static int getColourIndexFromName(String name)
- {
- int ret = 12;
-
- 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("User Defined"))
- {
- ret = USER_DEFINED;
- }
-
- return ret;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param cs DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static String getColourName(ColourSchemeI cs)
- {
- if (cs instanceof ConservationColourScheme)
- {
- cs = ((ConservationColourScheme) cs).cs;
- }
-
- int index = 12;
-
- 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)
- {
- 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 USER_DEFINED:
- ret = "User Defined";
-
- break;
-
- default:
- ret = "None";
-
- break;
- }
-
- 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);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param seqs DOCUMENT ME!
- * @param width DOCUMENT ME!
- * @param name DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
- String name)
- {
- 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:
- cs = new UserColourScheme(new Color[0]);
-
- 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;
- }
-}
+/*
+ * 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