X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;fp=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=355d717f15fc08e29b8a4676fd3a7e20813dc765;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=b586a0acea0598f151958705db30dc73c010e342;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index b586a0a..355d717 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,424 +1,424 @@
-/*
-* 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)
-    {
-
-        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:
-          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;
-    }
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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)
+    {
+
+        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:
+          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;
+    }
+}