X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=d3325cadb068cff3d0541e0a03ed0c41a8af3080;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=278cf6afcafad8b8de0d3f8c2cdc364ca805bfa1;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 278cf6a..d3325ca 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,24 +1,25 @@
 /*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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!
  *
@@ -27,398 +28,425 @@ import java.awt.*;
  */
 public class ColourSchemeProperty
 {
-    /** DOCUMENT ME!! */
-    public static final int CLUSTAL = 0;
+  /** DOCUMENT ME!! */
+  public static final int CLUSTAL = 0;
 
-    /** DOCUMENT ME!! */
-    public static final int BLOSUM = 1;
+  /** DOCUMENT ME!! */
+  public static final int BLOSUM = 1;
 
-    /** DOCUMENT ME!! */
-    public static final int PID = 2;
+  /** DOCUMENT ME!! */
+  public static final int PID = 2;
 
-    /** DOCUMENT ME!! */
-    public static final int ZAPPO = 3;
+  /** DOCUMENT ME!! */
+  public static final int ZAPPO = 3;
 
-    /** DOCUMENT ME!! */
-    public static final int TAYLOR = 4;
+  /** DOCUMENT ME!! */
+  public static final int TAYLOR = 4;
 
-    /** DOCUMENT ME!! */
-    public static final int HYDROPHOBIC = 5;
+  /** DOCUMENT ME!! */
+  public static final int HYDROPHOBIC = 5;
 
-    /** DOCUMENT ME!! */
-    public static final int HELIX = 6;
+  /** DOCUMENT ME!! */
+  public static final int HELIX = 6;
 
-    /** DOCUMENT ME!! */
-    public static final int STRAND = 7;
+  /** DOCUMENT ME!! */
+  public static final int STRAND = 7;
 
-    /** DOCUMENT ME!! */
-    public static final int TURN = 8;
+  /** DOCUMENT ME!! */
+  public static final int TURN = 8;
 
-    /** DOCUMENT ME!! */
-    public static final int BURIED = 9;
+  /** DOCUMENT ME!! */
+  public static final int BURIED = 9;
 
-    /** DOCUMENT ME!! */
-    public static final int NUCLEOTIDE = 10;
+  /** DOCUMENT ME!! */
+  public static final int NUCLEOTIDE = 10;
 
-    /** DOCUMENT ME!! */
-    public static final int USER_DEFINED = 11;
+  /** DOCUMENT ME!! */
+  public static final int USER_DEFINED = 11;
 
+  /** DOCUMENT ME!! */
+  public static final int NONE = 12;
 
-    /** 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;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static int getColourIndexFromName(String name)
+    if (name.equalsIgnoreCase("Clustal"))
     {
-        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;
+      ret = CLUSTAL;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static String getColourName(ColourSchemeI cs)
+    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;
+    }
 
-        int index = 12;
+    return ret;
+  }
 
-        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;
-        }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static String getColourName(ColourSchemeI cs)
+  {
 
-        return getColourName(index);
+    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;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param index DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static String getColourName(int index)
+    return getColourName(index);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param index DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public static String getColourName(int index)
+  {
+    String ret = null;
+
+    switch (index)
     {
-        String ret = null;
+      case CLUSTAL:
+        ret = "Clustal";
 
-        switch (index)
-        {
-        case CLUSTAL:
-            ret = "Clustal";
+        break;
 
-            break;
+      case BLOSUM:
+        ret = "Blosum62";
 
-        case BLOSUM:
-            ret = "Blosum62";
+        break;
 
-            break;
+      case PID:
+        ret = "% Identity";
 
-        case PID:
-            ret = "% Identity";
+        break;
 
-            break;
+      case ZAPPO:
+        ret = "Zappo";
 
-        case ZAPPO:
-            ret = "Zappo";
+        break;
 
-            break;
+      case TAYLOR:
+        ret = "Taylor";
+        break;
 
-        case TAYLOR:
-            ret = "Taylor";
-            break;
+      case HYDROPHOBIC:
+        ret = "Hydrophobic";
 
-        case HYDROPHOBIC:
-            ret = "Hydrophobic";
+        break;
 
-            break;
+      case HELIX:
+        ret = "Helix Propensity";
 
-        case HELIX:
-            ret = "Helix Propensity";
+        break;
 
-            break;
+      case STRAND:
+        ret = "Strand Propensity";
 
-        case STRAND:
-            ret = "Strand Propensity";
+        break;
 
-            break;
+      case TURN:
+        ret = "Turn Propensity";
 
-        case TURN:
-            ret = "Turn Propensity";
+        break;
 
-            break;
+      case BURIED:
+        ret = "Buried Index";
 
-        case BURIED:
-            ret = "Buried Index";
+        break;
 
-            break;
+      case NUCLEOTIDE:
+        ret = "Nucleotide";
 
-        case NUCLEOTIDE:
-            ret = "Nucleotide";
+        break;
 
-            break;
+      case USER_DEFINED:
+        ret = "User Defined";
 
-        case USER_DEFINED:
-            ret = "User Defined";
+        break;
 
-            break;
+      default:
+        ret = "None";
 
-        default:
-            ret = "None";
+        break;
+    }
 
-            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);
 
-        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;
 
-            break;
+      case BLOSUM:
+        cs = new Blosum62ColourScheme();
 
-        case BLOSUM:
-            cs = new Blosum62ColourScheme();
+        break;
 
-            break;
+      case PID:
+        cs = new PIDColourScheme();
 
-        case PID:
-            cs = new PIDColourScheme();
+        break;
 
-            break;
+      case ZAPPO:
+        cs = new ZappoColourScheme();
 
-        case ZAPPO:
-            cs = new ZappoColourScheme();
+        break;
 
-            break;
+      case TAYLOR:
+        cs = new TaylorColourScheme();
+        break;
 
-        case TAYLOR:
-            cs = new TaylorColourScheme();
-            break;
+      case HYDROPHOBIC:
+        cs = new HydrophobicColourScheme();
 
-        case HYDROPHOBIC:
-            cs = new HydrophobicColourScheme();
+        break;
 
-            break;
+      case HELIX:
+        cs = new HelixColourScheme();
 
-        case HELIX:
-            cs = new HelixColourScheme();
+        break;
 
-            break;
+      case STRAND:
+        cs = new StrandColourScheme();
 
-        case STRAND:
-            cs = new StrandColourScheme();
+        break;
 
-            break;
+      case TURN:
+        cs = new TurnColourScheme();
 
-        case TURN:
-            cs = new TurnColourScheme();
+        break;
 
-            break;
+      case BURIED:
+        cs = new BuriedColourScheme();
 
-        case BURIED:
-            cs = new BuriedColourScheme();
+        break;
 
-            break;
+      case NUCLEOTIDE:
+        cs = new NucleotideColourScheme();
 
-        case NUCLEOTIDE:
-            cs = new NucleotideColourScheme();
+        break;
 
-            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;
 
-        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;
+    }
 
-        default:
-            break;
-        }
+    return cs;
+  }
 
-        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 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;
+  }
 }