X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=278cf6afcafad8b8de0d3f8c2cdc364ca805bfa1;hb=9451924e2cdf30878359420a35d669ccee881043;hp=6e7a711e8c8fc74ce63282e4ca6be2c10084cf54;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 6e7a711..278cf6a 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* 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
@@ -18,88 +18,195 @@
 */
 package jalview.schemes;
 
-public class ColourSchemeProperty {
+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;
-    public static final int HYDROPHOBIC = 4;
-    public static final int HELIX = 5;
-    public static final int STRAND = 6;
-    public static final int TURN = 7;
-    public static final int BURIED = 8;
-    public static final int NUCLEOTIDE = 9;
-    public static final int USER_DEFINED = 10;
-    public static final int NONE = 11;
-
-    public static int getColourIndexFromName(String name) {
-        int ret = 11;
-
-        if (name.equalsIgnoreCase("Clustal")) {
+
+    /** 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")) {
+        }
+        else if (name.equalsIgnoreCase("Blosum62"))
+        {
             ret = BLOSUM;
-        } else if (name.equalsIgnoreCase("% Identity")) {
+        }
+        else if (name.equalsIgnoreCase("% Identity"))
+        {
             ret = PID;
-        } else if (name.equalsIgnoreCase("Zappo")) {
+        }
+        else if (name.equalsIgnoreCase("Zappo"))
+        {
             ret = ZAPPO;
-        } else if (name.equalsIgnoreCase("Hydrophobic")) {
+        }
+        else if (name.equalsIgnoreCase("Taylor"))
+        {
+          ret = TAYLOR;
+        }
+        else if (name.equalsIgnoreCase("Hydrophobic"))
+        {
             ret = HYDROPHOBIC;
-        } else if (name.equalsIgnoreCase("Helix Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Helix Propensity"))
+        {
             ret = HELIX;
-        } else if (name.equalsIgnoreCase("Strand Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Strand Propensity"))
+        {
             ret = STRAND;
-        } else if (name.equalsIgnoreCase("Turn Propensity")) {
+        }
+        else if (name.equalsIgnoreCase("Turn Propensity"))
+        {
             ret = TURN;
-        } else if (name.equalsIgnoreCase("Buried Index")) {
+        }
+        else if (name.equalsIgnoreCase("Buried Index"))
+        {
             ret = BURIED;
-        } else if (name.equalsIgnoreCase("Nucleotide")) {
+        }
+        else if (name.equalsIgnoreCase("Nucleotide"))
+        {
             ret = NUCLEOTIDE;
-        } else if (name.equalsIgnoreCase("User Defined")) {
+        }
+        else if (name.equalsIgnoreCase("User Defined"))
+        {
             ret = USER_DEFINED;
         }
 
         return ret;
     }
 
-    public static String getColourName(ColourSchemeI cs) {
-        if (cs instanceof ConservationColourScheme) {
-            cs = ((ConservationColourScheme) cs).cs;
-        }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(ColourSchemeI cs)
+    {
 
-        int index = 11;
+        int index = 12;
 
-        if (cs instanceof ClustalxColourScheme) {
+        if (cs instanceof ClustalxColourScheme)
+        {
             index = CLUSTAL;
-        } else if (cs instanceof Blosum62ColourScheme) {
+        }
+        else if (cs instanceof Blosum62ColourScheme)
+        {
             index = BLOSUM;
-        } else if (cs instanceof PIDColourScheme) {
+        }
+        else if (cs instanceof PIDColourScheme)
+        {
             index = PID;
-        } else if (cs instanceof ZappoColourScheme) {
+        }
+        else if (cs instanceof ZappoColourScheme)
+        {
             index = ZAPPO;
-        } else if (cs instanceof HydrophobicColourScheme) {
+        }
+        else if (cs instanceof TaylorColourScheme)
+        {
+            index = TAYLOR;
+        }
+        else if (cs instanceof HydrophobicColourScheme)
+        {
             index = HYDROPHOBIC;
-        } else if (cs instanceof HelixColourScheme) {
+        }
+        else if (cs instanceof HelixColourScheme)
+        {
             index = HELIX;
-        } else if (cs instanceof StrandColourScheme) {
+        }
+        else if (cs instanceof StrandColourScheme)
+        {
             index = STRAND;
-        } else if (cs instanceof TurnColourScheme) {
+        }
+        else if (cs instanceof TurnColourScheme)
+        {
             index = TURN;
-        } else if (cs instanceof BuriedColourScheme) {
+        }
+        else if (cs instanceof BuriedColourScheme)
+        {
             index = BURIED;
-        } else if (cs instanceof NucleotideColourScheme) {
+        }
+        else if (cs instanceof NucleotideColourScheme)
+        {
             index = NUCLEOTIDE;
-        } else if (cs instanceof UserColourScheme) {
+        }
+        else if (cs instanceof UserColourScheme)
+        {
             index = USER_DEFINED;
         }
 
         return getColourName(index);
     }
 
-    public static String getColourName(int index) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param index DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public static String getColourName(int index)
+    {
         String ret = null;
 
-        switch (index) {
+        switch (index)
+        {
         case CLUSTAL:
             ret = "Clustal";
 
@@ -120,6 +227,10 @@ public class ColourSchemeProperty {
 
             break;
 
+        case TAYLOR:
+            ret = "Taylor";
+            break;
+
         case HYDROPHOBIC:
             ret = "Hydrophobic";
 
@@ -164,18 +275,53 @@ public class ColourSchemeProperty {
         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, getColourIndexFromName(name));
+        String name)
+    {
+        return getColour(al.getSequences(), al.getWidth(), name);
     }
 
-    public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
-        int index) {
+    /**
+     * 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) {
+        switch (index)
+        {
         case CLUSTAL:
-            cs = new ClustalxColourScheme(al.getSequences(), al.getWidth());
+            cs = new ClustalxColourScheme(seqs, width);
 
             break;
 
@@ -194,6 +340,10 @@ public class ColourSchemeProperty {
 
             break;
 
+        case TAYLOR:
+            cs = new TaylorColourScheme();
+            break;
+
         case HYDROPHOBIC:
             cs = new HydrophobicColourScheme();
 
@@ -225,8 +375,10 @@ public class ColourSchemeProperty {
             break;
 
         case USER_DEFINED:
-            cs = new UserColourScheme(null);
-
+          Color[] col = new Color[24];
+          for (int i = 0; i < 24; i++)
+            col[i] = Color.white;
+          cs = new UserColourScheme(col);
             break;
 
         default:
@@ -235,4 +387,38 @@ public class ColourSchemeProperty {
 
         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;
+    }
 }