JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu

[jalview.git] / src / jalview / schemes / UserColourScheme.java

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 1865518..09cef92 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -24,13 +24,22 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;
+import jalview.util.StringUtils;
 
 import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.StringTokenizer;
 
 public class UserColourScheme extends ResidueColourScheme
 {
+  /*
+   * lookup (by symbol index) of lower case colours (if configured)
+   */
   Color[] lowerCaseColours;
 
   protected String schemeName;
@@ -47,13 +56,13 @@ public class UserColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     UserColourScheme usc = new UserColourScheme(colors);
     if (lowerCaseColours != null)
     {
-      usc.schemeName = new String(schemeName);
+      usc.schemeName = schemeName;
       usc.lowerCaseColours = new Color[lowerCaseColours.length];
       System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
               lowerCaseColours.length);
@@ -61,9 +70,30 @@ public class UserColourScheme extends ResidueColourScheme
     return usc;
   }
 
+  /**
+   * Constructor for an animino acid colour scheme. The colour specification may
+   * be one of
+   * <ul>
+   * <li>an AWT colour name e.g. red</li>
+   * <li>an AWT hex rgb colour e.g. ff2288</li>
+   * <li>residue colours list e.g. D,E=red;K,R,H=0022FF;c=yellow</li>
+   * </ul>
+   * 
+   * @param colour
+   */
   public UserColourScheme(String colour)
   {
     super(ResidueProperties.aaIndex);
+
+    if (colour.contains("="))
+    {
+      /*
+       * a list of colours per residue(s)
+       */
+      parseAppletParameter(colour);
+      return;
+    }
+
     Color col = ColorUtils.parseColourString(colour);
 
     if (col == null)
@@ -72,12 +102,31 @@ public class UserColourScheme extends ResidueColourScheme
       col = ColorUtils.createColourFromName(colour);
     }
 
-    colors = new Color[24];
-    for (int i = 0; i < 24; i++)
+    setAll(col);
+    schemeName = colour;
+  }
+
+  /**
+   * Sets all symbols to the specified colour
+   * 
+   * @param col
+   */
+  protected void setAll(Color col)
+  {
+    if (symbolIndex == null)
+    {
+      return;
+    }
+    int max = 0;
+    for (int index : symbolIndex)
+    {
+      max = Math.max(max, index);
+    }
+    colors = new Color[max + 1];
+    for (int i = 0; i <= max; i++)
     {
       colors[i] = col;
     }
-    schemeName = colour;
   }
 
   public Color[] getColours()
@@ -115,10 +164,10 @@ public class UserColourScheme extends ResidueColourScheme
    * 
    * @param paramValue
    */
-  public void parseAppletParameter(String paramValue)
+  void parseAppletParameter(String paramValue)
   {
-    // TODO: need a function to generate appletParameter colour string from a
-    // UCS
+    setAll(Color.white);
+
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
     String token = null, colour, residues;
@@ -145,9 +194,9 @@ public class UserColourScheme extends ResidueColourScheme
           {
             if (lowerCaseColours == null)
             {
-              lowerCaseColours = new Color[23];
+              lowerCaseColours = new Color[colors.length];
             }
-            for (int i = 0; i < 23; i++)
+            for (int i = 0; i < lowerCaseColours.length; i++)
             {
               if (lowerCaseColours[i] == null)
               {
@@ -162,7 +211,7 @@ public class UserColourScheme extends ResidueColourScheme
           {
             if (lowerCaseColours == null)
             {
-              lowerCaseColours = new Color[23];
+              lowerCaseColours = new Color[colors.length];
             }
             lowerCaseColours[colIndex] = ColorUtils.parseColourString(colour);
           }
@@ -245,7 +294,80 @@ public class UserColourScheme extends ResidueColourScheme
     {
       return schemeName;
     }
-    return JalviewColourScheme.UserDefined.toString();
+    return "User Defined";
   }
 
+  /**
+   * Generate an applet colour parameter like A,C,D=12ffe9;Q,W=2393fd;w=9178dd
+   * 
+   * @return
+   */
+  public String toAppletParameter()
+  {
+    /*
+     * step 1: build a map from colours to the symbol(s) that have the colour
+     */
+    Map<Color, List<String>> colours = new HashMap<Color, List<String>>();
+
+    for (char symbol = 'A'; symbol <= 'Z'; symbol++)
+    {
+      String residue = String.valueOf(symbol);
+      int index = symbolIndex[symbol];
+      Color c = colors[index];
+      if (c != null && !c.equals(Color.white))
+      {
+        if (colours.get(c) == null)
+        {
+          colours.put(c, new ArrayList<String>());
+        }
+        colours.get(c).add(residue);
+      }
+      if (lowerCaseColours != null)
+      {
+        c = lowerCaseColours[index];
+        if (c != null && !c.equals(Color.white))
+        {
+          residue = residue.toLowerCase();
+          if (colours.get(c) == null)
+          {
+            colours.put(c, new ArrayList<String>());
+          }
+          colours.get(c).add(residue);
+        }
+      }
+    }
+
+    /*
+     * step 2: make a list of { A,G,R=12f9d6 } residues/colour specs
+     */
+    List<String> residueColours = new ArrayList<String>();
+    for (Entry<Color, List<String>> cols : colours.entrySet())
+    {
+      boolean first = true;
+      StringBuilder sb = new StringBuilder();
+      for (String residue : cols.getValue())
+      {
+        if (!first)
+        {
+          sb.append(",");
+        }
+        sb.append(residue);
+        first = false;
+      }
+      sb.append("=");
+      /*
+       * get color as hex value, dropping the alpha (ff) part
+       */
+      String hexString = Integer.toHexString(cols.getKey().getRGB())
+              .substring(2);
+      sb.append(hexString);
+      residueColours.add(sb.toString());
+    }
+
+    /*
+     * sort and output
+     */
+    Collections.sort(residueColours);
+    return StringUtils.listToDelimitedString(residueColours, ";");
+  }
 }