X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=81947b3696e311cda68204dd2ebb63866ef62fe1;hb=3f89c3afc646bf1d83607110e538f20f9c01c3b2;hp=5f377b3e2abb759482bcf9f251a41a59802ffd36;hpb=223fc4baf5d7a97917755fe0c96c966aad71e6e6;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 5f377b3..81947b3 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.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) 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
@@ -18,68 +18,99 @@
  */
 package jalview.schemes;
 
+import java.util.*;
+
 import java.awt.*;
 
 public class UserColourScheme
     extends ResidueColourScheme
 {
+  Color[] lowerCaseColours;
+
   protected String schemeName;
 
   public UserColourScheme()
   {}
 
-  public UserColourScheme(String colour)
+  public UserColourScheme(Color[] newColors)
   {
-    Color col = null;
-    try{
-      int value = Integer.parseInt(colour, 16);
-      col = new Color(value);
-    }
-    catch(NumberFormatException ex){}
-
-    if(col==null)
-      col = ColourSchemeProperty.getAWTColorFromName(colour);
+    colors = newColors;
+  }
 
-    if(col==null)
-    {try{
-      java.util.StringTokenizer st = new java.util.StringTokenizer(colour, ",");
-      int r = Integer.parseInt( st.nextToken() );
-      int g = Integer.parseInt( st.nextToken() );
-      int b = Integer.parseInt( st.nextToken() );
-      col = new Color(r,g,b);
-    }catch(Exception ex){}
-    }
+  public UserColourScheme(String colour)
+  {
+    Color col = getColourFromString(colour);
 
-    if(col==null)
+    if (col == null)
     {
-      System.out.println("Unknown colour!! "+colour);
+      System.out.println("Unknown colour!! " + colour);
       col = createColourFromName(colour);
     }
 
     colors = new Color[24];
-    for(int i=0; i<24; i++)
+    for (int i = 0; i < 24; i++)
+    {
       colors[i] = col;
+    }
   }
 
-  public UserColourScheme(Color[] newColors)
+  public Color[] getColours()
   {
-    colors = newColors;
+    return colors;
   }
 
-  public Color[] getColours()
+  public Color[] getLowerCaseColours()
   {
-    return colors;
+    return lowerCaseColours;
   }
 
   public void setName(String name)
   {
     schemeName = name;
   }
+
   public String getName()
   {
     return schemeName;
   }
 
+  public Color getColourFromString(String colour)
+  {
+    colour = colour.trim();
+
+    Color col = null;
+    try
+    {
+      int value = Integer.parseInt(colour, 16);
+      col = new Color(value);
+    }
+    catch (NumberFormatException ex)
+    {}
+
+    if (col == null)
+    {
+      col = ColourSchemeProperty.getAWTColorFromName(colour);
+    }
+
+    if (col == null)
+    {
+      try
+      {
+        java.util.StringTokenizer st = new java.util.StringTokenizer(colour,
+            ",");
+        int r = Integer.parseInt(st.nextToken());
+        int g = Integer.parseInt(st.nextToken());
+        int b = Integer.parseInt(st.nextToken());
+        col = new Color(r, g, b);
+      }
+      catch (Exception ex)
+      {}
+    }
+
+    return col;
+
+  }
+
   public Color createColourFromName(String name)
   {
     int r, g, b;
@@ -93,7 +124,9 @@ public class UserColourScheme
     start = end;
     end += lsize / 3;
     if (end > lsize)
+    {
       end = lsize;
+    }
 
     g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
 
@@ -104,4 +137,103 @@ public class UserColourScheme
     return color;
   }
 
+  public void parseAppletParameter(String paramValue)
+  {
+    StringTokenizer st = new StringTokenizer(paramValue, ";");
+    StringTokenizer st2;
+    String token = null, colour, residues;
+    try
+    {
+      while (st.hasMoreElements())
+      {
+        token = st.nextToken().trim();
+        residues = token.substring(0, token.indexOf("="));
+        colour = token.substring(token.indexOf("=") + 1);
+
+        st2 = new StringTokenizer(residues, " ,");
+        while (st2.hasMoreTokens())
+        {
+          token = st2.nextToken();
+
+          if (ResidueProperties.aaIndex[token.charAt(0)] == -1)
+          {
+            continue;
+          }
+
+          int colIndex = ResidueProperties.aaIndex[token.charAt(0)];
+
+          if (token.equalsIgnoreCase("lowerCase"))
+          {
+            if (lowerCaseColours == null)
+            {
+              lowerCaseColours = new Color[23];
+            }
+            for (int i = 0; i < 23; i++)
+            {
+              if (lowerCaseColours[i] == null)
+              {
+                lowerCaseColours[i] = getColourFromString(colour);
+              }
+            }
+
+            continue;
+          }
+
+          if (token.equals(token.toLowerCase()))
+          {
+            if (lowerCaseColours == null)
+            {
+              lowerCaseColours = new Color[23];
+            }
+            lowerCaseColours[colIndex] = getColourFromString(colour);
+          }
+          else
+          {
+            colors[colIndex] = getColourFromString(colour);
+          }
+        }
+      }
+    }
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing userDefinedColours:\n"
+                         + token + "\n" + ex);
+    }
+
+  }
+
+  public Color findColour(char c, int j)
+  {
+    Color currentColour;
+    int index = ResidueProperties.aaIndex[c];
+
+    if ( (threshold == 0) || aboveThreshold(c, j))
+    {
+      if (lowerCaseColours != null && 'a' <= c && c <= 'z')
+      {
+        currentColour = lowerCaseColours[index];
+      }
+      else
+      {
+        currentColour = colors[index];
+      }
+    }
+    else
+    {
+      currentColour = Color.white;
+    }
+
+    if (conservationColouring)
+    {
+      currentColour = applyConservation(currentColour, j);
+    }
+
+    return currentColour;
+  }
+
+  public void setLowerCaseColours(Color[] lcolours)
+  {
+    lowerCaseColours = lcolours;
+  }
+
 }