X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=81947b3696e311cda68204dd2ebb63866ef62fe1;hb=6de402db90987d3645f3429d9073c13678d8e980;hp=0e037977b54caff62acdd07f078cc9c351dd1491;hpb=94c3c55a91089b85b9e4eccf6ea0b82750d6f405;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 0e03797..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
@@ -18,16 +18,19 @@
  */
 package jalview.schemes;
 
+import java.util.*;
+
 import java.awt.*;
-import java.util.StringTokenizer;
 
 public class UserColourScheme
     extends ResidueColourScheme
 {
+  Color[] lowerCaseColours;
+
   protected String schemeName;
 
   public UserColourScheme()
-  {  }
+  {}
 
   public UserColourScheme(Color[] newColors)
   {
@@ -38,15 +41,17 @@ public class UserColourScheme
   {
     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 Color[] getColours()
@@ -54,6 +59,11 @@ public class UserColourScheme
     return colors;
   }
 
+  public Color[] getLowerCaseColours()
+  {
+    return lowerCaseColours;
+  }
+
   public void setName(String name)
   {
     schemeName = name;
@@ -78,7 +88,9 @@ public class UserColourScheme
     {}
 
     if (col == null)
+    {
       col = ColourSchemeProperty.getAWTColorFromName(colour);
+    }
 
     if (col == null)
     {
@@ -112,7 +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;
 
@@ -127,8 +141,9 @@ public class UserColourScheme
   {
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
-    String token=null, colour, residues;
-    try{
+    String token = null, colour, residues;
+    try
+    {
       while (st.hasMoreElements())
       {
         token = st.nextToken().trim();
@@ -138,20 +153,87 @@ public class UserColourScheme
         st2 = new StringTokenizer(residues, " ,");
         while (st2.hasMoreTokens())
         {
-          int colIndex =
-              ( (Integer) ResidueProperties.aaHash.
-               get(st2.nextToken())).intValue();
-
-          colors[colIndex] = getColourFromString(colour);
+          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)
+    catch (Exception ex)
+    {
+      System.out.println("Error parsing userDefinedColours:\n"
+                         + token + "\n" + ex);
+    }
+
+  }
+
+  public Color findColour(char c, int j)
   {
-    System.out.println("Error parsing userDefinedColours:\n"
-                       +token+"\n"+ex);
+    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;
   }
 
 }