X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=bd70c5d6c51bb6f03eba8f4f6415cc855f25b0c6;hb=9451924e2cdf30878359420a35d669ccee881043;hp=24e35bbe020e9559a7bf6a164f47ed45d18592e3;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 24e35bb..bd70c5d 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,5 +1,6 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
+/*
+ * 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
@@ -13,18 +14,209 @@
  *
  * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.schemes;
 
-import java.util.*;
 import java.awt.*;
+import java.util.StringTokenizer;
 
-public class UserColourScheme extends ResidueColourScheme
+public class UserColourScheme
+    extends ResidueColourScheme
 {
-  public void setColourScheme(Color [] newColors)
+  Color [] lowerCaseColours;
+
+  protected String schemeName;
+
+  public UserColourScheme()
+  {  }
+
+  public UserColourScheme(Color[] newColors)
   {
     colors = newColors;
   }
+
+  public UserColourScheme(String colour)
+  {
+    Color col = getColourFromString(colour);
+
+    if(col==null)
+    {
+      System.out.println("Unknown colour!! "+colour);
+      col = createColourFromName(colour);
+    }
+
+    colors = new Color[24];
+    for(int i=0; i<24; i++)
+      colors[i] = col;
+  }
+
+  public Color[] getColours()
+  {
+    return colors;
+  }
+
+  public Color[] getLowerCaseColours()
+  {
+    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;
+
+    int lsize = name.length();
+    int start = 0, end = lsize / 3;
+
+    int rgbOffset = Math.abs(name.hashCode() % 10) * 15;
+
+    r = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+    start = end;
+    end += lsize / 3;
+    if (end > lsize)
+      end = lsize;
+
+    g = Math.abs(name.substring(start, end).hashCode() + rgbOffset) % 210 + 20;
+
+    b = Math.abs(name.substring(end).hashCode() + rgbOffset) % 210 + 20;
+
+    Color color = new Color(r, g, b);
+
+    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.aaHash.get(token) == null)
+            continue;
+
+          int colIndex =
+              ( (Integer) ResidueProperties.aaHash.
+               get(token)).intValue();
+
+           //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+
+          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(String s, int j)
+  {
+      int index = ((Integer) (ResidueProperties.aaHash.get(s))).intValue();
+
+      if ((threshold == 0) || aboveThreshold(ResidueProperties.aa[index], j))
+      {
+       //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release
+        if(lowerCaseColours!=null && 'a' <= s.charAt(0) && s.charAt(0) <= 'z')
+          currentColour = lowerCaseColours[index];
+        else
+          currentColour = colors[index];
+      }
+      else
+      {
+          currentColour = Color.white;
+      }
+
+      if(conservationColouring)
+        applyConservation(j);
+
+
+      return currentColour;
+   }
+
+   public void setLowerCaseColours(Color [] lcolours)
+   {
+     lowerCaseColours = lcolours;
+   }
+
 }