Formatted source

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index b0a5caa..a688593 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,65 +1,79 @@
+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+*/\r
 package jalview.schemes;\r
 \r
-import jalview.datamodel.*;\r
-import java.util.*;\r
 import java.awt.*;\r
 \r
-public class ResidueColourScheme implements ColourSchemeI{\r
-    Color    [] colors;\r
-    int       threshold = 0;\r
+import java.util.*;\r
+\r
+\r
+public class ResidueColourScheme implements ColourSchemeI {\r
+    Color[] colors;\r
+    int threshold = 0;\r
+    public Vector consensus;\r
 \r
     public ResidueColourScheme(Color[] colors, int threshold) {\r
-       this.colors    = colors;\r
-       this.threshold = threshold;\r
+        this.colors = colors;\r
+        this.threshold = threshold;\r
     }\r
 \r
     public ResidueColourScheme() {\r
     }\r
 \r
-    public Color findColour(String aa)\r
-    {\r
-      return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
+    public void setConsensus(Vector consensus) {\r
+        this.consensus = consensus;\r
     }\r
 \r
-    public Color findColour(String s, int j, Vector aa) {\r
-\r
-       if( threshold==0 || aboveThreshold(aa,s,j))\r
-          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
-       else\r
-          return Color.white;\r
+    public Color findColour(String aa) {\r
+        return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];\r
+    }\r
 \r
+    public Color findColour(String s, int j) {\r
+        if ((threshold == 0) || aboveThreshold(s, j)) {\r
+            return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];\r
+        } else {\r
+            return Color.white;\r
+        }\r
     }\r
 \r
     public int getThreshold() {\r
-       return threshold;\r
+        return threshold;\r
     }\r
 \r
     public void setThreshold(int ct) {\r
-       threshold = ct;\r
+        threshold = ct;\r
     }\r
 \r
-    public boolean aboveThreshold(Vector aa,String s, int j)\r
-    {\r
-\r
-       Hashtable hash = (Hashtable)aa.elementAt(j);\r
-\r
-        if ( ( (Integer) hash.get("maxCount")).intValue() != -1 && hash.contains(s))\r
-        {\r
-               ////  resCount////////////////////                  ///////////////seq count////////////\r
-          double sc = ( (Integer) hash.get(s)).intValue()  * 100.0 / ( (Integer) hash.get("size")).intValue();\r
+    public boolean aboveThreshold(String s, int j) {\r
+        Hashtable hash = (Hashtable) consensus.elementAt(j);\r
 \r
-          if (sc >= threshold)\r
-            return true;\r
+        if ((((Integer) hash.get("maxCount")).intValue() != -1) &&\r
+                hash.contains(s)) {\r
+            ////  resCount////////////////////                  ///////////////seq count////////////\r
+            double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(\r
+                    "size")).intValue();\r
 \r
+            if (sc >= threshold) {\r
+                return true;\r
+            }\r
         }\r
 \r
-       return false;\r
-    }\r
-\r
-    public boolean canThreshold() {\r
-       return true;\r
-    }\r
-    public boolean isUserDefinable() {\r
-       return false;\r
+        return false;\r
     }\r
 }\r