GPL

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

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index 48f7c38..e90e6cc 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -1,19 +1,43 @@
+/*\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
+\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 = 90;\r
+    int       threshold = 0;\r
+    public Vector   consensus;\r
 \r
     public ResidueColourScheme(Color[] colors, int threshold) {\r
-       this.colors    = colors;\r
+        this.colors    = colors;\r
        this.threshold = threshold;\r
     }\r
 \r
-    public ResidueColourScheme() {\r
+    public ResidueColourScheme()\r
+    {   }\r
+\r
+    public void setConsensus(Vector consensus)\r
+    {\r
+      this.consensus = consensus;\r
     }\r
 \r
     public Color findColour(String aa)\r
@@ -21,31 +45,15 @@ public class ResidueColourScheme implements ColourSchemeI{
       return colors[((Integer)(ResidueProperties.aaHash.get(aa))).intValue()];\r
     }\r
 \r
-    public Color findColour(SequenceI seq,String s, int j, Vector aa) {\r
-  try {\r
-           return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
-       } catch (Exception e) {\r
-           return Color.white;\r
-       }\r
-    }\r
-\r
-    // aa should maybe be a class\r
-    public Color getColour(SequenceI seq, int j,Vector aa) {\r
-\r
-       Color  c       = Color.white;\r
-       String s       = seq.getSequence(j,j+1);\r
-\r
-       if (threshold > 0 && aa != null)\r
-        {\r
-           if (aboveThreshold(aa,seq,j,threshold))\r
-               c = findColour(seq,s,j,aa);\r
-       }\r
-        else\r
-           c = findColour(seq,s,j,aa);\r
+    public Color findColour(String s, int j) {\r
 \r
+       if( threshold==0 || aboveThreshold(s,j))\r
+          return colors[((Integer)(ResidueProperties.aaHash.get(s))).intValue()];\r
+       else\r
+          return Color.white;\r
 \r
-      return c;\r
     }\r
+\r
     public int getThreshold() {\r
        return threshold;\r
     }\r
@@ -54,58 +62,20 @@ public class ResidueColourScheme implements ColourSchemeI{
        threshold = ct;\r
     }\r
 \r
-    public Vector  getColours(SequenceI s, Vector aa) {\r
-       Vector colours = new Vector();\r
-\r
-       for (int j = 0; j < s.getLength(); j++)\r
-           colours.addElement(getColour(s,j,aa));\r
-\r
-       return colours;\r
-    }\r
-\r
-    public Vector getColours(SequenceGroup sg, Vector aa) {\r
-       Vector colours = new Vector();\r
-\r
-       for (int j = 0; j < sg.getSize(); j++) {\r
-           SequenceI s = sg.getSequenceAt(j);\r
-\r
-           for (int i = 0; i < s.getLength();i++) {\r
-               colours.addElement(getColour(s,i,aa));\r
-           }\r
-       }\r
-       return colours;\r
-    }\r
-\r
-    public boolean aboveThreshold(Vector aa,SequenceI seq, int j, int threshold) {\r
-       String    s    = seq.getSequence(j,j+1);\r
-       Hashtable hash = (Hashtable)aa.elementAt(j);\r
-\r
-       if (j < aa.size()) {\r
-           String maxRes = (String)hash.get("maxResidue");\r
-\r
-           double sc = 0;\r
+    public boolean aboveThreshold(String s, int j)\r
+    {\r
+       Hashtable hash = (Hashtable)consensus.elementAt(j);\r
 \r
-           if (((Integer)hash.get("maxCount")).intValue() != -1  && hash.contains(s)) {\r
-               int maxCount = ((Integer)hash.get("maxCount")).intValue();\r
-               int resCount = ((Integer)hash.get(s)).intValue();\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
 \r
-               sc = resCount * 100.0 / resCount;\r
+          if (sc >= threshold)\r
+            return true;\r
 \r
-               // This should be isGap somewhere\r
-               if  ( !s.equals("-")  && !s.equals(".") && !s.equals(" ")) {\r
-                   if (sc >= (double)threshold) {\r
-                       return true;\r
-                   }\r
-               }\r
-           }\r
-       }\r
-       return false;\r
-    }\r
+        }\r
 \r
-    public boolean canThreshold() {\r
-       return true;\r
-    }\r
-    public boolean isUserDefinable() {\r
        return false;\r
     }\r
 }\r