X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=1780a4acf50bcdbac7b3e09768eeb69aed95a065;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=2050147453381a354c07b4c2a292a1f222cff6ad;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 2050147..1780a4a 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
@@ -1420,41 +1422,62 @@ public class ResidueProperties
   }
   static
   {
-    int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
+    int[][] propMatrixF = new int[maxProteinIndex][maxProteinIndex],
+            propMatrixPos = new int[maxProteinIndex][maxProteinIndex],
+            propMatrixEpos = new int[maxProteinIndex][maxProteinIndex];
     for (int i=0;i<maxProteinIndex;i++)
     {
+      int maxF=0,maxP=0,maxEP=0;
       String ic="";
-      if (aa.length<i) {
+      if (aa.length>i) {
         ic+=aa[i];
       }
       else {ic = "-";}
-      propMatrix[0][i][i]=propHash.size();
-      propMatrix[1][i][i]=propHash.size();
-      propMatrix[2][i][i]=propHash.size();
       for (int j=i+1;j<maxProteinIndex; j++)
       {
         String jc="";
-        if (aa.length<j) {
+        if (aa.length>j) {
           jc+=aa[j];
         }
         else {jc = "-";}
-        propMatrix[0][i][j]=0;
-        propMatrix[1][i][j]=0;
-        propMatrix[2][i][j]=0;
+        propMatrixF[i][j]=0;
+        propMatrixPos[i][j]=0;
+        propMatrixEpos[i][j]=0;
         for (Enumeration<String> en= (Enumeration<String>)propHash.keys(); en.hasMoreElements(); )
         {
           String ph = en.nextElement();
           Map<String,Integer> pph=(Map<String,Integer>)propHash.get(ph);
-          propMatrix[0][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic) : -1;
-          propMatrix[1][i][j]+= pph.get(ic).equals(pph.get(jc)) ? 1 : -1;
-          propMatrix[2][i][j]+= pph.get(ic).equals(pph.get(jc)) ? pph.get(ic)*2 : 0;
+          if (pph.get(ic)!=null && pph.get(jc)!=null) {
+            int icp=pph.get(ic).intValue(),jcp=pph.get(jc).intValue();
+            // Still working on these definitions.
+            propMatrixPos[i][j] += icp == jcp && icp>0 ? 2 : 0;
+            propMatrixPos[j][i] += icp == jcp && icp>0 ? 2 : 0;
+            propMatrixF[i][j] += icp == jcp ? 2 : 0;
+            propMatrixF[j][i] += icp == jcp ? 2 : 0;
+            propMatrixEpos[i][j] += icp == jcp ? (1+icp * 2) : 0;
+            propMatrixEpos[j][i] += icp == jcp ? (1+icp * 2) : 0;
+        }}
+        if (maxF<propMatrixF[i][j])
+        {
+          maxF=propMatrixF[i][j];
+        }
+        if (maxP<propMatrixPos[i][j])
+        {
+          maxP=propMatrixPos[i][j];
+        }
+        if (maxEP<propMatrixEpos[i][j])
+        {
+          maxEP=propMatrixEpos[i][j];
         }
       }
+      propMatrixF[i][i]=maxF;
+      propMatrixPos[i][i]=maxP;
+      propMatrixEpos[i][i]=maxEP;
     }
-    
-    scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrix[0],0));
-    scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrix[1],0));
-    scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrix[2],0));
+    // JAL-1512 comment out physicochemical score matrices for 2.8.1 release
+    //scoreMatrices.put("Conservation Pos", new ScoreMatrix("Conservation Pos",propMatrixPos,0));
+    //scoreMatrices.put("Conservation Both", new ScoreMatrix("Conservation Both",propMatrixF,0));
+    //scoreMatrices.put("Conservation EnhPos", new ScoreMatrix("Conservation EnhPos",propMatrixEpos,0));
     scoreMatrices.put("PID", new PIDScoreModel());
   }
 
@@ -1658,9 +1681,68 @@ public class ResidueProperties
   public static Hashtable toRNAssState;
   static
   {
-    toRNAssState = new Hashtable();
-    toRNAssState.put(")", "S");
-    toRNAssState.put("(", "S");
+	toRNAssState = new Hashtable<String,String>();
+    toRNAssState.put(")", "(");
+    toRNAssState.put("(", "(");
+    toRNAssState.put("]", "[");
+    toRNAssState.put("[", "[");
+    toRNAssState.put("{", "{");
+    toRNAssState.put("}", "{");
+    toRNAssState.put(">", ">");
+    toRNAssState.put("<", ">");
+    toRNAssState.put("A", "A");
+    toRNAssState.put("a", "A");
+    toRNAssState.put("B", "B");
+    toRNAssState.put("b", "B");
+    toRNAssState.put("C", "C");
+    toRNAssState.put("c", "C");
+    toRNAssState.put("D", "D");
+    toRNAssState.put("d", "D");
+    toRNAssState.put("E", "E");
+    toRNAssState.put("e", "E");
+    toRNAssState.put("F", "F");
+    toRNAssState.put("f", "F");
+    toRNAssState.put("G", "G");
+    toRNAssState.put("g", "G");
+    toRNAssState.put("H", "H");
+    toRNAssState.put("h", "H");
+    toRNAssState.put("I", "I");
+    toRNAssState.put("i", "I");
+    toRNAssState.put("J", "J");
+    toRNAssState.put("j", "J");
+    toRNAssState.put("K", "K");
+    toRNAssState.put("k", "K");
+    toRNAssState.put("L", "L");
+    toRNAssState.put("l", "L");
+    toRNAssState.put("M", "M");
+    toRNAssState.put("m", "M");
+    toRNAssState.put("N", "N");
+    toRNAssState.put("n", "N");
+    toRNAssState.put("O", "O");
+    toRNAssState.put("o", "O");
+    toRNAssState.put("P", "P");
+    toRNAssState.put("p", "P");
+    toRNAssState.put("Q", "Q");
+    toRNAssState.put("q", "Q");
+    toRNAssState.put("R", "R");
+    toRNAssState.put("r", "R");
+    toRNAssState.put("S", "S");
+    toRNAssState.put("s", "S");
+    toRNAssState.put("T", "T");
+    toRNAssState.put("t", "T");
+    toRNAssState.put("U", "U");
+    toRNAssState.put("u", "U");
+    toRNAssState.put("V", "V");
+    toRNAssState.put("v", "V");
+    toRNAssState.put("W", "W");
+    toRNAssState.put("w", "W");
+    toRNAssState.put("X", "X");
+    toRNAssState.put("x", "X");
+    toRNAssState.put("Y", "Y");
+    toRNAssState.put("y", "Y");
+    toRNAssState.put("Z", "Z");
+    toRNAssState.put("z", "Z");
+    
   }
 
   /**