Merge branch 'jims_marckhacks' into develop

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 98be0c8..aecce4b 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1420,6 +1420,41 @@ public class ResidueProperties
   }
   static
   {
+    int[][][] propMatrix = new int[3][maxProteinIndex][maxProteinIndex];
+    for (int i=0;i<maxProteinIndex;i++)
+    {
+      String ic="";
+      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) {
+          jc+=aa[j];
+        }
+        else {jc = "-";}
+        propMatrix[0][i][j]=0;
+        propMatrix[1][i][j]=0;
+        propMatrix[2][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;
+        }
+      }
+    }
+    
+    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));
     scoreMatrices.put("PID", new PIDScoreModel());
   }
 
@@ -1623,9 +1658,68 @@ 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");
+    
   }
 
   /**