X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;fp=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=8338c9dda01a6b4826498813562d0a2c559e95d1;hb=41138135cca24db61dc2ce16a8dc0b6dd6dfc6dd;hp=a5dd030d48c78f6003be5ddc6a676a8ce51c588f;hpb=1b75ecd55d73289607632bfb247205913542c352;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index a5dd030..8338c9d 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -202,7 +202,7 @@ public class StructureFrequency
    */
   public static final void calculate(SequenceI[] sequences, int start,
 		  int end, Hashtable[] result, boolean profile, AlignmentAnnotation rnaStruc){
-	  System.out.println("StructureFrequency.calculate");
+	  //System.out.println("StructureFrequency.calculateNEW4");
 	  Hashtable residueHash;
 	  String maxResidue;
 	  char[] seq, struc=rnaStruc.getRNAStruc().toCharArray();
@@ -211,12 +211,7 @@ public class StructureFrequency
 	  int count,nonGap=0,i,bpEnd=-1,j,jSize = sequences.length;
 	  int[] values = new int[255];
 	  float percentage;
-	  
-	  /*for(int x=(rna.length-1); x>=0; x--){
-		  System.out.println("BP-"+((rna.length-1)-x)+" "+rna[x].getBegin()+","+rna[x].getEnd()+" "+rna[x].getFeatureGroup());
-	  }*/
-	  
-	  
+	  	  
 	  for (i = start; i < end; i++) //foreach column
 	  {
 		  residueHash = new Hashtable();
@@ -231,7 +226,9 @@ public class StructureFrequency
 		  }
 
 		  if(s != '('){
-			  values['-']++;
+			  if(s == '-'){
+				  values['-']++;
+			  }
 		  }
 		  else
 		  {
@@ -259,27 +256,24 @@ public class StructureFrequency
 						  values['-']++;
 						  continue;
 					  }
-					  //if(s == '('){
-						  //bpEnd=rna[(rna.length-1-nonGap)].getEnd();
-						  bpEnd=findPair(rna,i);
-						  cEnd=seq[bpEnd];
-						  //System.out.println(i+","+bpEnd);
-						  if(checkBpType(c,cEnd)){
-							  values['H']++; //H means it's a helix (structured)
-						  }
-						  maxResidue="H";
-				  //}
+					  bpEnd=findPair(rna,i);
+					  cEnd=seq[bpEnd];
+					  if(checkBpType(c,cEnd)){
+						  values['H']++; //H means it's a helix (structured)
+					  }
+					  maxResidue="H";
 				  }
 			  }
-			  nonGap++;
+//			  nonGap++;
 		  }
 		  //UPDATE this for new values
-	      //if (profile)
-	      //{
-	     //   residueHash.put(PROFILE, new int[][]
-	      //  { values, new int[]
-	     //   { jSize, nongap } });
-	     // }
+	      if (profile)
+	      {
+	    	  //System.out.println("profile");
+	        residueHash.put(PROFILE, new int[][]
+	        { values, new int[]
+	        { jSize, values['H'] } });
+	      }
 		   
 
 		  count=values['H'];
@@ -375,6 +369,7 @@ public class StructureFrequency
           boolean ignoreGapsInConsensusCalculation,
           boolean includeAllConsSymbols, char[] alphabet)
   {
+	System.out.println("StructureFrequency.completeConsensus "+includeAllConsSymbols);
     float tval, value;
     if (consensus == null || consensus.annotations == null
             || consensus.annotations.length < width)
@@ -412,8 +407,9 @@ public class StructureFrequency
         maxRes = "+";
       }
       int[][] profile = (int[][]) hconsensus[i].get(StructureFrequency.PROFILE);
-      if (profile != null && includeAllConsSymbols)
+      if (profile != null && includeAllConsSymbols) //Just responsible for the tooltip
       {
+    	//System.out.println("StructureFrequency.includeAllConsSymbols");
         mouseOver = "";
         if (alphabet != null)
         {
@@ -429,6 +425,7 @@ public class StructureFrequency
         }
         else
         {
+          //System.out.println("StructureFrequency.NOTincludeAllConsSymbols");
           Object[] ca = new Object[profile[0].length];
           float[] vl = new float[profile[0].length];
           for (int c = 0; c < ca.length; c++)
@@ -472,38 +469,37 @@ public class StructureFrequency
    * @return
    */
   public static int[] extractProfile(Hashtable hconsensus,
-          boolean ignoreGapsInConsensusCalculation)
+		  boolean ignoreGapsInConsensusCalculation)
   {
-    int[] rtnval = new int[64];
-    int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
-    if (profile == null)
-      return null;
-    Object[] ca = new Object[profile[0].length];
-    float[] vl = new float[profile[0].length];
-    for (int c = 0; c < ca.length; c++)
-    {
-      ca[c] = new char[]
-      { (char) c };
-      vl[c] = (float) profile[0][c];
-    }
-    ;
-    jalview.util.QuickSort.sort(vl, ca);
-    rtnval[0] = 1;
-    for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
-    {
-      if (((char[]) ca[c])[0] != '-')
-      {
-        rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
-        rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
-                : 0]);
-      }
-    }
-    return rtnval;
+	  //System.out.println("StructureFrequency.extractProfile");
+	  int[] rtnval = new int[11];
+	  int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE);
+	  if (profile == null)
+		  return null;
+	  
+	  Object[] ca = new Object[profile[0].length];
+	  float[] vl = new float[profile[0].length];
+	  for (int c = 0; c < ca.length; c++)
+	  {
+		  ca[c] = new char[]
+		                   { (char) c };
+		  vl[c] = (float) profile[0][c];
+	  }
+	  ;
+	  jalview.util.QuickSort.sort(vl, ca);
+	  rtnval[0] = 1;
+	  for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+	  {
+		  if (((char[]) ca[c])[0] != '-')
+		  {
+			  rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
+			  rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+					  : 0]);
+		  }
+	  }
+	  return rtnval;
   }
 
-  enum base {A,T,g,C};
- 
-  
   public static void main(String args[]){
 	  //Short test to see if checkBpType works
 	  ArrayList<String> test = new ArrayList<String>();