JAL-885; Multi-helix bug is solved; One should think about a more

efficient solution; either by creating a Hashtable of pairs in
StructureFrequency or directly in a RNA class;

Change-Id: I7bd21eb4d952f22579c786f3d78395949fa046d0

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index f2ef118..71ccbd1 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -21,6 +21,7 @@
 
 package jalview.analysis;
 
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Vector;
 
@@ -28,6 +29,7 @@ import jalview.datamodel.SequenceFeature;
 
 public class Rna
 {
+       static Hashtable<Integer, Integer> pairHash = new Hashtable();
   /**
    * Based off of RALEE code ralee-get-base-pairs. Keeps track of open bracket
    * positions in "stack" vector. When a close bracket is reached, pair this
@@ -62,7 +64,7 @@ public class Rna
         Object temp = stack.lastElement();
         stack.remove(stack.size() - 1);
         pairs.addElement(temp);
-        pairs.addElement(i);
+        pairs.addElement(i);        
       }
 
       i++;
@@ -79,10 +81,27 @@ public class Rna
       
        outPairs[p / 2] = new SequenceFeature("RNA helix", "", "", begin,
               end, "");
+       //pairHash.put(begin, end);
+
     }
 
     return outPairs;
   }
+  
+  
+  /**
+   * Function to get the end position corresponding to a given start position
+   * @param indice - start position of a base pair
+   * @return - end position of a base pair
+   */
+  /*makes no sense at the moment :(
+  public int findEnd(int indice){
+         //TODO: Probably extend this to find the start to a given end?
+         //could be done by putting everything twice to the hash
+         ArrayList<Integer> pair = new ArrayList<Integer>();
+         return pairHash.get(indice);
+  }*/
+  
 
   /**
    * Figures out which helix each position belongs to and stores the helix

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 29c0a0b..a5dd030 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -181,6 +181,15 @@ public class StructureFrequency
     }
   }
   
+  public static int findPair(SequenceFeature[] pairs,int indice){
+         for(int i=0; i<pairs.length; i++){
+                 if(pairs[i].getBegin()==indice){
+                         return pairs[i].getEnd();
+                 }
+         }
+         return -1;
+  }
+  
   /**
    * Method to calculate a 'base pair consensus row', very similar 
    * to nucleotide consensus but takes into account a given structure
@@ -193,7 +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");
          Hashtable residueHash;
          String maxResidue;
          char[] seq, struc=rnaStruc.getRNAStruc().toCharArray();
@@ -203,10 +212,15 @@ public class StructureFrequency
          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();
-                 maxResidue="";
+                 maxResidue="-";
                  values = new int[255];
                  bpEnd=-1;
 
@@ -216,7 +230,7 @@ public class StructureFrequency
                          s = '-';
                  }
 
-                 if(s == '-'){
+                 if(s != '('){
                          values['-']++;
                  }
                  else
@@ -245,35 +259,31 @@ public class StructureFrequency
                                                  values['-']++;
                                                  continue;
                                          }
-                                         if(s == '('){
-                                                 bpEnd=rna[(rna.length-1-nonGap)].getEnd();              
+                                         //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";
+                                 //}
                                  }
                          }
                          nonGap++;
                  }
-                 /*UPDATE this for new values
-             if (profile)
-             {
-               residueHash.put(PROFILE, new int[][]
-               { values, new int[]
-               { jSize, nongap } });
-             }
-                  */
+                 //UPDATE this for new values
+             //if (profile)
+             //{
+            //   residueHash.put(PROFILE, new int[][]
+             //  { values, new int[]
+            //   { jSize, nongap } });
+            // }
+                  
 
                  count=values['H'];
-                 
-                 if (count == 0)
-                 {
-                         maxResidue = "-";
-                 }else{
-                         maxResidue="H";
-                 }
-                 
+                                 
                  residueHash.put(MAXCOUNT, new Integer(count));
              residueHash.put(MAXRESIDUE, maxResidue);
              
@@ -288,7 +298,6 @@ public class StructureFrequency
                  if(bpEnd>0){
                          result[bpEnd]=residueHash;
                  }
-
          }
   }