formatting

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 32a4e29..dbba0f4 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -16,7 +16,6 @@
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-
 package jalview.analysis;
 
 import java.util.*;
@@ -59,15 +58,15 @@ public class StructureFrequency
    */
   public static int findPair(SequenceFeature[] pairs, int indice)
   {
-         System.out.print("indice"+indice+"    ");
+
     for (int i = 0; i < pairs.length; i++)
     {
       if (pairs[i].getBegin() == indice)
-        
+
       {
-         System.out.println(pairs[i].getEnd());
+
         return pairs[i].getEnd();
-        
+
       }
     }
     return -1;
@@ -88,19 +87,11 @@ public class StructureFrequency
           int end, Hashtable[] result, boolean profile,
           AlignmentAnnotation rnaStruc)
   {
-//     System.out.println("longueur="+sequences.length);
-//     for(int l=0;l<=(sequences.length-1);l++){  
-//     System.out.println("sequences "+l+":"+sequences[l].getSequenceAsString());
-//     }
-//     System.out.println("start="+start);
-       System.out.println("end="+end);
-//     System.out.println("result="+result.length);
-//
-//     System.out.println("profile="+profile);
-//     System.out.println("rnaStruc="+rnaStruc);
+
     Hashtable residueHash;
     String maxResidue;
     char[] struc = rnaStruc.getRNAStruc().toCharArray();
+
     SequenceFeature[] rna = rnaStruc._rnasecstr;
     char c, s, cEnd;
     int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
@@ -108,7 +99,6 @@ public class StructureFrequency
     int[][] pairs;
     float percentage;
     boolean wooble = true;
-
     for (i = start; i < end; i++) // foreach column
     {
       residueHash = new Hashtable();
@@ -116,11 +106,11 @@ public class StructureFrequency
       values = new int[255];
       pairs = new int[255][255];
       bpEnd = -1;
-      //System.out.println("s="+struc[i]);
+      // System.out.println("s="+struc[i]);
       if (i < struc.length)
       {
         s = struc[i];
-        
+
       }
       else
       {
@@ -140,57 +130,54 @@ public class StructureFrequency
       }
       else
       {
-        
-         
+
         bpEnd = findPair(rna, i);
-       
-        if (bpEnd>-1)
-        {
-        for (j = 0; j < jSize; j++) // foreach row
+
+        if (bpEnd > -1)
         {
-          if (sequences[j] == null)
+          for (j = 0; j < jSize; j++) // foreach row
           {
-            System.err
-                    .println("WARNING: Consensus skipping null sequence - possible race condition.");
-            continue;
-          }
-          c = sequences[j].getCharAt(i);
-          //System.out.println("c="+c);
-          
+            if (sequences[j] == null)
+            {
+              System.err
+                      .println("WARNING: Consensus skipping null sequence - possible race condition.");
+              continue;
+            }
+            c = sequences[j].getCharAt(i);
+            // System.out.println("c="+c);
 
             // standard representation for gaps in sequence and structure
             if (c == '.' || c == ' ')
             {
-              System.err
-                      .println("WARNING: Consensus skipping null sequence - possible race condition.");
+              c = '-';
+            }
+
+            if (c == '-')
+            {
+              values['-']++;
               continue;
             }
             cEnd = sequences[j].getCharAt(bpEnd);
-         
-         
-            System.out.println("pairs ="+c+","+cEnd);
-            if (checkBpType(c, cEnd)==true)
+
+            // System.out.println("pairs ="+c+","+cEnd);
+            if (checkBpType(c, cEnd) == true)
             {
               values['(']++; // H means it's a helix (structured)
               maxResidue = "(";
-              wooble=true;
-              System.out.println("It's a pair wc");
-              
+              wooble = true;
+              // System.out.println("It's a pair wc");
+
             }
-            if (checkBpType(c, cEnd)==false)
+            if (checkBpType(c, cEnd) == false)
             {
-              wooble =false;
+              wooble = false;
               values['[']++; // H means it's a helix (structured)
               maxResidue = "[";
-              System.out.println("It's an pair non canonic");
-              System.out.println(sequences[j].getRNA());
-              System.out.println(rnaStruc.getRNAStruc().charAt(i));
+
             }
-            pairs[c][cEnd]++;  
-           
-          
-               }
+            pairs[c][cEnd]++;
 
+          }
         }
         // nonGap++;
       }
@@ -203,13 +190,13 @@ public class StructureFrequency
 
         residueHash.put(PAIRPROFILE, pairs);
       }
-      if (wooble==true)
+      if (wooble == true)
       {
-      count = values['('];
+        count = values['('];
       }
-      if (wooble==false)
+      if (wooble == false)
       {
-      count = values['['];
+        count = values['['];
       }
       residueHash.put(MAXCOUNT, new Integer(count));
       residueHash.put(MAXRESIDUE, maxResidue);
@@ -225,18 +212,20 @@ public class StructureFrequency
       }
       if (bpEnd > 0)
       {
-       values[')'] = values['('];
+        values[')'] = values['('];
         values[']'] = values['['];
         values['('] = 0;
         values['['] = 0;
         residueHash = new Hashtable();
-        if (wooble==true){
-               System.out.println(maxResidue+","+wooble);
-               maxResidue = ")";
+        if (wooble == true)
+        {
+          // System.out.println(maxResidue+","+wooble);
+          maxResidue = ")";
         }
-        if(wooble==false){
-               System.out.println(maxResidue+","+wooble);
-               maxResidue = "]";
+        if (wooble == false)
+        {
+          // System.out.println(maxResidue+","+wooble);
+          maxResidue = "]";
         }
         if (profile)
         {
@@ -254,6 +243,7 @@ public class StructureFrequency
         residueHash.put(PID_GAPS, new Float(percentage));
 
         result[bpEnd] = residueHash;
+
       }
     }
   }