X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FStructureFrequency.java;h=1342bb273760f0efc2524e1d3e2840ddf30b2f9c;hb=ce93212014c116c4c516c6dc85c5032449d311eb;hp=479c8562dbe7fecc5f17b101f0ccdf793dabba7f;hpb=5c5161b61d3dc11a22c10fc176f0f967ed40bf52;p=jalview.git

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 479c8562..1342bb2 100644
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -112,8 +112,9 @@ public class StructureFrequency
 
     for (int i = start; i < end; i++) // foreach column
     {
-      int canonicalOrWobblePairCount = 0;
+      int canonicalOrWobblePairCount = 0, canonical = 0;
       int otherPairCount = 0;
+      int nongap = 0;
       maxResidue = "-";
       values = new int[255];
       pairs = new int[255][255];
@@ -148,8 +149,8 @@ public class StructureFrequency
           {
             if (sequences[j] == null)
             {
-              System.err
-                      .println("WARNING: Consensus skipping null sequence - possible race condition.");
+              System.err.println(
+                      "WARNING: Consensus skipping null sequence - possible race condition.");
               continue;
             }
 
@@ -161,7 +162,7 @@ public class StructureFrequency
               values['-']++;
               continue;
             }
-
+            nongap++;
             /*
              * ensure upper-case for counting purposes
              */
@@ -175,32 +176,34 @@ public class StructureFrequency
             }
             if (Rna.isCanonicalOrWobblePair(c, cEnd))
             {
-              values['(']++;
-              maxResidue = "(";
               canonicalOrWobblePairCount++;
+              if (Rna.isCanonicalPair(c, cEnd))
+              {
+                canonical++;
+              }
             }
             else
             {
-              values['[']++;
-              maxResidue = "[";
               otherPairCount++;
             }
             pairs[c][cEnd]++;
           }
         }
-        // nonGap++;
       }
 
       residueHash = new Hashtable();
       if (profile)
       {
         // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
-        residueHash.put(PROFILE, new int[][] { values,
-            new int[] { jSize, (jSize - values['-']) } });
+        residueHash.put(PROFILE,
+                new int[][]
+                { values, new int[] { jSize, (jSize - values['-']) } });
 
         residueHash.put(PAIRPROFILE, pairs);
       }
-
+      values['('] = canonicalOrWobblePairCount;
+      values['['] = canonical;
+      values['{'] = otherPairCount;
       /*
        * the count is the number of valid pairs (as a percentage, determines
        * the relative size of the profile logo)
@@ -208,22 +211,31 @@ public class StructureFrequency
       int count = canonicalOrWobblePairCount;
 
       /*
-       * currently displaying as '(' if most pairs are valid, or as
-       * '[' if there are more invalid than valid pairs 
+       * display '(' if most pairs are canonical, or as
+       * '[' if there are more wobble pairs. 
        */
-      if (!maxResidue.equals("-"))
+      if (canonicalOrWobblePairCount > 0 || otherPairCount > 0)
       {
-        maxResidue = canonicalOrWobblePairCount >= otherPairCount ? "("
-                : "[";
+        if (canonicalOrWobblePairCount >= otherPairCount)
+        {
+          maxResidue = (canonicalOrWobblePairCount - canonical) < canonical
+                  ? "("
+                  : "[";
+        }
+        else
+        {
+          maxResidue = "{";
+        }
       }
-      residueHash.put(MAXCOUNT, new Integer(count));
+      residueHash.put(MAXCOUNT, Integer.valueOf(count));
       residueHash.put(MAXRESIDUE, maxResidue);
 
       percentage = ((float) count * 100) / jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
+      residueHash.put(PID_GAPS, Float.valueOf(percentage));
+
+      percentage = ((float) count * 100) / nongap;
+      residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
-      // percentage = ((float) count * 100) / (float) nongap;
-      // residueHash.put(PID_NOGAPS, new Float(percentage));
       if (result[i] == null)
       {
         result[i] = residueHash;
@@ -232,24 +244,31 @@ public class StructureFrequency
       {
         values[')'] = values['('];
         values[']'] = values['['];
+        values['}'] = values['{'];
         values['('] = 0;
         values['['] = 0;
-        maxResidue = maxResidue.equals("(") ? ")" : "]";
+        values['{'] = 0;
+        maxResidue = maxResidue.equals("(") ? ")"
+                : maxResidue.equals("[") ? "]" : "}";
 
         residueHash = new Hashtable();
         if (profile)
         {
-          residueHash.put(PROFILE, new int[][] { values,
-              new int[] { jSize, (jSize - values['-']) } });
+          residueHash.put(PROFILE,
+                  new int[][]
+                  { values, new int[] { jSize, (jSize - values['-']) } });
 
           residueHash.put(PAIRPROFILE, pairs);
         }
 
-        residueHash.put(MAXCOUNT, new Integer(count));
+        residueHash.put(MAXCOUNT, Integer.valueOf(count));
         residueHash.put(MAXRESIDUE, maxResidue);
 
         percentage = ((float) count * 100) / jSize;
-        residueHash.put(PID_GAPS, new Float(percentage));
+        residueHash.put(PID_GAPS, Float.valueOf(percentage));
+
+        percentage = ((float) count * 100) / nongap;
+        residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
         result[bpEnd] = residueHash;
       }
@@ -428,7 +447,8 @@ public class StructureFrequency
     int valuesCount = 0;
     rtnval[1] = 0;
     int offset = 2;
-    final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1 : 0];
+    final int divisor = profile[1][ignoreGapsInConsensusCalculation ? 1
+            : 0];
     for (int c = 624; c > 0; c--)
     {
       if (vl[c] > 0)