JAL-1841, bug fix in rna SS consensus, additions to Rna[Test]

[jalview.git] / src / jalview / analysis / StructureFrequency.java

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 88387dd..29d02fe 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -103,23 +103,23 @@ public class StructureFrequency
 
     SequenceFeature[] rna = rnaStruc._rnasecstr;
     char c, s, cEnd;
-    int count = 0, nonGap = 0, i, bpEnd = -1, j, jSize = sequences.length;
+    int bpEnd = -1;
+    int jSize = sequences.length;
     int[] values;
     int[][] pairs;
     float percentage;
-    boolean wooble = true;
-    for (i = start; i < end; i++) // foreach column
+
+    for (int i = start; i < end; i++) // foreach column
     {
-      residueHash = new Hashtable();
+      int canonicalOrWobblePairCount = 0;
+      int otherPairCount = 0;
       maxResidue = "-";
       values = new int[255];
       pairs = new int[255][255];
       bpEnd = -1;
-      // System.out.println("s="+struc[i]);
       if (i < struc.length)
       {
         s = struc[i];
-
       }
       else
       {
@@ -130,7 +130,7 @@ public class StructureFrequency
         s = '-';
       }
 
-      if (s != '(' && s != '[')
+      if (!Rna.isOpeningParenthesis(s))
       {
         if (s == '-')
         {
@@ -139,12 +139,11 @@ public class StructureFrequency
       }
       else
       {
-
         bpEnd = findPair(rna, i);
 
         if (bpEnd > -1)
         {
-          for (j = 0; j < jSize; j++) // foreach row
+          for (int j = 0; j < jSize; j++) // foreach row
           {
             if (sequences[j] == null)
             {
@@ -153,7 +152,6 @@ public class StructureFrequency
               continue;
             }
             c = sequences[j].getCharAt(i);
-            // System.out.println("c="+c);
 
             // standard representation for gaps in sequence and structure
             if (c == '.' || c == ' ')
@@ -168,29 +166,36 @@ public class StructureFrequency
             }
             cEnd = sequences[j].getCharAt(bpEnd);
 
-            // System.out.println("pairs ="+c+","+cEnd);
-            if (checkBpType(c, cEnd) == true)
+            /*
+             * ensure upper-case for counting purposes
+             */
+            if ('a' <= c && 'z' >= c)
+            {
+              c += 'A' - 'a';
+            }
+            if ('a' <= cEnd && 'z' >= cEnd)
             {
-              values['(']++; // H means it's a helix (structured)
+              cEnd += 'A' - 'a';
+            }
+            if (Rna.isCanonicalOrWobblePair(c, cEnd))
+            {
+              values['(']++;
               maxResidue = "(";
-              wooble = true;
-              // System.out.println("It's a pair wc");
-
+              canonicalOrWobblePairCount++;
             }
-            if (checkBpType(c, cEnd) == false)
+            else
             {
-              wooble = false;
-              values['[']++; // H means it's a helix (structured)
+              values['[']++;
               maxResidue = "[";
-
+              otherPairCount++;
             }
             pairs[c][cEnd]++;
-
           }
         }
         // nonGap++;
       }
-      // UPDATE this for new values
+
+      residueHash = new Hashtable();
       if (profile)
       {
         // TODO 1-dim array with jsize in [0], nongapped in [1]; or Pojo
@@ -199,13 +204,11 @@ public class StructureFrequency
 
         residueHash.put(PAIRPROFILE, pairs);
       }
-      if (wooble == true)
-      {
-        count = values['('];
-      }
-      if (wooble == false)
+      int count = Math.max(canonicalOrWobblePairCount, otherPairCount);
+      if (!maxResidue.equals("-"))
       {
-        count = values['['];
+        maxResidue = canonicalOrWobblePairCount >= otherPairCount ? "("
+                : "[";
       }
       residueHash.put(MAXCOUNT, new Integer(count));
       residueHash.put(MAXRESIDUE, maxResidue);
@@ -225,17 +228,9 @@ public class StructureFrequency
         values[']'] = values['['];
         values['('] = 0;
         values['['] = 0;
+        maxResidue = maxResidue.equals("(") ? ")" : "]";
+
         residueHash = new Hashtable();
-        if (wooble == true)
-        {
-          // System.out.println(maxResidue+","+wooble);
-          maxResidue = ")";
-        }
-        if (wooble == false)
-        {
-          // System.out.println(maxResidue+","+wooble);
-          maxResidue = "]";
-        }
         if (profile)
         {
           residueHash.put(PROFILE, new int[][] { values,
@@ -251,80 +246,8 @@ public class StructureFrequency
         residueHash.put(PID_GAPS, new Float(percentage));
 
         result[bpEnd] = residueHash;
-
-      }
-    }
-  }
-
-  /**
-   * Method to check if a base-pair is a canonical or a wobble bp
-   * 
-   * @param up
-   *          5' base
-   * @param down
-   *          3' base
-   * @return True if it is a canonical/wobble bp
-   */
-  public static boolean checkBpType(char up, char down)
-  {
-    if (up > 'Z')
-    {
-      up -= 32;
-    }
-    if (down > 'Z')
-    {
-      down -= 32;
-    }
-
-    switch (up)
-    {
-    case 'A':
-      switch (down)
-      {
-      case 'T':
-        return true;
-      case 'U':
-        return true;
-      }
-      break;
-    case 'C':
-      switch (down)
-      {
-      case 'G':
-        return true;
-      }
-      break;
-    case 'T':
-      switch (down)
-      {
-      case 'A':
-        return true;
-      case 'G':
-        return true;
-      }
-      break;
-    case 'G':
-      switch (down)
-      {
-      case 'C':
-        return true;
-      case 'T':
-        return true;
-      case 'U':
-        return true;
-      }
-      break;
-    case 'U':
-      switch (down)
-      {
-      case 'A':
-        return true;
-      case 'G':
-        return true;
       }
-      break;
     }
-    return false;
   }
 
   /**
@@ -534,7 +457,7 @@ public class StructureFrequency
       for (String j : test)
       {
         System.out.println(i + "-" + j + ": "
-                + StructureFrequency.checkBpType(i.charAt(0), j.charAt(0)));
+                + Rna.isCanonicalOrWobblePair(i.charAt(0), j.charAt(0)));
       }
     }
   }