JAL-885; Structure conservation row is just added if alignment

isNucleotide(); StructureFrequency.java cleaned;

Change-Id: Ic86908cbea0791e7174b440cc4c7e7b12b978927

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index 4d83019..9bdaa10 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -46,143 +46,12 @@ public class StructureFrequency
 
   public static final String PAIRPROFILE = "B";
 
-  public static final Hashtable[] calculate(Vector sequences, int start,
-          int end)
-  {
-    return calculate(sequences, start, end, false);
-  }
-
-  public static final Hashtable[] calculate(Vector sequences, int start,
-          int end, boolean profile)
-  {
-    SequenceI[] seqs = new SequenceI[sequences.size()];
-    int width = 0;
-    for (int i = 0; i < sequences.size(); i++)
-    {
-      seqs[i] = (SequenceI) sequences.elementAt(i);
-      if (seqs[i].getLength() > width)
-      {
-        width = seqs[i].getLength();
-      }
-    }
-
-    Hashtable[] reply = new Hashtable[width];
-
-    if (end >= width)
-    {
-      end = width;
-    }
-
-    calculate(seqs, start, end, reply, profile);
-
-    return reply;
-  }
-
-  public static final void calculate(SequenceI[] sequences, int start,
-          int end, Hashtable[] result)
-  {
-    calculate(sequences, start, end, result, false);
-  }
-
-  public static final void calculate(SequenceI[] sequences, int start,
-          int end, Hashtable[] result, boolean profile)
-  {
-    Hashtable residueHash;
-    int maxCount, nongap, i, j, v, jSize = sequences.length;
-    String maxResidue;
-    char c;
-    float percentage;
-
-    int[] values = new int[255];
-
-    char[] seq;
-
-    for (i = start; i < end; i++)
-    {
-      residueHash = new Hashtable();
-      maxCount = 0;
-      maxResidue = "";
-      nongap = 0;
-      values = new int[255];
-
-      for (j = 0; j < jSize; j++)
-      {
-        if (sequences[j] == null)
-        {
-          System.err
-                  .println("WARNING: Consensus skipping null sequence - possible race condition.");
-          continue;
-        }
-        seq = sequences[j].getSequence();
-        if (seq.length > i)
-        {
-          c = seq[i];
-
-          if (c == '.' || c == ' ')
-          {
-            c = '-';
-          }
-
-          if (c == '-')
-          {
-            values['-']++;
-            continue;
-          }
-          else if ('a' <= c && c <= 'z')
-          {
-            c -= 32; // ('a' - 'A');
-          }
-
-          nongap++;
-          values[c]++;
-
-        }
-        else
-        {
-          values['-']++;
-        }
-      }
-
-      for (v = 'A'; v < 'Z'; v++)
-      {
-        if (values[v] < 2 || values[v] < maxCount)
-        {
-          continue;
-        }
-
-        if (values[v] > maxCount)
-        {
-          maxResidue = String.valueOf((char) v);
-        }
-        else if (values[v] == maxCount)
-        {
-          maxResidue += String.valueOf((char) v);
-        }
-        maxCount = values[v];
-      }
-
-      if (maxResidue.length() == 0)
-      {
-        maxResidue = "-";
-      }
-      if (profile)
-      {
-        residueHash.put(PROFILE, new int[][]
-        { values, new int[]
-        { jSize, nongap } });
-      }
-      residueHash.put(MAXCOUNT, new Integer(maxCount));
-      residueHash.put(MAXRESIDUE, maxResidue);
-
-      percentage = ((float) maxCount * 100) / (float) jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
-
-      percentage = ((float) maxCount * 100) / (float) nongap;
-      residueHash.put(PID_NOGAPS, new Float(percentage));
-      result[i] = residueHash;
-    }
-  }
-
+/**
+ * Returns the 3' position of a base pair
+ * @param pairs Secondary structure annotation
+ * @param indice 5' position of a base pair
+ * @return 3' position of a base pair
+ */
   public static int findPair(SequenceFeature[] pairs, int indice)
   {
     for (int i = 0; i < pairs.length; i++)
@@ -210,7 +79,6 @@ public class StructureFrequency
           int end, Hashtable[] result, boolean profile,
           AlignmentAnnotation rnaStruc)
   {
-    // System.out.println("StructureFrequency.calculateNEW4");
     Hashtable residueHash;
     String maxResidue;
     char[] seq, struc = rnaStruc.getRNAStruc().toCharArray();
@@ -275,9 +143,7 @@ public class StructureFrequency
             {
               values['H']++; // H means it's a helix (structured)
             }
-            // System.out.println("pair: "+c+","+cEnd);
             pairs[c][cEnd]++;
-            // System.out.println("pairs: "+c+","+cEnd+" - "+pairs[c][cEnd]);
 
             maxResidue = "H";
           }
@@ -287,7 +153,6 @@ public class StructureFrequency
       // UPDATE this for new values
       if (profile)
       {
-        // System.out.println("profile");
         residueHash.put(PROFILE, new int[][]
         { values, new int[]
         { jSize, (jSize - values['-']) } });
@@ -415,8 +280,6 @@ 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)
@@ -460,7 +323,6 @@ public class StructureFrequency
       if (profile != null && includeAllConsSymbols) // Just responsible for the
       // tooltip
       {
-        // System.out.println("StructureFrequency.includeAllConsSymbols");
         mouseOver = "";
         if (alphabet != null)
         {
@@ -476,7 +338,6 @@ 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++)
@@ -514,10 +375,10 @@ public class StructureFrequency
   }
 
   /**
-   * get the sorted profile for the given position of the consensus
+   * get the sorted base-pair profile for the given position of the consensus
    * 
    * @param hconsensus
-   * @return
+   * @return profile of the given column
    */
   public static int[] extractProfile(Hashtable hconsensus,
           boolean ignoreGapsInConsensusCalculation, int column)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1dbcf56..0a9cad4 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -413,17 +413,22 @@ public class AlignViewport implements SelectionSource, VamsasSource
       consensus.hasText = true;
       consensus.autoCalculated = true;
 
-      // TODO check if this can done accordingly
-      strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      strucConsensus.hasText = true;
-      strucConsensus.autoCalculated = true;
-
+      if (alignment.isNucleotide())
+      {
+        strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+                new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+        strucConsensus.hasText = true;
+        strucConsensus.autoCalculated = true;
+      }
+      
       if (Cache.getDefault("SHOW_IDENTITY", true))
       {
         alignment.addAnnotation(consensus);
         // TODO: Make own if for structure
-        alignment.addAnnotation(strucConsensus);
+        if (alignment.isNucleotide())
+        {
+          alignment.addAnnotation(strucConsensus);
+        }
       }
 
     }