store symbol profile and extract it for display

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 6c21c74..fc8cb4c 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -43,9 +43,17 @@ public class AAFrequency
 
   public static final String PID_NOGAPS = "N";
 
+  public static final String PROFILE = "P";
+
   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++)
@@ -64,7 +72,7 @@ public class AAFrequency
       end = width;
     }
 
-    calculate(seqs, start, end, reply);
+    calculate(seqs, start, end, reply, profile);
 
     return reply;
   }
@@ -72,6 +80,12 @@ public class AAFrequency
   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;
@@ -144,7 +158,12 @@ public class AAFrequency
       {
         maxResidue = "-";
       }
-
+      if (profile)
+      {
+        residueHash.put(PROFILE, new int[][]
+        { values, new int[]
+        { jSize, nongap } });
+      }
       residueHash.put(MAXCOUNT, new Integer(maxCount));
       residueHash.put(MAXRESIDUE, maxResidue);
 
@@ -158,20 +177,37 @@ public class AAFrequency
   }
 
   /**
-   * Compute all or part of the annotation row from the given consensus hashtable
-   * @param consensus - pre-allocated annotation row 
+   * Compute all or part of the annotation row from the given consensus
+   * hashtable
+   * 
+   * @param consensus
+   *          - pre-allocated annotation row
    * @param hconsensus
    * @param iStart
    * @param width
    * @param ignoreGapsInConsensusCalculation
+   * @param includeAllConsSymbols
    */
   public static void completeConsensus(AlignmentAnnotation consensus,
           Hashtable[] hconsensus, int iStart, int width,
-          boolean ignoreGapsInConsensusCalculation)
+          boolean ignoreGapsInConsensusCalculation,
+          boolean includeAllConsSymbols)
   {
+    completeConsensus(consensus, hconsensus, iStart, width,
+            ignoreGapsInConsensusCalculation, includeAllConsSymbols,
+            null); //new char[]
+            // { 'A', 'C', 'G', 'T', 'U' });
+  }
+
+  public static void completeConsensus(AlignmentAnnotation consensus,
+          Hashtable[] hconsensus, int iStart, int width,
+          boolean ignoreGapsInConsensusCalculation,
+          boolean includeAllConsSymbols, char[] alphabet)
+  {
+    float tval, value;
     for (int i = iStart; i < width; i++)
     {
-      float value = 0;
+      value = 0;
       if (ignoreGapsInConsensusCalculation)
       {
         value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
@@ -183,20 +219,100 @@ public class AAFrequency
                 .floatValue();
       }
 
-      String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE)
-              .toString();
-      String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE)
-              + " ";
-
+      String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+      String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
       if (maxRes.length() > 1)
       {
         mouseOver = "[" + maxRes + "] ";
         maxRes = "+";
       }
+      int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
+      if (profile != null && includeAllConsSymbols)
+      {
+        mouseOver = "";
+        if (alphabet!=null)
+        {
+          for (int c = 0; c < alphabet.length; c++)
+          {
+            tval = ((float) profile[0][alphabet[c]])
+                    * 100f
+                    / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+                            : 0];
+            mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " "
+                    + ((int) tval) + "%";
+          }
+        }
+        else
+        {
+          Object[] ca = new Object[profile[0].length];
+          float[] vl = new float[profile[0].length];
+          for (int c = 0; c < ca.length; c++)
+          {
+            ca[c] = new char[]
+            { (char) c };
+            vl[c] = (float) profile[0][c];
+          }
+          ;
+          jalview.util.QuickSort.sort(vl, ca);
+          for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+          {
+            if (((char[]) ca[c])[0] != '-')
+            {
+              tval = ((float) profile[0][((char[]) ca[c])[0]])
+                      * 100f
+                      / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+                              : 0];
+              mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0]
+                      + " " + ((int) tval) + "%";
+              p++;
+
+            }
+          }
 
-      mouseOver += ((int) value + "%");
+        }
+      }
+      else
+      {
+        mouseOver += ((int) value + "%");
+      }
       consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);
     }
   }
+
+  /**
+   * get the sorted profile for the given position of the consensus
+   * 
+   * @param hconsensus
+   * @return
+   */
+  public static int[] extractProfile(Hashtable hconsensus,
+          boolean ignoreGapsInConsensusCalculation)
+  {
+    int[] rtnval = new int[64];
+    int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE);
+    if (profile == null)
+      return null;
+    Object[] ca = new Object[profile[0].length];
+    float[] vl = new float[profile[0].length];
+    for (int c = 0; c < ca.length; c++)
+    {
+      ca[c] = new char[]
+      { (char) c };
+      vl[c] = (float) profile[0][c];
+    }
+    ;
+    jalview.util.QuickSort.sort(vl, ca);
+    rtnval[0] = 1;
+    for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--)
+    {
+      if (((char[]) ca[c])[0] != '-')
+      {
+        rtnval[rtnval[0]++] = ((char[]) ca[c])[0];
+        rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1
+                : 0]);
+      }
+    }
+    return rtnval;
+  }
 }