X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=f409f8c59e50d43aa675c63aedda44a0e46799f8;hb=49b625d7c10b85425059a51706a2aca96deed955;hp=15618de9beddc09413c338604d622d8041b3eef1;hpb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 15618de..f409f8c 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -24,10 +24,8 @@ import java.util.*;
 
 
 /**
- * Takes in a vector of sequences and column start and column end
- * and returns a vector of size (end-start+1). Each element of the
- * vector contains a hashtable with the keys being residues and
- * the values being the count of each residue in that column.
+ * Takes in a vector or array of sequences and column start and column end
+ * and returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
  * This class is used extensively in calculating alignment colourschemes
  * that depend on the amount of conservation in each alignment column.
  * @author $author$
@@ -35,12 +33,12 @@ import java.util.*;
  */
 public class AAFrequency
 {
-    /** Takes in a !!ARRAY!! of sequences and column start and column end
-    * and fills given Vector of size (end-start+1). Each element of the
-    * vector contains a hashtable with the keys being residues and
-    * the values being the count of each residue in that column.
-    * This class is used extensively in calculating alignment colourschemes
-    * that depend on the amount of conservation in each alignment column. */
+  //No need to store 1000s of strings which are not
+  //visible to the user.
+  public static final String MAXCOUNT = "C";
+  public static final String MAXRESIDUE="R";
+  public static final String PID_GAPS = "G";
+  public static final String PID_NOGAPS="N";
 
    public static final Hashtable [] calculate(Vector sequences, int start, int end)
    {
@@ -72,34 +70,37 @@ public static final void calculate(SequenceI[] sequences,
 
   int[] values = new int[132];
 
+  String seq;
+
   for (i = start; i < end; i++)
   {
     residueHash = new Hashtable();
     maxCount = 0;
-    maxResidue = "-";
+    maxResidue = "";
     nongap = 0;
     values = new int[132];
 
     for (j = 0; j < jSize; j++)
     {
-      if (sequences[j].getLength() > i)
+      seq = sequences[j].getSequence();
+      if (seq.length() > i)
       {
-        c = sequences[j].getCharAt(i);
+        c = seq.charAt(i);
 
-        if ('a' <= c && c <= 'z')
-        {
-          c -= ('a' - 'A');
-        }
+        if(c == '.' || c==' ')
+          c = '-';
 
-        if (jalview.util.Comparison.isGap(c))
+        if(c=='-')
         {
-          c = '-'; // we always use this for gaps in the property vectors
+          values['-']++;
+          continue;
         }
-        else
+        else if ('a' <= c && c <= 'z')
         {
-          nongap++;
+          c -= 32 ;//('a' - 'A');
         }
 
+        nongap++;
         values[c]++;
 
       }
@@ -111,7 +112,7 @@ public static final void calculate(SequenceI[] sequences,
 
     for (v = 'A'; v < 'Z'; v++)
     {
-      if (values[v] == 0 || values[v] < maxCount)
+      if (values[v] < 2 || values[v] < maxCount)
         continue;
 
       if (values[v] > maxCount)
@@ -125,15 +126,17 @@ public static final void calculate(SequenceI[] sequences,
       maxCount = values[v];
     }
 
+    if(maxResidue.length()==0)
+      maxResidue = "-";
 
-    residueHash.put("maxCount", new Integer(maxCount));
-    residueHash.put("maxResidue", maxResidue);
+    residueHash.put(MAXCOUNT, new Integer(maxCount));
+    residueHash.put(MAXRESIDUE, maxResidue);
 
     percentage = ( (float) maxCount * 100) / (float) jSize;
-    residueHash.put("pid_gaps", new Float(percentage));
+    residueHash.put(PID_GAPS, new Float(percentage));
 
     percentage = ( (float) maxCount * 100) / (float) nongap;
-    residueHash.put("pid_nogaps", new Float(percentage));
+    residueHash.put(PID_NOGAPS, new Float(percentage));
     result[i] = residueHash;
   }
 }