X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=03cdc15ecba02e2bd677df853c65d177a99aa922;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=4a68f819e8a7dd7cf1fd28d964c67e6a75a53f0e;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 4a68f81..03cdc15 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -1,27 +1,26 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.analysis;
 
-import jalview.datamodel.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
 
 /**
  * Takes in a vector or array of sequences and column start and column end
@@ -36,115 +35,122 @@ public class AAFrequency
   //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 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)
-   {
-     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);
-
-     return reply;
-   }
-
-public static final void calculate(SequenceI[] sequences,
-                                  int start, int end,
-                                  Hashtable [] result)
-{
-  Hashtable residueHash;
-  int maxCount, nongap, i, j, v, jSize = sequences.length;
-  String maxResidue;
-  char c;
-  float percentage;
+  public static final String PID_NOGAPS = "N";
 
-  int[] values = new int[255];
+  public static final Hashtable[] calculate(Vector sequences, int start,
+                                            int end)
+  {
+    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();
+      }
+    }
 
-  char [] seq;
+    Hashtable[] reply = new Hashtable[width];
 
-  for (i = start; i < end; i++)
+    if (end >= width)
+    {
+      end = width;
+    }
+
+    calculate(seqs, start, end, reply);
+
+    return reply;
+  }
+
+  public static final void calculate(SequenceI[] sequences,
+                                     int start, int end,
+                                     Hashtable[] result)
   {
-    residueHash = new Hashtable();
-    maxCount = 0;
-    maxResidue = "";
-    nongap = 0;
-    values = new int[255];
+    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 (j = 0; j < jSize; j++)
+    for (i = start; i < end; i++)
     {
-      seq = sequences[j].getSequence();
-      if (seq.length > i)
-      {
-        c = seq[i];
+      residueHash = new Hashtable();
+      maxCount = 0;
+      maxResidue = "";
+      nongap = 0;
+      values = new int[255];
 
-        if(c == '.' || c==' ')
-          c = '-';
+      for (j = 0; j < jSize; j++)
+      {
+        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]++;
 
-        if(c=='-')
+        }
+        else
         {
           values['-']++;
-          continue;
         }
-        else if ('a' <= c && c <= 'z')
+      }
+
+      for (v = 'A'; v < 'Z'; v++)
+      {
+        if (values[v] < 2 || values[v] < maxCount)
         {
-          c -= 32 ;//('a' - 'A');
+          continue;
         }
 
-        nongap++;
-        values[c]++;
-
-      }
-      else
-      {
-        values['-']++;
+        if (values[v] > maxCount)
+        {
+          maxResidue = String.valueOf( (char) v);
+        }
+        else if (values[v] == maxCount)
+        {
+          maxResidue += String.valueOf( (char) v);
+        }
+        maxCount = values[v];
       }
-    }
-
-    for (v = 'A'; v < 'Z'; v++)
-    {
-      if (values[v] < 2 || values[v] < maxCount)
-        continue;
 
-      if (values[v] > maxCount)
+      if (maxResidue.length() == 0)
       {
-        maxResidue = String.valueOf( (char) v);
+        maxResidue = "-";
       }
-      else if (values[v] == maxCount)
-      {
-        maxResidue += String.valueOf( (char) v);
-      }
-      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));
 
-    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;
+      percentage = ( (float) maxCount * 100) / (float) nongap;
+      residueHash.put(PID_NOGAPS, new Float(percentage));
+      result[i] = residueHash;
+    }
   }
 }
-}
-
-