X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=4a8955bee6bf8ee3f8d4da23bc5cffd6a50392d5;hb=83ff5551a4f4b4fb92a7cdb5f519ad6453c56cc4;hp=bb4796faa2e3aa7f52eefe294afa9acb7fbb8dd2;hpb=e851b6e27ddf19394510347c1af298f1c377f101;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index bb4796f..4a8955b 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview 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 
@@ -382,13 +382,13 @@ public class AlignSeq
     {
       intToStr = pep;
       charToInt = ResidueProperties.aaIndex;
-      defInt = 23;
+      defInt = ResidueProperties.maxProteinIndex;
     }
     else if (type.equals(AlignSeq.DNA))
     {
       intToStr = dna;
       charToInt = ResidueProperties.nucleotideIndex;
-      defInt = 4;
+      defInt = ResidueProperties.maxNucleotideIndex;
     }
     else
     {
@@ -921,33 +921,41 @@ public class AlignSeq
 
   /**
    * compute the PID vector used by the redundancy filter.
-   * @param originalSequences - sequences in alignment that are to filtered
-   * @param omitHidden - null or strings to be analysed (typically, visible portion of each sequence in alignment) 
-   * @param start - first column in window for calculation
-   * @param end - last column in window for calculation
-   * @param ungapped - if true then use ungapped sequence to compute PID
-   * @return vector containing maximum PID for i-th sequence and any sequences longer than that seuqence 
+   * 
+   * @param originalSequences
+   *          - sequences in alignment that are to filtered
+   * @param omitHidden
+   *          - null or strings to be analysed (typically, visible portion of
+   *          each sequence in alignment)
+   * @param start
+   *          - first column in window for calculation
+   * @param end
+   *          - last column in window for calculation
+   * @param ungapped
+   *          - if true then use ungapped sequence to compute PID
+   * @return vector containing maximum PID for i-th sequence and any sequences
+   *         longer than that seuqence
    */
-  public static float[] computeRedundancyMatrix(SequenceI[] originalSequences,
-          String[] omitHidden, int start, int end, boolean ungapped)
+  public static float[] computeRedundancyMatrix(
+          SequenceI[] originalSequences, String[] omitHidden, int start,
+          int end, boolean ungapped)
   {
-    int height=originalSequences.length;
+    int height = originalSequences.length;
     float[] redundancy = new float[height];
-    int[] lngth=new int[height];
+    int[] lngth = new int[height];
     for (int i = 0; i < height; i++)
     {
       redundancy[i] = 0f;
-      lngth[i]=-1;
+      lngth[i] = -1;
     }
 
-
     // long start = System.currentTimeMillis();
 
     float pid;
     String seqi, seqj;
     for (int i = 0; i < height; i++)
     {
-      
+
       for (int j = 0; j < i; j++)
       {
         if (i == j)
@@ -965,28 +973,28 @@ public class AlignSeq
           seqi = omitHidden[i];
           seqj = omitHidden[j];
         }
-        if (lngth[i]==-1)
+        if (lngth[i] == -1)
         {
-          String ug=AlignSeq.extractGaps(Comparison.GapChars, seqi);
-          lngth[i]=ug.length();
+          String ug = AlignSeq.extractGaps(Comparison.GapChars, seqi);
+          lngth[i] = ug.length();
           if (ungapped)
           {
-            seqi=ug;
+            seqi = ug;
           }
         }
-        if (lngth[j]==-1)
+        if (lngth[j] == -1)
         {
-          String ug=AlignSeq.extractGaps(Comparison.GapChars, seqj);
-          lngth[j]=ug.length();
+          String ug = AlignSeq.extractGaps(Comparison.GapChars, seqj);
+          lngth[j] = ug.length();
           if (ungapped)
           {
-            seqj=ug;
+            seqj = ug;
           }
         }
         pid = Comparison.PID(seqi, seqj);
 
-        // use real sequence length rather than string length 
-        if (lngth[j]<lngth[i])
+        // use real sequence length rather than string length
+        if (lngth[j] < lngth[i])
         {
           redundancy[j] = Math.max(pid, redundancy[j]);
         }