X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=0af85f145b8236d4c2a8d2d5590721d277ed6f8c;hb=ae83cc59079dc5374a41402889b6f4192f66e9e2;hp=464abb025e826fcf08669e0128e9c6e20cb9994a;hpb=88eaada36951276cf8b2863bb95aa37148166ea2;p=jalview.git

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 464abb0..0af85f1 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* 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
@@ -63,14 +63,14 @@ public class AlignSeq
     int[] seq2;
     SequenceI s1;
     SequenceI s2;
-    String s1str;
-    String s2str;
+    public String s1str;
+    public String s2str;
     int maxi;
     int maxj;
     int[] aseq1;
     int[] aseq2;
-    public String astr1 = "";
-    public String astr2 = "";
+    public String astr1="";
+    public String astr2="";
 
     /** DOCUMENT ME!! */
     public int seq1start;
@@ -96,7 +96,6 @@ public class AlignSeq
     int defInt = 23;
     StringBuffer output = new StringBuffer();
     String type;
-    Runtime rt;
 
     /**
      * Creates a new AlignSeq object.
@@ -107,7 +106,6 @@ public class AlignSeq
      */
     public AlignSeq(SequenceI s1, SequenceI s2, String type)
     {
-        rt = Runtime.getRuntime();
         SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);
     }
 
@@ -124,7 +122,6 @@ public class AlignSeq
                     String string2,
                     String type)
     {
-        rt = Runtime.getRuntime();
         SeqInit(s1, string1, s2,  string2,  type);
     }
 
@@ -261,9 +258,18 @@ public class AlignSeq
                         String string2,
                         String type)
     {
+
         s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
         s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
 
+        if(s1str.length()==0 || s2str.length()==0)
+        {
+          System.out.println("ALL GAPS: " +
+                             (s1str.length()==0?s1.getName():" ")
+                             +(s2str.length()==0?s2.getName():""));
+          return;
+        }
+
         this.s1 = s1;
         this.s2 = s2;
 
@@ -745,17 +751,24 @@ public class AlignSeq
 
         for (int i = 0; i < s.length(); i++)
         {
-            String ss = s.substring(i, i + 1).toUpperCase();
+           // String ss = s.substring(i, i + 1).toUpperCase();
+            char c = s.charAt(i);
+            if ('a' <= c && c <= 'z')
+            {
+              // TO UPPERCASE !!!
+              c -= ('a' - 'A');
+            }
+
 
             try
             {
                 if (type.equals("pep"))
                 {
-                    seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();
+                    seq1[i] = ResidueProperties.aaIndex[c];
                 }
                 else if (type.equals("dna"))
                 {
-                    seq1[i] = ((Integer) dnaHash.get(ss)).intValue();
+                    seq1[i] = ResidueProperties.nucleotideIndex[c];
                 }
 
                 if (seq1[i] > 23)