sequence is char []

[jalview.git] / src / jalview / analysis / AlignSeq.java

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 464abb0..d0c5869 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -63,14 +63,14 @@ public class AlignSeq
     int[] seq2;\r
     SequenceI s1;\r
     SequenceI s2;\r
-    String s1str;\r
-    String s2str;\r
+    public String s1str;\r
+    public String s2str;\r
     int maxi;\r
     int maxj;\r
     int[] aseq1;\r
     int[] aseq2;\r
-    public String astr1 = "";\r
-    public String astr2 = "";\r
+    public String astr1="";\r
+    public String astr2="";\r
 \r
     /** DOCUMENT ME!! */\r
     public int seq1start;\r
@@ -96,7 +96,6 @@ public class AlignSeq
     int defInt = 23;\r
     StringBuffer output = new StringBuffer();\r
     String type;\r
-    Runtime rt;\r
 \r
     /**\r
      * Creates a new AlignSeq object.\r
@@ -107,8 +106,7 @@ public class AlignSeq
      */\r
     public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
     {\r
-        rt = Runtime.getRuntime();\r
-        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);\r
+        SeqInit(s1, s1.getSequenceAsString(), s2,  s2.getSequenceAsString(), type);\r
     }\r
 \r
     /**\r
@@ -124,7 +122,6 @@ public class AlignSeq
                     String string2,\r
                     String type)\r
     {\r
-        rt = Runtime.getRuntime();\r
         SeqInit(s1, string1, s2,  string2,  type);\r
     }\r
 \r
@@ -261,9 +258,18 @@ public class AlignSeq
                         String string2,\r
                         String type)\r
     {\r
+\r
         s1str = extractGaps(jalview.util.Comparison.GapChars, string1);\r
         s2str = extractGaps(jalview.util.Comparison.GapChars, string2);\r
 \r
+        if(s1str.length()==0 || s2str.length()==0)\r
+        {\r
+          System.out.println("ALL GAPS: " +\r
+                             (s1str.length()==0?s1.getName():" ")\r
+                             +(s2str.length()==0?s2.getName():""));\r
+          return;\r
+        }\r
+\r
         this.s1 = s1;\r
         this.s2 = s2;\r
 \r
@@ -745,17 +751,24 @@ public class AlignSeq
 \r
         for (int i = 0; i < s.length(); i++)\r
         {\r
-            String ss = s.substring(i, i + 1).toUpperCase();\r
+           // String ss = s.substring(i, i + 1).toUpperCase();\r
+            char c = s.charAt(i);\r
+            if ('a' <= c && c <= 'z')\r
+            {\r
+              // TO UPPERCASE !!!\r
+              c -= ('a' - 'A');\r
+            }\r
+\r
 \r
             try\r
             {\r
                 if (type.equals("pep"))\r
                 {\r
-                    seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();\r
+                    seq1[i] = ResidueProperties.aaIndex[c];\r
                 }\r
                 else if (type.equals("dna"))\r
                 {\r
-                    seq1[i] = ((Integer) dnaHash.get(ss)).intValue();\r
+                    seq1[i] = ResidueProperties.nucleotideIndex[c];\r
                 }\r
 \r
                 if (seq1[i] > 23)\r