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 2fd1773..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
@@ -96,8 +96,6 @@ public class AlignSeq
     int defInt = 23;\r
     StringBuffer output = new StringBuffer();\r
     String type;\r
-    Runtime rt;\r
-\r
 \r
     /**\r
      * Creates a new AlignSeq object.\r
@@ -108,8 +106,23 @@ public class AlignSeq
      */\r
     public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
     {\r
-        rt = Runtime.getRuntime();\r
-        SeqInit(s1, s2, type);\r
+        SeqInit(s1, s1.getSequenceAsString(), s2,  s2.getSequenceAsString(), type);\r
+    }\r
+\r
+    /**\r
+     * Creates a new AlignSeq object.\r
+     *\r
+     * @param s1 DOCUMENT ME!\r
+     * @param s2 DOCUMENT ME!\r
+     * @param type DOCUMENT ME!\r
+     */\r
+    public AlignSeq(SequenceI s1,\r
+                    String string1,\r
+                    SequenceI s2,\r
+                    String string2,\r
+                    String type)\r
+    {\r
+        SeqInit(s1, string1, s2,  string2,  type);\r
     }\r
 \r
     /**\r
@@ -239,10 +252,23 @@ public class AlignSeq
      * @param s2 DOCUMENT ME!\r
      * @param type DOCUMENT ME!\r
      */\r
-    public void SeqInit(SequenceI s1, SequenceI s2, String type)\r
+    public void SeqInit(SequenceI s1,\r
+                        String string1,\r
+                        SequenceI s2,\r
+                        String string2,\r
+                        String type)\r
     {\r
-        s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());\r
-        s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());\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
@@ -424,11 +450,11 @@ public class AlignSeq
         output.append("Length of alignment = " + (aseq1.length - count) + "\n");\r
         output.append("Sequence ");\r
         output.append(new Format("%" + maxid + "s").form(s1.getName()));\r
-        output.append(" :  " + seq1start + " - " + seq1end + " (Sequence length = " +\r
+        output.append(" :  " + s1.getStart() + " - " + s1.getEnd() + " (Sequence length = " +\r
             s1str.length() + ")\n");\r
         output .append("Sequence ");\r
         output.append(new Format("%" + maxid + "s").form(s2.getName()));\r
-        output .append(" :  " + seq2start + " - " + seq2end + " (Sequence length = " +\r
+        output.append(" :  " + s2.getStart() + " - " + s2.getEnd() + " (Sequence length = " +\r
             s2str.length() + ")\n\n");\r
 \r
         for (int j = 0; j < nochunks; j++)\r
@@ -500,7 +526,7 @@ public class AlignSeq
         output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid));\r
 \r
         try{\r
-          os.println(output.toString());\r
+          os.print(output.toString());\r
         }catch(Exception ex){}\r
     }\r
 \r
@@ -725,17 +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