Description added

[jalview.git] / src / jalview / datamodel / SeqCigar.java

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 816e531..7363e9e 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -1,3 +1,21 @@
+/*
+ * 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
+ */
 package jalview.datamodel;
 
 import jalview.analysis.*;
@@ -41,7 +59,7 @@ public class SeqCigar
   public String getSequenceString(char GapChar)
   {
     return (length == 0) ? "" :
-        (String) getSequenceAndDeletions(refseq.getSequence().substring(start, end), GapChar)[0];
+        (String) getSequenceAndDeletions(refseq.getSequenceAsString(start, end), GapChar)[0];
   }
 
   /**
@@ -55,18 +73,20 @@ public class SeqCigar
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq.getSequence().substring(start,end),
+    Object[] edit_result = getSequenceAndDeletions(refseq.getSequenceAsString(start,end),
         GapChar);
     if (edit_result == null)
     {
       throw new Error(
           "Implementation Error - unexpected null from getSequenceAndDeletions");
     }
-
+    int bounds[] = (int[]) edit_result[1];
     seq = new Sequence(refseq.getName(), (String) edit_result[0],
-                       refseq.getStart() + start+( (int[]) edit_result[1])[0],
-                       refseq.getStart() + start+( (int[]) edit_result[1])[2]);
+                       refseq.getStart() + start+bounds[0],
+                       refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
+    // seq.checkValidRange(); probably not needed
     seq.setDatasetSequence(refseq);
+    seq.setDescription(refseq.getDescription());
     return seq;
   }
 
@@ -94,7 +114,7 @@ public class SeqCigar
     }
     if (_s<0)
       throw new Error("Implementation Error: _s="+_s);
-    String seq_string = seq.getSequence();
+    String seq_string = seq.getSequenceAsString();
     if (_e==0 || _e<_s || _e>seq_string.length())
       _e=seq_string.length();
     // resolve start and end positions relative to ungapped reference sequence
@@ -356,7 +376,7 @@ public class SeqCigar
     for (int i = 0; i < alseqs.length; i++)
     {
       alseqs_string[i]=alseqs[i].getRefSeq().
-          getSequence().substring(alseqs[i].start,alseqs[i].end);
+          getSequenceAsString(alseqs[i].start,alseqs[i].end);
       gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
       if (gs_regions[i] == null)
       {
@@ -416,8 +436,9 @@ public class SeqCigar
       SequenceI ref = alseqs[i].getRefSeq();
       seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
                              ref.getStart() + alseqs[i].start+bounds[0],
-                             ref.getStart() + alseqs[i].start+bounds[2]);
+                             ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
+      seqs[i].setDescription(ref.getDescription());
     }
     if (segments!=null) {
       for (int i=0; i<segments.length; i+=3) {
@@ -458,8 +479,8 @@ public class SeqCigar
     if (!gen_sgapped_s.getSequence().equals(s_gapped.getSequence()))
     {
       System.err.println("Couldn't reconstruct sequence.\n" +
-                         gen_sgapped_s.getSequence() + "\n" +
-                         s_gapped.getSequence());
+                         gen_sgapped_s.getSequenceAsString() + "\n" +
+                         s_gapped.getSequenceAsString());
       return false;
     }
     return true;
@@ -531,7 +552,7 @@ public class SeqCigar
                        + "\nCigar String:" + sub_se_gp.getCigarstring() + "\n"
         );
     SequenceI ssgp = sub_se_gp.getSeq('-');
-    System.out.println("\t " + ssgp.getSequence());
+    System.out.println("\t " + ssgp.getSequenceAsString());
     for (int r = 0; r < 10; r++)
     {
       sub_se_gp = new SeqCigar(s_subsequence_gapped, 8, 48);
@@ -541,7 +562,7 @@ public class SeqCigar
       {
         int e = st + rs;
         sub_se_gp.deleteRange(st, e);
-        String ssgapedseq = sub_se_gp.getSeq('-').getSequence();
+        String ssgapedseq = sub_se_gp.getSeq('-').getSequenceAsString();
         System.out.println(st + "," + e + "\t:" + ssgapedseq);
         st -=3;
       }
@@ -557,7 +578,7 @@ public class SeqCigar
         System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
                            al.getSequenceAt(i).getStart() + "\t" +
                            al.getSequenceAt(i).getEnd() + "\t" +
-                           al.getSequenceAt(i).getSequence());
+                           al.getSequenceAt(i).getSequenceAsString());
       }
     }
     {
@@ -573,7 +594,7 @@ public class SeqCigar
         System.out.println("" + al.getSequenceAt(i).getName() + "\t" +
                            al.getSequenceAt(i).getStart() + "\t" +
                            al.getSequenceAt(i).getEnd() + "\t" +
-                           al.getSequenceAt(i).getSequence());
+                           al.getSequenceAt(i).getSequenceAsString());
       }
     }
 //    if (!ssgapedseq.equals("ryas---dtqqwa----slchvh"))