X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=7363e9ef334537956f1fc4d517d25b8ebae2e986;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=84da27877cbb7fdb0684c4c9d3c15b09324a4361;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 84da278..7363e9e 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -59,7 +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];
   }
 
   /**
@@ -73,7 +73,7 @@ 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)
     {
@@ -86,6 +86,7 @@ public class SeqCigar
                        refseq.getStart() + start+((bounds[2]==0) ? -1 : bounds[2]));
     // seq.checkValidRange(); probably not needed
     seq.setDatasetSequence(refseq);
+    seq.setDescription(refseq.getDescription());
     return seq;
   }
 
@@ -113,7 +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
@@ -375,7 +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)
       {
@@ -437,6 +438,7 @@ public class SeqCigar
                              ref.getStart() + alseqs[i].start+bounds[0],
                              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) {
@@ -477,8 +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;
@@ -550,7 +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);
@@ -560,7 +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;
       }
@@ -576,7 +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());
       }
     }
     {
@@ -592,7 +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"))