Sequence is char []

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

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 74a7812..34e8487 100644 (file)
--- 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)
     {
@@ -113,7 +113,7 @@ 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 +375,7 @@ 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)
       {
@@ -561,7 +561,7 @@ 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;
       }