getSequenceAsString

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

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 07abd53..760123b 100644 (file)
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -479,8 +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;
@@ -552,7 +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);
@@ -594,7 +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"))