X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;fp=src%2Fjalview%2Fdatamodel%2FSeqCigar.java;h=b2a1f66759e012859d2afa6395ae67058c05337d;hb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;hp=f2777f499b469555ee0ed8bdb051658bd9063784;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index f2777f4..b2a1f66 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -68,8 +68,8 @@ public class SeqCigar extends CigarSimple
    */
   public String getSequenceString(char GapChar)
   {
-    return (length == 0) ? "" : (String) getSequenceAndDeletions(refseq
-            .getSequenceAsString(start, end), GapChar)[0];
+    return (length == 0) ? "" : (String) getSequenceAndDeletions(
+            refseq.getSequenceAsString(start, end), GapChar)[0];
   }
 
   /**
@@ -85,18 +85,17 @@ public class SeqCigar extends CigarSimple
     {
       return null;
     }
-    Object[] edit_result = getSequenceAndDeletions(refseq
-            .getSequenceAsString(start, end), GapChar);
+    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 + bounds[0], refseq.getStart() + start
-            + ((bounds[2] == 0) ? -1 : bounds[2]));
+    seq = new Sequence(refseq.getName(), (String) edit_result[0],
+            refseq.getStart() + start + bounds[0], refseq.getStart()
+                    + start + ((bounds[2] == 0) ? -1 : bounds[2]));
     seq.setDescription(refseq.getDescription());
     int sstart = seq.getStart(), send = seq.getEnd();
     // seq.checkValidRange(); probably not needed
@@ -170,9 +169,8 @@ public class SeqCigar extends CigarSimple
       }
       else
       {
-        ds = new Sequence(seq.getName(), ungapped, seq.getStart(), seq
-                .getStart()
-                + ungapped.length() - 1);
+        ds = new Sequence(seq.getName(), ungapped, seq.getStart(),
+                seq.getStart() + ungapped.length() - 1);
         // JBPNote: this would be consistent but may not be useful
         // seq.setDatasetSequence(ds);
       }
@@ -501,8 +499,8 @@ public class SeqCigar extends CigarSimple
             }
             else
             {
-              g_seqs[s].insert(inspos, alseqs_string[i].substring(
-                      region[0], region[1] + 1));
+              g_seqs[s].insert(inspos,
+                      alseqs_string[i].substring(region[0], region[1] + 1));
             }
           }
           shifts.addShift(region[2], insert.length); // update shift in
@@ -520,10 +518,9 @@ public class SeqCigar extends CigarSimple
     {
       int[] bounds = ((int[]) ((Object[]) gs_regions[i])[1]);
       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] == 0 ? -1 : bounds[2]));
+      seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
+              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());
     }