formatting

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index e668470..8b86a82 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -51,7 +51,7 @@ public class AlignmentView
     width = seqcigararray.getWidth(); // visible width
   }
   /**
-   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment 
+   * Create an alignmentView where the first column corresponds with the 'firstcol' column of some reference alignment
    * @param sdata
    * @param firstcol
    */
@@ -244,8 +244,8 @@ public class AlignmentView
                 }
                 else
                 {
-                  alignment[s].setSequence(alignment[s].getSequence() +
-                                           mseq[s].getSequence());
+                  alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                           mseq[s].getSequenceAsString());
                   if (mseq[s].getStart() <= mseq[s].getEnd())
                   {
                     alignment[s].setEnd(mseq[s].getEnd());
@@ -276,8 +276,8 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
-                                             oseq.getSequence());
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
                       alignment[s].setEnd(oseq.getEnd());
@@ -303,8 +303,8 @@ public class AlignmentView
             }
             else
             {
-              alignment[s].setSequence(alignment[s].getSequence() +
-                                       hseq.getSequence());
+              alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                       hseq.getSequenceAsString());
               if (hseq.getEnd() >= hseq.getStart())
               {
                 alignment[s].setEnd(hseq.getEnd());
@@ -332,8 +332,8 @@ public class AlignmentView
               }
               else
               {
-                alignment[s].setSequence(alignment[s].getSequence() +
-                                         mseq[s].getSequence());
+                alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                         mseq[s].getSequenceAsString());
                 if (mseq[s].getEnd() >= mseq[s].getStart())
                 {
                   alignment[s].setEnd(mseq[s].getEnd());
@@ -366,8 +366,8 @@ public class AlignmentView
                   }
                   else
                   {
-                    alignment[s].setSequence(alignment[s].getSequence() +
-                                             oseq.getSequence());
+                    alignment[s].setSequence(alignment[s].getSequenceAsString() +
+                                             oseq.getSequenceAsString());
                     if (oseq.getEnd() >= oseq.getStart())
                     {
                       alignment[s].setEnd(oseq.getEnd());
@@ -397,7 +397,7 @@ public class AlignmentView
   }
   /**
    * returns simple array of start end positions of visible range on alignment.
-   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment. 
+   * vis_start and vis_end are inclusive - use SequenceI.getSubSequence(vis_start, vis_end+1) to recover visible sequence from underlying alignment.
    * @return int[] { start_i, end_i } for 1<i<n visible regions.
    */
   public int[] getVisibleContigs() {
@@ -429,7 +429,7 @@ public class AlignmentView
           viscontigs[nvis+1]=contigs[contig+1]-1; // end is inclusive
           nvis+=2;
         }
-        start = contigs[contig + 1] + contigs[contig + 2];              
+        start = contigs[contig + 1] + contigs[contig + 2];
       }
       if (start<fwidth) {
         viscontigs[nvis] = start;
@@ -442,8 +442,8 @@ public class AlignmentView
     }
   }
   /**
-   * 
-   * @return position of first visible column of AlignmentView within its parent's alignment reference frame 
+   *
+   * @return position of first visible column of AlignmentView within its parent's alignment reference frame
    */
   public int getAlignmentOrigin() {
     // TODO Auto-generated method stub