X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=e6d3e83e31517fa891afd499aa729ea14c8f7ea0;hb=de75573aa38c4b40686256d4332c3a069b6a98ca;hp=a4aeac7abdb0270ed391b7e11185c0e36394cd25;hpb=5088f3a5830a92aca7db379a3b1d43a891611061;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index a4aeac7..e6d3e83 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -77,18 +77,22 @@ public class AlignmentUtils
     for (SequenceI s : core.getSequences())
     {
       SequenceI newSeq = s.deriveSequence();
-      if (newSeq.getStart() > maxoffset
+      final int newSeqStart = newSeq.getStart() - 1;
+      if (newSeqStart > maxoffset
               && newSeq.getDatasetSequence().getStart() < s.getStart())
       {
-        maxoffset = newSeq.getStart();
+        maxoffset = newSeqStart;
       }
       sq.add(newSeq);
     }
     if (flankSize > -1)
     {
-      maxoffset = flankSize;
+      maxoffset = Math.min(maxoffset, flankSize);
     }
-    // now add offset to create a new expanded alignment
+
+    /*
+     * now add offset left and right to create an expanded alignment
+     */
     for (SequenceI s : sq)
     {
       SequenceI ds = s;
@@ -98,8 +102,8 @@ public class AlignmentUtils
       }
       int s_end = s.findPosition(s.getStart() + s.getLength());
       // find available flanking residues for sequence
-      int ustream_ds = s.getStart() - ds.getStart(), dstream_ds = ds
-              .getEnd() - s_end;
+      int ustream_ds = s.getStart() - ds.getStart();
+      int dstream_ds = ds.getEnd() - s_end;
 
       // build new flanked sequence
 
@@ -115,27 +119,27 @@ public class AlignmentUtils
           offset = maxoffset - flankSize;
           ustream_ds = flankSize;
         }
-        if (flankSize < dstream_ds)
+        if (flankSize <= dstream_ds)
         {
-          dstream_ds = flankSize;
+          dstream_ds = flankSize - 1;
         }
       }
+      // TODO use Character.toLowerCase to avoid creating String objects?
       char[] upstream = new String(ds.getSequence(s.getStart() - 1
               - ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
-      char[] downstream = new String(ds.getSequence(s_end - 1, s_end + 1
+      char[] downstream = new String(ds.getSequence(s_end - 1, s_end
               + dstream_ds)).toLowerCase().toCharArray();
       char[] coreseq = s.getSequence();
       char[] nseq = new char[offset + upstream.length + downstream.length
               + coreseq.length];
       char c = core.getGapCharacter();
-      // TODO could lowercase the flanking regions
+
       int p = 0;
       for (; p < offset; p++)
       {
         nseq[p] = c;
       }
-      // s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) +
-      // new String(downstream).toLowerCase());
+
       System.arraycopy(upstream, 0, nseq, p, upstream.length);
       System.arraycopy(coreseq, 0, nseq, p + upstream.length,
               coreseq.length);
@@ -153,6 +157,7 @@ public class AlignmentUtils
       {
         for (AlignmentAnnotation aa : s.getAnnotation())
         {
+          aa.adjustForAlignment(); // JAL-1712 fix
           newAl.addAnnotation(aa);
         }
       }
@@ -1236,7 +1241,7 @@ public class AlignmentUtils
 
   /**
    * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
-   * that sequence name is structured as Source|AccessId.
+   * that sequence name is structured as Source|AccessionId.
    * 
    * @param seq1
    * @param seq2