X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=1158c53bb37dec432977f5bf1182587fe9d9ae3b;hb=9476b459d78a974bdb525600ada55d9f3ebde8f1;hp=403991a9311d49755a5c2442113737437471f228;hpb=4d5f77436c8d77a776ca7c042611f36238c97057;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 403991a..1158c53 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -184,10 +184,10 @@ public class AlignmentUtils
       // TODO use Character.toLowerCase to avoid creating String objects?
       char[] upstream = new String(ds
               .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
-              .toLowerCase(Locale.ROOT).toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] downstream = new String(
               ds.getSequence(s_end - 1, s_end + dstream_ds))
-              .toLowerCase(Locale.ROOT).toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] coreseq = s.getSequence();
       char[] nseq = new char[offset + upstream.length + downstream.length
               + coreseq.length];
@@ -1471,19 +1471,20 @@ public class AlignmentUtils
          */
         final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
                 .findAnnotations(seq, dsann.getCalcId(), dsann.label);
-        boolean found=false;
+        boolean found = false;
         if (matchedAlignmentAnnotations != null)
         {
-          for (AlignmentAnnotation matched:matchedAlignmentAnnotations)
+          for (AlignmentAnnotation matched : matchedAlignmentAnnotations)
           {
             if (dsann.description.equals(matched.description))
             {
-              found=true;
+              found = true;
               break;
             }
           }
         }
-        if (!found) {
+        if (!found)
+        {
           result.add(dsann);
           if (labelForCalcId != null)
           {
@@ -1503,7 +1504,8 @@ public class AlignmentUtils
 
   /**
    * Adds annotations to the top of the alignment annotations, in the same order
-   * as their related sequences. If you already have an annotation and want to add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
+   * as their related sequences. If you already have an annotation and want to
+   * add it to a sequence in an alignment use {@code addReferenceAnnotationTo}
    * 
    * @param annotations
    *          the annotations to add
@@ -1520,51 +1522,60 @@ public class AlignmentUtils
     {
       for (AlignmentAnnotation ann : annotations.get(seq))
       {
-        addReferenceAnnotationTo(alignment, seq,ann,selectionGroup);
+        addReferenceAnnotationTo(alignment, seq, ann, selectionGroup);
       }
     }
   }
+
   /**
-   * Make a copy of a reference annotation {@code ann} and add it to an alignment sequence {@code seq} in {@code alignment}, optionally limited to the extent of {@code selectionGroup}
+   * Make a copy of a reference annotation {@code ann} and add it to an
+   * alignment sequence {@code seq} in {@code alignment}, optionally limited to
+   * the extent of {@code selectionGroup}
+   * 
    * @param alignment
    * @param seq
    * @param ann
-   * @param selectionGroup - may be null
+   * @param selectionGroup
+   *          - may be null
    * @return annotation added to {@code seq and {@code alignment}
    */
-  public static AlignmentAnnotation addReferenceAnnotationTo(final AlignmentI alignment, final SequenceI seq,final AlignmentAnnotation ann,final SequenceGroup selectionGroup)
+  public static AlignmentAnnotation addReferenceAnnotationTo(
+          final AlignmentI alignment, final SequenceI seq,
+          final AlignmentAnnotation ann, final SequenceGroup selectionGroup)
   {
-        AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
-        int startRes = 0;
-        int endRes = ann.annotations.length;
-        if (selectionGroup != null)
-        {
-          startRes = selectionGroup.getStartRes();
-          endRes = selectionGroup.getEndRes();
-        }
-        copyAnn.restrict(startRes, endRes + 0);
+    AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+    int startRes = 0;
+    int endRes = ann.annotations.length;
+    if (selectionGroup != null)
+    {
+      startRes = -1 + Math.min(seq.getEnd(), Math.max(seq.getStart(),
+              seq.findPosition(selectionGroup.getStartRes())));
+      endRes = -1 + Math.min(seq.getEnd(),
+              seq.findPosition(selectionGroup.getEndRes()));
 
-        /*
-         * Add to the sequence (sets copyAnn.datasetSequence), unless the
-         * original annotation is already on the sequence.
-         */
-        if (!seq.hasAnnotation(ann))
-        {
-          ContactMatrixI cm = seq.getDatasetSequence()
-                  .getContactMatrixFor(ann);
-          if (cm != null)
-          {
-            seq.addContactListFor(copyAnn, cm);
-          }
-          seq.addAlignmentAnnotation(copyAnn);
-        }
-        // adjust for gaps
-        copyAnn.adjustForAlignment();
-        // add to the alignment and set visible
-        alignment.addAnnotation(copyAnn);
-        copyAnn.visible = true;
-      
-        return copyAnn;
+    }
+    copyAnn.restrict(startRes, endRes + 0);
+
+    /*
+     * Add to the sequence (sets copyAnn.datasetSequence), unless the
+     * original annotation is already on the sequence.
+     */
+    if (!seq.hasAnnotation(ann))
+    {
+      ContactMatrixI cm = seq.getDatasetSequence().getContactMatrixFor(ann);
+      if (cm != null)
+      {
+        seq.addContactListFor(copyAnn, cm);
+      }
+      seq.addAlignmentAnnotation(copyAnn);
+    }
+    // adjust for gaps
+    copyAnn.adjustForAlignment();
+    // add to the alignment and set visible
+    alignment.addAnnotation(copyAnn);
+    copyAnn.visible = true;
+
+    return copyAnn;
   }
 
   /**