X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=95f578051e5b41c685feb674b683b077c3df8317;hb=85299bc2db43c8b108169661ebc1c4d9b2d3d2e5;hp=4d3d5787566a502bd9d0dbe1c2edecfcd13cebef;hpb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4d3d578..95f5780 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1830,7 +1830,13 @@ public class Alignment implements AlignmentI, AutoCloseable
     {
       return AlignmentUtils.alignCdsAsProtein(this, al);
     }
-    return AlignmentUtils.alignAs(this, al);
+    else if (thatIsProtein && !thisIsNucleotide)
+    {
+    	// honour sense we were called - align this according to al 
+    	return AlignmentUtils.alignAs(this, al);
+    }
+    // otherwise doing a DNA to DNA alignment - so use legacy obverse sense
+    return AlignmentUtils.alignAs(this,al);    
   }
 
   /**
@@ -2057,7 +2063,7 @@ public class Alignment implements AlignmentI, AutoCloseable
     if (cm == null && _aa.sequenceRef != null)
     {
       cm = _aa.sequenceRef.getContactMatrixFor(_aa);
-      if (cm == null)
+      if (cm == null && _aa.sequenceRef.getDatasetSequence() != null)
       {
         // TODO fix up this logic and unify with getContactListFor
         cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@@ -2069,6 +2075,11 @@ public class Alignment implements AlignmentI, AutoCloseable
   @Override
   public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
   {
+    if (_aa.annotations == null || column >= _aa.annotations.length
+            || column < 0)
+    {
+      return null;
+    }
     ContactListI cl = cmholder.getContactListFor(_aa, column);
     if (cl == null && _aa.groupRef != null)
     {
@@ -2076,16 +2087,19 @@ public class Alignment implements AlignmentI, AutoCloseable
     }
     if (cl == null && _aa.sequenceRef != null)
     {
-      int spos = _aa.sequenceRef.findPosition(column);
-      if (spos >= _aa.sequenceRef.getStart()
-              && spos <= 1 + _aa.sequenceRef.getEnd())
+      if (_aa.annotations[column] != null)
       {
-        cl = _aa.sequenceRef.getContactListFor(_aa,
-                spos - _aa.sequenceRef.getStart());
+        // sequence associated
+        cl = _aa.sequenceRef.getContactListFor(_aa, column);
         if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
         {
-          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
-                  spos - _aa.sequenceRef.getStart());
+          int spos = _aa.sequenceRef.findPosition(column);
+          if (spos >= _aa.sequenceRef.getStart()
+                  && spos <= 1 + _aa.sequenceRef.getEnd())
+          {
+            cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+                    spos - _aa.sequenceRef.getStart());
+          }
         }
       }
     }
@@ -2098,8 +2112,7 @@ public class Alignment implements AlignmentI, AutoCloseable
     AlignmentAnnotation aa = cmholder.addContactList(cm);
 
     Annotation _aa[] = new Annotation[getWidth()];
-    Annotation dummy = new Annotation(0.0f);
-    for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+    for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
     {
       ;
     }