Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index e4e619c..228eede 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -353,7 +353,7 @@ public class PDBChain
       Residue tmpres = residues.lastElement();
       Atom tmpat = tmpres.atoms.get(0);
       // Make A new SequenceFeature for the current residue numbering
-        SequenceFeature sf = new SequenceFeature("RES NUM", tmpat.resName
+        SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
               + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
               + count, offset + count, pdbid);
       // MCview.PDBChain.PDBFILEFEATURE);

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 90c7e02..07cb689 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1567,7 +1567,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (alignment.getHiddenSequences() != null)
+      if (hasHiddenRows())
       {
         iSize = alignment.getHiddenSequences().getFullAlignment()
                 .getHeight();

diff --git a/test/jalview/analysis/TestAlignSeq.java b/test/jalview/analysis/TestAlignSeq.java
index d6342ef..43ebd63 100644 (file)
--- a/test/jalview/analysis/TestAlignSeq.java
+++ b/test/jalview/analysis/TestAlignSeq.java
@@ -119,7 +119,7 @@ public class TestAlignSeq
     String expected = "Score = 320\nLength of alignment = 10\nSequence Seq1 :  3 - 18 (Sequence length = 14)\nSequence Seq1 :  1 - 10 (Sequence length = 10)\n\n"
             + "Seq1 SDFAQQQRRR\n"
             + "     |||||||   \n"
-            + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
+            + "Seq1 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n";
     assertEquals(expected, baos.toString());
   }
 }