X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuild.java;h=0c47c1dd8011fc05ef682d1f39fb113439eb94ac;hb=0d519ae0c45b0b9962b4589e84c262a71bb2f346;hp=85abd502f01e8ffa21b4d87417a24acc0848d958;hpb=3e49da65865c812f4b2b81f40ef65c983f14aa83;p=jalview.git

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 85abd50..0c47c1d 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -4,7 +4,6 @@ import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentView;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.ResidueCount;
 import jalview.datamodel.SequenceGroup;
@@ -116,20 +115,18 @@ public class HMMBuild extends HmmerCommand
         else if (MessageManager.getString("label.groups_and_alignment")
                 .equals(value))
         {
-          AlignmentView av = viewport.getAlignmentView(true);
-          runBuildFor.add(av.getVisibleAlignment('-'));
-          runBuildFor.addAll(av.getVisibleGroups('-'));
+          runBuildFor.add(viewport.getAlignmentView(false)
+                  .getVisibleAlignment('-'));
+          runBuildFor.addAll(viewport.getAlignment().getGroups());
         }
         else if (MessageManager.getString("label.groups").equals(value))
         {
-          AlignmentView av = viewport.getAlignmentView(false);
-          runBuildFor.addAll(av.getVisibleGroups('-'));
+          runBuildFor.addAll(viewport.getAlignment().getGroups());
         }
         else if (MessageManager.getString("label.selected_group")
                 .equals(value))
         {
-          AlignmentView av = viewport.getAlignmentView(true);
-          runBuildFor.add(av.getVisibleAlignment('-'));
+          runBuildFor.add(viewport.getSelectionGroup());
         }
       }
       else if (MessageManager.getString("label.use_reference")
@@ -193,16 +190,20 @@ public class HMMBuild extends HmmerCommand
 						.getSelectionAsNewSequences((AlignmentI) ac.getContext());
         for (SequenceI seq : sel)
         {
-          copy.add(seq);
+          if (seq != null)
+          {
+            copy.add(seq);
+          }
         }
       }
       // TODO rather than copy alignment data we should anonymize in situ -
       // export/File import could use anonymization hash to reinstate references
       // at import level ?
+
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
       Hashtable sequencesHash = stashSequences(copyArray);
 
-      exportStockholm(copyArray, alignmentFile, ac, false);
+      exportStockholm(copyArray, alignmentFile, ac);
 
       recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
 
@@ -336,6 +337,9 @@ public class HMMBuild extends HmmerCommand
     HMMFile file = new HMMFile(
             new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
     SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+
+
+
     ResidueCount counts = new ResidueCount(alignment.getSequences());
     hmmSeq.getHMM().setBackgroundFrequencies(counts);