Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950

[jalview.git] / src / jalview / hmmer / HMMBuild.java

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 6de7029..b3cca40 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -4,6 +4,7 @@ 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.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -105,24 +106,29 @@ public class HMMBuild extends HmmerCommand
       {
         foundArg = true;
         String value = arg.getValue();
+
         if (MessageManager.getString("label.alignment").equals(value))
         {
-          runBuildFor.add(alignment);
+          runBuildFor.add(viewport.getAlignmentView(false)
+                  .getVisibleAlignment('-'));
         }
         else if (MessageManager.getString("label.groups_and_alignment")
                 .equals(value))
         {
-          runBuildFor.add(alignment);
-          runBuildFor.addAll(viewport.getAlignment().getGroups());
+          AlignmentView av = viewport.getAlignmentView(true);
+          runBuildFor.add(av.getVisibleAlignment('-'));
+          runBuildFor.addAll(av.getVisibleGroups('-'));
         }
         else if (MessageManager.getString("label.groups").equals(value))
         {
-          runBuildFor.addAll(viewport.getAlignment().getGroups());
+          AlignmentView av = viewport.getAlignmentView(false);
+          runBuildFor.addAll(av.getVisibleGroups('-'));
         }
         else if (MessageManager.getString("label.selected_group")
                 .equals(value))
         {
-          runBuildFor.add(viewport.getSelectionGroup());
+          AlignmentView av = viewport.getAlignmentView(true);
+          runBuildFor.add(av.getVisibleAlignment('-'));
         }
       }
       else if (MessageManager.getString("label.use_reference")
@@ -183,13 +189,16 @@ public class HMMBuild extends HmmerCommand
       else
       {
         SequenceI[] sel = ((SequenceGroup) ac)
-                .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+                .getSelectionAsNewSequences((AlignmentI) ac.getContext(),
+                        false);
         for (SequenceI seq : sel)
         {
           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);