X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=e4f11e09cf4d66de64e570d49c48b89ffe6ca2eb;hb=26ba864a6c290121fe6cf616794d2d0bea65fb7d;hp=3be32bb1e4a3e0f767415f5b6f0a5ec36b8140d7;hpb=7ba92fd0e87b8155e656cfb9562d024a2524086d;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 3be32bb..e4f11e0 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -86,20 +86,23 @@ public class AlignViewController implements AlignViewControllerI
     if (sg != null
             && (cs == null || cs.getSelected() == null || cs.size() == 0))
     {
-      gps = jalview.analysis.Grouping.makeGroupsFrom(
-              viewport.getSequenceSelection(),
-              viewport.getAlignmentView(true).getSequenceStrings(
-                      viewport.getGapCharacter()), viewport.getAlignment()
-                      .getGroups());
-    } else {
-      if (cs!=null) {
+      gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
+              .getSequenceSelection(), viewport.getAlignmentView(true)
+              .getSequenceStrings(viewport.getGapCharacter()), viewport
+              .getAlignment().getGroups());
+    }
+    else
+    {
+      if (cs != null)
+      {
         gps = jalview.analysis.Grouping.makeGroupsFromCols(
                 (sg == null) ? viewport.getAlignment().getSequencesArray()
                         : sg.getSequences().toArray(new SequenceI[0]), cs,
                 viewport.getAlignment().getGroups());
       }
     }
-    if (gps!=null) {
+    if (gps != null)
+    {
       viewport.getAlignment().deleteAllGroups();
       viewport.clearSequenceColours();
       viewport.setSelectionGroup(null);
@@ -289,17 +292,22 @@ public class AlignViewController implements AlignViewControllerI
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      avcg.setStatus(MessageManager.formatMessage("label.view_controller_toggled_marked",
-    		  new String[]{
-    	  			(toggle ? MessageManager.getString("label.toggled") : MessageManager.getString("label.marked")),
-    	  			(invert ? (Integer.valueOf((alw - alStart) - bs.cardinality()).toString()):(Integer.valueOf(bs.cardinality()).toString())),
-    	  			featureType, Integer.valueOf(nseq).toString()
-      		 	}));
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.view_controller_toggled_marked",
+              new String[] {
+                  (toggle ? MessageManager.getString("label.toggled")
+                          : MessageManager.getString("label.marked")),
+                  (invert ? (Integer.valueOf((alw - alStart)
+                          - bs.cardinality()).toString()) : (Integer
+                          .valueOf(bs.cardinality()).toString())),
+                  featureType, Integer.valueOf(nseq).toString() }));
       return true;
     }
     else
     {
-      avcg.setStatus(MessageManager.formatMessage("label.no_feature_of_type_found", new String[]{featureType}));
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.no_feature_of_type_found",
+              new String[] { featureType }));
       if (!extendCurrent && cs != null)
       {
         cs.clear();
@@ -309,8 +317,6 @@ public class AlignViewController implements AlignViewControllerI
     }
   }
 
-
-
   @Override
   public void sortAlignmentByFeatureDensity(String[] typ)
   {
@@ -322,10 +328,10 @@ public class AlignViewController implements AlignViewControllerI
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
     if (typ == null)
     {
-      typ = fr==null ? null : fr.getDisplayedFeatureTypes();
+      typ = fr == null ? null : fr.getDisplayedFeatureTypes();
     }
     String gps[] = null;
-    gps = fr==null ? null : fr.getDisplayedFeatureGroups();
+    gps = fr == null ? null : fr.getDisplayedFeatureGroups();
     if (typ != null)
     {
       ArrayList types = new ArrayList();
@@ -388,7 +394,7 @@ public class AlignViewController implements AlignViewControllerI
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(file, protocol).parse(viewport
+      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
               .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
               .getFeatureColours(), false, relaxedIdMatching);
     } catch (Exception ex)