JAL-1989 more unit tests and encapsulation for ColumnSelection

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 3be32bb..06b1e4c 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -83,23 +83,25 @@ public class AlignViewController implements AlignViewControllerI
     SequenceGroup sg = viewport.getSelectionGroup();
     ColumnSelection cs = viewport.getColumnSelection();
     SequenceGroup[] gps = null;
-    if (sg != null
-            && (cs == null || cs.getSelected() == null || cs.size() == 0))
+    if (sg != null && (cs == null || cs.isEmpty()))
     {
-      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 +291,22 @@ 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 +316,6 @@ public class AlignViewController implements AlignViewControllerI
     }
   }
 
-
-
   @Override
   public void sortAlignmentByFeatureDensity(String[] typ)
   {
@@ -322,10 +327,10 @@ 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();