JAL-3390 pull-up refactoring towards functional changes...

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index a5a3591..f45afa5 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -107,8 +107,7 @@ public class AlignViewController implements AlignViewControllerI
         viewport.getAlignment().addGroup(gps[g]);
         if (colours != null)
         {
-          gps[g].setColourScheme(colours.getInstance(viewport, gps[g],
-                  viewport.getHiddenRepSequences()));
+          gps[g].setColourScheme(colours.getInstance(viewport, gps[g]));
         }
         Color col = new Color((int) (Math.random() * 255),
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
@@ -167,9 +166,10 @@ public class AlignViewController implements AlignViewControllerI
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
-            || extendCurrent) ? viewport.getAlignment()
-                    : viewport.getSelectionGroup();
+    boolean searchSelection = viewport.getSelectionGroup() != null
+            && !extendCurrent;
+    SequenceCollectionI sqcol = searchSelection ? viewport
+            .getSelectionGroup() : viewport.getAlignment();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -205,9 +205,10 @@ public class AlignViewController implements AlignViewControllerI
     }
     else
     {
-      avcg.setStatus(MessageManager
-              .formatMessage("label.no_feature_of_type_found", new String[]
-              { featureType }));
+      String key = searchSelection ? "label.no_feature_found_selection"
+              : "label.no_feature_of_type_found";
+      avcg.setStatus(MessageManager.formatMessage(key,
+              new String[] { featureType }));
       if (!extendCurrent)
       {
         cs.clear();