JAL-4014 release notes for JAL-4026 patches

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 1fc1946..2fb9cdd 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -90,8 +90,7 @@ public class AlignViewController implements AlignViewControllerI
         gps = jalview.analysis.Grouping.makeGroupsFromCols(
                 (sg == null) ? viewport.getAlignment().getSequencesArray()
                         : sg.getSequences().toArray(new SequenceI[0]),
-                cs, viewport.getAlignment().getGroups(),
-                viewport.getAlignment().getHiddenColumns());
+                cs, viewport.getAlignment().getGroups());
       }
     }
     if (gps != null)
@@ -169,8 +168,9 @@ public class AlignViewController implements AlignViewControllerI
     BitSet bs = new BitSet();
     boolean searchSelection = viewport.getSelectionGroup() != null
             && !extendCurrent;
-    SequenceCollectionI sqcol = searchSelection ? viewport
-            .getSelectionGroup() : viewport.getAlignment();
+    SequenceCollectionI sqcol = searchSelection
+            ? viewport.getSelectionGroup()
+            : viewport.getAlignment();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -208,8 +208,9 @@ public class AlignViewController implements AlignViewControllerI
     {
       String key = searchSelection ? "label.no_feature_found_selection"
               : "label.no_feature_of_type_found";
-      avcg.setStatus(MessageManager.formatMessage(key,
-              new String[] { featureType }));
+      avcg.setStatus(
+              MessageManager.formatMessage(key, new String[]
+              { featureType }));
       if (!extendCurrent)
       {
         cs.clear();
@@ -230,11 +231,11 @@ public class AlignViewController implements AlignViewControllerI
    * @param bs
    * @return
    */
-  int findColumnsWithFeature(String featureType,
-          SequenceCollectionI sqcol, BitSet bs)
+  int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+          BitSet bs)
   {
-    FeatureRenderer fr = alignPanel == null ? null : alignPanel
-            .getFeatureRenderer();
+    FeatureRenderer fr = alignPanel == null ? null
+            : alignPanel.getFeatureRenderer();
 
     final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
     final int endColumn = sqcol.getEndRes() + 1;
@@ -245,8 +246,8 @@ public class AlignViewController implements AlignViewControllerI
       if (sq != null)
       {
         // int ist = sq.findPosition(sqcol.getStartRes());
-        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
-                endColumn, featureType);
+        List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+                featureType);
 
         boolean found = false;
         for (SequenceFeature sf : sfs)
@@ -316,17 +317,16 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   /**
-   * Sorts the alignment (or current selection) by either average score or density
-   * of the specified feature types, and adds to the command history. If
-   * {@code types} is null, all visible feature types are used for the sort. If no
-   * feature types apply, does nothing.
+   * Sorts the alignment (or current selection) by either average score or
+   * density of the specified feature types, and adds to the command history. If
+   * {@code types} is null, all visible feature types are used for the sort. If
+   * no feature types apply, does nothing.
    * 
    * @param types
    * @param methodText
-   *                     - text shown in Undo/Redo command
+   *          - text shown in Undo/Redo command
    * @param method
-   *                     - passed to
-   *                     jalview.analysis.AlignmentSorter.sortByFeatures()
+   *          - passed to jalview.analysis.AlignmentSorter.sortByFeatures()
    */
   protected void sortByFeatures(List<String> types, String methodText,
           final String method)
@@ -375,7 +375,7 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresAdded = false;
@@ -461,7 +461,7 @@ public class AlignViewController implements AlignViewControllerI
     else
     {
       avcg.setStatus(MessageManager
-              .formatMessage("No highlighted regions marked"));
+              .getString("label.no_highlighted_regions_marked"));
       if (!extendCurrent)
       {
         cs.clear();