X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;fp=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=2fb9cdde4123dfdd87d0208c5263733991cad964;hb=9c98d4bd666346f6ad3892c5394b7da3be82d93e;hp=757558308463d4eab722e686f0491092de8cabd1;hpb=c7b2143c9cf7c5e05ad63251f7d3910751b16d20;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 7575583..2fb9cdd 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -168,8 +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);
 
@@ -207,8 +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();
@@ -229,11 +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;
@@ -244,8 +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)
@@ -315,17 +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)
@@ -459,7 +460,8 @@ public class AlignViewController implements AlignViewControllerI
     }
     else
     {
-      avcg.setStatus(MessageManager.getString("label.no_highlighted_regions_marked"));
+      avcg.setStatus(MessageManager
+              .getString("label.no_highlighted_regions_marked"));
       if (!extendCurrent)
       {
         cs.clear();