Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index f45afa5..ee46a89 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -310,16 +310,34 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureDensity(List<String> typ)
   {
-    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+    String methodText = MessageManager.getString("label.sort_by_density");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
   }
 
-  protected void sortBy(List<String> typ, String methodText,
+  /**
+   * 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
+   * @param method
+   *                     - passed to
+   *                     jalview.analysis.AlignmentSorter.sortByFeatures()
+   */
+  protected void sortByFeatures(List<String> types, String methodText,
           final String method)
   {
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
-    if (typ == null && fr != null)
+    if (types == null && fr != null)
+    {
+      types = fr.getDisplayedFeatureTypes();
+    }
+    if (types.isEmpty())
     {
-      typ = fr.getDisplayedFeatureTypes();
+      return; // nothing to do
     }
     List<String> gps = null;
     if (fr != null)
@@ -341,7 +359,7 @@ public class AlignViewController implements AlignViewControllerI
       stop = al.getWidth();
     }
     SequenceI[] oldOrder = al.getSequencesArray();
-    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+    AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
     alignPanel.paintAlignment(true, false);
@@ -351,11 +369,12 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureScore(List<String> typ)
   {
-    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+    String methodText = MessageManager.getString("label.sort_by_score");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, DataSourceType protocol,
+  public boolean parseFeaturesFile(Object file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresAdded = false;