JAL-1482 JAL-653 refactor feature file import code to alignview controller

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

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 7e41f77..3be32bb 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -179,13 +180,7 @@ public class AlignViewController implements AlignViewControllerI
       int tfeat = 0;
       if (sq != null)
       {
-        SequenceI dsq = sq.getDatasetSequence();
-        while (dsq.getDatasetSequence() != null)
-        {
-          dsq = dsq.getDatasetSequence();
-        }
-        ;
-        SequenceFeature[] sf = dsq.getSequenceFeatures();
+        SequenceFeature[] sf = sq.getSequenceFeatures();
         if (sf != null)
         {
           int ist = sq.findIndex(sq.getStart());
@@ -385,4 +380,38 @@ public class AlignViewController implements AlignViewControllerI
   {
     sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
   }
+
+  @Override
+  public boolean parseFeaturesFile(String file, String protocol,
+          boolean relaxedIdMatching)
+  {
+    boolean featuresFile = false;
+    try
+    {
+      featuresFile = new FeaturesFile(file, protocol).parse(viewport
+              .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+              .getFeatureColours(), false, relaxedIdMatching);
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if (featuresFile)
+    {
+      avcg.refreshFeatureUI(true);
+      if (alignPanel.getFeatureRenderer() != null)
+      {
+        // update the min/max ranges where necessary
+        alignPanel.getFeatureRenderer().findAllFeatures(true);
+      }
+      if (avcg.getFeatureSettingsUI() != null)
+      {
+        avcg.getFeatureSettingsUI().discoverAllFeatureData();
+      }
+      alignPanel.paintAlignment(true);
+    }
+
+    return featuresFile;
+
+  }
 }