Merge branch 'develop' into features/JAL-653_gffalignments

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index db61f77..cd9c533 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -78,6 +78,7 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
@@ -107,7 +108,6 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
@@ -3159,6 +3159,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public FeatureSettings featureSettings;
 
   @Override
+  public FeatureSettingsControllerI getFeatureSettingsUI()
+  {
+    return featureSettings;
+  }
+
+  @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if (featureSettings != null)
@@ -5008,41 +5014,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          contents or path to retrieve file
    * @param type
    *          access mode of file (see jalview.io.AlignFile)
-   * @return true if features file was parsed corectly.
+   * @return true if features file was parsed correctly.
    */
   public boolean parseFeaturesFile(String file, String type)
   {
-    boolean featuresFile = false;
-    try
-    {
-      featuresFile = new FeaturesFile(file, type).parse(viewport
-              .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
-              .getFeatureRenderer().getFeatureColours(), false,
-              jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
+    return avc.parseFeaturesFile(file, type,
+            jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+    
+  }
 
-    if (featuresFile)
+  @Override
+  public void refreshFeatureUI(boolean enableIfNecessary)
+  {
+    // note - currently this is only still here rather than in the controller
+    // because of the featureSettings hard reference that is yet to be
+    // abstracted
+    if (enableIfNecessary)
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      if (alignPanel.getSeqPanel().seqCanvas.fr != null)
-      {
-        // update the min/max ranges where necessary
-        alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
-      }
-      if (featureSettings != null)
-      {
-        featureSettings.setTableData();
-      }
-      alignPanel.paintAlignment(true);
     }
 
-    return featuresFile;
-  }
 
+  }
   @Override
   public void dragEnter(DropTargetDragEvent evt)
   {