JAL-1824 corrected copy'n'paste error introduced from JAL-1821 refactor which causes...

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index dc0a127..940a216 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureSettingsControllerI;
 import jalview.bin.Cache;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -28,6 +29,7 @@ import jalview.io.JalviewFileChooser;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 import java.awt.BorderLayout;
@@ -87,7 +89,8 @@ import javax.swing.table.AbstractTableModel;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 
-public class FeatureSettings extends JPanel
+public class FeatureSettings extends JPanel implements
+        FeatureSettingsControllerI
 {
   DasSourceBrowser dassourceBrowser;
 
@@ -226,7 +229,7 @@ public class FeatureSettings extends JPanel
       fr.findAllFeatures(true); // display everything!
     }
 
-    setTableData();
+    discoverAllFeatureData();
     final PropertyChangeListener change;
     final FeatureSettings fs = this;
     fr.addPropertyChangeListener(change = new PropertyChangeListener()
@@ -420,7 +423,8 @@ public class FeatureSettings extends JPanel
    */
   Hashtable typeWidth = null;
 
-  synchronized public void setTableData()
+  @Override
+  synchronized public void discoverAllFeatureData()
   {
     Vector allFeatures = new Vector();
     Vector allGroups = new Vector();
@@ -428,15 +432,13 @@ public class FeatureSettings extends JPanel
     String group;
     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
-      if (af.getViewport().getAlignment().getSequenceAt(i)
-              .getDatasetSequence().getSequenceFeatures() == null)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
+              .getSequenceFeatures();
+      if (tmpfeatures == null)
       {
         continue;
       }
 
-      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getDatasetSequence().getSequenceFeatures();
-
       int index = 0;
       while (index < tmpfeatures.length)
       {
@@ -546,7 +548,7 @@ public class FeatureSettings extends JPanel
     {
 
       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getDatasetSequence().getSequenceFeatures();
+              .getSequenceFeatures();
       if (tmpfeatures == null)
       {
         continue;
@@ -1074,6 +1076,21 @@ public class FeatureSettings extends JPanel
         }
       }
     });
+    help.setFont(JvSwingUtils.getLabelFont());
+    help.setText(MessageManager.getString("action.help"));
+    help.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          Help.showHelpWindow(HelpId.SequenceFeatureSettings);
+        } catch (HelpSetException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
     cancel.setFont(JvSwingUtils.getLabelFont());
     cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
@@ -1198,7 +1215,7 @@ public class FeatureSettings extends JPanel
   {
     SequenceI[] dataset, seqs;
     int iSize;
-    AlignViewport vp = af.getViewport();
+    AlignmentViewport vp = af.getViewport();
     if (vp.getSelectionGroup() != null
             && vp.getSelectionGroup().getSize() > 0)
     {