JAL-1925 update source version in license

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index dc0a127..935d9c6 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 2.9.0b2)
+ * Copyright (C) 2015 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;
 
@@ -122,7 +125,8 @@ public class FeatureSettings extends JPanel
     this.af = af;
     fr = af.getFeatureRenderer();
     // allow transparency to be recovered
-    transparency.setMaximum(100 - (int) ((originalTransparency=fr.getTransparency()) * 100));
+    transparency.setMaximum(100 - (int) ((originalTransparency = fr
+            .getTransparency()) * 100));
 
     try
     {
@@ -132,15 +136,18 @@ public class FeatureSettings extends JPanel
       ex.printStackTrace();
     }
 
-    table = new JTable() {
+    table = new JTable()
+    {
       @Override
-      public String getToolTipText(MouseEvent e) {
-        if (table.columnAtPoint(e.getPoint()) == 0) {
+      public String getToolTipText(MouseEvent e)
+      {
+        if (table.columnAtPoint(e.getPoint()) == 0)
+        {
           /*
            * Tooltip for feature name only
            */
-          return JvSwingUtils.wrapTooltip(true,
-                MessageManager.getString("label.feature_settings_click_drag"));
+          return JvSwingUtils.wrapTooltip(true, MessageManager
+                  .getString("label.feature_settings_click_drag"));
         }
         return null;
       }
@@ -184,8 +191,7 @@ public class FeatureSettings extends JPanel
         {
           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
-                  evt.getX(),
-                  evt.getY());
+                  evt.getX(), evt.getY());
         }
       }
     });
@@ -214,8 +220,8 @@ public class FeatureSettings extends JPanel
         }
       }
     });
-//    table.setToolTipText(JvSwingUtils.wrapTooltip(true,
-//            MessageManager.getString("label.feature_settings_click_drag")));
+    // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
+    // MessageManager.getString("label.feature_settings_click_drag")));
     scrollPane.setViewportView(table);
 
     dassourceBrowser = new DasSourceBrowser(this);
@@ -226,7 +232,7 @@ public class FeatureSettings extends JPanel
       fr.findAllFeatures(true); // display everything!
     }
 
-    setTableData();
+    discoverAllFeatureData();
     final PropertyChangeListener change;
     final FeatureSettings fs = this;
     fr.addPropertyChangeListener(change = new PropertyChangeListener()
@@ -275,8 +281,7 @@ public class FeatureSettings extends JPanel
           final Object typeCol, final Hashtable minmax, int x, int y)
   {
     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
-            "label.settings_for_param", new String[]
-            { type }));
+            "label.settings_for_param", new String[] { type }));
     JMenuItem scr = new JMenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
@@ -286,8 +291,7 @@ public class FeatureSettings extends JPanel
 
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureScore(new String[]
-        { type });
+        me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
       }
 
     });
@@ -298,8 +302,7 @@ public class FeatureSettings extends JPanel
 
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureDensity(new String[]
-        { type });
+        me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
       }
 
     });
@@ -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)
       {
@@ -514,8 +516,7 @@ public class FeatureSettings extends JPanel
           af.alignPanel.overviewPanel.updateOverviewImage();
         }
 
-        resetTable(new String[]
-        { grp });
+        resetTable(new String[] { grp });
       }
     });
     groupPanel.add(check);
@@ -546,7 +547,7 @@ public class FeatureSettings extends JPanel
     {
 
       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
-              .getDatasetSequence().getSequenceFeatures();
+              .getSequenceFeatures();
       if (tmpfeatures == null)
       {
         continue;
@@ -703,11 +704,13 @@ public class FeatureSettings extends JPanel
   void load()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "fc" }, new String[]
-            { "Sequence Feature Colours" }, "Sequence Feature Colours");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "fc" },
+            new String[] { "Sequence Feature Colours" },
+            "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.load_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
 
     int value = chooser.showOpenDialog(this);
@@ -722,8 +725,7 @@ public class FeatureSettings extends JPanel
                 file), "UTF-8");
 
         jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-        jucs = jucs
-                .unmarshal(in);
+        jucs = jucs.unmarshal(in);
 
         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
         {
@@ -801,11 +803,13 @@ public class FeatureSettings extends JPanel
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "fc" }, new String[]
-            { "Sequence Feature Colours" }, "Sequence Feature Colours");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "fc" },
+            new String[] { "Sequence Feature Colours" },
+            "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours"));
+    chooser.setDialogTitle(MessageManager
+            .getString("label.save_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -940,9 +944,9 @@ public class FeatureSettings extends JPanel
       }
     }
     if (sort)
-     {
+    {
       jalview.util.QuickSort.sort(width, data);
-    // update global priority order
+      // update global priority order
     }
 
     updateFeatureRenderer(data, false);
@@ -1074,6 +1078,21 @@ 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()
@@ -1152,8 +1171,10 @@ public class FeatureSettings extends JPanel
       }
     });
     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-    tabbedPane.addTab(MessageManager.getString("label.feature_settings"), settingsPane);
-    tabbedPane.addTab(MessageManager.getString("label.das_settings"), dasSettingsPane);
+    tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
+            settingsPane);
+    tabbedPane.addTab(MessageManager.getString("label.das_settings"),
+            dasSettingsPane);
     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
     transbuttons.add(optimizeOrder);
     transbuttons.add(invert);
@@ -1198,7 +1219,7 @@ 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)
     {
@@ -1347,8 +1368,10 @@ public class FeatureSettings extends JPanel
       this.data = data;
     }
 
-    private String[] columnNames =
-    { MessageManager.getString("label.feature_type"), MessageManager.getString("action.colour"), MessageManager.getString("label.display") };
+    private String[] columnNames = {
+        MessageManager.getString("label.feature_type"),
+        MessageManager.getString("action.colour"),
+        MessageManager.getString("label.display") };
 
     private Object[][] data;