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JAL-1645 JAL-1355 UI/i18n: added missing messages, moved ‘…’ into action messages...
[jalview.git] / src / jalview / appletgui / AlignFrame.java
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 4f7e2b9..0861f2d 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -20,46 +20,13 @@
  */
 package jalview.appletgui;
 
-import java.awt.BorderLayout;
-import java.awt.Canvas;
-import java.awt.CheckboxMenuItem;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Label;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
@@ -93,7 +60,6 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
-import jalview.schemes.RNAInteractionColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -105,6 +71,42 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import org.jmol.viewer.Viewer;
+
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
@@ -209,7 +211,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     if (hiddenSeqs != null && hiddenSeqs.length > 0)
     {
       viewport.hideSequence(hiddenSeqs);
-      viewport.setHasHiddenRows(true);
     }
     if (columnSelection != null)
     {
@@ -927,7 +928,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               : showForSequences);
         aa.visible = visible;
     }
-    alignPanel.validateAnnotationDimensions(false);
+    alignPanel.validateAnnotationDimensions(true);
+    validate();
+    repaint();
   }
 
   private void setAnnotationSortOrder(SequenceAnnotationOrder order)
@@ -1226,10 +1229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new PurinePyrimidineColourScheme());
     }
-    else if (source == RNAInteractionColour)
-    {
-      changeColour(new RNAInteractionColourScheme());
-    }
+    // else if (source == RNAInteractionColour)
+    // {
+    // changeColour(new RNAInteractionColourScheme());
+    // }
     else if (source == RNAHelixColour)
     {
       new RNAHelicesColourChooser(viewport, alignPanel);
@@ -1340,8 +1343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             { e.getActionCommand() }), 600, 500);
 
     FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
-    viewport.setFeatureRenderer(fr);
-    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
+    cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -2572,7 +2574,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public void changeColour(ColourSchemeI cs)
   {
-    int threshold = 0;
 
     if (cs != null)
     {
@@ -2595,15 +2596,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     viewport.setGlobalColourScheme(cs);
 
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(viewport.applet)
-            .sequenceColoursChanged(alignPanel);
-
     alignPanel.paintAlignment(true);
   }
 
@@ -2999,10 +2991,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           MessageManager.getString("label.load_features_annotations"));
 
   MenuItem outputFeatures = new MenuItem(
-          MessageManager.getString("label.export_features").concat("..."));
+          MessageManager.getString("label.export_features"));
 
   MenuItem outputAnnotations = new MenuItem(
-          MessageManager.getString("label.export_annotations").concat("..."));
+          MessageManager.getString("label.export_annotations"));
 
   MenuItem closeMenuItem = new MenuItem(
           MessageManager.getString("action.close"));
@@ -3068,7 +3060,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem purinePyrimidineColour = new MenuItem();
 
-  MenuItem RNAInteractionColour = new MenuItem();
+  // MenuItem RNAInteractionColour = new MenuItem();
 
   MenuItem RNAHelixColour = new MenuItem();
 
@@ -3251,8 +3243,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     removeAllGapsMenuItem.setLabel(MessageManager
             .getString("action.remove_all_gaps"));
     removeAllGapsMenuItem.addActionListener(this);
-    removeRedundancyMenuItem.setLabel(MessageManager.getString(
-            "action.remove_redundancy").concat("..."));
+    removeRedundancyMenuItem.setLabel(MessageManager
+            .getString("action.remove_redundancy"));
     removeRedundancyMenuItem.addActionListener(this);
 
     /*
@@ -3276,7 +3268,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
-    annotationColumnSelection.setLabel("Select by Annotation");
+    annotationColumnSelection.setLabel(MessageManager
+            .getString("action.select_by_annotation"));
     annotationColumnSelection.addActionListener(this);
 
     /*
@@ -3306,7 +3299,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     hideAllSelection.addActionListener(this);
     showAllHidden.addActionListener(this);
     featureSettings.setLabel(MessageManager
-            .getString("label.feature_settings"));
+            .getString("action.feature_settings"));
     featureSettings.addActionListener(this);
     sequenceFeatures.setLabel(MessageManager
             .getString("label.show_sequence_features"));
@@ -3438,9 +3431,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     purinePyrimidineColour.setLabel(MessageManager
             .getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
-    RNAInteractionColour.setLabel(MessageManager
-            .getString("label.rna_interaction"));
-    RNAInteractionColour.addActionListener(this);
+    // RNAInteractionColour.setLabel(MessageManager
+    // .getString("label.rna_interaction"));
+    // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager
             .getString("action.by_rna_helixes"));
     RNAHelixColour.addActionListener(this);
@@ -3871,10 +3864,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public SequenceStructureBinding addStructureViewInstance(
           Object jmolviewer, String[] sequenceIds)
   {
-    org.jmol.api.JmolViewer viewer = null;
+    Viewer viewer = null;
     try
     {
-      viewer = (org.jmol.api.JmolViewer) jmolviewer;
+      viewer = (Viewer) jmolviewer;
     } catch (ClassCastException ex)
     {
       System.err.println("Unsupported viewer object :"
@@ -3947,7 +3940,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean needtoadd = false;
     if (toaddpdb != null)
     {
-      Vector pdbe = toaddpdb.getPDBId();
+      Vector pdbe = toaddpdb.getAllPDBEntries();
       PDBEntry pdbentry = null;
       if (pdbe != null && pdbe.size() > 0)
       {
@@ -4206,4 +4199,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     this.splitFrame = sf;
   }
+
+    // may not need this
+  @Override
+  public void setShowSeqFeatures(boolean b)
+  {
+    // showSeqFeatures.setSelected(b);
+    viewport.setShowSequenceFeatures(b);
+
+  }
+
+  @Override
+  public void setMenusForViewport()
+  {
+    // setMenusFromViewport(viewport);
+
+  }
+  @Override
+  public void refreshFeatureUI(boolean enableIfNecessary)
+  {
+    if (enableIfNecessary)
+    {
+      sequenceFeatures.setState(true);
+      alignPanel.av.setShowSequenceFeatures(true);
+    }
+  }
+
+  @Override
+  public FeatureSettingsControllerI getFeatureSettingsUI()
+  {
+    return alignPanel.av.featureSettings;
+  }
+
 }