Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 65b002b..34410f1 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
@@ -28,6 +29,7 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
@@ -40,6 +42,8 @@ import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -48,7 +52,6 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-
 /**
  * GUI elements for handling an external chimera display
  * 
@@ -59,6 +62,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 {
   private JalviewChimeraBinding jmb;
 
+
   /*
    * Path to Chimera session file. This is set when an open Jalview/Chimera
    * session is saved, or on restore from a Jalview project (if it holds the
@@ -66,11 +70,15 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   private String chimeraSessionFile = null;
 
+
   private int myWidth = 500;
 
   private int myHeight = 150;
 
-  /**
+  private JMenuItem writeFeatures=null;
+
+  private JMenu fetchAttributes=null;
+/**
    * Initialise menu options.
    */
   @Override
@@ -81,7 +89,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
-    JMenuItem writeFeatures = new JMenuItem(
+    writeFeatures = new JMenuItem(
             MessageManager.getString("label.create_viewer_attributes"));
     writeFeatures.setToolTipText(MessageManager
             .getString("label.create_viewer_attributes_tip"));
@@ -95,7 +103,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     });
     viewerActionMenu.add(writeFeatures);
 
-    final JMenu fetchAttributes = new JMenu(
+    fetchAttributes = new JMenu(
             MessageManager.getString("label.fetch_chimera_attributes"));
     fetchAttributes.setToolTipText(
             MessageManager.getString("label.fetch_chimera_attributes_tip"));
@@ -111,9 +119,18 @@ public class ChimeraViewFrame extends StructureViewerBase
     viewerActionMenu.add(fetchAttributes);
   }
 
+  @Override
+  protected void buildActionMenu()
+  {
+    super.buildActionMenu();
+    // add these back in after menu is refreshed
+    viewerActionMenu.add(writeFeatures);
+    viewerActionMenu.add(fetchAttributes);
+    
+  };
   /**
-   * Query Chimera for its residue attribute names and add them as items off the
-   * attributes menu
+   * Query the structure viewer for its residue attribute names and add them as
+   * items off the attributes menu
    * 
    * @param attributesMenu
    */
@@ -130,7 +147,11 @@ public class ChimeraViewFrame extends StructureViewerBase
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          getChimeraAttributes(attName);
+          if (getBinding().copyStructureAttributesToFeatures(attName,
+                  getAlignmentPanel()) > 0)
+          {
+            getAlignmentPanel().getFeatureRenderer().featuresAdded();
+          }
         }
       });
       attributesMenu.add(menuItem);
@@ -138,17 +159,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Read residues in Chimera with the given attribute name, and set as features
-   * on the corresponding sequence positions (if any)
-   * 
-   * @param attName
-   */
-  protected void getChimeraAttributes(String attName)
-  {
-    jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
-  }
-
-  /**
    * Sends command(s) to the structure viewer to create residue attributes for
    * visible Jalview features
    */
@@ -227,7 +237,6 @@ public class ChimeraViewFrame extends StructureViewerBase
     return new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, null);
   }
-
   /**
    * Create a new viewer from saved session state data including Chimera session
    * file
@@ -240,22 +249,34 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param colourBySequence
    * @param newViewId
    */
-  public ChimeraViewFrame(String chimeraSessionFile,
-          AlignmentPanel alignPanel, PDBEntry[] pdbArray,
-          SequenceI[][] seqsArray, boolean colourByChimera,
-          boolean colourBySequence, String newViewId)
+  public ChimeraViewFrame(StructureViewerModel viewerData,
+          AlignmentPanel alignPanel, String sessionFile, String vid)
   {
     this();
-    setViewId(newViewId);
-    this.chimeraSessionFile = chimeraSessionFile;
+    setViewId(vid);
+    this.chimeraSessionFile = sessionFile;
+    Map<File, StructureData> pdbData = viewerData.getFileData();
+    PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
+    SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
+    int i = 0;
+    for (StructureData data : pdbData.values())
+    {
+      PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+              PDBEntry.Type.PDB, data.getFilePath());
+      pdbArray[i] = pdbentry;
+      List<SequenceI> sequencesForPdb = data.getSeqList();
+      seqsArray[i] = sequencesForPdb
+              .toArray(new SequenceI[sequencesForPdb.size()]);
+      i++;
+    }
     openNewChimera(alignPanel, pdbArray, seqsArray);
-    if (colourByChimera)
+    if (viewerData.isColourByViewer())
     {
       jmb.setColourBySequence(false);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    else if (colourBySequence)
+    else if (viewerData.isColourWithAlignPanel())
     {
       jmb.setColourBySequence(true);
       seqColour.setSelected(true);
@@ -307,7 +328,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     if (!jmb.launchChimera())
     {
-      JvOptionPane.showMessageDialog(Desktop.desktop,
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
               MessageManager.formatMessage("label.open_viewer_failed",
                       getViewerName()),
               MessageManager.getString("label.error_loading_file"),
@@ -404,7 +425,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     if (errormsgs.length() > 0)
     {
 
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager.formatMessage(
                       "label.pdb_entries_couldnt_be_retrieved", new Object[]
                       { errormsgs.toString() }),
@@ -483,7 +504,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
       /*
        * ensure that any newly discovered features (e.g. RESNUM)
-       * are added to any open feature settings dialog
+       * are notified to the FeatureRenderer (and added to any 
+       * open feature settings dialog)
        */
       FeatureRenderer fr = getBinding().getFeatureRenderer(null);
       if (fr != null)
@@ -514,6 +536,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     worker = null;
   }
 
+
   @Override
   public void makePDBImage(TYPE imageType)
   {
@@ -527,11 +550,6 @@ public class ChimeraViewFrame extends StructureViewerBase
     return jmb;
   }
 
-  @Override
-  protected void fitToWindow_actionPerformed()
-  {
-    jmb.focusView();
-  }
 
   @Override
   public ViewerType getViewerType()