JAL-1761 pattern for structure viewer construction from project file

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 45ab9a9..0e5675c 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -25,10 +25,10 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
@@ -41,12 +41,13 @@ 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;
 import jalview.io.StructureFile;
 import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -80,16 +81,13 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     super.initMenus();
 
-    viewerActionMenu.setText(MessageManager.getString("label.chimera"));
-
-    helpItem.setText(MessageManager.getString("label.chimera_help"));
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
     JMenuItem writeFeatures = new JMenuItem(
-            MessageManager.getString("label.create_chimera_attributes"));
+            MessageManager.getString("label.create_viewer_attributes"));
     writeFeatures.setToolTipText(MessageManager
-            .getString("label.create_chimera_attributes_tip"));
+            .getString("label.create_viewer_attributes_tip"));
     writeFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -154,14 +152,12 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Send a command to Chimera to create residue attributes for Jalview features
-   * <p>
-   * The syntax is: setattr r &lt;attName&gt; &lt;attValue&gt; &lt;atomSpec&gt;
-   * <p>
-   * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
+   * Sends command(s) to the structure viewer to create residue attributes for
+   * visible Jalview features
    */
   protected void sendFeaturesToChimera()
   {
+    // todo pull up?
     int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
     statusBar.setText(
             MessageManager.formatMessage("label.attributes_set", count));
@@ -247,22 +243,34 @@ 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);
@@ -529,20 +537,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
-  public void showHelp_actionPerformed()
-  {
-    try
-    {
-      String url = jmb.getHelpURL();
-      BrowserLauncher.openURL(url);
-    } catch (IOException ex)
-    {
-      System.err
-              .println("Show Chimera help failed with: " + ex.getMessage());
-    }
-  }
-
-  @Override
   public AAStructureBindingModel getBinding()
   {
     return jmb;