JAL-3551 working proof of concept of Jalview driving PyMOL

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 22336b9..a6e479d 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -23,7 +23,6 @@ package jalview.gui;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
@@ -34,7 +33,6 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -164,9 +162,9 @@ public class ChimeraViewFrame extends StructureViewerBase
   /**
    * Send a command to Chimera to create residue attributes for Jalview features
    * <p>
-   * The syntax is: setattr r <attName> <attValue> <atomSpec>
+   * 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
+   * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
    */
   protected void sendFeaturesToChimera()
   {
@@ -208,8 +206,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqs)
   {
     createProgressBar();
-    jmb = new JalviewChimeraBindingModel(this,
-            ap.getStructureSelectionManager(), pdbentrys, seqs, null);
+    jmb = newBindingModel(ap, pdbentrys, seqs);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
@@ -237,6 +234,13 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   }
 
+  protected JalviewChimeraBindingModel newBindingModel(AlignmentPanel ap,
+          PDBEntry[] pdbentrys, SequenceI[][] seqs)
+  {
+    return new JalviewChimeraBindingModel(this,
+            ap.getStructureSelectionManager(), pdbentrys, seqs, null);
+  }
+
   /**
    * Create a new viewer from saved session state data including Chimera session
    * file
@@ -510,7 +514,7 @@ public class ChimeraViewFrame extends StructureViewerBase
             pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
                     jmb.getChains()[pos], pe.getFile(), protocol,
                     getProgressIndicator());
-            stashFoundChains(pdb, pe.getFile());
+            jmb.stashFoundChains(pdb, pe.getFile());
 
           } catch (OutOfMemoryError oomerror)
           {
@@ -566,71 +570,6 @@ public class ChimeraViewFrame extends StructureViewerBase
     worker = null;
   }
 
-  /**
-   * Fetch PDB data and save to a local file. Returns the full path to the file,
-   * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
-   * 
-   * @param processingEntry
-   * @return
-   * @throws Exception
-   */
-
-  private void stashFoundChains(StructureFile pdb, String file)
-  {
-    for (int i = 0; i < pdb.getChains().size(); i++)
-    {
-      String chid = new String(
-              pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
-      jmb.getChainNames().add(chid);
-      jmb.addChainFile(chid, file);
-    }
-  }
-
-  private String fetchPdbFile(PDBEntry processingEntry) throws Exception
-  {
-    String filePath = null;
-    Pdb pdbclient = new Pdb();
-    AlignmentI pdbseq = null;
-    String pdbid = processingEntry.getId();
-    long handle = System.currentTimeMillis()
-            + Thread.currentThread().hashCode();
-
-    /*
-     * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
-     */
-    String msg = MessageManager.formatMessage("status.fetching_pdb",
-            new Object[]
-            { pdbid });
-    getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
-    // long hdl = startProgressBar(MessageManager.formatMessage(
-    // "status.fetching_pdb", new Object[]
-    // { pdbid }));
-    try
-    {
-      pdbseq = pdbclient.getSequenceRecords(pdbid);
-    } catch (OutOfMemoryError oomerror)
-    {
-      new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
-    } finally
-    {
-      msg = pdbid + " " + MessageManager.getString("label.state_completed");
-      getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
-      // stopProgressBar(msg, hdl);
-    }
-    /*
-     * If PDB data were saved and are not invalid (empty alignment), return the
-     * file path.
-     */
-    if (pdbseq != null && pdbseq.getHeight() > 0)
-    {
-      // just use the file name from the first sequence's first PDBEntry
-      filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
-              .elementAt(0).getFile()).getAbsolutePath();
-      processingEntry.setFile(filePath);
-    }
-    return filePath;
-  }
-
   @Override
   public void eps_actionPerformed()
   {
@@ -650,9 +589,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     try
     {
-      String url = jmb.isChimeraX()
-              ? "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html"
-              : "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+      String url = jmb.getHelpURL();
       BrowserLauncher.openURL(url);
     } catch (IOException ex)
     {
@@ -682,7 +619,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     {
       if (pathUsed == null)
       {
-        String suffix = jmb.isChimeraX() ? ".cxs" : ".py";
+        String suffix = jmb.getSessionFileExtension();
         File tempFile = File.createTempFile("chimera", suffix);
         tempFile.deleteOnExit();
         pathUsed = tempFile.getPath();
@@ -755,20 +692,4 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     return "Chimera";
   }
-
-  /**
-   * Sends commands to align structures according to associated alignment(s).
-   * 
-   * @return
-   */
-  @Override
-  protected String alignStructsWithAllAlignPanels()
-  {
-    String reply = super.alignStructsWithAllAlignPanels();
-    if (reply != null)
-    {
-      statusBar.setText("Superposition failed: " + reply);
-    }
-    return reply;
-  }
 }