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 1a5e901..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;
@@ -516,7 +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)
           {
@@ -572,71 +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()
   {