JAL-3551 working proof of concept of Jalview driving PyMOL

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 6dd7d50..25d9998 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -36,6 +36,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
 
 import java.awt.Color;
 import java.awt.Component;
@@ -1087,4 +1088,57 @@ public abstract class StructureViewerBase extends GStructureViewer
     getBinding().showChains(toshow);
   }
 
+  /**
+   * Tries to fetch a PDB file and save to a temporary local file. Returns the
+   * saved file path if successful, or null if not.
+   * 
+   * @param processingEntry
+   * @return
+   */
+  protected String fetchPdbFile(PDBEntry processingEntry)
+  {
+    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 (Exception e)
+    {
+      System.err.println(
+              "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
+    } 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;
+  }
+
 }