X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=217d2b1c5f89b5b641e38e5c31120d100b1587f1;hb=2e57729baa0bc97fc03ab1fb8eb4dbc1a12f3d9a;hp=9280caa42d0635708f6031e9c6ba3753e4ecd0c0;hpb=023163e0fe8837c1ddb75eb30abc058f7747b5c2;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 9280caa..217d2b1 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -20,13 +20,14 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.io.File;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
@@ -38,7 +39,6 @@ import javax.swing.event.InternalFrameEvent;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
@@ -52,9 +52,6 @@ import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
-import jalview.ws.dbsources.Pdb;
-import jalview.ws.utils.UrlDownloadClient;
 
 public class AppJmol extends StructureViewerBase
 {
@@ -274,7 +271,7 @@ public class AppJmol extends StructureViewerBase
     _started = true;
     try
     {
-      List<String> files = fetchPdbFiles();
+      List<String> files = jmb.fetchPdbFiles(this);
       if (files.size() > 0)
       {
         showFilesInViewer(files);
@@ -420,132 +417,6 @@ public class AppJmol extends StructureViewerBase
   }
 
   /**
-   * Retrieves and saves as file any modelled PDB entries for which we do not
-   * already have a file saved. Returns a list of absolute paths to structure
-   * files which were either retrieved, or already stored but not modelled in
-   * the structure viewer (i.e. files to add to the viewer display).
-   * 
-   * @return
-   */
-  List<String> fetchPdbFiles()
-  {
-    // todo - record which pdbids were successfully imported.
-    StringBuilder errormsgs = new StringBuilder();
-
-    List<String> files = new ArrayList<>();
-    String pdbid = "";
-    try
-    {
-      String[] filesInViewer = jmb.getStructureFiles();
-      // TODO: replace with reference fetching/transfer code (validate PDBentry
-      // as a DBRef?)
-      Pdb pdbclient = new Pdb();
-      EBIAlfaFold afclient = new EBIAlfaFold();
-      
-      for (int pi = 0; pi < jmb.getPdbCount(); pi++)
-      {
-        String file = jmb.getPdbEntry(pi).getFile();
-        if (file == null)
-        {
-          // todo: extract block as method and pull up (also ChimeraViewFrame)
-          // retrieve the pdb and store it locally
-          AlignmentI pdbseq = null;
-          PDBEntry strucEntry = jmb.getPdbEntry(pi);
-          pdbid = strucEntry.getId();
-          long hdl = pdbid.hashCode() - System.currentTimeMillis();
-          setProgressMessage(MessageManager
-                  .formatMessage("status.fetching_pdb", new String[]
-                  { pdbid }), hdl);
-          try
-          {
-            if (afclient.isValidReference(pdbid))
-            {
-              pdbseq = afclient.getSequenceRecords(pdbid);
-            } else {
-              if (strucEntry.hasRetrievalUrl())
-              {
-                File tmpFile = File.createTempFile(pdbid, "cif");
-                String fromUrl = strucEntry.getRetrievalUrl();
-                UrlDownloadClient.download(fromUrl, tmpFile);
-                
-                // may not need this check ?
-                file = tmpFile.getAbsolutePath();
-                if (file != null)
-                {
-                  pdbseq = EBIAlfaFold.importDownloadedStructureFromUrl(fromUrl,tmpFile,pdbid,null,null,null);
-                }
-              } else {
-                pdbseq = pdbclient.getSequenceRecords(pdbid);
-              }
-            }
-          } catch (OutOfMemoryError oomerror)
-          {
-            new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-            errormsgs.append("'").append(pdbid).append("'");
-          } finally
-          {
-            setProgressMessage(
-                    MessageManager.getString("label.state_completed"), hdl);
-          }
-          if (pdbseq != null)
-          {
-            // just transfer the file name from the first sequence's first
-            // PDBEntry
-            file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
-                    .elementAt(0).getFile()).getAbsolutePath();
-            jmb.getPdbEntry(pi).setFile(file);
-            files.add(file);
-          }
-          else
-          {
-            errormsgs.append("'").append(pdbid).append("' ");
-          }
-        }
-        else
-        {
-          if (filesInViewer != null && filesInViewer.length > 0)
-          {
-            addingStructures = true; // already files loaded.
-            for (int c = 0; c < filesInViewer.length; c++)
-            {
-              if (Platform.pathEquals(filesInViewer[c], file))
-              {
-                file = null;
-                break;
-              }
-            }
-          }
-          if (file != null)
-          {
-            files.add(file);
-          }
-        }
-      }
-    } catch (OutOfMemoryError oomerror)
-    {
-      new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-      errormsgs.append("When retrieving pdbfiles : current was: '")
-              .append(pdbid).append("'");
-    }
-    if (errormsgs.length() > 0)
-    {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-              MessageManager.formatMessage(
-                      "label.pdb_entries_couldnt_be_retrieved", new String[]
-                      { errormsgs.toString() }),
-              MessageManager.getString("label.couldnt_load_file"),
-              JvOptionPane.ERROR_MESSAGE);
-    }
-    return files;
-  }
-
-  /**
    * Outputs the Jmol viewer image as an image file, after prompting the user to
    * choose a file and (for EPS) choice of Text or Lineart character rendering
    * (unless a preference for this is set)
@@ -565,7 +436,7 @@ public class AppJmol extends StructureViewerBase
         jmb.jmolViewer.renderScreenImage(g, width, height);
       }
     };
-    String view = MessageManager.getString("action.view").toLowerCase();
+    String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
     ImageExporter exporter = new ImageExporter(writer,
             getProgressIndicator(), type, getTitle());
     exporter.doExport(null, this, width, height, view);