Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 037b97e..844faa7 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -33,7 +33,7 @@ import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -91,7 +91,7 @@ public class AppJmolBinding extends JalviewJmolBinding
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception e)
     {
-      Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+      Console.error("Failed to launch Jmol-associated url " + url, e);
       // TODO: 2.6 : warn user if browser was not configured.
     }
   }
@@ -214,7 +214,7 @@ public class AppJmolBinding extends JalviewJmolBinding
   {
     // todo - record which pdbids were successfully imported.
     StringBuilder errormsgs = new StringBuilder();
-  
+
     List<String> files = new ArrayList<>();
     String pdbid = "";
     try
@@ -222,45 +222,18 @@ public class AppJmolBinding extends JalviewJmolBinding
       String[] filesInViewer = 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 < getPdbCount(); pi++)
       {
-        String file = getPdbEntry(pi).getFile();
+        PDBEntry strucEntry = getPdbEntry(pi);
+
+        String file = strucEntry.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 = getPdbEntry(pi);
           pdbid = strucEntry.getId();
-          long hdl = pdbid.hashCode() - System.currentTimeMillis();
-          structureViewer.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);
-              }
-            }
+            file = structureViewer.fetchPdbFile(strucEntry);
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
@@ -268,18 +241,10 @@ public class AppJmolBinding extends JalviewJmolBinding
           {
             ex.printStackTrace();
             errormsgs.append("'").append(pdbid).append("'");
-          } finally
-          {
-            structureViewer.setProgressMessage(
-                    MessageManager.getString("label.state_completed"), hdl);
           }
-          if (pdbseq != null)
+          if (file != null)
           {
-            // just transfer the file name from the first sequence's first
-            // PDBEntry
-            file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
-                    .elementAt(0).getFile()).getAbsolutePath();
-            getPdbEntry(pi).setFile(file);
+            // success
             files.add(file);
           }
           else
@@ -318,7 +283,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     }
     if (errormsgs.length() > 0)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+       JvOptionPane.showInternalMessageDialog(Desktop.getInstance(),
               MessageManager.formatMessage(
                       "label.pdb_entries_couldnt_be_retrieved", new String[]
                       { errormsgs.toString() }),