Allows Jmol to share cached files

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index c1dc77c..407f87d 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -22,6 +22,7 @@ package jalview.datamodel;
 
 import jalview.util.CaseInsensitiveString;
 
+import java.io.File;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -38,7 +39,9 @@ public class PDBEntry
 
   private static final int PDB_ID_LENGTH = 4;
 
-  private String file;
+  private String fileName;
+  
+  private File file;
 
   private String type;
 
@@ -133,8 +136,8 @@ public class PDBEntry
      */
     boolean idMatches = id == o.id
             || (id != null && id.equalsIgnoreCase(o.id));
-    boolean fileMatches = file == o.file
-            || (file != null && file.equals(o.file));
+    boolean fileMatches = fileName == o.fileName
+            || (fileName != null && fileName.equals(o.fileName));
     boolean typeMatches = type == o.type
             || (type != null && type.equals(o.type));
     if (idMatches && fileMatches && typeMatches)
@@ -164,12 +167,12 @@ public class PDBEntry
    * @param entryType
    * @param filePath
    */
-  void init(String pdbId, String chain, PDBEntry.Type entryType,
+  private void init(String pdbId, String chain, PDBEntry.Type entryType,
           String filePath)
   {
     this.id = pdbId;
     this.type = entryType == null ? null : entryType.toString();
-    this.file = filePath;
+    this.fileName = filePath;
     setChainCode(chain);
   }
 
@@ -180,7 +183,7 @@ public class PDBEntry
    */
   public PDBEntry(PDBEntry entry)
   {
-    file = entry.file;
+    fileName = entry.fileName;
     type = entry.type;
     id = entry.id;
     if (entry.properties != null)
@@ -220,12 +223,22 @@ public class PDBEntry
 
   public void setFile(String f)
   {
+    this.fileName = f;
+  }
+
+  public void setFile(File f)
+  {
     this.file = f;
   }
 
   public String getFile()
   {
-    return file;
+    return (file != null ? file.getAbsolutePath() : fileName);
+  }
+
+  public File getFileF()
+  {
+    return (file == null ? new File(fileName) : file);
   }
 
   public void setType(String t)
@@ -420,6 +433,7 @@ public class PDBEntry
     {
       setFile(newFile);
       setType(newType);
+      setFile(newEntry.getFileF());
     }
 
     /*

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 7179a18..f937f22 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -140,7 +140,7 @@ public class AppJmol extends StructureViewerBase
         closeViewer(false);
       }
     });
-    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
+    initJmol(loadStatus, null); // pdbentry, seq, JBPCHECK!
   }
 
   @Override
@@ -199,8 +199,6 @@ public class AppJmol extends StructureViewerBase
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     addingStructures = false;
-    worker = new Thread(this);
-    worker.start();
 
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
@@ -212,6 +210,8 @@ public class AppJmol extends StructureViewerBase
       }
     });
 
+    worker = new Thread(this);
+    worker.start();
   }
 
   /**
@@ -231,7 +231,7 @@ public class AppJmol extends StructureViewerBase
   }
 
 
-  void initJmol(String command)
+  private void initJmol(String command, List<File> files)
   {
     jmb.setFinishedInit(false);
     renderPanel = new RenderPanel();
@@ -255,6 +255,8 @@ public class AppJmol extends StructureViewerBase
     if (command == null)
     {
       command = "";
+    } else if (files != null) {
+               jmb.cacheFiles(files);
     }
     jmb.evalStateCommand(command);
     jmb.evalStateCommand("set hoverDelay=0.1");
@@ -302,7 +304,7 @@ public class AppJmol extends StructureViewerBase
     _started = true;
     try
     {
-      List<String> files = fetchPdbFiles();
+      List<File> files = fetchPdbFiles();
       if (files.size() > 0)
       {
         showFilesInViewer(files);
@@ -321,12 +323,13 @@ public class AppJmol extends StructureViewerBase
    * @param files
    *          list of absolute paths to structure files
    */
-  void showFilesInViewer(List<String> files)
+  void showFilesInViewer(List<File> files)
   {
     long lastnotify = jmb.getLoadNotifiesHandled();
     StringBuilder fileList = new StringBuilder();
-    for (String s : files)
+    for (File f : files)
     {
+      String s = f.getAbsolutePath();
       fileList.append(SPACE).append(QUOTE)
               .append(Platform.escapeString(s)).append(QUOTE);
     }
@@ -336,7 +339,7 @@ public class AppJmol extends StructureViewerBase
     {
       try
       {
-        initJmol("load FILES " + filesString);
+        initJmol("load FILES " + filesString, files);
       } catch (OutOfMemoryError oomerror)
       {
         new OOMWarning("When trying to open the Jmol viewer!", oomerror);
@@ -359,6 +362,7 @@ public class AppJmol extends StructureViewerBase
 
       try
       {
+       jmb.cacheFiles(files);
         jmb.evalStateCommand(command);
       } catch (OutOfMemoryError oomerror)
       {
@@ -453,12 +457,12 @@ public class AppJmol extends StructureViewerBase
    * 
    * @return
    */
-  List<String> fetchPdbFiles()
+  List<File> fetchPdbFiles()
   {
     // todo - record which pdbids were successfully imported.
     StringBuilder errormsgs = new StringBuilder();
 
-    List<String> files = new ArrayList<>();
+    List<File> files = new ArrayList<>();
     String pdbid = "";
     try
     {
@@ -468,7 +472,7 @@ public class AppJmol extends StructureViewerBase
       Pdb pdbclient = new Pdb();
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
       {
-        String file = jmb.getPdbEntry(pi).getFile();
+        File file = jmb.getPdbEntry(pi).getFileF();
         if (file == null)
         {
           // todo: extract block as method and pull up (also ChimeraViewFrame)
@@ -506,7 +510,7 @@ public class AppJmol extends StructureViewerBase
             // just transfer the file name from the first sequence's first
             // PDBEntry
             file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
-                    .elementAt(0).getFile()).getAbsolutePath();
+                    .elementAt(0).getFile());
             jmb.getPdbEntry(pi).setFile(file);
             files.add(file);
           }
@@ -520,9 +524,10 @@ public class AppJmol extends StructureViewerBase
           if (filesInViewer != null && filesInViewer.length > 0)
           {
             addingStructures = true; // already files loaded.
+            String filename = file.getAbsolutePath();
             for (int c = 0; c < filesInViewer.length; c++)
             {
-              if (filesInViewer[c].equals(file))
+              if (filesInViewer[c].equals(filename))
               {
                 file = null;
                 break;

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index eeb4888..5c2addc 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -28,12 +28,16 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
 
 import java.awt.Container;
+import java.io.File;
+import java.util.List;
 import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import javajs.util.BS;
+
 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
 public class AppJmolBinding extends JalviewJmolBinding
@@ -215,4 +219,17 @@ public class AppJmolBinding extends JalviewJmolBinding
 
     return null;
   }
+
+  @SuppressWarnings("unused")
+public void cacheFiles(List<File> files) {
+         if (files == null)
+                 return;
+         for (File f : files) {
+                 String path = f.getAbsolutePath();
+                 byte[] data = Platform.getFileBytes(f);
+                 if (data != null) {
+                         Platform.cacheFileData(path, data);
+                 }
+         }
+  }
 }

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 084f886..5c8360c 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -120,6 +120,7 @@ public abstract class StructureFile extends AlignFile
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
     entry.setType(getStructureFileType());
+    entry.setFile(inFile);
     if (chain.id != null)
     {
       entry.setChainCode(chain.id);