X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=ae2128bdb016298204c15e708c9efc24caf1a844;hb=36f083dc674297be2157d9f291a7cddba9d3250a;hp=4f746cbed4330f609ccbfb97d2b0ff804f29190e;hpb=8f08ed712138cea8987594a62b6053a0bfdba327;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 4f746cb..ae2128b 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1156,12 +1156,14 @@ public abstract class StructureViewerBase extends GStructureViewer
     {
       if (afclient.isValidReference(pdbid))
       {
-        pdbseq = afclient.getSequenceRecords(pdbid);
+        pdbseq = afclient.getSequenceRecords(pdbid,processingEntry.getRetrievalUrl());
       } else {
           if (processingEntry.hasRetrievalUrl())
           {
+            String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+                     
             // retrieve from URL to new local tmpfile
-            File tmpFile = File.createTempFile(pdbid,
+            File tmpFile = File.createTempFile(safePDBId,
                     "." + (PDBEntry.Type.MMCIF.toString().equals(
                             processingEntry.getType().toString()) ? "cif"
                                     : "pdb"));
@@ -1210,8 +1212,23 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   public File saveSession()
   {
-    // TODO: a wait loop to ensure the file is written fully before returning?
-    return getBinding() == null ? null : getBinding().saveSession();
+    if (getBinding() == null) { return  null;}
+    File session = getBinding().saveSession();
+    long l = session.length();
+    int wait=50;
+    do {
+      try {
+        Thread.sleep(5);
+      } catch (InterruptedException e) {
+      } 
+      long nextl = session.length();
+      if (nextl!=l)
+      {
+        wait = 50;
+        l=nextl;
+      }
+    } while (--wait>0);
+    return session;
   }
 
   /**