X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=1c0dfe6c2e534bddc3d733588bfdc9542c17e5a0;hb=62cdf4a06bef088c02f81c66ab2fe0bc3264e321;hp=2299c2602b767098e161817d5615d4481337545e;hpb=7d34fe9736520832bd6269cf2bbde3a8739e5e82;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 2299c26..1c0dfe6 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -79,6 +79,9 @@ import javax.swing.event.MenuListener;
 
 public class AppJmol extends StructureViewerBase
 {
+  // ms to wait for Jmol to load files
+  private static final int JMOL_LOAD_TIMEOUT = 20000;
+
   private static final String SPACE = " ";
 
   private static final String BACKSLASH = "\"";
@@ -309,12 +312,10 @@ public class AppJmol extends StructureViewerBase
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
-    worker = null;
-    {
-      addingStructures = false;
-      worker = new Thread(this);
-      worker.start();
-    }
+    addingStructures = false;
+    worker = new Thread(this);
+    worker.start();
+
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
@@ -381,10 +382,7 @@ public class AppJmol extends StructureViewerBase
       scriptWindow.setVisible(false);
     }
 
-    /*
-     * -i for no info logging (less verbose)
-     */
-    jmb.allocateViewer(renderPanel, true, "", null, null, "-i",
+    jmb.allocateViewer(renderPanel, true, "", null, null, "",
             scriptWindow, null);
     // jmb.newJmolPopup("Jmol");
     if (command == null)
@@ -511,8 +509,8 @@ public class AppJmol extends StructureViewerBase
     StringBuilder fileList = new StringBuilder();
     for (String s : files)
     {
-      fileList.append(SPACE).append(BACKSLASH).append(Platform.escapeString(s))
-              .append(BACKSLASH);
+      fileList.append(SPACE).append(BACKSLASH)
+              .append(Platform.escapeString(s)).append(BACKSLASH);
     }
     String filesString = fileList.toString();
 
@@ -544,8 +542,7 @@ public class AppJmol extends StructureViewerBase
         jmb.evalStateCommand(command);
       } catch (OutOfMemoryError oomerror)
       {
-        new OOMWarning(
-                "When trying to add structures to the Jmol viewer!",
+        new OOMWarning("When trying to add structures to the Jmol viewer!",
                 oomerror);
         Cache.log.debug("File locations are " + filesString);
       } catch (Exception ex)
@@ -555,7 +552,7 @@ public class AppJmol extends StructureViewerBase
     }
 
     // need to wait around until script has finished
-    int waitMax = 5000; // give up after 5 seconds
+    int waitMax = JMOL_LOAD_TIMEOUT;
     int waitFor = 35;
     int waitTotal = 0;
     while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
@@ -572,7 +569,13 @@ public class AppJmol extends StructureViewerBase
       }
       if (waitTotal > waitMax)
       {
-        System.err.println("Timed out waiting for Jmol to load files");
+        System.err
+                .println("Timed out waiting for Jmol to load files after "
+                        + waitTotal + "ms");
+//        System.err.println("finished: " + jmb.isFinishedInit()
+//                + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+//                + "; files: " + files.toString());
+        jmb.getPdbFile();
         break;
       }
     }