Merge branch 'update/JAL-3949_jalview_bin_Console_to_cure_sanity_even_more' into...

diff --git a/getdown/lib/getdown-core.jar b/getdown/lib/getdown-core.jar
index 4edf9b0..a11a269 100644 (file)
Binary files a/getdown/lib/getdown-core.jar and b/getdown/lib/getdown-core.jar differ

diff --git a/getdown/lib/getdown-launcher-local.jar b/getdown/lib/getdown-launcher-local.jar
index 500b38b..4ac9d5d 100644 (file)
Binary files a/getdown/lib/getdown-launcher-local.jar and b/getdown/lib/getdown-launcher-local.jar differ

diff --git a/getdown/lib/getdown-launcher.jar b/getdown/lib/getdown-launcher.jar
index 2ead1c7..999c3fa 100644 (file)
Binary files a/getdown/lib/getdown-launcher.jar and b/getdown/lib/getdown-launcher.jar differ

diff --git a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
index 684844a..9deb5bc 100644 (file)
--- a/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
+++ b/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/Application.java
@@ -1264,7 +1264,9 @@ public class Application
         String[] sargs = args.toArray(new String[args.size()]);
         log.info("Running " + StringUtil.join(sargs, "\n  "));
 
-        return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+        // don't set the working dir, leave it the same as the working dir of the invocation
+        //return Runtime.getRuntime().exec(sargs, envp, getAppDir());
+        return Runtime.getRuntime().exec(sargs, envp);
     }
 
     /**

diff --git a/j11lib/getdown-core.jar b/j11lib/getdown-core.jar
index 4edf9b0..a11a269 100644 (file)
Binary files a/j11lib/getdown-core.jar and b/j11lib/getdown-core.jar differ

diff --git a/j8lib/getdown-core.jar b/j8lib/getdown-core.jar
index 4edf9b0..a11a269 100644 (file)
Binary files a/j8lib/getdown-core.jar and b/j8lib/getdown-core.jar differ

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 8290dd9..349871d 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -1161,7 +1161,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       } else {
           if (processingEntry.hasRetrievalUrl())
           {
-            String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8");
+            String safePDBId = java.net.URLEncoder.encode(pdbid,"UTF-8").replace("%","__");
                      
             // retrieve from URL to new local tmpfile
             File tmpFile = File.createTempFile(safePDBId,