From fee427f136e57790d514cec293de7a0fff173afd Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 2 Nov 2005 16:56:37 +0000
Subject: [PATCH] Java 1.5 bug note

---
 src/jalview/io/SequenceFeatureFetcher.java |   38 ++++++++++++++++++----------
 src/jalview/io/WSWUBlastClient.java        |    2 ++
 2 files changed, 26 insertions(+), 14 deletions(-)

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 108fe08..2bfbfd9 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -57,7 +57,7 @@ public class SequenceFeatureFetcher implements Runnable
     {
       // 1. Load the mapping information from the file
       Mapping map = new Mapping(uni.getClass().getClassLoader());
-      java.net.URL url = uni.getClass().getResource("/uniprot_mapping.xml");
+      java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
       map.loadMapping(url);
 
       // 2. Unmarshal the data
@@ -156,19 +156,29 @@ public class SequenceFeatureFetcher implements Runnable
 
     }
 
-    if (unknownSequences.size() > 0)
-    {
-      int reply = javax.swing.JOptionPane.showInternalConfirmDialog(
-          Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."
-              +"\nPerform blast for unknown sequences?",
-                  "Blast for Unidentified Sequences",
-                   javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);
-
-      if(reply == javax.swing.JOptionPane.YES_OPTION)
-       new WSWUBlastClient(ap, align, unknownSequences);
-    }
-    else
-       ((Alignment)dataset).featuresAdded = true;
+    promptBeforeBlast();
+
+  }
+
+
+  void promptBeforeBlast()
+   {
+     // This must be outside the run() body as java 1.5
+     // will not return any value from the OptionPane to the expired thread.
+      if (unknownSequences.size() > 0)
+      {
+        int reply = javax.swing.JOptionPane.showConfirmDialog(
+            Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."
+                +"\nPerform blast for unknown sequences?",
+                    "Blast for Unidentified Sequences",
+                     javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);
+
+        System.out.println("response ?? "+reply);
+        if(reply == javax.swing.JOptionPane.YES_OPTION)
+         new WSWUBlastClient(ap, align, unknownSequences);
+      }
+      else
+         ((Alignment)dataset).featuresAdded = true;
 
 
     ap.repaint();
diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 36e5dfd..41729ce 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -141,6 +141,8 @@ public class WSWUBlastClient
 
     void updateIds()
     {
+        // This must be outside the run() body as java 1.5
+     // will not return any value from the OptionPane to the expired thread.
       int reply = JOptionPane.showConfirmDialog(
           Desktop.desktop, "Automatically update suggested ids?",
           "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
-- 
1.7.10.2