From 25a1c531a180d6d5620c0d065c3515b06464dd29 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 31 Oct 2005 15:53:31 +0000
Subject: [PATCH] Prompt before blasting

---
 src/jalview/io/SequenceFeatureFetcher.java |   16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/src/jalview/io/SequenceFeatureFetcher.java b/src/jalview/io/SequenceFeatureFetcher.java
index 520ba03..35a9a95 100755
--- a/src/jalview/io/SequenceFeatureFetcher.java
+++ b/src/jalview/io/SequenceFeatureFetcher.java
@@ -96,7 +96,7 @@ public class SequenceFeatureFetcher implements Runnable
   public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)
   {
     unknownSequences = new ArrayList();
-    this.align = align;
+    this.align = align.getDataset();
     this.ap = ap;
 
     Thread thread = new Thread(this);
@@ -139,6 +139,7 @@ public class SequenceFeatureFetcher implements Runnable
                                           "xml", null);
 
 
+
           if (file != null)
           {
             ReadUniprotFile(file, align, ids);
@@ -163,6 +164,13 @@ 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
@@ -194,18 +202,20 @@ public class SequenceFeatureFetcher implements Runnable
     for (i = 0; i < iSize; i++)
     {
       entry = (UniprotEntry) entries.elementAt(i);
-      String idmatch = entry.getAccession();
+      String idmatch = entry.getAccession().elementAt(0).toString();
       sequence = align.findName(idmatch);
 
       if (sequence == null)
       {
         //Sequence maybe Name, not Accession
-        idmatch = entry.getName();
+
+        idmatch = entry.getName().elementAt(0).toString();;
         sequence = align.findName(idmatch);
       }
 
       if (sequence == null)
       {
+        System.out.println("not found");
         continue;
       }
 
-- 
1.7.10.2