From d5ae51f80441c008a5e23741b40ab095720ff618 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 12:00:25 +0000
Subject: [PATCH] Catch exceptions

---
 src/jalview/gui/SequenceFetcher.java |   69 ++++++++++++++++++++--------------
 1 file changed, 41 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 74312e2..4fa215f 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -128,35 +128,43 @@ public class SequenceFetcher
   public void run()
   {
     StringBuffer result = new StringBuffer();
-    if (database.getSelectedItem().equals("Uniprot")
-        || database.getSelectedItem().equals("EMBL")
-        || database.getSelectedItem().equals("EMBLCDS"))
-    {
-      EBIFetchClient dbFetch = new EBIFetchClient();
-      String[] reply = dbFetch.fetchData(
-          database.getSelectedItem().toString().toLowerCase(
-          ) + ":" + textfield.getText(),
-          "fasta", "raw");
-
-      for (int i = 0; i < reply.length; i++)
-        result.append(reply[i]+"\n");
-    }
-    else if (database.getSelectedItem().equals("PDB"))
-    {
-      EBIFetchClient ebi = new EBIFetchClient();
-      String[] reply = ebi.fetchData("pdb:" + textfield.getText(), "pdb",
-                                     "raw");
-      PDBfile pdbfile = new PDBfile(reply);
-      for (int i = 0; i < pdbfile.chains.size(); i++)
+      if (database.getSelectedItem().equals("Uniprot")
+          || database.getSelectedItem().equals("EMBL")
+          || database.getSelectedItem().equals("EMBLCDS"))
       {
-        result.append("\n>" +
-                     ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.getName() +
-                     "\n"
-                     +
-                     ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
-                     getSequence());
+        EBIFetchClient dbFetch = new EBIFetchClient();
+        String[] reply = dbFetch.fetchData(
+            database.getSelectedItem().toString().toLowerCase(
+            ) + ":" + textfield.getText(),
+            "fasta", "raw");
+
+        for (int i = 0; i < reply.length; i++)
+          result.append(reply[i] + "\n");
+      }
+      else if (database.getSelectedItem().equals("PDB"))
+      {
+        EBIFetchClient ebi = new EBIFetchClient();
+        String[] reply = ebi.fetchData("pdb:" + textfield.getText(), "pdb",
+                                       "raw");
+        try{
+          PDBfile pdbfile = new PDBfile(reply);
+          for (int i = 0; i < pdbfile.chains.size(); i++)
+          {
+            result.append("\n>" +
+                          ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
+                          getName() +
+                          "\n"
+                          +
+                          ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
+                          getSequence());
+          }
+        }catch(Exception ex)// Problem parsing PDB file
+        {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+         "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem(),
+         "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+        }
       }
-    }
 
     if (result.length() > 0)
     {
@@ -166,7 +174,7 @@ public class SequenceFetcher
       if (FormatAdapter.formats.contains(format))
       {
         sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);
-        if (sequences != null)
+        if (sequences != null && sequences.length>0)
         {
           if(alignFrame==null)
           {
@@ -219,6 +227,11 @@ public class SequenceFetcher
           }
 
         }
+        else
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+         "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem(),
+         "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+
       }
     }
 
-- 
1.7.10.2