From 36269160d91eccc05eb4def98d2a6362f462eda2 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 8 Dec 2005 16:10:39 +0000
Subject: [PATCH] added some error checking and instruction dialogs

---
 src/jalview/gui/SequenceFetcher.java |   43 +++++++++++++++++++++++++---------
 1 file changed, 32 insertions(+), 11 deletions(-)

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index ca2e375..e7d03fe 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -36,10 +36,11 @@ public class SequenceFetcher
   JInternalFrame frame;
   AlignFrame alignFrame;
   StringBuffer result;
+  final String noDbSelected = "-- Select Database --";
   public SequenceFetcher(AlignFrame af)
   {
     alignFrame = af;
-    database.addItem("-- Select Database --");
+    database.addItem(noDbSelected);
     database.addItem("Uniprot");
     database.addItem("EMBL");
     database.addItem("EMBLCDS");
@@ -146,8 +147,29 @@ public class SequenceFetcher
     worker.start();
   }
 
+  private void resetDialog() {
+    database.setEnabled(true);
+    textfield.setEnabled(true);
+    ok.setEnabled(true);
+    cancel.setEnabled(true);
+    frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");
+  }
+
   public void run()
   {
+    String error = "";
+    if (database.getSelectedItem().equals(noDbSelected))
+      error += "Please select the source database\n";
+    com.stevesoft.pat.Regex empty=new com.stevesoft.pat.Regex("\\s+","");
+    textfield.setText(empty.replaceAll(textfield.getText()));
+    if (textfield.getText().length()==0)
+      error+="Please enter a (semi-colon separated list of) database id(s)";
+    if (error.length()>0) {
+      showErrorMessage(error);
+      resetDialog();
+      return;
+    }
+
    result = new StringBuffer();
     if (database.getSelectedItem().equals("Uniprot"))
     {
@@ -170,20 +192,17 @@ public class SequenceFetcher
     else if (database.getSelectedItem().equals("PDB"))
     {
       result = getPDBFile(textfield.getText().toUpperCase());
-      parseResult(result.toString());
+      if (result!=null)
+        parseResult(result.toString());
     }
 
 
     if (result == null || result.length() == 0)
       showErrorMessage("Error retrieving " + textfield.getText()
                        + " from " + database.getSelectedItem());
-
-
-      database.setEnabled(true);
-      textfield.setEnabled(true);
-      ok.setEnabled(true);
-      cancel.setEnabled(true);
-      frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");
+    else
+      textfield.setText("");
+    resetDialog();
   }
 
   void getUniprotFile(String id)
@@ -256,6 +275,8 @@ public class SequenceFetcher
 
       EBIFetchClient ebi = new EBIFetchClient();
       String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
+      if (reply==null)
+        return null;
       try
       {
         PDBfile pdbfile = new PDBfile(reply);
@@ -275,8 +296,8 @@ public class SequenceFetcher
       }
       catch (Exception ex) // Problem parsing PDB file
       {
-        showErrorMessage("Error retrieving " + textfield.getText() + " from " +
-            database.getSelectedItem());
+        jalview.bin.Cache.log.warn("Exception when retrieving " + textfield.getText() + " from " +
+            database.getSelectedItem(), ex);
         return null;
       }
 
-- 
1.7.10.2