From b619c31a9a4e3b548e9e166028a12b5db96eb070 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 9 Apr 2014 09:50:35 +0100
Subject: [PATCH] prompt to concatenate or use GFF tabix index
---
uk/ac/sanger/artemis/io/DocumentEntryFactory.java | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/DocumentEntryFactory.java b/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
index f530a0863..a83b7b235 100644
--- a/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
+++ b/uk/ac/sanger/artemis/io/DocumentEntryFactory.java
@@ -31,6 +31,8 @@ import uk.ac.sanger.artemis.util.LinePushBackReader;
import java.io.File;
import java.io.IOException;
+import javax.swing.JOptionPane;
+
/**
* This class contains the method makeDocumentEntry (), which creates a
@@ -79,7 +81,18 @@ abstract public class DocumentEntryFactory
document.getInputStream() instanceof net.sf.samtools.util.BlockCompressedInputStream)
{
if(IndexedGFFDocumentEntry.isIndexed( ((File)document.getLocation()) ))
- return new IndexedGFFDocumentEntry(document);
+ {
+ Object[] possibleValues = { "Use index", "Ignore index" };
+ int sel = JOptionPane.showOptionDialog(null,
+ "Use the GFF index file (to increase the performance)\n"+
+ "or concatenate the sequences together?",
+ "Indexed GFF",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, possibleValues, possibleValues[0]);
+
+ if(sel == 0)
+ return new IndexedGFFDocumentEntry(document);
+ }
}
final LinePushBackReader document_reader =
--
GitLab