From f070197de234808f57a1871c9f7ee419447bcee9 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Wed, 27 Nov 2013 15:01:28 +0000
Subject: [PATCH] warn when overlaying a GFF with a sequence onto a sequence
entry
---
uk/ac/sanger/artemis/SimpleEntryGroup.java | 10 ++++++++++
1 file changed, 10 insertions(+)
diff --git a/uk/ac/sanger/artemis/SimpleEntryGroup.java b/uk/ac/sanger/artemis/SimpleEntryGroup.java
index 8c6d82c88..9d1d8ee70 100644
--- a/uk/ac/sanger/artemis/SimpleEntryGroup.java
+++ b/uk/ac/sanger/artemis/SimpleEntryGroup.java
@@ -26,6 +26,7 @@
package uk.ac.sanger.artemis;
import uk.ac.sanger.artemis.sequence.*;
+import uk.ac.sanger.artemis.components.MessageDialog;
import uk.ac.sanger.artemis.io.GFFDocumentEntry;
import uk.ac.sanger.artemis.io.IndexedGFFDocumentEntry;
import uk.ac.sanger.artemis.io.Range;
@@ -646,7 +647,16 @@ public class SimpleEntryGroup extends EntryVector
if(entry.getEMBLEntry() instanceof IndexedGFFDocumentEntry)
((IndexedGFFDocumentEntry)entry.getEMBLEntry()).setEntryGroup(this);
else if(entry.getEMBLEntry() instanceof GFFDocumentEntry)
+ {
((GFFDocumentEntry)entry.getEMBLEntry()).adjustCoordinates( getSequenceEntry() );
+ if(!Options.isBlackBeltMode() && size() > 1 &&
+ entry.getEMBLEntry().getSequence() != null )
+ {
+ new MessageDialog (null, "Warning",
+ "Overlaying a GFF with a sequence onto an entry with a sequence.",
+ false);
+ }
+ }
addElement(entry);
}
--
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