From dc12bf83656ccdfcf0d7f6c2983c50a11bc50fb4 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 13 Sep 2013 12:37:55 +0100
Subject: [PATCH] fix for splitting GFF genes and then undo-ing the split
---
uk/ac/sanger/artemis/components/EditMenu.java | 24 ++++++++-----------
1 file changed, 10 insertions(+), 14 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/EditMenu.java b/uk/ac/sanger/artemis/components/EditMenu.java
index 1b5546a6b..50d124a6d 100644
--- a/uk/ac/sanger/artemis/components/EditMenu.java
+++ b/uk/ac/sanger/artemis/components/EditMenu.java
@@ -1641,7 +1641,7 @@ public class EditMenu extends SelectionMenu
* @param entry_group Used to get the ActionController for calling
* startAction() and endAction().
**/
- private static void unmergeFeature(final JFrame frame,
+ protected static void unmergeFeature(final JFrame frame,
final Selection selection,
final EntryGroup entry_group)
{
@@ -1710,16 +1710,15 @@ public class EditMenu extends SelectionMenu
{
final FeatureVector chadoGenes = new FeatureVector();
chadoGenes.add(segment_feature);
- final Vector duplicateGenes = duplicateGeneFeatures(frame, chadoGenes, entry_group);
+ final Vector<ChadoCanonicalGene> duplicateGenes = duplicateGeneFeatures(frame, chadoGenes, entry_group);
// get the new duplicate spliced feature
- ChadoCanonicalGene chado_gene = (ChadoCanonicalGene)duplicateGenes.get(0);
+ ChadoCanonicalGene chado_gene = duplicateGenes.get(0);
// assumes single transcript
- uk.ac.sanger.artemis.io.Feature transcript =
- (uk.ac.sanger.artemis.io.Feature)chado_gene.getTranscripts().get(0);
+ uk.ac.sanger.artemis.io.Feature transcript = chado_gene.getTranscripts().get(0);
// get the spliced feature with the same key as the segment
// selected to unmerge
- uk.ac.sanger.artemis.io.Feature spliced = (uk.ac.sanger.artemis.io.Feature)
+ uk.ac.sanger.artemis.io.Feature spliced =
chado_gene.getSpliceSitesOfTranscript(GeneUtils.getUniqueName(transcript),
first_segment.getFeature().getKey().getKeyString()).get(0);
new_feature = (Feature)spliced.getUserData();
@@ -1733,11 +1732,8 @@ public class EditMenu extends SelectionMenu
// segment_feature and delete the segments up to (and including)
// index_of_first_segment from new_feature
- for(int i = all_feature_segments.size() - 1;
- i >= index_of_second_segment; --i)
- {
+ for(int i = all_feature_segments.size() - 1; i >= index_of_second_segment; --i)
segment_feature.getSegments ().elementAt (i).removeFromFeature ();
- }
// remove the first segment of new_feature index_of_first_segment times
for (int i = 0; i <= index_of_first_segment; ++i)
@@ -1747,15 +1743,15 @@ public class EditMenu extends SelectionMenu
{
final FeatureVector chadoGenes = new FeatureVector();
chadoGenes.add(segment_feature);
- final Vector duplicateGenes = duplicateGeneFeatures(frame, chadoGenes, entry_group);
+ final Vector<ChadoCanonicalGene> duplicateGenes = duplicateGeneFeatures(frame, chadoGenes, entry_group);
final GFFStreamFeature orig_feature = (GFFStreamFeature)segment_feature.getEmblFeature();
final ChadoCanonicalGene orig_chado_gene = orig_feature.getChadoGene();
final String prevId = GeneUtils.getUniqueName(orig_chado_gene.getGene());
GeneUtils.deleteAllFeature(
- ((uk.ac.sanger.artemis.Feature)orig_chado_gene.getGene().getUserData()), orig_chado_gene);
+ ((uk.ac.sanger.artemis.Feature)orig_chado_gene.getGene().getUserData()), orig_chado_gene, false);
- final ChadoCanonicalGene gene1 = (ChadoCanonicalGene)duplicateGenes.get(0);
+ final ChadoCanonicalGene gene1 = duplicateGenes.get(0);
final ChadoCanonicalGene gene2 = ((GFFStreamFeature)new_feature.getEmblFeature()).getChadoGene();
if(!prevId.startsWith("DUP"))
{
@@ -2176,7 +2172,7 @@ public class EditMenu extends SelectionMenu
}
- protected static Vector duplicateGeneFeatures(final JFrame frame,
+ private static Vector<ChadoCanonicalGene> duplicateGeneFeatures(final JFrame frame,
final FeatureVector features,
final EntryGroup entry_group)
{
--
GitLab