From af7a78d94ac6d9907bb9d38b2c32a9a124b69964 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 26 Apr 2011 08:59:18 +0000
Subject: [PATCH] changes for the "Create introns" function to transfer sys_id
and allow for 3'UTR and 5'UTR
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15998 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/AddMenu.java | 18 +++++++++++++++++-
1 file changed, 17 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/components/AddMenu.java b/uk/ac/sanger/artemis/components/AddMenu.java
index 6cf182217..68705b8ad 100644
--- a/uk/ac/sanger/artemis/components/AddMenu.java
+++ b/uk/ac/sanger/artemis/components/AddMenu.java
@@ -40,6 +40,7 @@ import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
+import uk.ac.sanger.artemis.io.InvalidRelationException;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.RangeVector;
@@ -750,7 +751,9 @@ public class AddMenu extends SelectionMenu
final Feature selection_feature =
selected_features.elementAt (feature_index);
- if (!selection_feature.isProteinFeature ()) {
+ if (!(selection_feature.isProteinFeature () ||
+ selection_feature.getKey().equals("5'UTR") ||
+ selection_feature.getKey().equals("3'UTR"))) {
continue;
}
@@ -814,6 +817,19 @@ public class AddMenu extends SelectionMenu
new Location (intron_ranges, cds_location.isComplement ());
final QualifierVector qualifiers = new QualifierVector ();
+ try {
+ StringVector sysNames = Options.getOptions().getSystematicQualifierNames();
+ for(int i=0; i<sysNames.size(); i++) {
+ Qualifier qual = selection_feature.getQualifierByName((String) sysNames.get(i));
+ if(qual != null && qual.getValues() != null && qual.getValues().size() > 0) {
+ qualifiers.addQualifierValues(qual);
+ break;
+ }
+ }
+ } catch (InvalidRelationException e) {
+ throw new Error ("internal error - unexpected exception: " + e);
+ }
+
try {
selection_feature.getEntry ().createFeature (intron_key,
intron_location,
--
GitLab