From 2171719cedb0c2a40af2c83fff332fbb36b6149b Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 29 Mar 2007 08:35:59 +0000
Subject: [PATCH] add autoGeneratePepName()
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5819 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/io/ChadoCanonicalGene.java | 49 ++++++++++++++++++-
1 file changed, 48 insertions(+), 1 deletion(-)
diff --git a/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java b/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java
index 0d800492b..8fe25545f 100644
--- a/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java
+++ b/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java,v 1.20 2007-03-28 09:15:34 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/ChadoCanonicalGene.java,v 1.21 2007-03-29 08:35:59 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -683,6 +683,53 @@ public class ChadoCanonicalGene
return null;
}
+
+ /**
+ * Generate new names for peptide features for this gene model
+ * @param transcript_id
+ * @return
+ */
+ public String autoGeneratePepName(final String transcript_id)
+ {
+ try
+ {
+ int index = transcript_id.lastIndexOf(':');
+ int transcript_number = -1;
+
+ if(index > -1)
+ {
+ try
+ {
+ transcript_number = Integer.parseInt(transcript_id.substring(index+1));
+ }
+ catch(NumberFormatException nfe)
+ {
+ transcript_number = -1;
+ }
+ }
+
+ if(transcript_number < 1)
+ {
+ for(transcript_number = 1; transcript_number <= transcripts.size();
+ transcript_number++)
+ {
+ Feature transcript = (Feature) transcripts.get(transcript_number - 1);
+ if(transcript_id.equals(getQualifier(transcript, "ID")))
+ break;
+ }
+ }
+
+ String name = (String)getGene().getQualifierByName("ID").getValues().get(0);
+
+ return name + ":" + transcript_number + ":pep";
+ }
+ catch(InvalidRelationException e)
+ {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
/**
* Search for the feature with a particular uniquename
* @param name uniquename
--
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