From d48ae6f29746b720adbbd23c043d832153e72419 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 2 Feb 2010 10:13:43 +0000
Subject: [PATCH] when changing groups of featurelocs check they are not
partial
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13143 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/IBatisDAO.java | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 3c68fc3e5..c62bb08f6 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -878,11 +878,25 @@ public class IBatisDAO extends GmodDAO
FeatureLoc thisFeatureLoc = (FeatureLoc) featureLocs.get(i);
int thisSrcFeatureId =
thisFeatureLoc.getFeatureBySrcFeatureId().getFeatureId();
+
if(srcFeatureId != thisSrcFeatureId)
{
- thisFeatureLoc.setFmin(thisFeatureLoc.getFmin()+diffFmin);
- thisFeatureLoc.setFmax(thisFeatureLoc.getFmax()+diffFmax);
- sqlMap.update("updateFeatureLoc", thisFeatureLoc);
+ // check to see if the featureloc fmin/fmax are marked as partial
+ // if they are then ignore as they are likely to be the end of
+ // a contig
+ boolean changed = false;
+ if(!thisFeatureLoc.isFminPartial())
+ {
+ thisFeatureLoc.setFmin(thisFeatureLoc.getFmin()+diffFmin);
+ changed = true;
+ }
+ if(!thisFeatureLoc.isFmaxPartial())
+ {
+ thisFeatureLoc.setFmax(thisFeatureLoc.getFmax()+diffFmax);
+ changed = true;
+ }
+ if(changed)
+ sqlMap.update("updateFeatureLoc", thisFeatureLoc);
}
}
}
--
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