From 8b62506da19ac1487ee078481da07dcef8f65f0b Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 1 Nov 2012 16:28:09 +0000
Subject: [PATCH] fix for setting fmin fmax partial so that this is not set for
internal exons
---
.../chado/ChadoTransactionManager.java | 21 +++++++++++++++----
1 file changed, 17 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 784265694..418c67d4d 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -2210,17 +2210,30 @@ public class ChadoTransactionManager
}
else
featureloc.setPhase(null);
-
- if(gffFeature.getQualifierByName("isFminPartial") != null)
+
+ final RangeVector ranges = gffFeature.getLocation().getRanges();
+ boolean firstSeg = true;
+ boolean lastSeg = true;
+ if(ranges.size() > 1) // define if first/last segment
+ {
+ firstSeg = false;
+ lastSeg = false;
+ if(range_new.getStart() == gffFeature.getFirstBase())
+ firstSeg = true;
+ if(range_new.getEnd() == gffFeature.getLastBase())
+ lastSeg = true;
+ }
+
+ if(firstSeg && gffFeature.getQualifierByName("isFminPartial") != null)
featureloc.setFminPartial(true);
else
featureloc.setFminPartial(false);
- if(gffFeature.getQualifierByName("isFmaxPartial") != null)
+ if(lastSeg && gffFeature.getQualifierByName("isFmaxPartial") != null)
featureloc.setFmaxPartial(true);
else
featureloc.setFmaxPartial(false);
-
+
return featureloc;
}
--
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