From 46978828b4b9d0dabeec8f35e2c5f8831ea9f6b1 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 19 Aug 2013 16:20:18 +0100
Subject: [PATCH] add predicate to check partial settings
---
uk/ac/sanger/artemis/io/ValidateFeature.java | 23 ++++++++++++++------
1 file changed, 16 insertions(+), 7 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/ValidateFeature.java b/uk/ac/sanger/artemis/io/ValidateFeature.java
index 027893ec3..eb3551cdf 100644
--- a/uk/ac/sanger/artemis/io/ValidateFeature.java
+++ b/uk/ac/sanger/artemis/io/ValidateFeature.java
@@ -133,6 +133,7 @@ public class ValidateFeature
showFeatureList(STRAND_PREDICATE, "Gene Strand Errors", grp, sel, gotoSrc, plotGrp);
showFeatureList(BOUNDARY_PREDICATE, "Gene Boundary Errors", grp, sel, gotoSrc, plotGrp);
showFeatureList(COMPLETE_GENE_MODEL_PREDICATE, "Incomplete Gene Model", grp, sel, gotoSrc, plotGrp);
+ showFeatureList(PARTIAL_PREDICATE, "Partial Settings", grp, sel, gotoSrc, plotGrp);
}
showFeatureList(INTERNAL_STOP, "Internal Stop Codons", grp, sel, gotoSrc, plotGrp);
@@ -212,15 +213,11 @@ public class ValidateFeature
report.put("Gene features found on different strand", Level.FATAL);
}
- if(!isPartialConsistent(gffFeature, "Start_range"))
+ if(!isPartialConsistent(gffFeature, "Start_range") ||
+ !isPartialConsistent(gffFeature, "End_range"))
{
pass = false;
- report.put("Partial attribute 'Start_range' not consistent", Level.FATAL);
- }
- if(!isPartialConsistent(gffFeature, "End_range"))
- {
- pass = false;
- report.put("Partial attribute 'End_range' not consistent", Level.FATAL);
+ report.put("Partial settings not consistent", Level.FATAL);
}
}
@@ -547,6 +544,7 @@ public class ValidateFeature
return true;
}
+
/**
* The phase is REQUIRED for all CDS features.
* @param gffFeature
@@ -903,6 +901,17 @@ public class ValidateFeature
}
};
+ private static FeaturePredicate PARTIAL_PREDICATE = new FeaturePredicate()
+ {
+ public boolean testPredicate(uk.ac.sanger.artemis.Feature feature)
+ {
+ if( isPartialConsistent((GFFStreamFeature) feature.getEmblFeature(), "Start_range") &&
+ isPartialConsistent((GFFStreamFeature) feature.getEmblFeature(), "End_range") )
+ return false;
+ return true;
+ }
+ };
+
private FeaturePredicate INTERNAL_STOP = new FeaturePredicate()
{
public boolean testPredicate(uk.ac.sanger.artemis.Feature feature)
--
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