From 1d18975c8ab39177e201f3791108472d20f4a269 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 31 Jan 2014 11:24:58 +0000
Subject: [PATCH] use reserved attribute list in
GFF3AttributeBuilder.reserved_a
---
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 14 ++++----------
1 file changed, 4 insertions(+), 10 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 6279f57ef..bfec1da89 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -713,12 +713,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
/**
* Return a String containing the qualifiers of this feature in a form
- * suitable for using as the last field of a GFF line. The codon_start
- * attribute is not included since GFF has a frame field. gff_seqname,
- * gff_source and score aren't included since they have corresponding fields.
+ * suitable for using as the last field of a GFF line.
**/
private String unParseAttributes(final String myId) {
- //final StringBuffer buffer = new StringBuffer();
final QualifierVector qualifiers = getQualifiers();
GFF3AttributeBuilder abuf = new GFF3AttributeBuilder();
prepareProcessors(abuf);
@@ -727,10 +724,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
abuf.ignore(attr);
}
- final String names[] = { "ID", "Name", "Alias", "Parent", "Derives_from",
- "Target", "Gap", "Note", "Dbxref", "Ontology_term", "Start_range",
- "End_range", "Is_circular" };
- final int names_length = names.length;
+ final int names_length = abuf.reserved_a.length;
// add ID attribute
if (myId != null) {
@@ -739,7 +733,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
// build reserved attributes
for (int i = 1; i < names_length; i++) {
- Qualifier this_qualifier = qualifiers.getQualifierByName(names[i]);
+ Qualifier this_qualifier = qualifiers.getQualifierByName(abuf.reserved_a[i]);
if (this_qualifier == null)
continue;
@@ -754,7 +748,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature implements
// skip reserved names
for (int j = 0; j < names_length; j++)
- if (this_qualifier.getName().equals(names[j]))
+ if (this_qualifier.getName().equals(abuf.reserved_a[j]))
lname = true;
if (lname)
continue;
--
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