diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java index 6279f57efc5f57bb9f8d0b375e2734dae003303b..bfec1da894ca1d501f6e59cf8c971b9984bae9ac 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;