diff --git a/etc/feature_keys_gff b/etc/feature_keys_gff index a5bcc0d5e7c3fdc79ffcb50a4e35fb5f12ce651a..afb9f5642294a91cb248675527928d1c73a10b92 100644 --- a/etc/feature_keys_gff +++ b/etc/feature_keys_gff @@ -14,8 +14,8 @@ gene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ont #CDS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified codon_start description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score results note comment job polypeptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref product molecule_type size organism_name strain topology localization gff_source gff_seqname score mass isoelectric charge source private signal_peptide membrane_structure cytoplasmic_polypeptide_region non_cytoplasmic_polypeptide_region transmembrane_polypeptide_region cytoplasm_location transmembrane non_cytoplasm_location GPI_anchor_cleavage_site comment curation translation pseudogene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private -pseudogenic_exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private -pseudogenic_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score product +pseudogenic_exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score private +pseudogenic_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score product intron ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id isObsolete timelastmodified description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified codon_start description locus stable_id EC_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score three_prime_UTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term Start_range End_range feature_id isObsolete timelastmodified systematic_id note comment private curation diff --git a/etc/versions b/etc/versions index b920a1143ebc3d7491bf5017b550cc39de728008..31b100847539325d3bc50615cd3aca2fdb9a675a 100644 --- a/etc/versions +++ b/etc/versions @@ -1,4 +1,4 @@ -Artemis Release 16.0.6 -ACT Release 13.0.6 +Artemis Release 16.0.7 +ACT Release 13.0.7 DNAPlotter Release 1.11 BamView 1.2.13 \ No newline at end of file diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java index 11284b4b93d9bff5e14ec4085372efc33223bb9f..1c1756fc63724ce0e8e0d99fbea6caa0ddc8f91d 100644 --- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java +++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java @@ -473,27 +473,31 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry { final StringVector values = productQualifier.getValues(); final StringVector tmpNewValues = new StringVector(); - for(int j=0; j<values.size(); j++) + for(String val: values) { - String val = (String)values.get(j); - int ind = 0; - if((ind=val.indexOf(";db_xref="))>-1 && this instanceof EmblDocumentEntry) val = val.substring(0,ind); - + if((ind=val.indexOf(";evidence="))>-1 && this instanceof EmblDocumentEntry) val = val.substring(0,ind); - + if((ind=val.indexOf(";with="))>-1 && this instanceof EmblDocumentEntry) val = val.substring(0,ind); - + + if((ind=val.indexOf("rank="))>-1 && this instanceof EmblDocumentEntry) + { + int ind2 = val.indexOf(";", ind); + if(ind == 0 && ind2 > -1) + val = val.substring(ind2+1); + } + if(val.startsWith("term=")) val = val.substring(5, val.length()); - + if(val.endsWith(";")) val = val.substring(0, val.length()-1); - + tmpNewValues.add(val); } return tmpNewValues; @@ -741,7 +745,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry Enumeration qualifiersenum = qualifierMapProperties.propertyNames(); n = 0; - Vector qualifiersToRemove = new Vector(); + Vector<String> qualifiersToRemove = new Vector<String>(); while(qualifiersenum.hasMoreElements()) { String current_map_name = (String) qualifiersenum.nextElement();