add gene_synonym and ncRNA_class

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11432 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/feature_keys

@@ -31,7 +31,7 @@ conflict        @citation allele db_xref evidence gene inference label locus_tag
 enhancer        allele citation db_xref evidence gene inference label locus_tag map note partial standard_name usedin
 exon            EC_number allele citation codon codon_start db_xref evidence function gene inference label locus_tag map note number partial product pseudo standard_name transl_except usedin
 gap             @estimated_length
-gene            allele citation db_xref evidence function gene inference label locus_tag map note operon partial phenotype product pseudo standard_name usedin
+gene            allele citation db_xref evidence function gene inference label locus_tag map note operon partial phenotype product pseudo standard_name usedin gene_synonym
 iDNA            allele citation db_xref evidence function gene inference label locus_tag map note number partial standard_name usedin
 intron          allele citation cons_splice db_xref evidence function gene inference label locus_tag map note number partial standard_name usedin
 mRNA            allele citation db_xref evidence exception function gene inference label locus_tag map note operon partial product pseudo standard_name transcript_id usedin
@@ -44,6 +44,7 @@ misc_recomb     allele citation db_xref evidence gene inference label locus_tag
 misc_signal     allele citation db_xref evidence function gene inference label locus_tag map note operon partial phenotype standard_name usedin
 misc_structure  allele citation db_xref evidence function gene inference label locus_tag map note partial standard_name usedin
 modified_base   @mod_base allele citation db_xref evidence frequency gene inference label locus_tag map note usedin
+ncRNA            allele citation db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name usedin ncRNA_class
 old_sequence    @citation allele db_xref evidence gene inference label locus_tag map note partial replace usedin
 operon          @operon allele citation db_xref evidence function inference label map note phenotype pseudo standard_name usedin
 oriT            allele bound_moiety citation db_xref direction evidence gene inference label locus_tag map note rpt_family rpt_type rpt_unit standard_name usedin
@@ -54,7 +55,7 @@ prim_transcript allele citation db_xref evidence function gene inference label l
 primer_bind     PCR_conditions allele citation db_xref evidence gene inference label locus_tag map note partial standard_name usedin
 promoter        allele citation db_xref evidence function gene inference label locus_tag map note operon partial phenotype pseudo standard_name usedin
 protein_bind    @bound_moiety allele citation db_xref evidence function gene inference label locus_tag map note partial standard_name usedin
-rRNA            allele citation db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name usedin
+rRNA            allele citation db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name usedin ncRNA_class
 rep_origin      allele citation db_xref direction evidence gene inference label locus_tag map note partial standard_name usedin
 repeat_region   allele citation db_xref evidence function gene inference insertion_seq label locus_tag map note partial rpt_family rpt_type rpt_unit standard_name transposon usedin
 repeat_unit     allele citation db_xref evidence function gene inference label locus_tag map note partial rpt_family rpt_type rpt_unit usedin
@@ -65,7 +66,7 @@ snRNA           allele citation db_xref evidence function gene inference label l
 snoRNA          allele citation db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name usedin
 source          @organism cell_line cell_type chloroplast chromoplast chromosome citation clone clone_lib country cultivar cyanelle db_xref dev_stage ecotype environmental_sample evidence focus frequency germline haplotype inference insertion_seq isolate isolation_source kinetoplast lab_host label macronuclear map mitochondrion mol_type note organelle plasmid pop_variant proviral rearranged segment sequenced_mol serotype serovar sex specific_host specimen_voucher strain sub_clone sub_species sub_strain tissue_lib tissue_type transgenic transposon usedin variety virion
 stem_loop       allele citation db_xref evidence function gene inference label locus_tag map note operon partial standard_name usedin
-tRNA            allele anticodon citation db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name usedin
+tRNA            allele anticodon citation db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name usedin ncRNA_class
 terminator      allele citation db_xref evidence gene inference label locus_tag map note operon partial standard_name usedin
 transit_peptide allele citation codon codon_start db_xref evidence function gene inference label locus_tag map note partial product pseudo standard_name transl_except usedin
 unsure          allele citation db_xref evidence gene inference label locus_tag map note replace usedin

etc/qualifier_types

@@ -50,6 +50,7 @@ focus            no         none
 frequency        yes        real    0.0  1.0
 function         yes        "text"
 gene             no         "text"
+gene_synonym     no         "text"
 germline         yes        none
 haplotype        no         "text"
 inference        no         "text"
@@ -65,6 +66,10 @@ map              no         "text"
 mod_base         no         modbase
 mol_type         no         "text"
 note             no         "text"
+ncRNA_class      no         list    antisense_RNA autocatalytically_spliced_intron \
+                                    ribozyme hammerhead_ribozyme RNase_P_RNA RNase_MRP_RNA \
+                                    telomerase_RNA guide_RNA rasiRNA scRNA siRNA \
+                                    miRNA piRNA snoRNA snRNA SRP_RNA vault_RNA Y_RNA other
 number           yes        number  1 99999999
 operon           no         "text"
 organell         no         "text"