X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=333a4e4460327a327143b1d8308ce552c70e4178;hb=b4f40b3f92e17f4373ecf047b393f579bc88164d;hp=847c9034bcacb5236d628de4468ba3e0c12569da;hpb=45964a5011035526f997fb39bfc58dec53ffbcec;p=jalview.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 847c903..333a4e4 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,5 +1,28 @@ + + @@ -7,59 +30,256 @@ - + + + + developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes + + + This effectively represents a java.util.MapList object + + + + + + a region from start to end inclusive + + + + + + + + + a region from start to end inclusive + + + + + + + + + + number of dictionary symbol widths involved in each + mapped position on this sequence (for example, 3 for a dna sequence exon + region that is being mapped to a protein sequence). This is optional, + since the unit can be usually be inferred from the dictionary type of + each sequence involved in the mapping. + + + + + number of dictionary symbol widths involved in each + mapped position on this sequence (for example, 3 for a dna sequence exon + region that is being mapped to a protein sequence). This is optional, + since the unit can be usually be inferred from the dictionary type of + each sequence involved in the mapping. + + + + + + + + Represent the jalview.datamodel.Mapping object - it also provides + a way of storing sequences that are mapped 'to' without adding them + to the sequence set (which will mean they are then added to the alignment too). + + + + + + + + + + + + The sequence whose dataset sequence is to be referenced here + + + + + + + + + Biotype of the mapping e.g. CdsToPeptide + + + + + + + - + - - - - - - - - - - - - - + + + specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment. + Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide). + + + + + - + - - - - - - - - - + + + + a Mapping entry and an associated protein sequence + + - - - - - - - - - + + + + internal jalview id for the dnasq for this mapping. + + + + + + + + + + + + + + + + + + + + + + + + + true for gene locus mapping, source=species, version=assembly, accession=chromosome + + + + + + + true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot) + + + + + + + + + + dataset sequence id for this sequence. Will be created as union of sequences. + + + + + + + Biotype of the sequence (if known) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + height in pixels for the graph if this is a graph-type annotation. + + + + + + + + + + + is an autocalculated annotation row + + + is to be shown below the alignment - introduced in Jalview 2.8 for visualizing T-COFFEE alignment scores + + Optional string identifier used to group sets of annotation produced by a particular calculation. Values are opaque strings but have semantic meaning to Jalview's renderer, data importer and calculation system. + + + + + + + + + + + + + reference to set where jalview will gather the dataset sequences for all sequences in the set. + + +