X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=65a1307ea4ee955ddaed2da58a5121728920bf42;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=9ba791979f9f0c818436b36df7ec736741f6e680;hpb=855f7a4bb3e8d5fcfa9059df64262fc73f0164be;p=jalview.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 9ba7919..65a1307 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,4 +1,22 @@ + @@ -7,52 +25,230 @@ - + + + + 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 + + + + + + + + + + + - + - - - - - - - - - - - - - + + + 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. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + dataset sequence id for this sequence. Will be created as union of sequences. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + +