X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=364bfbe31016f89e5a5bf8ca54affaf36256d4e2;hb=HEAD;hp=22b7aac75111e71bb35d2817f5f7ab8ad52bb6c5;hpb=3ee6d0992179d26e9feffcea304c5e6149a5965d;p=jalview.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 22b7aac..364bfbe 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -23,58 +23,83 @@ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview Note this also generates code for included schemas --> - + - - + + - - developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes + + developed after mapRangeType from + http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes - This effectively represents a java.util.MapList object + This effectively represents a java.util.MapList + object - + - a region from start to end inclusive + a region from start to end inclusive + - - + + - - + + - 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. + - + - 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. + @@ -82,69 +107,94 @@ - 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). + 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 + 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). + 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 + a Mapping entry and an associated protein + sequence - + - internal jalview id for the dnasq for this mapping. + internal jalview id for the dnasq for this + mapping. - + - + @@ -153,21 +203,52 @@ - + - - - - - + + + + + + + + + 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. + + + + - dataset sequence id for this sequence. Will be created as union of sequences. + Biotype of the sequence (if known) @@ -190,15 +271,16 @@ - - - - - + + - - + + - - height in pixels for the graph if this is a graph-type annotation. + + + 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. + + + 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. + + - + - - - + + + - - + + - + + + + Matrices referred to by this set of sequences. + + + - - + + - reference to set where jalview will gather the dataset sequences for all sequences in the set. + reference to set where jalview will gather the + dataset sequences for all sequences in the set. @@ -259,27 +379,113 @@ - - + + - + - + - - + + - - + + + + + + + + + Represents matrix data imported to Jalview, and the + results of any derived calculations (independent of a particular + view + on the matrix). + + + + + + serialised representation of matrix as one or + more sets of comma separated values + + + + + + Comma separated series of longs formed from + bitsets defining partitions on the rows/columns of the matrix + + + + + + tree computed for this + + + + + + + + + + + + + + + + Defines a mapping from the local frame to a matrix + and its associated data specified by MatrixType + + + + + + + mapping from the matrix row and column positions + to + associated reference frame + + + - - + + + + + reference to the matrix type this Map refers to + + + + + + + + + +