X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=364bfbe31016f89e5a5bf8ca54affaf36256d4e2;hb=HEAD;hp=f73c01be8ea40c73bb95092ccacebf85b77edec6;hpb=7418f2aca1d88b04abebcce7940006e202c5f19c;p=jalview.git
diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index f73c01b..364bfbe 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,82 +1,491 @@
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+ developed after mapRangeType from
+ http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+
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+ This effectively represents a java.util.MapList
+ object
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+ a region from start to end inclusive
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+ a region from start to end inclusive
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+ 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.
+
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+
+
+ 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.
+
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+ 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).
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+ The sequence whose dataset sequence is to
+ be referenced here
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+ Biotype of the mapping e.g. CdsToPeptide
+
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+ 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).
+
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+ a Mapping entry and an associated protein
+ sequence
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+ internal jalview id for the dnasq for this
+ mapping.
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+ true for gene locus mapping, source=species,
+ version=assembly, accession=chromosome
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+ true for the representative accession for
+ databases where multiple accessions map to the same entry
+ (eg. Uniprot)
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+ dataset sequence id for this sequence. Will be
+ created as union of sequences.
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+ Biotype of the sequence (if known)
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+ height in pixels for the graph if this is a
+ graph-type annotation.
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+ is an autocalculated annotation row
+
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+ is to be shown below the alignment - introduced
+ in Jalview 2.8 for visualizing T-COFFEE alignment scores
+
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+
+ 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.
+
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+ Matrices referred to by this set of sequences.
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+ reference to set where jalview will gather the
+ dataset sequences for all sequences in the set.
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+ Represents matrix data imported to Jalview, and the
+ results of any derived calculations (independent of a particular
+ view
+ on the matrix).
+
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+
+ serialised representation of matrix as one or
+ more sets of comma separated values
+
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+ Comma separated series of longs formed from
+ bitsets defining partitions on the rows/columns of the matrix
+
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+ tree computed for this
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+ Defines a mapping from the local frame to a matrix
+ and its associated data specified by MatrixType
+
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+ mapping from the matrix row and column positions
+ to
+ associated reference frame
+
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+ reference to the matrix type this Map refers to
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