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. Matrices referred to by this set of sequences. reference to set where jalview will gather the dataset sequences for all sequences in the set. 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