X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=22b7aac75111e71bb35d2817f5f7ab8ad52bb6c5;hb=1d6ce1bd2d0cf108d6207694e4aa6b845de11049;hp=f73c01be8ea40c73bb95092ccacebf85b77edec6;hpb=7418f2aca1d88b04abebcce7940006e202c5f19c;p=jalview.git
diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index f73c01b..22b7aac 100755
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -1,82 +1,285 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+