X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=schemas%2Fvamsas.xsd;h=80f5d91272c45a6b85aa985963fb7b989bb74946;hb=717959cb5ca21c6183c3588361f43782767a88df;hp=5eb52d18371f1594b9540da227913e17e6c0a269;hpb=dbd740ddfe6329c369196ee6ad440aca23252a4d;p=vamsas.git diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 5eb52d1..80f5d91 100644 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -1,8 +1,9 @@ - Vorba ID - Vamsas Object Request Broker Address ID (name needs to be @@ -25,8 +26,7 @@ Primary Key for vamsas object referencing - - + @@ -56,12 +56,38 @@ - - + + + + node identity and mapping data between tree + representations and vamsas document objects + + + + + + + reference to one or more trees containing + the node being described. + + + + + String uniquely identifying a particular + node in the referenced tree according to the format of + the tree representation that is referenced. + + + + + + + + @@ -70,10 +96,62 @@ Primary Key for vamsas object referencing - - + + + + base type for citing arbitrary links between vamsas objects + + + + + + Optional human readable description of the relationship + + + + + Primary Key for vamsas object referencing + + + + + + List of one or more vamsas object + references + + + + + + + + + + Short name for this node + + + + + Descriptive text for this node + + + + + Direct associations between this node and any vamsas + objects + + + + + + + Primary Key for vamsas object referencing + + + + @@ -211,8 +289,7 @@ - - + Annotation with the same non-empty group name are grouped @@ -266,7 +343,7 @@ - + Reference Frame for rangeType specfication @@ -301,9 +378,9 @@ Did what - + - When + When @@ -337,7 +414,11 @@ - A collection of sequences, alignments, trees and other things. + A collection of sequences, alignments, trees and other things. + TODO: Add a title field and properties for programs that can + present the user with different distinct datasets For the moment, the program + just presents them as a list and perhaps lets the user work out which dataset it + wants based on the alignments that it contains. (Dominik and Jim 7th June 2007) @@ -360,27 +441,29 @@ - - From: Offset to first - position in dataset sequence record that - this database entry maps to To: Offset - to last position in dataset sequence - record that this database entry maps to - Start: Offset to first last position in - database entry that first (or offset) - position in sequence maps to End: Offset - to last position in database entry that - last (offset) position in sequence maps - to - - - - - - - - + + + + the local mapType maps from the parent + sequence coordinate frame to the reference + frame defined by the dbRef element. + The mapped mapType is the mapped range defined + on the dbRef element's reference frame. + Conventionally, the unit attribute defaults to 1, or + will be inferred from the local sequence's + dictionary type and any dictionary type associated + with the database being mapped to. + However, it may be used to avoid ambiguity. + + + + + + + + + @@ -422,6 +505,13 @@ + + + explicitly named cross reference to + other objects in the document. + + @@ -439,6 +529,37 @@ + + + + + A mapping between the specified 'local' and 'mapped' sequence coordinate frames. + The step size between each coordinate frame depends on the sequence + dictionary types, or alternatively specified in the optional unit + attribute on each range element. + + + + + + + + + Object on which the local + range is defined. + + + + + Object on which the mapped + range is defined. + + + + + + + @@ -450,7 +571,7 @@ - + annotation is associated with a particular dataset sequence @@ -485,6 +606,15 @@ graph + + + annotation is associated with + a range on a particular group of alignment + sequences + + + @@ -574,9 +704,7 @@ - - - + @@ -667,20 +795,6 @@ additional typed properties - - - - - - - object to which the mapping is being mapped - - - - - - - @@ -793,42 +907,53 @@ - - - - Offset to first position in dataset sequence record that start - position on 'onto' maps to - - - - - Offset to last position in dataset sequence record that end - position on 'onto' maps to - - - - - Offset to first position in database entry that first (or offset) - position in sequence maps to - - - - - Offset to last position in database entry that last (offset) - position in sequence maps to - - + + + Two sets of ranges defined between objects - usually sequences, indicating which + regions on each are mapped. + + + + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + - - Contains lock information: - locktype:ApplicationHandle - locktype is 'local' or 'full' - A lock is only valid if the ApplicationHandle resolves to a living application in the vamsas session. - A local lock means that the application has locked changes to all local properties on the object. - A full lock means that the application has locked changes to all properties on the object, and any objects that it holds references to. - + Contains lock information: locktype:ApplicationHandle locktype is + 'local' or 'full' A lock is only valid if the ApplicationHandle resolves to a living + application in the vamsas session. A local lock means that the application has + locked changes to all local properties on the object. A full lock means that the + application has locked changes to all properties on the object, and any objects that + it holds references to.