Specify positions and/or regions on the principle dimension of some associated vamsas object
TODO: this is abstract. should provide context to scope the range of ids for each use
Keeping to jaxb-1.0 specification for the moment - this choice should become a substitution group when we use jaxb-2.0 capable bindings
a position within the associated object's coordinate system
a region from start to end, with flag for inclusivity of terminii
when false, a consecutive range like 'start=1, end=2' means the region lying after position 1 and before position 2
contains unassociated trees and a number of analysis sets
Primary Key for vamsas object referencing
objects with modifiable=false will not be modified by a vamsas client update
Properties. Generally, these are mutable so an application should check them each time. This may change depending on the context of the property
Contains a named collection of trees TODO: define way of referencing leaves of global tree for any sequence/alignment object
Primary Key for vamsas object referencing
objects with modifiable=false will not be modified by a vamsas client update
Primary Key for vamsas object referencing
objects with modifiable=false will not be modified by a vamsas client update
Named and typed property string
The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types
provenance contains source of annotation
polymorphism for having collection of single points,
or ordered set of regions with polarity (start.lt.end or end.lt.start)
Note:These are mutable so an application should check them each time.
Primary Key for vamsas object referencing
objects with modifiable=false will not be modified by a vamsas client update
Annotation with the same non-empty group name are grouped together
Specifies a named and typed value used to perform some data transformation.
LATER: experiment with xml validation of property set prototypes for services
Named and typed property string
The type specifies how the property will be parsed. Empty property strings are allowed, and can be used to prototype the input to a document. TODO: specify allowed types
Selects all or part of a collection of vamsas objects as a named input to some transformation process.
Reference Frame for rangeType specfication
Defines the origin and series of operations applied directly to the object that references it.
Who
With which application
Did what
When
additional information
parameter for the action
bioinformatic objects input to action
Primary Key for vamsas object referencing
A collection of sequences, alignments, trees and other things.
a primary or secondary sequence record from which all other sequences may be derived
Primary Key for vamsas object referencing
Primary Key for vamsas object referencing
symbol class for sequence
Annotate over positions and regions of dataset sequences
annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef
Annotate over positions and regions of the alignment
annotation may be associated with a particular sequence lying within the same reference frame as the rangeType's objRef
TODO: hard to distinguish this from the alignment features element. Do we merge them and leave the applications
Primary Key for vamsas object referencing
Annotate over positions and regions of the ungapped sequences in the alignment
TODO: have to remove id rangeSpec or require it to be the same as dataset sequence reference
Primary Key for vamsas object referencing
Dataset Sequence from which this alignment sequence is taken from
typical properties may be alignment score objects
Primary Key for vamsas object referencing
objects with modifiable=false will not be modified by a vamsas client update
Primary Key for vamsas object referencing
per-site symbolic and/or quantitative annotation
SecondaryStructure and display character (from Jalview) have been subsumed into the glyph element
Free text at this position
Discrete symbol - possibly graphically represented
specifies the symbol dictionary for this glyph - eg utf8 (the default), aasecstr_3 or kd_hydrophobicity - the content is not validated so applications must ensure they gracefully deal with invalid entries here
TODO: specify a minimum list of glyph dictionaries to get us started and provide a way for the vamsasClient to validate their content if regexes are specified
Ordered set of float values - an application may treat the values together as a vector with common support for a set of annotation elements - but this is, again, not validated so applications should deal gracefully with varying numbers of dimensions
position with respect to the coordinate frame defined by a rangeType specification
true means the annotation element appears between the specified position and the next
Primary Key for vamsas object referencing
additional typed properties
Data specific to a particular type and version of vamsas application
Data available to just a particular user
Data available to just a specific instance of the application
VAMSAS/Pierre: Is this data volatile ? Application instances may not be accessible after the session has closed - the user may have to be presented with the option of picking up the data in that instance
General data container to attach a typed data object to any vamsas object
true implies data will be decompresses with Zip before presenting to application
Type of arbitrary data - TODO: decide format - use (extended) MIME types ?
Object the arbitrary data is associated with
Primary Key for vamsas object referencing