src/objects/gbproj/gbproj.asn

--- -------------------------------------------------------------------------
--- Definitions for GB project
--- GUI projects are the basic units of data used in Genome Workbench
---
--- -------------------------------------------------------------------------

NCBI-GBProject DEFINITIONS ::=
BEGIN

IMPORTS Annotdesc, Seq-annot     FROM NCBI-Sequence
        Seq-submit               FROM NCBI-Submit
        Seq-entry                FROM NCBI-Seqset
        Seq-id, Seq-loc          FROM NCBI-Seqloc
        Seq-align, Seq-align-set FROM NCBI-Seqalign
        Date, User-object        FROM NCBI-General;

EXPORTS ProjectFolder, ProjectItem, ProjectHistoryItem, ProjectDescr, ProjectAnnot,
        FolderInfo, AbstractProjectItem, LoaderDescriptor, ViewDescriptor;


-- A dummy type used for replacing 'removed' or deprecated optional fields that
-- have not been used and won't be used any more.
DummyObsoleteType ::= CHOICE {
	null NULL
}

--
-- Version 2 project
-- With version two we start a new paradigm
-- The first item in the project *MUST* be a non-optional version stamp,
-- composed as an integer.  This allows us to use a binary ASN.1 fingerprint to
-- determine the version prior to reading a file.
--
GBProject-ver2 ::= SEQUENCE {

    -- the version for this project
    -- for this particular instance, this should always be 2
    -- this data element *MUST* be first
    project-version VisibleString,

    -- next counter for project items
    counter INTEGER DEFAULT 0,

    -- standard descriptors
    descr ProjectDescr,

    -- a set of extra analyses perfromed by the user
    -- each of these may have descriptors
    data ProjectFolder,

    -- a copy of the original plugin message used to generate this project
    -- This is deprecated. DO NOT USE THIS FIELD.
    -- The original spec is: orig-message PluginMessage OPTIONAL.
	  -- It is intended to be removed, but a complete
		-- removal will cause order shift for the rest of 
		-- fields in this choice, and cause deserialization
		-- failure for existing ASN file since this filed is
		-- in the middle of the spec.
    obsolete-orig-message DummyObsoleteType OPTIONAL,

    -- history of things done to this object
    history SET OF ProjectHistoryItem OPTIONAL,

    --name of the plugin that can handle External Data for the project
    data-plugin VisibleString OPTIONAL,

    --optional parameter for the data-plugin
    plugin-param VisibleString OPTIONAL,

    -- arbitrary annotations
    annot SET OF ProjectAnnot OPTIONAL,
    
    -- a set of data sources including data loader and data
    loaders SET OF LoaderDescriptor OPTIONAL,

    --- set of views, associated with project
    views SET OF ViewDescriptor OPTIONAL,
	
    -- set of view-specific settings
    view-settings SET OF User-object OPTIONAL
}


ViewDataLink ::= SEQUENCE {
    --- if both are absent - link goes to project
    --- if both present - fingerprinted object inside project item
    --- if only project-item-id present - link goes to project item
    
    --- project item id
    project-item-id INTEGER OPTIONAL,
    
    --- fingerprint of object to show in view
    fingerprint CHOICE {
        crc32 INTEGER,
        md5   OCTET STRING
    } OPTIONAL,
    
    type VisibleString
}

ViewDescriptor ::= SEQUENCE {
    --- data for view opening
    data CHOICE {
        --- link to retrieve data
        link  ViewDataLink,  
        
        --- virtual project item, if link cannot be created
        item  ProjectItem
    },        
    
    --- plugin name of saved view
    view-plugin     VisibleString,
    
    --- view id
    view-id         INTEGER,
    
    --- optional settings, requered to open view
    view-memento    ViewMemento OPTIONAL
}


ViewMemento ::= SEQUENCE {
    options-id  INTEGER
}


ProjectFolder ::= SEQUENCE {
    info    FolderInfo,
    folders SET OF ProjectFolder    OPTIONAL,
    items   SET OF ProjectItem      OPTIONAL
}


ProjectItem ::= SEQUENCE {
    -- serial number - must be unique in a project (GBProject)
    id INTEGER,

    -- user-defined label
    label VisibleString OPTIONAL,

    -- user-defined descriptors
    descr SET OF Annotdesc OPTIONAL,

    -- the item we represent
    item CHOICE {
        -- for projects that simply import a far-pointer
        id     Seq-id,

        -- for projects that contain something else
        entry  Seq-entry,

        -- annotation only
        annot  Seq-annot,

        -- for submission
        submit Seq-submit,

        -- seq-align and seq-align-set as registered items
        seq-align     Seq-align,
        seq-align-set Seq-align-set,

        -- plugin message
        -- This is deprecated. DO NOT USE THIS FIELD.
        -- The original spec is: plugin PluginMessage.
	      -- It is intended to be removed, but a complete
		    -- removal will cause order shift for the rest of 
		    -- fields in this choice, and cause deserialization
		    -- failure for existing ASN files since this filed is
		    -- in the middle of the spec.
		    obsolete-plugin DummyObsoleteType,

        -- arbitrary object (use with care!)
        other AbstractProjectItem,
        
        -- PubMed ID
        pmid   SET OF INTEGER,

        -- Taxonomy ID
        taxid  SET OF INTEGER
    },

    --name of the plugin that can handle External Data for the project
    data-plugin VisibleString OPTIONAL,

    -- "folder open" state
    disabled    BOOLEAN OPTIONAL
}

AbstractProjectItem ::= SEQUENCE {
    type VisibleString,
    data OCTET STRING
}


ProjectHistoryItem ::= SEQUENCE {
    -- ID of ProjectItem referenced
    id INTEGER,

    -- date of modification
    date Date,

    -- label for this item (terse description)
    label VisibleString,

    -- optional longer description
    comment VisibleString OPTIONAL
}


FolderInfo ::= SEQUENCE {
    title VisibleString,

    -- basic descriptors
    create-date Date,

    -- optional comments
    comment VisibleString OPTIONAL,

    -- "folder open" state
    open    BOOLEAN OPTIONAL,

    -- arbitrary annotations
    annot SET OF Annotdesc OPTIONAL
}


ProjectDescr ::= SEQUENCE {
    -- user-defined title for the workspace
    title VisibleString,

    -- basic (required) descriptors
    create-date Date,
    modified-date Date OPTIONAL,

    -- optional descriptors
    comment VisibleString OPTIONAL
}


ProjectAnnot ::= SEQUENCE {
    create-date Date,
    modified-date Date OPTIONAL,
    annot Annotdesc
}


LoaderDescriptor ::= SEQUENCE {
    -- data loader label 
    label VisibleString,

    -- loader data source type
    loader-type VisibleString,

    -- data, depends on loader type
    data User-object,
    
    -- flag: is this data loader enabled?
    enabled BOOLEAN DEFAULT TRUE,

    -- loader priority used in object manager
    priority INTEGER OPTIONAL
}


END