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--$Revision: 63097 $
--  Definitions for CDD's 
--  NCBI Structure Group
--  National Center for Biotechnology Information
--  National Institutes of Health
--  Bethesda, MD 20894 USA
--  October 1999
--  asntool -m cdd.asn -w 100 -o cdd.h
--  asntool -B objcdd -m cdd.asn -G -w 100 -I objseq.h objsset.h -K cdd.h \
--          -M asn.all

-- NCBI Conserved Domain Definition


EXPORTS  Cdd-id, Cdd-id-set, Cdd, Cdd-set, Cdd-tree, Cdd-tree-set, Cdd-pref-nodes, Cdd-Project;

IMPORTS  Date                    FROM NCBI-General
         Pub                     FROM NCBI-Pub
         Biostruc-annot-set      FROM MMDB
         Bioseq                  FROM NCBI-Sequence
         Seq-annot               FROM NCBI-Sequence
         Seq-entry               FROM NCBI-Seqset
         Org-ref                 FROM NCBI-Organism
         Seq-id                  FROM NCBI-Seqloc
         Seq-interval            FROM NCBI-Seqloc
         Seq-loc                 FROM NCBI-Seqloc
         Seq-feat                FROM NCBI-Seqfeat
         Score-set               FROM NCBI-Seqalign
         Cn3d-user-annotations   FROM NCBI-Cn3d
         PssmWithParameters      FROM NCBI-ScoreMat;
-- dealing with lists of preferred tax-nodes 

Cdd-org-ref ::= SEQUENCE {
  reference     Org-ref,
  active        BOOLEAN DEFAULT TRUE,
  parent-tax-id INTEGER OPTIONAL,
  rank          VisibleString OPTIONAL
Cdd-org-ref-set ::= SET OF Cdd-org-ref

Cdd-pref-node-descr ::= CHOICE {
  create-date      Date,
  description      VisibleString

Cdd-pref-node-descr-set ::= SET OF Cdd-pref-node-descr

Cdd-pref-nodes ::= SEQUENCE {
   preferred-nodes Cdd-org-ref-set,
   model-organisms Cdd-org-ref-set OPTIONAL,
   optional-nodes  Cdd-org-ref-set OPTIONAL,
   description     Cdd-pref-node-descr-set OPTIONAL

-- Cdd's should not exist without a unique accession, but alternative id's may
-- be present as well. It is conceivable that a CD which is created as a merged
-- product of two highly redundant CDs will retain the source ids in addition 
-- to its new unique id

Global-id ::= SEQUENCE {
  accession     VisibleString,          -- SMART, Pfam, LOAD or CD accession
  release       VisibleString OPTIONAL, -- to hold CD-Database release number
                                        -- if desired, currently not used
  version       INTEGER       OPTIONAL, -- version 0 is the seed, version
                                        -- numbers increase with update/curate
                                        -- cycles
  database      VisibleString OPTIONAL  -- this is NOT the source!, rather the
}                                       -- database the object resides in
                                        -- currently not in use

Cdd-id ::= CHOICE {
  uid           INTEGER,                -- for synchronization with Entrez
                                        -- holds PSSM-Ids
  gid           Global-id               -- holds accession/version pairs

Cdd-id-set ::= SEQUENCE OF Cdd-id

Cdd-repeat ::= SEQUENCE {               -- record whether the CD contains
                                        -- repeated sequence/structure motifs
  count         INTEGER,                -- number of tandem repeats in the CD
  location      Seq-loc OPTIONAL,       -- location on the representative
  avglen        INTEGER OPTIONAL        -- average repeat length

Cdd-book-ref ::= SEQUENCE {             -- record a link to Entrez Books
  bookname      VisibleString,          -- abbreviated book title
  textelement   ENUMERATED { unassigned(0),   -- type of element 
                             section(1),      -- a section or paragraph
                             figgrp(2),       -- a figure or set of figures
                             table(3),        -- a table
                             chapter(4),      -- a whole chapter
                             biblist(5),      -- a lisf of references
                             box(6),          -- an inserted box
                             glossary(7),     -- glossary
                             appendix(8),     -- appendix
                             other(255) },
  elementid     INTEGER OPTIONAL,       -- numerical address of the text-element
  subelementid  INTEGER OPTIONAL,       -- exact address, used with section
  celementid    VisibleString OPTIONAL, -- address of the text element, if character string
  csubelementid VisibleString OPTIONAL  -- exact address, if character string


-- The description of CDD's refers to the specific set of aligned sequences,
-- the region that is being aligned and the information contained in the
-- alignment. It may contain a lengthy comment
-- describing the function of the domain as well as its origin and all
-- other anecdotal information that can't be pressed into a rigid scheme.
-- Crosslinks to reference papers available in PubMed are possible as well.
-- There can be as many of these as you want in the CDD.

Cdd-descr ::= CHOICE {
  othername     VisibleString,          -- alternative names for the CDD
                                        -- if domain has several common names
  category      VisibleString,          -- intracellular, extracellular, etc.
                                        -- to record spatial and/or temporal
                                        -- expression in free-text format
  comment       VisibleString,          -- this is where descriptions go
  reference     Pub,                    -- a citation describing the domain
  create-date   Date,                   -- Date of first creation/dump
  tax-source    Org-ref,                -- holds the highest common tax node
  source        VisibleString,          -- the database the seeds were created
                                        -- from, e.g. SMART, PFAM, etc..
  status        INTEGER { unassigned(0),
                          finished-ok(1),     -- a public curated CD
                          pending-release(2), -- needs work done, not yet released
                          other-asis(3),      -- imported as-is, immediate release
                          matrix-only(4),     -- CD holds a Psi-Blast PSSM only,
                                              -- does not contain alignment data
                          update-running(5),  -- has been flagged for
                                              -- update (in queue)
                          auto-updated(6),    -- update finished, no
                                              -- work necessary
                          claimed(7),         -- is earmarked for curation
                          curated-complete(8),-- public curated member of a
                                              -- completed family
                          other(255) },       -- for CD production?
  update-date   Date,                         -- Date of last version change
  scrapbook     SEQUENCE OF VisibleString,    -- for storing curation notes
                                              -- those won't make it into public
                                              -- distributions
  source-id     Cdd-id-set,                   -- for linking back to source db
  repeats       Cdd-repeat,                   -- to record repeat counts
  old-root      Cdd-id-set,                   -- to record short-term history
  curation-status INTEGER { unassigned(0),    -- to record curation status
                            prein (1),        -- when CD is checked out from
                            ofc (2),          -- the tracking database, for 
                            iac (3),          -- use within curation software
                            ofv1 (4),
                            iav1 (5),
                            ofv2 (6),
                            iav2 (7),
                            postin (8),
                            other (255) },
  readonly-status INTEGER { unassigned(0),    -- to record read-only status
                            readonly (1),     -- when CD is checked out from
                            readwrite (2),    -- the tracking database, for
                            other (255) },    -- use within curation software
  book-ref      Cdd-book-ref,                 -- links to Entrez/books
  attribution   Pub,                          -- add citations and/or author names
  title         VisibleString                 -- hold short descriptive text

Cdd-descr-set ::= SET OF Cdd-descr

-- the Cdd-tree stores the hierarchy of CDDs. These objects are stored separate
-- from the CDs to allow for fast retrieval and use as an 'index' into CDs
-- all the components in a CD-tree match components in the full-sized CD
-- and should be synchronized

Cdd-tree ::= SEQUENCE {
  name          VisibleString,          -- short name  copied from CD
  id            Cdd-id-set,             -- IDs         copied from CD
  description   Cdd-descr-set OPTIONAL, -- description copied from CD
  parent        Cdd-id     OPTIONAL,    -- CD is the result of a split/merge
  children      Cdd-id-set OPTIONAL,    -- this CD has been split
  siblings      Cdd-id-set OPTIONAL,    -- related CDs (have common hits)
  neighbors     Cdd-id-set OPTIONAL     -- co-occurring CDs (non-overlapping 
                                        -- hits to same sequences)

Cdd-tree-set ::= SEQUENCE OF Cdd-tree

-- Matrix definitions, these are supposed to store PSSMs and corresponding 
-- matrices of relative residue frequencies.
-- the number of columns and rows is listed explicitly, values in columns
-- are stored column by column, i.e. in groups of nrows values for each column

Matrix ::= SEQUENCE {
  ncolumns      INTEGER,
  nrows         INTEGER,
  row-labels    SEQUENCE OF VisibleString OPTIONAL,
  scale-factor  INTEGER,
  columns       SEQUENCE OF INTEGER

-- definition for matrix of pairwise "distances", stored as the upper 
-- triangle of a squared n x n matrix (excluding the diagonal), this is
-- supposed to store pairwise percentages of identical residues, pairwise
-- alignment scores or E-values from pairwise BLAST sequence comparisons

Triangle ::= SEQUENCE {
  nelements     INTEGER,
  scores        Score-set OPTIONAL,

-- Update-align is supposed to contain alignments that still need some work
-- done to fit into the CD-proper alignment. These originate from the
-- CD update process (generated by Blast, for example) or may be created in
-- an editing session to save its state

Update-comment ::= CHOICE {
  comment       VisibleString,          -- free text to describe nature of
                                        -- Update-align
  addthis       Seq-loc,                -- suggestion for inclusion in the CD
                                        -- without corresponding alignment
  replaces      Seq-loc,                -- if one or several alignment rows are
                                        -- to be replaced by the Update-align
  reject-loc    Seq-loc,                -- if used with Reject-id, specify a
                                        -- location on a sequence which should
                                        -- not be used
  reference     Pub                     -- if update alignment imported from
                                        -- citation and for whenever it seems
                                        -- necessary to cite

-- Both fields are optional, as the Update-align may be a Seq-annot without
-- description, or a suggestion to add a sequence without the corresponding
-- alignment

Update-align ::= SEQUENCE {
  description   SEQUENCE OF Update-comment OPTIONAL,  
  seqannot      Seq-annot OPTIONAL,     -- contains the SeqAlign
  type          INTEGER { unassigned(0),

Reject-id ::= SEQUENCE {
  description   SEQUENCE OF Update-comment OPTIONAL,
  ids           SET OF Seq-id

Feature-evidence ::= CHOICE {
  comment       VisibleString,          -- so we can spell out what doesn't
                                        -- fit in any other category
  reference     Pub,                    -- evidence via a literature reference
  bsannot       Biostruc-annot-set,     -- evidence via Biostruc-features, such
                                        -- as structure superpositions 
  seqfeat       Seq-feat,               -- evidence is a Sequence feature found
                                        -- elsewhere
  book-ref      Cdd-book-ref            -- evidence is a book chapter or figure

Align-annot ::= SEQUENCE {
  location      Seq-loc,                -- points to a location in one of the
                                        -- aligned sequences, usually the
                                        -- master/representative
  description   VisibleString OPTIONAL, -- to hold descriptions/names like
                                        -- "Heme binding site" or "catalytic
                                        -- triad" etc., something that should
                                        -- be used for labels in visualization
  evidence      SEQUENCE OF Feature-evidence OPTIONAL,  -- evidence we can
                                                        -- compute with
  type          INTEGER OPTIONAL,       -- for typing annotated features
                                        -- 0 .. no type assigned
                                        -- 1 .. active site
                                        -- 2 .. polypeptide binding site
                                        -- 3 .. nucleic acid binding site
                                        -- 4 .. ion binding site
                                        -- 5 .. chemical binding site
                                        -- 6 .. posttranslational modification site
                                        -- 7 .. structural motif
  aliases       SEQUENCE OF VisibleString OPTIONAL, -- adding more names for indexing
  motif         VisibleString OPTIONAL, -- to validate mapping of sites
  motifuse      INTEGER OPTIONAL        -- 0 for validation,
                                        -- 1 for motif somewhere in seqloc
                                        -- 2 for multiple motifs in seqloc

Align-annot-set ::= SEQUENCE OF Align-annot

-- the Domain-parent records an evolutionary relationship which may not be
-- as simple as a classical parent-child relationship in a typical hierarchy,
-- i.e. where a CD is merely a specific subgroup ("child") of a more general
-- diverse alignment model ("parent"). A CD alignment model may be the result
-- of an ancient fusion event, combining two or more domains into a bigger unit
-- which has subsequently undergone a divergent evolutionary process similar to
-- what may have happened to a single "domain". A CD alignment model may 
-- also reflect the result of a deletion event, where a specific subgroup
-- lacks part of a (set of) domain(s), but where the part present is found to
-- be highly similar to a putative "parent", with some added evidence for
-- an actual deletion, like from the distribution of truncated copies in phylogenetic
-- lineages. Deletion events which affect different parts of a set of
-- duplicated domain architectures may be indistinguishable from actual
-- fission events, which means that we may want to represent the latter as
-- deletions after duplication and do not need a special case for fissions.

Domain-parent ::= SEQUENCE {

  parent-type    INTEGER { classical           (0), -- the classification of parent child relations
                           fusion              (1),
                           deletion            (2),
                           permutation         (3),
                           other               (255) },
  parentid       Cdd-id,                -- identify the section parent by accession
  seqannot       Seq-annot OPTIONAL     -- contains the sequence alignment linking
                                        -- CD alignment models, should align the 
                                        -- masters/representatives of each CD

-- record sequence trees generated by a suitable algorithm.

Sequence-tree ::= SEQUENCE {
  cdAccession    VisibleString OPTIONAL,
  algorithm      Algorithm-type,
  root           SeqTree-node

SeqTree-node ::= SEQUENCE {
  name           VisibleString           OPTIONAL,
  distance       REAL                    OPTIONAL,
  children       CHOICE {
    children SEQUENCE OF SeqTree-node,
    footprint SEQUENCE {
      seqRange   Seq-interval,
      rowId      INTEGER OPTIONAL
  annotation     Node-annotation         OPTIONAL

Algorithm-type ::= SEQUENCE {
  scoring-Scheme    INTEGER { unassigned           (0),
                              percent-id           (1),
                              kimura-corrected     (2),
                              aligned-score        (3),
                              aligned-score-ext    (4),
                              aligned-score-filled (5),
                              blast-footprint      (6),
                              blast-full           (7),
			      hybrid-aligned-score (8),
                              other           (255) },
  clustering-Method INTEGER { unassigned             (0),
                              single-linkage         (1),
                              neighbor-joining       (2),
                              fast-minimum-evolution (3),
                              other                (255) },
  score-Matrix      INTEGER { unassigned (0),
                              blosum45   (1),
                              blosum62   (2),
                              blosum80   (3),
                              pam30      (4),
                              pam70      (5),
                              pam250     (6),
                              other    (255) } OPTIONAL,
  gapOpen           INTEGER OPTIONAL,
  gapExtend         INTEGER OPTIONAL,
  gapScaleFactor    INTEGER OPTIONAL,
  nTerminalExt      INTEGER OPTIONAL,
  cTerminalExt      INTEGER OPTIONAL,
  tree-scope        INTEGER { allDescendants       (0),
		                  selfOnly             (2),
		                  other              (255) } OPTIONAL,
  coloring-scope    INTEGER { allDescendants        (0),
		                  immediateChildrenOnly (1),
		                  other               (255) } OPTIONAL

Node-annotation ::= SEQUENCE {
  presentInChildCD VisibleString OPTIONAL,
  note             VisibleString OPTIONAL

-- the Cdd is the basic ASN.1 object storing an annotated and curated set of
-- alignments (formulated as a set of pairwise master-slave alignments). 
-- The alignment data are contained in Seq-annots, and a special type of
-- object, the Update-align, contains additional alignment data from unfinished
-- editing sessions and update processes. The Biostruc-annot-set holds 
-- structure superposition information for multiple structure-derived rows in
-- the alignment.
-- Version numbers in Global-ids are meant to be updated every time the Cdd is
-- changed in a way that does not require Global-ids to be changed (sequences
-- added in update cycle, annotation changed, alignment errors fixed)

Cdd ::= SEQUENCE {
  name          VisibleString,          -- a short name (can be the accession..)
  id            Cdd-id-set,             -- this CD's Ids
  description   Cdd-descr-set OPTIONAL, -- status, references, etc.
  seqannot      SEQUENCE OF Seq-annot    OPTIONAL,  -- contains the CD alignment
  features      Biostruc-annot-set       OPTIONAL,  -- contains structure
                                                    -- alignment data
                                                    -- or "core" definitions
  sequences     Seq-entry     OPTIONAL, -- store as bioseq-set inside seq-entry
  profile-range Seq-interval  OPTIONAL, -- profile for this region only
                                        -- also stores the Seq-id of the master
  trunc-master  Bioseq        OPTIONAL, -- holds the truncated master, which
                                        -- may be something like a consensus,
                                        -- uses the same sequence coordinate
                                        -- frame as the profile-range
  posfreq       Matrix        OPTIONAL, -- relative residue frequencies
  scoremat      Matrix        OPTIONAL, -- Position dependent score matrix
  distance      Triangle      OPTIONAL, -- pairwise distances for all seqs.
  parent        Cdd-id        OPTIONAL, -- this CD is the result of a split
  children      Cdd-id-set    OPTIONAL, -- this CD has been split, not used
  siblings      Cdd-id-set    OPTIONAL, -- related CDs (common hits), clusters
  neighbors     Cdd-id-set    OPTIONAL, -- co-occurring CDs, not used
  pending       SEQUENCE OF Update-align OPTIONAL,  -- contains alignments from
                                                    -- update or "lower panel"
  rejects       SEQUENCE OF Reject-id    OPTIONAL,  -- SeqIds of rejected CD-
                                                    -- members, ignore in update
  master3d      SET OF Seq-id OPTIONAL, -- record if CD has a 3D representative
  alignannot    Align-annot-set OPTIONAL,           -- alignment annotation
  style-dictionary Cn3d-style-dictionary OPTIONAL,  -- record rendering styles
  user-annotations Cn3d-user-annotations OPTIONAL,  -- user annotations in Cn3D
  ancestors     SEQUENCE OF Domain-parent OPTIONAL, -- list of parents
  scoreparams   PssmWithParameters       OPTIONAL,
  seqtree       Sequence-tree            OPTIONAL

Cdd-set ::= SET OF Cdd

-- Cdd projects store a set of CDs, typically related to each other
-- relationships would be specified using the ancestors fields in the
-- individual CD objects. For use with CD-Tree, a program to visualize
-- curated CD hierarchies and evidence for hierarchical family structures.

Cdd-Viewer-Rect ::= SEQUENCE {
  top           INTEGER,           -- top coordinate
  left          INTEGER,           -- left  coordinate
  width         INTEGER,           -- width 
  height        INTEGER            -- height

Cdd-Viewer ::= SEQUENCE {
  ctrl          INTEGER {                   -- viewer type
                  unassigned          (0),
		  cd-info             (1),
		  align-annot         (2),
		  seq-list            (3),
		  seq-tree            (4),
		  merge-preview       (5),
		  cross-hits          (6),
		  notes               (7),
		  tax-tree            (8),
		  dart                (9),
		  dart-selected-rows (10),
		  other (255)
  rect          Cdd-Viewer-Rect OPTIONAL,  -- viewer rectangle
  accessions    SEQUENCE OF VisibleString  -- list of accessions associated with a viewer

Cdd-Script ::= SEQUENCE {
  type          INTEGER {
                  unassigned (0),
                  user-recorded (1),
		  server-generated (2),
                  other (255)
                } OPTIONAL,
  name          VisibleString OPTIONAL,   -- user assigned name/description
  commands      VisibleString             -- actual script commands

-- cd colors are as:  0000FF for red, 00FF00 for green, FF0000 for blue

Cdd-Project ::= SEQUENCE {
  cds           SEQUENCE OF Cdd ,         -- cds
  cdcolor       SEQUENCE OF INTEGER,      -- colors  
  viewers       SEQUENCE OF Cdd-Viewer,   -- Sequence viewers
  log           VisibleString,            -- log
  scripts       SEQUENCE OF Cdd-Script OPTIONAL,    -- command scripts
  id            Cdd-id-set  OPTIONAL,               -- to assign unique project id
  rids          SEQUENCE OF VisibleString OPTIONAL, -- to store request IDs for batch CD-Searches
  create-date   Date OPTIONAL,
  update-date   Date OPTIONAL,
  project-id    INTEGER OPTIONAL          -- for temporary tracking in the database