HomoloGene DEFINITIONS ::=
BEGIN

IMPORTS Date FROM NCBI-General
        Seq-loc FROM NCBI-Seqloc
	Seq-align FROM NCBI-Seqalign;


-- HomoloGeneEntry taxid is the tax id of the group node, which can
-- be the same as the Gene tax id in case of singletons

HG-EntrySet ::= SEQUENCE {
	entries		SET OF HG-Entry -- homologene entry
}


HG-Entry ::= SEQUENCE {
	hg-id		INTEGER,
	version		INTEGER OPTIONAL,
	title		VisibleString OPTIONAL,
	caption		VisibleString OPTIONAL,
	taxid		INTEGER OPTIONAL,
	genes		SET OF HG-Gene OPTIONAL,
	cr-date		Date OPTIONAL,
	up-date		Date OPTIONAL,
	distances	SET OF HG-Stats OPTIONAL,
	commentaries	SET OF HG-CommentarySet OPTIONAL,
	warnings	SET OF VisibleString OPTIONAL,
	node		HG-Node OPTIONAL
}


HG-Gene ::= SEQUENCE {
	geneid			INTEGER,
	otherid			INTEGER OPTIONAL,  							-- internal use only!!!!!
	symbol			VisibleString OPTIONAL,
	aliases			SET OF VisibleString OPTIONAL,
	title				VisibleString,
	taxid				INTEGER,	 											--taxid of gene node
	prot-gi			INTEGER OPTIONAL,
	prot-acc		VisibleString OPTIONAL,
	prot-len		INTEGER OPTIONAL,
	nuc-gi			INTEGER OPTIONAL,
	nuc-acc			VisibleString OPTIONAL,
	gene-links	SET OF HG-Link OPTIONAL,
	prot-links	SET OF HG-Link OPTIONAL,
	domains			SET OF HG-Domain OPTIONAL,
	chr     		VisibleString OPTIONAL,
	location		Seq-loc OPTIONAL,        				-- location on the genome
	locus-tag		VisibleString OPTIONAL
}


HG-Stats ::= SEQUENCE {
	gi1		INTEGER,
	gi2		INTEGER,
	nuc-change	REAL,
	nuc-change-jc	REAL,
	prot-change	REAL,
	ka		REAL,
	ks		REAL,
	knr		REAL,
	knc		REAL,
	recip-best	BOOLEAN OPTIONAL
}


HG-Commentary ::= SEQUENCE {
	link			HG-Link,
	description		VisibleString OPTIONAL, -- main description
	caption			VisibleString OPTIONAL, -- extra text
	provider		VisibleString OPTIONAL,
	other-links		SET OF HG-Link OPTIONAL,
	other-commentaries	SET OF HG-Commentary OPTIONAL,
	taxid			INTEGER OPTIONAL,
	geneid			INTEGER OPTIONAL
}

HG-CommentarySet ::= SEQUENCE {
	hg-id		INTEGER OPTIONAL,
	title		VisibleString,
	commentaries	SET OF HG-Commentary
}

HG-CommentaryContainer ::= SET OF HG-CommentarySet

HG-Link ::= SEQUENCE {
	hypertext	VisibleString,
	url		VisibleString OPTIONAL
}

HG-Domain ::= SEQUENCE {
	begin		INTEGER,
	end		INTEGER,
	pssm-id		INTEGER OPTIONAL,	-- entrez uid
	cdd-id		VisibleString OPTIONAL,
	cdd-name	VisibleString OPTIONAL
}

HG-Node ::= SEQUENCE {
	type		ENUMERATED {
				family(0),
				ortholog(1),
				paralog(2),
				leaf(3)
			},
	id		HG-Node-id,
	caption		VisibleString OPTIONAL,
	current-node	BOOLEAN DEFAULT FALSE,
	children	SET OF HG-Node OPTIONAL,
	branch-len	INTEGER OPTIONAL
}

HG-Node-id ::= SEQUENCE {
	id		INTEGER OPTIONAL,
	id-type		ENUMERATED {
				none(0),
				geneid(1),
				hid(2)
			}
}

HG-Alignment ::= SEQUENCE {
	hg-id		INTEGER,
	alignment	Seq-align
}

HG-AlignmentSet ::= SET OF HG-Alignment

END