ajseqwrite

Data type AjPSeqout

Holds definition of sequence output.

Alias name(s)

Name
AjSSeqout
AjOSeqout

Attributes

Name	Type	Description
Name	AjPStr	Name (ID)
Acc	AjPStr	Accession number (primary only)
Sv	AjPStr	SeqVersion number
Gi	AjPStr	GI NCBI version number
Desc	AjPStr	One-line description
Tax	AjPStr	Main taxonomy (species)
Taxid	AjPStr	Main taxonomy (species) id in NCBI taxonomy
Organelle	AjPStr	Organelle taxonomy
Type	AjPStr	Type N or P
Outputtype	AjPStr	Output sequence known type
Molecule	AjPStr	Molecule type
Class	AjPStr	Class of entry
Division	AjPStr	Database division
Evidence	AjPStr	Experimental evidence (e.g. from UniProt)
Db	AjPStr	Database name from input name
Setdb	AjPStr	Database name from input command line
Setoutdb	AjPStr	Database name from command line
Full	AjPStr	Full name
Date	AjPSeqDate	Dates
Fulldesc	AjPSeqDesc	Dates
Doc	AjPStr	Obsolete - see TextPtr
Usa	AjPStr	USA for re-reading
Ufo	AjPStr	UFO for re-reading
Fttable	AjPFeattable	Feature table
Ftquery	AjPFeattabOut	Feature table output
FtFormat	AjPStr	Feature output format (if not in UFO)
FtFilename	AjPStr	Feature output filename (if not in UFO)
Informatstr	AjPStr	Input format
Formatstr	AjPStr	Output format
EType	AjEnum	unused, obsolete
Format	AjEnum	Output format index
Filename	AjPStr	Output filename (if not in USA)
Directory	AjPStr	Output directory
Entryname	AjPStr	Entry name
Acclist	AjPList	Secondary accessions
Keylist	AjPList	Keyword list
Taxlist	AjPList	Taxonomy list
Genelist	AjPList	Gene list
Reflist	AjPList	References (citations)
Cmtlist	AjPList	Comment block list
Xreflist	AjPList	Database cross reference list
Seq	AjPStr	The sequence
File	AjPFile	Output file
Knownfile	AjPFile	Already open output file (we don't close this one)
Extension	AjPStr	File extension
Savelist	AjPList	Previous sequences saved for later output (e.g. MSF format)
Accuracy	float*	Accuracy values (one per base) from base calling
Data	void*	Format data for reuse, e.g. multiple sequence output
Cleanup	(void*)	Function to write remaining lines on closing
Rev	AjBool	true: to be reverse-complemented
Circular	AjBool	true: circular nucleotide molecule
Single	AjBool	If true, single sequence in each file (-ossingle)
Features	AjBool	If true, save features with sequence or in file
Qualsize	ajuint	Size of Accuracy array
Count	ajint	Number of sequences
Offset	ajint	offset from start

Constructor(s)

Name	Description
ajSeqoutNew	Default constructor

Destructor(s)

Name	Description
ajSeqoutDel	Default destructor

Modifier(s)

Name	Description
ajSeqoutUsa	Resets using a new USA
ajSeqoutClear	Resets ready for reuse.
ajSeqoutOpen	If the file is not yet open, calls seqoutUsaProcess

Cast(s)

Name	Description
ajSeqoutCheckGcg	Calculates the GCG checksum for a sequence set.

Modifier(s)

Name	Description
ajSeqWrite	Master sequence output routine
ajSeqsetWrite	Master sequence set output routine
ajSeqFileNewOut	Opens an output file for sequence writing.

Other related data structure(s)

Name	Description
AjPSeq	Sequences

Attributes

Name	Type	Description
Padding	char[4]	Padding to alignment boundary