ajseqwrite

Data type AjPSeqout

Holds definition of sequence output.

Attributes

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