ajalign

Data type AjPAlign

Holds definition of feature align output.

Alias name(s)

Name
AjSAlign
AjOAlign

Constructor(s)

Name	Description
ajAlignNew	Default constructor

Destructor(s)

Name	Description
ajAlignDel	Default destructor

Modifier(s)

Name	Description
ajAlignReset	Resets ready for reuse.

Output

Name	Description
ajAlignWrite	Master alignment output routine
ajAlignWriteHeader	Master header output routine
ajAlignWriteTail	Master footer output routine

Cast(s)

Name	Description
ajAlignGetFormat	Returns the format of an alignment

Other related data structure(s)

Name	Description
AjPSeqout	Sequence output
AjPFeatout	Feature output
AjPReport	Report output
AjPFile	Input and output files

Attributes

Name	Type	Description
Type	AjPStr	"P" Protein or "N" Nucleotide
Formatstr	AjPStr	Report format (-aformat qualifier)
File	AjPFile	Output file object
Header	AjPStr	Text to add to header with newlines
SubHeader	AjPStr	Text to add to align subheader with newlines
Tail	AjPStr	Text to add to tail with newlines
SubTail	AjPStr	Text to add to subtail with newlines
Showacc	AjBool	Report accession number if ajTrue
Showdes	AjBool	Report sequence description if ajTrue
Showusa	AjBool	Report full USA (-ausa qualifier) if ajTrue or only seqname if ajFalse
Multi	AjBool	if true, assume >1 alignment
Global	AjBool	if true, show full sequence beyond match
Format	AjEnum	Report format (index number)
Data	AjPList	Alignment specific data - see ajalign.c
Nseqs	ajint	Number of sequences in all alignments
Nmin	ajint	Minimum number of sequences e.g. 2
Nmax	ajint	Maximum number of sequences e.g. 2
Width	ajint	Output width (minimum 10)
IMatrix	AjPMatrix	Integer matrix (see also FMatrix)
FMatrix	AjPMatrixf	Floating point matrix (see also IMatrix)
Matrix	AjPStr	Matrix name
GapPen	AjPStr	Gap penalty (converted to string)
ExtPen	AjPStr	Gap extend penalty (converted to string)
SeqOnly	AjBool	Sequence output only, no head or tail
SeqExternal	AjBool	Sequence is non-local, do not delete
Count	ajint	Use count
RefSeq	ajint	Index of the reference sequences in AlignOData objects of the Data list