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