| Name | Type | Description |
|---|
| Name | AjPStr | As "Source" for features, usually empty
|
| Type | AjPStr | "P" Protein or "N" Nucleotide
|
| Formatstr | AjPStr | Report format (-rformat)
|
| Fttable | AjPFeattable | Feature table to use (obsolete?)
|
| Ftquery | AjPFeattabOut | Output definition for features
|
| Extension | AjPStr | Output file extension
|
| File | AjPFile | Output file object
|
| Tagnames | AjPList | List of extra tag names (from ACD)
|
| Tagprints | AjPList | List of extra tag printnames (from ACD)
|
| Tagtypes | AjPList | List of extra tag datatypes (from ACD)
|
| Header | AjPStr | Text to add to header with newlines
|
| SubHeader | AjPStr | Text to add to subheader with newlines
|
| Tail | AjPStr | Text to add to tail with newlines
|
| SubTail | AjPStr | Text to add to subtail with newlines
|
| FileNames | AjPList | Names of extra files (see FileTypes)
|
| FileTypes | AjPList | Types of extra files (see FileNames)
|
| Totseqs | ajlong | Total number of sequences processed
|
| Totlength | ajlong | Total length of sequences processed
|
| Precision | ajint | Floating precision for score
|
| Showacc | AjBool | Report accession number
|
| Showdes | AjBool | Report sequence description
|
| Showusa | AjBool | Report USA (-rusa) or only seqname
|
| Showscore | AjBool | Report score (if optional for format)
|
| Showstrand | AjBool | Report nucleotide strand (if optional for format)
|
| Multi | AjBool | if true, assume >1 sequence
|
| Mintags | ajint | Minimum number of tags to report
|
| CountSeq | ajint | Number of sequences reported so far
|
| CountHit | ajint | Number of features reported so far
|
| TotHits | ajint | Number of features found so far
|
| MaxHitAll | ajint | Maximum number of hits to report overall
|
| MaxHitSeq | ajint | Maximum number of hits to report for each sequence
|
| MaxLimit | AjBool | if true, maximum hits reached
|
| Format | AjEnum | Report format (index number)
|
| Padding | char[4] | Padding to alignment boundary
|