C.2. Datatype-specific Qualifiers

C.2. Datatype-specific Qualifiers
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C.2.1. Sequence Input

Table C.2. Sequence Reading Qualifiers
ACD datatype	Qualifier	Description	Default value
`sequence`	`-sbegin integer`	Start of the sequence to be used	`0`
	`-send integer`	End of the sequence to be used	`0`
	`-sreverse Y/N`	Reverse (if DNA)	`N`
	`-sask Y/N`	Ask for begin/end/reverse	`N`
	`-snucleotide Y/N`	Sequence is nucleotide	`N`
	`-sprotein Y/N`	Sequence is protein	`N`
	`-slower Y/N`	Make lower case	`N`
	`-supper Y/N`	Make upper case	`N`
	`-sformat string`	Input sequence format	`""`
	`-sdbname string`	Database name	`""`
	`-sid string`	Entryname	`""`
	`-ufo string`	UFO features	`""`
	`-fformat string`	Features format	`""`
	`-fopenfile string`	Features file name	`""`
`seqall`	`-sbegin integer`	Start of each sequence to be used	`0`
	`-send integer`	End of each sequence to be used	`0`
	`-sreverse Y/N`	Reverse (if DNA)	`N`
	`-sask Y/N`	Ask for begin/end/reverse	`N`
	`-snucleotide Y/N`	Sequence is nucleotide	`N`
	`-sprotein Y/N`	Sequence is protein	`N`
	`-slower Y/N`	Make lower case	`N`
	`-supper Y/N`	Make upper case	`N`
	`-sformat string`	Input sequence format	`""`
	`-sdbname string`	Database name	`""`
	`-sid string`	Entryname	`""`
	`-ufo string`	UFO features	`""`
	`-fformat string`	Features format	`""`
	`-fopenfile string`	Features file name	`""`
`seqset`	`-sbegin integer`	Start of each sequence to be used	`0`
	`-send integer`	End of each sequence to be used	`0`
	`-sreverse Y/N`	Reverse (if DNA)	`N`
	`-sask Y/N`	Ask for begin/end/reverse	`N`
	`-snucleotide Y/N`	Sequence is nucleotide	`N`
	`-sprotein Y/N`	Sequence is protein	`N`
	`-slower Y/N`	Make lower case	`N`
	`-supper Y/N`	Make upper case	`N`
	`-sformat string`	Input sequence format	`""`
	`-sdbname string`	Database name	`""`
	`-sid string`	Entryname	`""`
	`-ufo string`	UFO features	`""`
	`-fformat string`	Features format	`""`
	`-fopenfile string`	Features file name	`""`
`seqsetall`	`-sbegin integer`	Start of each sequence to be used	`0`
	`-send integer`	End of each sequence to be used	`0`
	`-sreverse Y/N`	Reverse (if DNA)	`N`
	`-sask Y/N`	Ask for begin/end/reverse	`N`
	`-snucleotide Y/N`	Sequence is nucleotide	`N`
	`-sprotein Y/N`	Sequence is protein	`N`
	`-slower Y/N`	Make lower case	`N`
	`-supper Y/N`	Make upper case	`N`
	`-sformat string`	Input sequence format	`""`
	`-sdbname string`	Database name	`""`
	`-sid string`	Entryname	`""`
	`-ufo string`	UFO features	`""`
	`-fformat string`	Features format	`""`
	`-fopenfile string`	Features file name	`""`

C.2.2. Sequence Output

Table C.3. Sequence Writing Qualifiers.
ACD datatype	Qualifier	Description	Default value
`seqout`	`-osformat string`	Output seq format	`""`
	`-osextension string`	File name extension	`""`
	`-osname string`	Base file name	`""`
	`-osdirectory string`	Output directory	`""`
	`-osdbname string`	Database name to add	`""`
	`-ossingle Y/N`	Separate file for each entry	`N`
	`-oufo string`	UFO features	`""`
	`-offormat string`	Features format	`""`
	`-ofname string`	Features file name	`""`
	`-ofdirectory string`	Output directory	`""`
`seqoutall`	`-osformat string`	Output seq format	`""`
	`-osextension string`	File name extension	`""`
	`-osname string`	Base file name	`""`
	`-osdirectory string`	Output directory	`""`
	`-osdbname string`	Database name to add	`""`
	`-ossingle Y/N`	Separate file for each entry	`N`
	`-oufo string`	UFO features	`""`
	`-offormat string`	Features format	`""`
	`-ofname string`	Features file name	`""`
	`-ofdirectory string`	Output directory	`""`
`seqoutset`	`-osformat string`	Output seq format	`""`
	`-osextension string`	File name extension	`""`
	`-osname string`	Base file name	`""`
	`-osdirectory string`	Output directory	`""`
	`-osdbname string`	Database name to add	`""`
	`-ossingle Y/N`	Separate file for each entry	`N`
	`-oufo string`	UFO features	`""`
	`-offormat string`	Features format	`""`
	`-ofname string`	Features file name	`""`
	`-ofdirectory string`	Output directory	`""`

C.2.3. Features

Table C.4. Feature Qualifiers
ACD datatype	Qualifier	Description	Default value
`features`	`-fformat string`	Features format	`""`
	`-fopenfile string`	Features file name	`""`
	`-fask Y/N`	Prompt for begin/end/reverse	`N`
	`-fbegin integer`	Start of the features to be used	`0`
	`-fend integer`	End of the features to be used	`0`
	`-freverse Y/N`	Reverse (if DNA)	`N`

C.2.4. Alignments

Table C.5. Alignment qualifiers
ACD datatype	Qualifier	Description	Default value
Data type	Qualifier definition	Description
`align`	`-aformat string`	Alignment format	`""`
	`-aextension string`	File name extension	`""`
	`-adirectory string`	Output directory	`""`
	`-aname string`	Base file name	`""`
	`-awidth integer`	Alignment width	`0`
	`-aaccshow Y/N`	Show accession number in the header	`N`
	`-adesshow Y/N`	Show description in the header	`N`
	`-ausashow Y/N`	Show the full USA in the alignment	`N`
	`-aglobal Y/N`	Show the full sequence in alignment	`N`

C.2.5. Patterns

Table C.6. Pattern qualifiers
ACD datatype	Qualifier	Description	Default value
`pattern`	`-pformat string`	File format	`""`
	`-pmismatch integer`	Pattern mismatch	`""`
	`-pname string`	Pattern base name	`""`
`regexp`	`-pformat string`	File format	`""`
	`-pname string`	Pattern base name	`""`

C.2.6. Outputs

Table C.7. Output qualifiers.
ACD datatype	Qualifier	Description	Default value
`align`	`-aformat string`	Alignment format	`""`
	`-aextension string`	File name extension	`""`
	`-adirectory string`	Output directory	`""`
	`-aname string`	Base file name	`""`
	`-awidth integer`	Alignment width	`0`
	`-aaccshow Y/N`	Show accession number in the header	`N`
	`-adesshow Y/N`	Show description in the header	`N`
	`-ausashow Y/N`	Show the full USA in the alignment	`N`
	`-aglobal Y/N`	Show the full sequence in alignment	`N`
`featout`	`-offormat string`	Output feature format	`""`
	`-ofopenfile string`	Features file name	`""`
	`-ofextension string`	File name extension	`""`
	`-ofdirectory string`	Output directory	`""`
	`-ofname string`	Base file name	`""`
	`-ofsingle Y/N`	Separate file for each entry	`N`
`outcodon`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outdata`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outdiscrete`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outfile`	`-odirectory string`	Output directory	`""`
`outfileall`	`-odirectory string`	Output directory	`""`
`outfreq`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outmatrix`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outmatrixf`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outproperties`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outscop`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`outtree`	`-odirectory string`	Output directory	`""`
	`-oformat string`	Output format specific to this data type	`""`
`report`	`-rformat string`	Report format	`""`
	`-rname string`	Base file name	`""`
	`-rextension string`	File name extension	`""`
	`-rdirectory string`	Output directory	`""`
	`-raccshow Y/N`	Show accession number in the report	`N`
	`-rdesshow Y/N`	Show description in the report	`N`
	`-rscoreshow Y/N`	Show the score in the report	`Y`
	`-rusashow Y/N`	Show the full USA in the report	`N`
	`-rmaxall integer`	Maximum total hits to report	`0`
	`-rmaxseq integer`	Maximum total hits to report for any one sequence	`0`
`seqout`	`-osformat string`	Output seq format	`""`
	`-osextension string`	File name extension	`""`
	`-osname string`	Base file name	`""`
	`-osdirectory string`	Output directory	`""`
	`-osdbname string`	Database name to add	`""`
	`-ossingle Y/N`	Separate file for each entry	`N`
	`-oufo string`	UFO features	`""`
	`-offormat string`	Features format	`""`
	`-ofname string`	Features file name	`""`
	`-ofdirectory string`	Output directory	`""`
`seqoutall`	`-osformat string`	Output seq format	`""`
	`-osextension string`	File name extension	`""`
	`-osname string`	Base file name	`""`
	`-osdirectory string`	Output directory	`""`
	`-osdbname string`	Database name to add	`""`
	`-ossingle Y/N`	Separate file for each entry	`N`
	`-oufo string`	UFO features	`""`
	`-offormat string`	Features format	`""`
	`-ofname string`	Features file name	`""`
	`-ofdirectory string`	Output directory	`""`
`seqoutset`	`-osformat string`	Output seq format	`""`
	`-osextension string`	File name extension	`""`
	`-osname string`	Base file name	`""`
	`-osdirectory string`	Output directory	`""`
	`-osdbname string`	Database name to add	`""`
	`-ossingle Y/N`	Separate file for each entry	`N`
	`-oufo string`	UFO features	`""`
	`-offormat string`	Features format	`""`
	`-ofname string`	Features file name	`""`
	`-ofdirectory string`	Output directory	`""`

C.2.7. Reports

Table C.8. Report Qualifiers
ACD datatype	Qualifier	Description	Default value
`report`	`-rformat string`	Report format	`""`
	`-rname string`	Base file name	`""`
	`-rextension string`	File name extension	`""`
	`-rdirectory string`	Output directory	`""`
	`-raccshow Y/N`	Show accession number in the report	`N`
	`-rdesshow Y/N`	Show description in the report	`N`
	`-rscoreshow Y/N`	Show the score in the report	`Y`
	`-rstrandshow Y/N`	Show the nucleotide strand in the report	`N`
	`-rusashow Y/N`	Show the full USA in the report	`N`
	`-rmaxall integer`	Maximum total hits to report	`0`
	`-rmaxseq integer`	Maximum total hits to report for any one sequence	`0`

C.2.8. Graphics

Table C.9. Graph qualifiers.
ACD datatype	Qualifier	Description	Default value
`graph`	`-gprompt Y/N`	Graph prompting	`N`
	`-gdesc string`	Graph description	`""`
	`-gtitle string`	Graph title	`""`
	`-gsubtitle string`	Graph subtitle	`""`
	`-gxtitle string`	Graph x axis title	`""`
	`-gytitle string`	Graph y axis title	`""`
	`-goutfile string`	Output file for non interactive displays	`""`
	`-gdirectory string`	Output directory	`""`
`xygraph`	`-gprompt Y/N`	Graph prompting	`N`
	`-gdesc string`	Graph description	`""`
	`-gtitle string`	Graph title	`""`
	`-gsubtitle string`	Graph subtitle	`""`
	`-gxtitle string`	Graph x axis title	`""`
	`-gytitle string`	Graph y axis title	`""`
	`-goutfile string`	Output file for non interactive displays	`""`
	`-gdirectory string`	Output directory	`""`

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