—
—
Hide Show 142 lines of Pod
@ISA
=
qw(Bio::Tools::Run::PiseApplication)
;
Hide Show 14 lines of Pod
sub
new {
my
(
$class
,
$location
,
$email
,
@params
) =
@_
;
my
$self
=
$class
->SUPER::new(
$location
,
$email
);
$self
->{COMMAND} =
"lindna"
;
$self
->{VERSION} =
"5.a"
;
$self
->{TITLE} =
"LINDNA"
;
$self
->{DESCRIPTION} =
"Draws linear maps of DNA constructs (EMBOSS)"
;
$self
->{OPT_EMAIL} = 0;
$self
->{CATEGORIES} = [
"display"
,
];
$self
->{_INTERFACE_STANDOUT} =
undef
;
$self
->{_STANDOUT_FILE} =
undef
;
$self
->{TOP_PARAMETERS} = [
"lindna"
,
"init"
,
"graphout"
,
"inputfile"
,
"ruler"
,
"blocktype"
,
"intersymbol"
,
"intercolour"
,
"interticks"
,
"gapsize"
,
"ticklines"
,
"textheight"
,
"textlength"
,
"margin"
,
"tickheight"
,
"blockheight"
,
"rangeheight"
,
"gapgroup"
,
"postext"
,
"auto"
,
"psouput"
,
"psresults"
,
"metaresults"
,
"dataresults"
,
"pngresults"
,
];
$self
->{PARAMETERS_ORDER} = [
"lindna"
,
"init"
,
"graphout"
,
"inputfile"
,
"ruler"
,
"blocktype"
,
"intersymbol"
,
"intercolour"
,
"interticks"
,
"gapsize"
,
"ticklines"
,
"textheight"
,
"textlength"
,
"margin"
,
"tickheight"
,
"blockheight"
,
"rangeheight"
,
"gapgroup"
,
"postext"
,
"auto"
,
"psouput"
,
"psresults"
,
"metaresults"
,
"dataresults"
,
"pngresults"
,
];
$self
->{TYPE} = {
"lindna"
=>
'String'
,
"init"
=>
'String'
,
"graphout"
=>
'Excl'
,
"inputfile"
=>
'InFile'
,
"ruler"
=>
'Switch'
,
"blocktype"
=>
'Excl'
,
"intersymbol"
=>
'Excl'
,
"intercolour"
=>
'Integer'
,
"interticks"
=>
'Switch'
,
"gapsize"
=>
'Integer'
,
"ticklines"
=>
'Switch'
,
"textheight"
=>
'Float'
,
"textlength"
=>
'Float'
,
"margin"
=>
'Float'
,
"tickheight"
=>
'Float'
,
"blockheight"
=>
'Float'
,
"rangeheight"
=>
'Float'
,
"gapgroup"
=>
'Float'
,
"postext"
=>
'Float'
,
"auto"
=>
'String'
,
"psouput"
=>
'String'
,
"psresults"
=>
'Results'
,
"metaresults"
=>
'Results'
,
"dataresults"
=>
'Results'
,
"pngresults"
=>
'Results'
,
};
$self
->{FORMAT} = {
"init"
=> {
"perl"
=>
' "" '
,
},
"graphout"
=> {
"perl"
=>
'($value)? " -graphout=$value" : ""'
,
},
"inputfile"
=> {
"perl"
=>
'($value && $value ne $vdef)? " -inputfile=$value" : ""'
,
},
"ruler"
=> {
"perl"
=>
'($value)? "" : " -noruler"'
,
},
"blocktype"
=> {
"perl"
=>
'($value && $value ne $vdef)? " -blocktype=$value" : ""'
,
},
"intersymbol"
=> {
"perl"
=>
'($value && $value ne $vdef)? " -intersymbol=$value" : ""'
,
},
"intercolour"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -intercolour=$value" : ""'
,
},
"interticks"
=> {
"perl"
=>
'($value)? " -interticks" : ""'
,
},
"gapsize"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -gapsize=$value" : ""'
,
},
"ticklines"
=> {
"perl"
=>
'($value)? " -ticklines" : ""'
,
},
"textheight"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -textheight=$value" : ""'
,
},
"textlength"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -textlength=$value" : ""'
,
},
"margin"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -margin=$value" : ""'
,
},
"tickheight"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -tickheight=$value" : ""'
,
},
"blockheight"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -blockheight=$value" : ""'
,
},
"rangeheight"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -rangeheight=$value" : ""'
,
},
"gapgroup"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -gapgroup=$value" : ""'
,
},
"postext"
=> {
"perl"
=>
'(defined $value && $value != $vdef)? " -postext=$value" : ""'
,
},
"auto"
=> {
"perl"
=>
'" -auto -stdout"'
,
},
"psouput"
=> {
"perl"
=>
'" -goutfile=lindna"'
,
},
"psresults"
=> {
},
"metaresults"
=> {
},
"dataresults"
=> {
},
"pngresults"
=> {
},
"lindna"
=> {
"perl"
=>
'"lindna"'
,
}
};
$self
->{FILENAMES} = {
"psresults"
=>
'*.ps'
,
"metaresults"
=>
'*.meta'
,
"dataresults"
=>
'*.dat'
,
"pngresults"
=>
'*.png *.2 *.3'
,
};
$self
->{SEQFMT} = {
};
$self
->{GROUP} = {
"init"
=> -10,
"graphout"
=> 1,
"inputfile"
=> 2,
"ruler"
=> 3,
"blocktype"
=> 4,
"intersymbol"
=> 5,
"intercolour"
=> 6,
"interticks"
=> 7,
"gapsize"
=> 8,
"ticklines"
=> 9,
"textheight"
=> 10,
"textlength"
=> 11,
"margin"
=> 12,
"tickheight"
=> 13,
"blockheight"
=> 14,
"rangeheight"
=> 15,
"gapgroup"
=> 16,
"postext"
=> 17,
"auto"
=> 18,
"psouput"
=> 100,
"lindna"
=> 0
};
$self
->{BY_GROUP_PARAMETERS} = [
"init"
,
"pngresults"
,
"lindna"
,
"metaresults"
,
"psresults"
,
"dataresults"
,
"graphout"
,
"inputfile"
,
"ruler"
,
"blocktype"
,
"intersymbol"
,
"intercolour"
,
"interticks"
,
"gapsize"
,
"ticklines"
,
"textheight"
,
"textlength"
,
"margin"
,
"tickheight"
,
"blockheight"
,
"rangeheight"
,
"gapgroup"
,
"postext"
,
"auto"
,
"psouput"
,
];
$self
->{SIZE} = {
};
$self
->{ISHIDDEN} = {
"init"
=> 1,
"graphout"
=> 0,
"inputfile"
=> 0,
"ruler"
=> 0,
"blocktype"
=> 0,
"intersymbol"
=> 0,
"intercolour"
=> 0,
"interticks"
=> 0,
"gapsize"
=> 0,
"ticklines"
=> 0,
"textheight"
=> 0,
"textlength"
=> 0,
"margin"
=> 0,
"tickheight"
=> 0,
"blockheight"
=> 0,
"rangeheight"
=> 0,
"gapgroup"
=> 0,
"postext"
=> 0,
"auto"
=> 1,
"psouput"
=> 1,
"psresults"
=> 0,
"metaresults"
=> 0,
"dataresults"
=> 0,
"pngresults"
=> 0,
"lindna"
=> 1
};
$self
->{ISCOMMAND} = {
"init"
=> 0,
"graphout"
=> 0,
"inputfile"
=> 0,
"ruler"
=> 0,
"blocktype"
=> 0,
"intersymbol"
=> 0,
"intercolour"
=> 0,
"interticks"
=> 0,
"gapsize"
=> 0,
"ticklines"
=> 0,
"textheight"
=> 0,
"textlength"
=> 0,
"margin"
=> 0,
"tickheight"
=> 0,
"blockheight"
=> 0,
"rangeheight"
=> 0,
"gapgroup"
=> 0,
"postext"
=> 0,
"auto"
=> 0,
"psouput"
=> 0,
"psresults"
=> 0,
"metaresults"
=> 0,
"dataresults"
=> 0,
"pngresults"
=> 0,
};
$self
->{ISMANDATORY} = {
"init"
=> 0,
"graphout"
=> 0,
"inputfile"
=> 0,
"ruler"
=> 0,
"blocktype"
=> 0,
"intersymbol"
=> 0,
"intercolour"
=> 0,
"interticks"
=> 0,
"gapsize"
=> 0,
"ticklines"
=> 0,
"textheight"
=> 0,
"textlength"
=> 0,
"margin"
=> 0,
"tickheight"
=> 0,
"blockheight"
=> 0,
"rangeheight"
=> 0,
"gapgroup"
=> 0,
"postext"
=> 0,
"auto"
=> 0,
"psouput"
=> 0,
"psresults"
=> 0,
"metaresults"
=> 0,
"dataresults"
=> 0,
"pngresults"
=> 0,
};
$self
->{PROMPT} = {
"init"
=>
""
,
"graphout"
=>
"graphout [device to be displayed on] (-graphout)"
,
"inputfile"
=>
"input file containing mapping data (-inputfile)"
,
"ruler"
=>
"do you want a ruler (-ruler)"
,
"blocktype"
=>
"type of blocks (enter Open, Filled, or Outline) (-blocktype)"
,
"intersymbol"
=>
"type of junctions between blocks (-intersymbol)"
,
"intercolour"
=>
"colour of junctions between blocks (enter a colour number) (-intercolour)"
,
"interticks"
=>
"do you want horizontal junctions between ticks (-interticks)"
,
"gapsize"
=>
"interval between ticks in the ruler (enter an integer) (-gapsize)"
,
"ticklines"
=>
"do you want vertical lines at the ruler's ticks (-ticklines)"
,
"textheight"
=>
"height of text (enter a number to multiply the default height) (-textheight)"
,
"textlength"
=>
"length of text (enter a number to multiply the default length) (-textlength)"
,
"margin"
=>
"width of left margin (enter a number to multiply the default width) (-margin)"
,
"tickheight"
=>
"height of ticks (enter a number to multiply the default height) (-tickheight)"
,
"blockheight"
=>
"height of blocks (enter a number to multiply the default height) (-blockheight)"
,
"rangeheight"
=>
"height of range ends (enter a number to multiply the default height) (-rangeheight)"
,
"gapgroup"
=>
"space between groups (enter a number to multiply the default space) (-gapgroup)"
,
"postext"
=>
"space between text and ticks, blocks, and ranges (enter a number to multiply the default space) (-postext)"
,
"auto"
=>
""
,
"psouput"
=>
""
,
"psresults"
=>
""
,
"metaresults"
=>
""
,
"dataresults"
=>
""
,
"pngresults"
=>
""
,
};
$self
->{ISSTANDOUT} = {
"init"
=> 0,
"graphout"
=> 0,
"inputfile"
=> 0,
"ruler"
=> 0,
"blocktype"
=> 0,
"intersymbol"
=> 0,
"intercolour"
=> 0,
"interticks"
=> 0,
"gapsize"
=> 0,
"ticklines"
=> 0,
"textheight"
=> 0,
"textlength"
=> 0,
"margin"
=> 0,
"tickheight"
=> 0,
"blockheight"
=> 0,
"rangeheight"
=> 0,
"gapgroup"
=> 0,
"postext"
=> 0,
"auto"
=> 0,
"psouput"
=> 0,
"psresults"
=> 0,
"metaresults"
=> 0,
"dataresults"
=> 0,
"pngresults"
=> 0,
};
$self
->{VLIST} = {
"graphout"
=> [
'x11'
,
'x11'
,
'hp7470'
,
'hp7470'
,
'postscript'
,
'postscript'
,
'cps'
,
'cps'
,
'hp7580'
,
'hp7580'
,
'null'
,
'null'
,
'data'
,
'data'
,
'colourps'
,
'colourps'
,
'text'
,
'text'
,
'none'
,
'none'
,
'tek4107t'
,
'tek4107t'
,
'tekt'
,
'tekt'
,
'xwindows'
,
'xwindows'
,
'hpgl'
,
'hpgl'
,
'xterm'
,
'xterm'
,
'meta'
,
'meta'
,
'ps'
,
'ps'
,
'tek'
,
'tek'
,
'png'
,
'png'
,
'tektronics'
,
'tektronics'
,],
"blocktype"
=> [
'1'
,
'Open'
,
'2'
,
'Filled'
,
'3'
,
'Outline'
,],
"intersymbol"
=> [
'1'
,
'Straight'
,
'2'
,
'Up'
,
'3'
,
'Down'
,
'4'
,
'No'
,],
};
$self
->{FLIST} = {
};
$self
->{SEPARATOR} = {
};
$self
->{VDEF} = {
"graphout"
=>
'postscript'
,
"ruler"
=>
'1'
,
"blocktype"
=>
'Filled'
,
"intersymbol"
=>
'Straight'
,
"intercolour"
=>
'1'
,
"interticks"
=>
'0'
,
"gapsize"
=>
'500'
,
"ticklines"
=>
'0'
,
"textheight"
=>
'1'
,
"textlength"
=>
'1'
,
"margin"
=>
'1'
,
"tickheight"
=>
'1'
,
"blockheight"
=>
'1'
,
"rangeheight"
=>
'1'
,
"gapgroup"
=>
'1'
,
"postext"
=>
'1'
,
};
$self
->{PRECOND} = {
"init"
=> {
"perl"
=>
'1'
},
"graphout"
=> {
"perl"
=>
'1'
},
"inputfile"
=> {
"perl"
=>
'1'
},
"ruler"
=> {
"perl"
=>
'1'
},
"blocktype"
=> {
"perl"
=>
'1'
},
"intersymbol"
=> {
"perl"
=>
'1'
},
"intercolour"
=> {
"perl"
=>
'1'
},
"interticks"
=> {
"perl"
=>
'1'
},
"gapsize"
=> {
"perl"
=>
'1'
},
"ticklines"
=> {
"perl"
=>
'1'
},
"textheight"
=> {
"perl"
=>
'1'
},
"textlength"
=> {
"perl"
=>
'1'
},
"margin"
=> {
"perl"
=>
'1'
},
"tickheight"
=> {
"perl"
=>
'1'
},
"blockheight"
=> {
"perl"
=>
'1'
},
"rangeheight"
=> {
"perl"
=>
'1'
},
"gapgroup"
=> {
"perl"
=>
'1'
},
"postext"
=> {
"perl"
=>
'1'
},
"auto"
=> {
"perl"
=>
'1'
},
"psouput"
=> {
"perl"
=>
'$graphout eq "postscript" || $graphout eq "ps" || $graphout eq "colourps" || $graphout eq "cps" || $graphout eq "png"'
,
},
"psresults"
=> {
"perl"
=>
'$graphout eq "postscript" || $graphout eq "ps" || $graphout eq "colourps" || $graphout eq "cps"'
,
},
"metaresults"
=> {
"perl"
=>
'$graphout eq "meta"'
,
},
"dataresults"
=> {
"perl"
=>
'$graphout eq "data"'
,
},
"pngresults"
=> {
"perl"
=>
'$graphout eq "png"'
,
},
};
$self
->{CTRL} = {
};
$self
->{PIPEOUT} = {
};
$self
->{WITHPIPEOUT} = {
};
$self
->{PIPEIN} = {
};
$self
->{WITHPIPEIN} = {
};
$self
->{ISCLEAN} = {
"init"
=> 0,
"graphout"
=> 0,
"inputfile"
=> 0,
"ruler"
=> 0,
"blocktype"
=> 0,
"intersymbol"
=> 0,
"intercolour"
=> 0,
"interticks"
=> 0,
"gapsize"
=> 0,
"ticklines"
=> 0,
"textheight"
=> 0,
"textlength"
=> 0,
"margin"
=> 0,
"tickheight"
=> 0,
"blockheight"
=> 0,
"rangeheight"
=> 0,
"gapgroup"
=> 0,
"postext"
=> 0,
"auto"
=> 0,
"psouput"
=> 0,
"psresults"
=> 0,
"metaresults"
=> 0,
"dataresults"
=> 0,
"pngresults"
=> 0,
};
$self
->{ISSIMPLE} = {
"init"
=> 0,
"graphout"
=> 0,
"inputfile"
=> 0,
"ruler"
=> 0,
"blocktype"
=> 0,
"intersymbol"
=> 0,
"intercolour"
=> 0,
"interticks"
=> 0,
"gapsize"
=> 0,
"ticklines"
=> 0,
"textheight"
=> 0,
"textlength"
=> 0,
"margin"
=> 0,
"tickheight"
=> 0,
"blockheight"
=> 0,
"rangeheight"
=> 0,
"gapgroup"
=> 0,
"postext"
=> 0,
"auto"
=> 0,
"psouput"
=> 0,
"psresults"
=> 0,
"metaresults"
=> 0,
"dataresults"
=> 0,
"pngresults"
=> 0,
};
$self
->{PARAMFILE} = {
};
$self
->{COMMENT} = {
"blocktype"
=> [
"type of blocks: Open, Filled, or Outline. Option \'Outline\' draws filled blocks surrounded by a black border"
,
],
"textheight"
=> [
"height of text. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"textlength"
=> [
"length of text. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"margin"
=> [
"width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"tickheight"
=> [
"height of ticks. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"blockheight"
=> [
"height of blocks. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"rangeheight"
=> [
"height of range ends. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"gapgroup"
=> [
"space between groups. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
"postext"
=> [
"space between text and ticks, blocks, and ranges. Enter a number <1 or >1 to decrease or increase the size, respectively"
,
],
};
$self
->{SCALEMIN} = {
};
$self
->{SCALEMAX} = {
};
$self
->{SCALEINC} = {
};
$self
->{INFO} = {
};
$self
->_init_params(
@params
);
return
$self
;
}
1;