#-------------------------  D3HOM/D4HOM ( 2/ 8/05) --------------------------
item:DXHOM - Dot-matrix similarity (DNA)

# The directory fsapdoc must also be available in the $GDE_HELP_DIR,
# containing the file hom.asc from the FSAP package. Again, this
# directory can be implemented as a symbolic link.
itemmethod:readseq -i1 -fGenBank -o=in1.seq1 in1; readseq -i2 -fGenBank -o=in1.seq2 in1; hom.csh in1.seq1 $STRAND in1.seq2 in1.out $STARTX $FINISHX $STARTY $FINISHY $RANGE $MINPER $COMPFACT $KIND $LINESIZE $PROGRAM; ($GDE_TEXTEDIT in1.out; $RM_CMD in1*) &
itemhelp:doc/fsap/hom.txt
itemopen:gde_help_viewer.csh

arg:STARTX
argtype:slider
arglabel:STARTX
argmin:1
argmax:500000
argvalue:1

arg:FINISHX
argtype:slider
arglabel:FINISHX
argmin:1
argmax:500000
argvalue:500000

arg:STARTY
argtype:slider
arglabel:STARTY
argmin:1
argmax:500000
argvalue:1

arg:FINISHY
argtype:slider
arglabel:FINISHY
argmin:1
argmax:500000
argvalue:500000

arg:STRAND
arglabel:Which strand is X-axis?
argtype:chooser
argchoice:original:n
argchoice:opposite:y
argvalue:0

arg:PROGRAM
arglabel:K-tuple
argtype:chooser
argchoice:3:d3hom
argchoice:4:d4hom
argvalue:0

arg:RANGE
argtype:slider
arglabel:Dist. from center of window
argmin:1
argmax:30
argvalue:10

arg:MINPER
argtype:slider
arglabel:min. % similarity printed
argmin:40
argmax:100
argvalue:60

arg:COMPFACT
argtype:slider
arglabel:compression factor
argmin:1
argmax:500
argvalue:10

arg:KIND
argtype:chooser
argchoice:DNA:D
argchoice:RNA:R
argvalue:0

arg:LINESIZE
argtype:slider
arglabel:width (columns) of output line
argmin:40
argmax:150
argvalue:70

in:in1
informat:genbank
insave: