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#
# Copyright (c) Medical Research Council, Laboratory of Molecular Biology,
# 1995. All rights reserved.
#
# This file is part of the Staden Package. See the Staden Package copyright
# notice for information on the restrictions for usage and distribution, and
# for a disclaimer of all warranties.
#
proc PlotBaseComp { } {
global nip_defs
set t .plot_base_comp
if {[xtoplevel $t -resizable 0] == ""} return
wm title $t "Plot base composition"
set seq_id [get_active_seq_id]
global $seq_id.start $seq_id.end
set seq_length [seq_info $seq_id length]
set seq_start [seq_info $seq_id start]
set seq_end [seq_info $seq_id end]
if {[info exists $seq_id.start]} {
set seq_start [set $seq_id.start]
}
if {[info exists $seq_id.end]} {
set seq_end [set $seq_id.end]
}
keylset us RANGE [keylget nip_defs NIP.PBC.RANGE]
seq_id $t.range -range 1 -browse 1 -from 1 -to $seq_length \
-start_value $seq_start -end_value $seq_end -min_value 1 \
-default [seq_info $seq_id name] \
-update_cmd [list [list seq_range_updates $t.range]]\
-browse_cmd seq_browser
global $t.t $t.c $t.a $t.g
set $t.t [keylget nip_defs NIP.PBC.T]
set $t.c [keylget nip_defs NIP.PBC.C]
set $t.a [keylget nip_defs NIP.PBC.A]
set $t.g [keylget nip_defs NIP.PBC.G]
frame $t.nt
checkbutton $t.nt.cb_t -text T -variable $t.t
checkbutton $t.nt.cb_c -text C -variable $t.c
checkbutton $t.nt.cb_a -text A -variable $t.a
checkbutton $t.nt.cb_g -text G -variable $t.g
keylset wl WIN_LEN [keylget nip_defs NIP.PBC.WIN_LEN]
set win_length [keylget wl WIN_LEN.VALUE]
set seq_length [expr [seq_id_to $t.range] - [seq_id_from $t.range] + 1]
if {$win_length > $seq_length} {
set win_length [expr $seq_length / 2]
}
set max_length [keylget wl WIN_LEN.MAX]
entrybox $t.win_len \
-title "[keylget wl WIN_LEN.NAME] ([keylget wl WIN_LEN.MIN]\
to $max_length)" \
-default $win_length \
-width 5 \
-type "CheckIntRange [keylget wl WIN_LEN.MIN] $max_length "
#########################################################################
#ok cancel help buttons
okcancelhelp $t.button -bd 2 -relief groove \
-ok_command "PlotBaseComp2 $t $t.range $t.win_len"\
-cancel_command "seq_id_destroy $t.range; destroy $t" \
-help_command "show_help spin {SPIN-Plot-Base-Composition}"
pack $t.range
pack $t.nt.cb_t $t.nt.cb_c $t.nt.cb_a $t.nt.cb_g -side left -fill x -expand 1
pack $t.nt -fill x
pack $t.win_len -fill x
pack $t.button -side bottom -fill x
}
proc plot_base_comp {seq_id result_id} {
global nip_defs tk_utils_defs
global HORIZONTAL SCALE_BAR
set type [keylget nip_defs BASECOMP]
set r_id [CreateRasterGraph raster [list [list $seq_id $HORIZONTAL]] $type 0\
[keylget nip_defs RASTER.TITLE]\
[keylget nip_defs RASTER.PLOT_HEIGHT] \
[keylget nip_defs RASTER.PLOT_WIDTH] \
[keylget nip_defs RULER.PLOT_HEIGHT] \
[keylget nip_defs RULER.PLOT_WIDTH]]
nip_base_comp plot -window $raster \
-window_id $r_id \
-seq_id $seq_id \
-result_id $result_id \
-fill [keylget nip_defs NIP.PBC.COLOUR] \
-width [keylget nip_defs NIP.PBC.L_WIDTH]
set r_win [winfo parent $raster]
#add key for all results
keybox_add $r_win.key$r_id \
-text "[seq_result_key_name -index $result_id]" \
-background [keylget nip_defs NIP.PBC.COLOUR]\
-enter "EnterKey $raster $result_id" -motion MotionRaster \
-leave "LeaveKey $raster" \
-drop "DropResult $result_id $SCALE_BAR" \
-menu "seq_result_keybox_update $r_win $result_id \[seq_result_names -result_id $result_id\]"
fit_on_screen $r_win
#update result list
seq_result_list_update [keylget tk_utils_defs RASTER.RESULTS.WIN]
}
proc PlotBaseComp2 { t range win_len} {
global nip_defs tk_utils_defs
global $t.t $t.c $t.a $t.g
global HORIZONTAL SCALE_BAR PROTEIN
if {![set $t.a] && ![set $t.c] && ![set $t.g] && ![set $t.t]} {
bell
verror ERR_WARN "plot base composition" "no base types selected"
return
}
set window_length [entrybox_get $win_len]
if {[expr $window_length % 2] == 0} {
bell
verror ERR_WARN "plot base composition" "window length must be odd"
return
}
if {$window_length > [expr [seq_id_to $range] - [seq_id_from $range] + 1]} {
bell
verror ERR_WARN "plot base composition" "window length must be less than sequence length"
return
}
set seq_id [name_to_seq_id [seq_id_name $range]]
if {[seq_info $seq_id type] == $PROTEIN} {
verror ERR_WARN "base composition" "unable to process protein sequences"
seq_id_destroy $range
return
}
SetBusy
set result_id [nip_base_comp create -seq_id $seq_id \
-start [seq_id_from $range] \
-end [seq_id_to $range] \
-win_len $window_length \
-a [set $t.a] -c [set $t.c] \
-g [set $t.g] -t [set $t.t]]
# stop windows from hiding the plot
wm withdraw $t
plot_base_comp $seq_id $result_id
ClearBusy
#failed to do base composition
if {$result_id == "-1"} {
seq_result_update -index $result_id -job QUIT
return
}
seq_id_destroy $range
global $seq_id.start $seq_id.end
set $seq_id.start [seq_id_from $range]
set $seq_id.end [seq_id_to $range]
destroy $t
}
proc CountBaseComp { } {
global nip_defs
set t .count_base_comp
if {[xtoplevel $t -resizable 0] == ""} return
wm title $t "Count sequence composition"
set seq_id [get_active_seq_id]
global $seq_id.start $seq_id.end
set seq_length [seq_info $seq_id length]
set seq_start [seq_info $seq_id start]
set seq_end [seq_info $seq_id end]
if {[info exists $seq_id.start]} {
set seq_start [set $seq_id.start]
}
if {[info exists $seq_id.end]} {
set seq_end [set $seq_id.end]
}
keylset us RANGE [keylget nip_defs NIP.PBC.RANGE]
seq_id $t.range -range 1 -browse 1 -from 1 -to $seq_length \
-start_value $seq_start -end_value $seq_end -min_value 1 \
-default [seq_info $seq_id name] \
-update_cmd [list [list seq_range_updates $t.range]]\
-browse_cmd nip_seq_browser
#########################################################################
#ok cancel help buttons
okcancelhelp $t.button -bd 2 -relief groove \
-ok_command "CountBaseComp2 $t.range; destroy $t"\
-cancel_command "seq_id_destroy $t.range; destroy $t" \
-help_command "show_help spin {SPIN-Base-Composition}"
pack $t.range
pack $t.button -side bottom -fill x
}
proc CountBaseComp2 {range} {
set seq_id [name_to_seq_id [seq_id_name $range]]
count_base_comp -seq_id $seq_id \
-start [seq_id_from $range] \
-end [seq_id_to $range]
seq_id_destroy $range
global $seq_id.start $seq_id.end
set $seq_id.start [seq_id_from $range]
set $seq_id.end [seq_id_to $range]
}
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