#!/usr/bin/env tclsh

#
# Copyright (C) Navraj S. Pannu 2006-2007, Leiden University
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
#

proc rename_input_columns { step mtzin mtzout } {
    global XMLParse
   
    set c $XMLParse([join "crank parameters ref_crystal" __])
    set d $XMLParse([join "crank parameters ref_dataset" __])
    set in_fp $XMLParse([join "crank soap run step=$step input exp_columns crystal=$c data=$d f" __])
    set in_sigfp $XMLParse([join "crank soap run step=$step input exp_columns crystal=$c data=$d sigf" __])

    if { [info exists XMLParse([join "crank soap run step=$step buccaneer phase_restrain" __])] } {
       set phase_restrain $XMLParse([join "crank soap run step=$step buccaneer phase_restrain" __])
    } else {
       set phase_restrain "MLHL"
    }

    if { $phase_restrain == "DIRECT"} {
	# Set parameters specific to the SAD target
	# only SAD at the moment for refmac, so find crystal and data set with maximal f"
	set maxc 0
	set maxd 0
	set nc 0
	set maxfpp 0
	set c $XMLParse([join "crank parameters ref_crystal" __])
	set d $XMLParse([join "crank parameters ref_dataset" __])
	set i 1
	while { [info exists XMLParse([join "crank parameters crystal=$i data=1 type" __])] } {
	    set j 1
	    while { [info exists XMLParse([join "crank parameters crystal=$i data=$j type" __])] } {
		if { $XMLParse([join "crank parameters crystal=$i data=$j anomalous" __]) == 1 } {
		    set k 1
		    while { [info exists XMLParse([join "crank parameters crystal=$i data=$j atom=$k fprimeprime" __])] } {
			if { $XMLParse([join "crank parameters crystal=$i data=$j atom=$k fprimeprime" __]) > $maxfpp } {
			    set maxc $i
			    set maxd $j
			    set maxfpp $XMLParse([join "crank parameters crystal=$i data=$j atom=$k fprimeprime" __])
			}
			incr k
		    }
		} elseif { $XMLParse([join "crank parameters crystal=$i native" __]) == 1 } {
		    set nc $i
		}
		incr j
	    }
	    incr i
	}

	if { ($maxc < 1) || ($maxd < 1) } {
	    crank_error "Only SAD or SIRAS data is supported in refmac at the moment, so one anomalous data set is needed"
	}

	if { ($nc > 0) } {
	    set in_fp $XMLParse([join "crank soap run step=$step input exp_columns crystal=$nc data=1 f" __])
	    set in_sigfp $XMLParse([join "crank soap run step=$step input exp_columns crystal=$nc data=1 sigf" __])
	} else {
	    set in_fp $XMLParse([join "crank soap run step=$step input exp_columns crystal=$maxc data=$maxd f" __])
	    set in_sigfp $XMLParse([join "crank soap run step=$step input exp_columns crystal=$maxc data=$maxd sigf" __])
	}
    }

    set outf $XMLParse([join "crank soap run step=$step output phase_columns f" __])
    set outsigf $XMLParse([join "crank soap run step=$step output phase_columns sigf" __])
    set outphib $XMLParse([join "crank soap run step=$step output phase_columns phib" __])
    set outfom $XMLParse([join "crank soap run step=$step output phase_columns fom" __])

    set sftools_script "read $mtzin\n set label col $in_fp \n $outf \n set label col $in_sigfp \n $outsigf \n"
    set sftools_script "$sftools_script set label col PHIC \n $outphib\n set label col FOM \n $outfom \n"

    if { [info exists XMLParse([join "crank soap run step=$step input freer_columns freer" __])] } {
	set in_freer $XMLParse([join "crank soap run step=$step input freer_columns freer" __])
	set out_freer $XMLParse([join "crank soap run step=$step output freer_columns freer" __])
	set sftools_script "$sftools_script set label col $in_freer \n $out_freer \n"
	set sftools_script "$sftools_script write $mtzout col $outf $outsigf $outphib $outfom $out_freer\n"
    } else {
	set sftools_script "$sftools_script write $mtzout col $outf $outsigf $outphib $outfom\n"
    }
    set sftools_script "$sftools_script quit \n"

    set command "sftools << \"$sftools_script\""
#   puts $command
    catch {eval exec $command } output 
#   puts $output
}

global env

set mtzin    [lindex $argv 0]
set mtzout   [lindex $argv 1]

set inputxml [file join .. xml input.xml]

source [file join $env(CRANK) bin crankutils.tcl]

if { [file exists $inputxml] == 0 } {
    crank_error "crank::inputxml file does not exist"
}

XMLParsefile $inputxml

set step $XMLParse(crank__soap__current_step)

rename_input_columns $step $mtzin $mtzout

exit