#!/bin/sh

# A short test for mrbump. Requires that clustalw and fasta be installed.
# The first test does not require internet connectivity.

# Test first for the clustalw and fasta executables in the PATH

clustalw_found=False
mafft_found=False
fasta_found=False

PATH_list=`echo $PATH | sed s'|:| |'g | xargs` 

# Look for new location of clustalw2 and mafft
if test -x $CCP4/libexec/clustalw2; then clustalw_found=True; fi;
if test -x $CCP4/libexec/mafft; then mafft_found=True; fi;

# Look for clustalw
for i in $PATH_list; do if test -x $i/clustalw; then clustalw_found=True; fi; done
for i in $PATH_list; do if test -x $i/clustalw2; then clustalw_found=True; fi; done

# Look for fasta
for i in $PATH_list; do if test -x $i/fasta34; then fasta_found=True; fi; done
for i in $PATH_list; do if test -x $i/fasta35; then fasta_found=True; fi; done
for i in $PATH_list; do if test -x $i/fasta36; then fasta_found=True; fi; done

# If both are missing
if [ ${fasta_found} = False ] && [ ${clustalw_found} = False ] 
then
   echo "Error: Clustalw executable not found. MrBUMP requires the alignment"  1>&2
   echo "       program Clustalw be installed in order to run this test." 1>&2
   echo "" 1>&2
   echo "Error: Fasta executable not found. MrBUMP requires the Fasta"  1>&2
   echo "       program (fasta34 or fasta35 or fasta36) be installed in order to" 1>&2
   echo "       run this test." 1>&2
   echo "" 1>&2
   exit
fi

# If clustalw is missing
if [ $clustalw_found = False ] 
then
   echo "Error: Clustalw executable not found. MrBUMP requires the alignment" 1>&2 
   echo "       program Clustalw be installed in order to run this test." 1>&2
   echo "" 1>&2
   exit
else
   echo "Clustalw executable found in PATH."
   echo ""
fi

# If fasta is missing
if [ $fasta_found = False ] 
then
   echo "Error: Fasta executable not found. MrBUMP requires the Fasta"  1>&2
   echo "       program (fasta34 or fasta35 or fasta36) be installed in order to" 1>&2
   echo "       run this test." 1>&2
   echo "" 1>&2
   exit
else
   echo "Fasta executable found in PATH."
   echo ""
fi

# Remove any files left over from a previous run of this test

rm -rf $CCP4_SCR/mrbump_test_temp.mtz $CCP4_SCR/mrbump_test_temp.pdb $CCP4_SCR/search_test_mrbump

# Run the simple test (Toxd example)

mrbump HKLIN $CEXAM/toxd/toxd.mtz SEQIN $CEXAM/toxd/toxd.seq HKLOUT $CCP4_SCR/mrbump_test_temp.mtz XYZOUT $CCP4_SCR/mrbump_test_temp.pdb <<eof
JOBID test_mrbump
LABIN F=FTOXD3 SIGF=SIGFTOXD3 FreeR_flag=FreeR_flag
MAPROGRAM clustalw
MRPROGRAM molrep phaser 
USEENSEM False
MRNUM 1
MDLP False
MDLC False
MDLM True
MDLS False
MDLD False
LOCALFILE $CEXAM/toxd/toxd.pdb CHAIN A
DOFASTA False
SSMSEARCH False
PQSSEARCH False
SCOPSEARCH False
CHECK False
ROOTDIR $CCP4_SCR
TRYALL True
DEBUG True
END
eof

exit