#!/bin/sh
# Adapted from the SRS5 srsinstall script
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# analyse command line and print usage if wrong
#

ERR='codonWinstall: Stopping due to Error'

if [ "$#" = 0 ]; then
  option="all"
elif [ "$1" = "all" ]; then
  option="all"
elif [ "$1" = "clean" ]; then
  option="clean"
elif [ "$1" = "codonw" ]; then
  option="codonw"
elif [ "$1" = "links" ]; then
  option="links"
elif [ "$1" = "cleanall" ]; then
  option="cleanall"
elif [ "$1" = "realclean" ]; then
  option="cleanall"
else
  option="usage"
  echo "unknown option '$1'"
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# print "usage"
#

if [ "$option" = 'usage' ]; then
  cat << END

  Usage: ./codonWinstall option

  Options:

  all        does a complete installation
  codonw     compile codonw only .. no linked programmes
  links      generate links to pseudo programmes
  clean      removes all object files
  cleanall   removes all the object files, codonW, linked files and Makefile
  realclean  removes all the object files, codonW, linked files and Makefile
  
END
  exit 1
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

if [ "$option" = 'all' ]; then
  echo "... starting installation of codonW"
fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# put correct "make" and "cc" commands 
#

OS=`uname`

if [ "$OS" = "SunOS" ]; then
    case "`uname -r`" in
	[56]*)   OS='Solaris' ;;
    esac
fi

# some echo commands do not support -n
# generally /usr/bin/echo doesn't but /usr/ucb/echo does, so one can hardwire
# to be independent of users path.
if [ -r /usr/ucb/echo ]; then
  ECHON="/usr/ucb/echo -n"
else
  ECHON="echo -n"
fi

# OSF/1 v4.0 /usr/ucb is symlink to /usr/bin, but /bin/sh has builtin -n
if [ "$OS" = "OSF1" ]; then
  case "`uname -r`" in
    V[4]*)  ECHON="echo -n"
	    # or can
	    #CMD_ENV=bsd ; export CMD_ENV
    ;;
  esac
fi

# we did our best, but now let's test
ECHONT="`$ECHON | wc -c`"
if [ $ECHONT != 0 ]; then
  ECHONEND="\c"
  ECHON=echo
else
  ECHONEND=""
fi


if [ ! -f "Makefile" ]; then

  $ECHON "enter the make command [make]: $ECHONEND"
  read makeCom
  if [ "$makeCom" = "" ]; then makeCom='make' ; fi

  # for OSF1 need to know if it is osf1 make or gnu make
  if [ "$OS" = "OSF1" ]; then
	$ECHON "is this OSF1 make [y]: $ECHONEND"
	read OSFmake
	if [ "$OSFmake" = "" ]; then OSFmake='y' ; fi
  fi

  if [ "$OS" = "SunOS" -o "$OS" = "Solaris" ]; then
    ccComDef='gcc'
  else
    ccComDef='cc'    
  fi

  $ECHON "enter the cc command [${ccComDef}]: $ECHONEND"
  read ccCom

  if [ "$ccCom" = "" ]; then ccCom="$ccComDef" ; fi

  echo 'choose between optimised code, or code for debugging'
  $ECHON "optimised code [y]: $ECHONEND"
  read optimCom
  if [ "$optimCom" = "" ]; then optimCom="y" ; fi


  $ECHON "enter the link command [ln]: $ECHONEND"
  read ccLn

  if [ "$ccLn" = "" ]; then ccLn="ln -f" ; fi


  $ECHON "Do you want hard or soft links [hard]: $ECHONEND"
  read ccLnflag

  if [ "$ccLnflag" = "" ]; then ccLnflag="hard" ; fi

  echo 'choose between optimised code, or code for debugging'
  $ECHON "optimised code [y]: $ECHONEND"
  read optimCom
  if [ "$optimCom" = "" ]; then optimCom="y" ; fi



  echo "...creating makefile for '$OS'"

#better rename the old makefiles
  if [ -f  "Makefile" ]; then \mv  Makefile Makefile.pre ; fi
  if [ -f  "makefile" ]; then \mv  makefile makefile.pre ; fi
  touch Makefile

# Add the logical parts of the make file

  if [ "$OS" = "OSF1" ]; then
    echo "override cflags  = $(CFLAGS) -g" >> Makefile;
  fi

  if [ "$optimCom" = "y" ]; then
    cflags="-O";
  else
    cflags="-g -DDEBUG" ;
  fi

  if [ "$ccLnflag" = "hard" ]; then
    lncmd=$ccLn;
  else
    lncmd="$ccLn -s";
  fi

 link_prog="rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc" 

cat <<EOF >> Makefile

objects  = codon_us.o codons.o open_fil.o commline.o menu.o tester.o coresp.o
linked   = $link_prog

CC=$ccComDef
CFLAGS= $cflags -DBSD
LN=$lncmd


all: codonw links   

codonw: $(objects)
	$(CC) $(CFLAGS)  $(objects) -o codonw -lm

clean:
	\rm -f $(objects)

cleanall:
	\rm -f $(objects) codonw Makefile $(linked)

realclean:
	\rm -f $(objects) codonw Makefile $(linked)

codon_us.o: codon_us.c codonW.h 
	$(CC) -c $(CFLAGS) codon_us.c  

menu.o: menu.c codonW.h 
	$(CC) -c $(CFLAGS) menu.c

codons.o: codons.c codonW.h 
	$(CC) -c $(CFLAGS) codons.c

coresp.o: coresp.c codonW.h 
	$(CC) -c $(CFLAGS) coresp.c

open_fil.o:    open_fil.c codonW.h
	$(CC) -c $(CFLAGS) open_fil.c

commline.o:    commline.c codonW.h 
	$(CC) -c $(CFLAGS) commline.c

tester.o:      tester.c codonW.h
	$(CC) -c $(CFLAGS) tester.c

links: codonw
EOF


for file in $link_prog 
do
 echo "\t\t$(LN) codonw $file"  >> Makefile
done

 echo >> Makefile

fi

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# cleans the object
#

if [ "$option" = 'clean' ]; then
  echo '...cleaning the old object files '
  echo '...make clean'
  make clean
fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

if [ "$option" = 'cleanall' -o "$option" = 'realclean' ]; then
  echo '...cleaning the old object files, linked files and executables'
  echo '...make realclean '
  make realclean
fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

if [ "$option" = 'all' ]; then
  echo '...Starting to make codonW, with auxillary programs '
  echo '...make all'
  make all
fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

if [ "$option" = 'codonw' ]; then
  echo '...checking codonW is up to date'
  echo '...make codonw'
  make codonw
fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

if [ "$option" = 'links' ]; then
  echo '... Linking auxilliary programs to  '
  echo '...make links'
  make links
fi
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~