#!/bin/sh
#Use this section to describe what goes on what line
name=alllis          # name.blc -> name.als -> name.ps
nb=1                 # number of lines before sequences
na=5                 # number of lines after sequences
#ss=top               # Comment out to have SS after sequences
color=yes            # "yes" for color 
gap=.                # Gap character
indent=9            # Indent width

# Necessary Calculations -- no changes should be necessary
ns=`grep -c ">" $name.blc`        # number of seqs
fs=`expr $nb + 1`                 # line of first sequence
ls=`expr $nb + $ns`               # line of last sequence
if [ -z $ss ]; then               # Decides where ss will be
  ss=`expr $nb + $ns + 2`           # SS after sequence
  else ss=1                         # SS at top
fi
ssl=`expr $ss + 1`                # line of secondary sstructure labels
ss2=`expr $ss + 2`                # line of secondary structure
ssl2=`expr $ss + 3`               # line of secondary sstructure labels
b11=`echo $b1 |awk '{print $2}'`  # The seq# of block 1
b22=`echo $b2 |awk '{print $2}'`  # The seq# of block 2
b33=`echo $b3 |awk '{print $2}'`  # The seq# of block 3
                                  # ab / ae = alignment begin / end
ab=`grep -n "*" $name.blc |head -1 |awk -F ":" '{print $1}'`
ae=`grep -n "*" $name.blc |tail -1 |awk -F ":" '{print $1}'`
loa=`expr  $ae - $ab - 1`         #Length of alignment
#nc defines the percentage of conservation
nc=`expr $ns \* 6 / 10`

#Generate Alscript Input
cat << end-top > temp.als
     #Comments in ALscript command files start with a #
     #Commands are free format - separated by blank, tab or comma characters
     #But no blank lines.  Blank lines must have a comment character #
     #
     BLOCK_FILE         $name.blc
     OUTPUT_FILE        $name.ps
     PORTRAIT
     POINTSIZE 7
     DEFINE_FONT 0 Helvetica DEFAULT
     DEFINE_FONT 1 Helvetica-Bold DEFAULT
     DEFINE_FONT 2 Helvetica REL .2
     DEFINE_FONT 3 Symbol REL 1.2
     DEFINE_FONT 4 Courier-Bold DEFAULT
     IDENT_WIDTH $indent
     ADD_SEQ 0 $nb
     ADD_SEQ $ns $na
SINGLE_PAGE
  bw#DEFINE_COLOUR 1 .2 .2 .2
  bw#DEFINE_COLOUR 2 .4 .4 .4
  bw#DEFINE_COLOUR 3 .8 .8 .8
 col#DEFINE_COLOUR 1 1 0 0
 col#DEFINE_COLOUR 2 0 0 1
 col#DEFINE_COLOUR 3 0 1 0
 col#DEFINE_COLOUR 4 0 1 1
 col#DEFINE_COLOUR 5 1 0 1
 col#DEFINE_COLOUR 6 1 .4 .4
 col#DEFINE_COLOUR 7 .4 .4 1
 col#DEFINE_COLOUR 8 .4  1 .4
  #   NUMBER_SEQS
  #   DO_TICKS
     NO_NUMBERS
     SETUP              #Tell the program to get on with the formatting.
     ID_FONT ALL 4
FONT_REGION ALL 1
FONT_REGION 1 $fs $loa $ls 0
     RELATIVE_TO $fs   #assumes your sequence on top
end-top

sed -e s/\$ssl/$ssl/g -e s/\$ss/$ss/g -e s/\$loa/$loa/g $name-c.ss >> temp.als
sed -e s/\$ssl/$ssl2/g -e s/\$ss/$ss2/g -e s/\$loa/$loa/g $name-d.ss >> temp.als

cat << end-bottom >> temp.als
     #
     #  Mask for conservative substitution
     #  Next line assumes your sequence is on top of the alignment
     RELATIVE_TO 0
     SUB_CHARS 1 $fs $loa $ls SPACE "$gap" 
     #  Mask for conserved
     calcons  1 $fs $loa $ls
#Last number on next line is % conserved  (times ten) for conservative sub
     mask SETUP
     mask ILLEGAL "$gap"
     mask SETUP
     mask CONSERVATION 1 $fs $loa $ls 6
     mask CCOL 1 $fs $loa $ls 100
     mask FONT 1 $fs $loa $ls 1
     mask SCOL 1 $fs $loa $ls 3
     mask RESET
#Last number on next line is #/total seqs for conserved
     mask SETUP
     mask ILLEGAL "$gap"
     mask  ID 1 $fs $loa $ls $nc 
     mask SCOL 1 $fs $loa $ls 2
     mask CCOL 1 $fs $loa $ls 99 
     mask FONT 1 $fs $loa $ls 1
     mask RESET
     #  Mask for total identity
     mask CONSERVATION 1 $fs $loa $ls 10 
     mask SCOL 1 $fs $loa $ls 1
     mask CCOL 1 $fs $loa $ls 99
    # mask FONT 1 $fs $loa $ls 1
     mask RESET
#TEXT 36 30 "(2 - 35)"
SUB_ID 2  "Mm    7305363"
SUB_ID 3  "Hs    4557741"
SUB_ID 4  "Ss   11276042"
SUB_ID 5  "Bt    1170793"
SUB_ID 6  "Mf   23574762"
SUB_ID 7  "Gg    6601335"
SUB_ID 8  "Xl   14132774"
SUB_ID 9  "Dr   27882549"
SUB_ID 10 "Dm    3983137"
SUB_ID 11 "Ce   17554220"
SUB_ID 12 "Dd   24210418"
SUB_ID 13 "Ag   31240513"
SUB_ID 14 "Ci   23575733"
SUB_ID 15 "Pc   14599401"
SUB_ID 16 "Nc   28950172"
SUB_ID 17 "En    3024219"
# Text commands created for numbering
# Sequence Number: 1
# Starting Number: 1
# Interval:        10
# Position:        1
TEXT 20 1 "10"
TEXT 30 1 "20"
TEXT 40 1 "30"
TEXT 55 1 "40"
TEXT 65 1 "50"
TEXT 75 1 "60"
TEXT 85 1 "70"
TEXT 95 1 "80"
TEXT 108 1 "90"
RELATIVE_TO 1 1
TEXT 71 1 "@fcircle"
TEXT 72 1 "@fcircle"
     # End of Alscript input file
end-bottom

if [ $color == "yes" ] ; then grep -v "bw#" temp.als | sed 's/col#/    /g' > $name.als
 else grep -v "col#" temp.als | sed 's/bw#/   /g' > $name.als
fi
alscript $name.als > $name.ps  && kghostview $name.ps &
gs -dBATCH -dNOPAUSE -sDEVICE=jpeg -sOutputFile=$name.jpg -r100 $name.ps