# sortlines.sh   Usage:  sortlines.sh files >out

# Eats a sequence
# and prints lines in canonical order

# If you download this from my web page, it is important to
# use the SOURCE FILE.  DON'T mouse it off the screen
# because many of the characters will not be visible.

# Call this file  sortlines.sh (not sortlines.sh.txt)

# Note to myself: remember to maintain the link
# ln sortlines.sh /usr/njas/wwwfiles/sequences/sortlines.sh.txt

# Jan 26 2000
# Comments improved Nov 04 2002

if [ "$#" -eq 0 ]
then
echo "Incorrect no of arguments. Usage: sortlines.sh file(s) >bigout " >& 2
echo "Eats sequences and prints lines in canonical order" >& 2
exit 1
fi

# define directories, files, etc
AWK=/bin/gawk

# % lines used are ACDEFHIKNORSTUVWXYeopt

# eat a sequence
cat $* | $AWK '
# Sets p[%I]=1 if %I line is present, etc; seic=1 if S line "ends in comma"

# Initiate the arrays etc
BEGIN {
	p["%A"] = 0;
	p["%B"] = 0;
        p["%C"] = 0;
        p["%D"] = 0;
        p["%E"] = 0;
        p["%F"] = 0;
        p["%G"] = 0;
        p["%H"] = 0;
        p["%I"] = 0; 
        p["%J"] = 0;
        p["%K"] = 0;
        p["%L"] = 0;
        p["%M"] = 0;
        p["%N"] = 0;
        p["%O"] = 0;
        p["%P"] = 0;
        p["%Q"] = 0;
        p["%R"] = 0;
        p["%S"] = 0;
        p["%T"] = 0;
        p["%U"] = 0;
        p["%V"] = 0;
        p["%W"] = 0;
        p["%X"] = 0;
        p["%Y"] = 0;
        p["%Z"] = 0;
	p["%a"] = 0;
	p["%b"] = 0;
        p["%c"] = 0;
        p["%d"] = 0;
        p["%e"] = 0;
        p["%f"] = 0;
        p["%g"] = 0;
        p["%h"] = 0;
        p["%i"] = 0; 
        p["%j"] = 0;
        p["%k"] = 0;
        p["%l"] = 0;
        p["%m"] = 0;
        p["%n"] = 0;
        p["%o"] = 0;
        p["%p"] = 0;
        p["%q"] = 0;
        p["%r"] = 0;
        p["%s"] = 0;
        p["%t"] = 0;
        p["%u"] = 0;
        p["%v"] = 0;
        p["%w"] = 0;
        p["%x"] = 0;
        p["%y"] = 0;
        p["%z"] = 0;
      }
# end of BEGIN stuff

# AAAAA start of main program
$1 == "%I" {					# start section %I
# now we have found a new %I line
# so now is time to print previous sequence if any

# PPPPPP the main print section
if ( p["%I"] == 1 )
	{									# start print
# print ID line
printf("%s\n", line["%I", 1] )

# print %S
if ( p["%S"] >= 1 ) printf("%s\n", line["%S", 1] )
for ( i = 2; i <= p["%S"]; i++ ) printf("%s\n", line["%S", i] )
# print %T
if ( p["%T"] >= 1 ) printf("%s\n", line["%T", 1] )
for ( i = 2; i <= p["%T"]; i++ ) printf("%s\n", line["%T", i] )
# print %U
if ( p["%U"] >= 1 ) printf("%s\n", line["%U", 1] )
for ( i = 2; i <= p["%U"]; i++ ) printf("%s\n", line["%U", i] )
# print %V
if ( p["%V"] >= 1 ) printf("%s\n", line["%V", 1] )
for ( i = 2; i <= p["%V"]; i++ ) printf("%s\n", line["%V", i] )
# print %W
if ( p["%W"] >= 1 ) printf("%s\n", line["%W", 1] )
for ( i = 2; i <= p["%V"]; i++ ) printf("%s\n", line["%W", i] )
# print %X
if ( p["%X"] >= 1 ) printf("%s\n", line["%X", 1] )
for ( i = 2; i <= p["%X"]; i++ ) printf("%s\n", line["%X", i] )
# print %N line
if ( p["%N"] >= 1 ) printf("%s\n", line["%N", 1] )
for ( i = 2; i <= p["%N"]; i++ ) printf("%s\n", line["%N", i] )
# print %Cs
if ( p["%C"] >= 1 ) printf("%s\n", line["%C", 1] )
for ( i = 2; i <= p["%C"]; i++ ) printf("%s\n", line["%C", i] )
# Print %R line
if ( p["%R"] >= 1 ) printf("%s\n", line["%R", 1] )
for ( i = 2; i <= p["%R"]; i++ ) printf("%s\n", line["%R", i] )
# print refs
if ( p["%D"] >= 1 ) printf("%s\n", line["%D", 1] )
for ( i = 2; i <= p["%D"]; i++ ) printf("%s\n", line["%D", i] )
# print %Hs
if ( p["%H"] >= 1 ) printf("%s\n", line["%H", 1] )
for ( i = 2; i <= p["%H"]; i++ ) printf("%s\n", line["%H", i] )
# print %Fs
if ( p["%F"] >= 1 ) printf("%s\n", line["%F", 1] )
for ( i = 2; i <= p["%F"]; i++ ) printf("%s\n", line["%F", i] )
# print %es
if ( p["%e"] >= 1 ) printf("%s\n", line["%e", 1] )
for ( i = 2; i <= p["%e"]; i++ ) printf("%s\n", line["%e", i] )
# print %ps
if ( p["%p"] >= 1 ) printf("%s\n", line["%p", 1] )
for ( i = 2; i <= p["%p"]; i++ ) printf("%s\n", line["%p", i] )
# print %ts
if ( p["%t"] >= 1 ) printf("%s\n", line["%t", 1] )
for ( i = 2; i <= p["%t"]; i++ ) printf("%s\n", line["%t", i] )
# print %os
if ( p["%o"] >= 1 ) printf("%s\n", line["%o", 1] )
for ( i = 2; i <= p["%o"]; i++ ) printf("%s\n", line["%o", i] )
# print %Ys
if ( p["%Y"] >= 1 ) printf("%s\n", line["%Y", 1] )
for ( i = 2; i <= p["%Y"]; i++ ) printf("%s\n", line["%Y", i] )
# print %Ks
if ( p["%K"] >= 1 ) printf("%s\n", line["%K", 1] )
for ( i = 2; i <= p["%K"]; i++ ) printf("%s\n", line["%K", i] )
# Print %O line
if ( p["%O"] == 1 ) printf("%s\n", line["%O", 1] )
# Print author line
if ( p["%A"] >= 1 ) printf("%s\n", line["%A", 1] )
for ( i = 2; i <= p["%A"]; i++ ) printf("%s\n", line["%A", i] )
# Print %E line
if ( p["%E"] >= 1 ) printf("%s\n", line["%E", 1] )
for ( i = 2; i <= p["%E"]; i++ ) printf("%s\n", line["%E", i] )
# print blank line
printf("\n")

	}									#   end print
# end of printing section
# weve just printed the previous sequence, triggered by reading a %I line

# reset
	p["%A"] = 0;
	p["%B"] = 0;
        p["%C"] = 0;
        p["%D"] = 0;
        p["%E"] = 0;
        p["%F"] = 0;
        p["%G"] = 0;
        p["%H"] = 0;
        p["%I"] = 1; 
# (because we had the %I line in hand)
        p["%J"] = 0;
        p["%K"] = 0;
        p["%L"] = 0;
        p["%M"] = 0;
        p["%N"] = 0;
        p["%O"] = 0;
        p["%P"] = 0;
        p["%Q"] = 0;
        p["%R"] = 0;
        p["%S"] = 0;
        p["%T"] = 0;
        p["%U"] = 0;
        p["%V"] = 0;
        p["%W"] = 0;
        p["%X"] = 0;
        p["%Y"] = 0;
        p["%Z"] = 0;
	p["%a"] = 0;
	p["%b"] = 0;
        p["%c"] = 0;
        p["%d"] = 0;
        p["%e"] = 0;
        p["%f"] = 0;
        p["%g"] = 0;
        p["%h"] = 0;
        p["%i"] = 0; 
        p["%j"] = 0;
        p["%k"] = 0;
        p["%l"] = 0;
        p["%m"] = 0;
        p["%n"] = 0;
        p["%o"] = 0;
        p["%p"] = 0;
        p["%q"] = 0;
        p["%r"] = 0;
        p["%s"] = 0;
        p["%t"] = 0;
        p["%u"] = 0;
        p["%v"] = 0;
        p["%w"] = 0;
        p["%x"] = 0;
        p["%y"] = 0;
        p["%z"] = 0;
	seq = "";
	signseq = "";
	trig = 0;
	signtrig = 0;
        seic = 0;
        teic = 0;
        ueic = 0;

# save %I line for new seq
line[$1, 1 ] = $0

           }					# end section %I

# end of %I line stuff

# BBBBB
# accept a %*-line but not a %I-line
$1 ~ "%[^I]" {							# start non-%I line

p[$1]++
line[$1, p[$1]] = $0

	     }							# end non-%I line
	

END  {
# print final sequence

# QQQQQQ the main print section
if ( p["%I"] == 1 )
	{									# start print
# print ID line
printf("%s\n", line["%I", 1] )

# print %S
if ( p["%S"] >= 1 ) printf("%s\n", line["%S", 1] )
for ( i = 2; i <= p["%S"]; i++ ) printf("%s\n", line["%S", i] )
# print %T
if ( p["%T"] >= 1 ) printf("%s\n", line["%T", 1] )
for ( i = 2; i <= p["%T"]; i++ ) printf("%s\n", line["%T", i] )
# print %U
if ( p["%U"] >= 1 ) printf("%s\n", line["%U", 1] )
for ( i = 2; i <= p["%U"]; i++ ) printf("%s\n", line["%U", i] )
# print %V
if ( p["%V"] >= 1 ) printf("%s\n", line["%V", 1] )
for ( i = 2; i <= p["%V"]; i++ ) printf("%s\n", line["%V", i] )
# print %W
if ( p["%W"] >= 1 ) printf("%s\n", line["%W", 1] )
for ( i = 2; i <= p["%V"]; i++ ) printf("%s\n", line["%W", i] )
# print %X
if ( p["%X"] >= 1 ) printf("%s\n", line["%X", 1] )
for ( i = 2; i <= p["%X"]; i++ ) printf("%s\n", line["%X", i] )
# print %N line
if ( p["%N"] >= 1 ) printf("%s\n", line["%N", 1] )
for ( i = 2; i <= p["%N"]; i++ ) printf("%s\n", line["%N", i] )
# print %Cs
if ( p["%C"] >= 1 ) printf("%s\n", line["%C", 1] )
for ( i = 2; i <= p["%C"]; i++ ) printf("%s\n", line["%C", i] )
# Print %R line
if ( p["%R"] >= 1 ) printf("%s\n", line["%R", 1] )
for ( i = 2; i <= p["%R"]; i++ ) printf("%s\n", line["%R", i] )
# print refs
if ( p["%D"] >= 1 ) printf("%s\n", line["%D", 1] )
for ( i = 2; i <= p["%D"]; i++ ) printf("%s\n", line["%D", i] )
# print %Hs
if ( p["%H"] >= 1 ) printf("%s\n", line["%H", 1] )
for ( i = 2; i <= p["%H"]; i++ ) printf("%s\n", line["%H", i] )
# print %Fs
if ( p["%F"] >= 1 ) printf("%s\n", line["%F", 1] )
for ( i = 2; i <= p["%F"]; i++ ) printf("%s\n", line["%F", i] )
# print %es
if ( p["%e"] >= 1 ) printf("%s\n", line["%e", 1] )
for ( i = 2; i <= p["%e"]; i++ ) printf("%s\n", line["%e", i] )
# print %ps
if ( p["%p"] >= 1 ) printf("%s\n", line["%p", 1] )
for ( i = 2; i <= p["%p"]; i++ ) printf("%s\n", line["%p", i] )
# print %ts
if ( p["%t"] >= 1 ) printf("%s\n", line["%t", 1] )
for ( i = 2; i <= p["%t"]; i++ ) printf("%s\n", line["%t", i] )
# print %os
if ( p["%o"] >= 1 ) printf("%s\n", line["%o", 1] )
for ( i = 2; i <= p["%o"]; i++ ) printf("%s\n", line["%o", i] )
# print %Ys
if ( p["%Y"] >= 1 ) printf("%s\n", line["%Y", 1] )
for ( i = 2; i <= p["%Y"]; i++ ) printf("%s\n", line["%Y", i] )
# print %Ks
if ( p["%K"] >= 1 ) printf("%s\n", line["%K", 1] )
for ( i = 2; i <= p["%K"]; i++ ) printf("%s\n", line["%K", i] )
# Print %O line
if ( p["%O"] == 1 ) printf("%s\n", line["%O", 1] )
# Print author line
if ( p["%A"] >= 1 ) printf("%s\n", line["%A", 1] )
for ( i = 2; i <= p["%A"]; i++ ) printf("%s\n", line["%A", i] )
# Print %E line
if ( p["%E"] >= 1 ) printf("%s\n", line["%E", 1] )
for ( i = 2; i <= p["%E"]; i++ ) printf("%s\n", line["%E", i] )
# print blank line
printf("\n")

	}									#   end print
# end of printing section

}'