#!/usr/bin/perl -w

#  ^---- edit the above path if perl is located elsewhere on your
#        system (use 'which perl' to find out).  Then tell your system
#        manager they put perl in the wrong place.
#
#  Specify your bibliography directory. Comment out if not desired.
#  Description in bibliography section below.
#
$bibdirectory = "/home/bvl/Publications";
#
#############################################################################
#
# reftex v0.3 by Ben Vollmayr-Lee, bvollmay@bucknell.edu, Apr 2002
#
# Purpose: to make references humane in revtex (versions 3 and 4) and conform
#    to Phys Rev endnote style (which their recommendation, bibtex, does not).
# Copyright: you may freely use, modify, and distribute this.  But it would
#    be nice if you informed me because I might like your modifications too.
#
# Installation: just make this file executable with 'chmod u+x reftex' and
#    put it in your executable path
# Usage: exactly like latex: type 'reftex paper.tex' to get paper.dvi
#
# Documentation: 
#   This program can be used simply as a reference ordering system for a
#   single revtex paper, or it can be used with a bibliography file
#   similar to bibtex, or you can do a combination of the two.  This latter
#   option allows making endnotes within the paper while keeping references
#   in a bibliography file, for example.
# 
# Here's a summary of how reftex works (paper.tex means your file):
#    1) steps through paper.tex and makes a list of your citation names
#    2) reads in your bibliography file entries, if you have one
#    3) reads in the \bibitem entries in paper.tex
#    4) creates ordered set of appropriate \bibitem entries in a new
#       version of your paper called paper.ref.tex (in suitable form for 
#       cond-mat or journal submission)
#    5) runs latex on paper.ref.tex and moves the result to paper.dvi
# Thus you can do your editing on paper.tex, compile with reftex to get
# paper.dvi with the references done properly, and when you're ready to
# submit the paper, use the paper.ref.tex version.
#
# Bibliography file:
#   You specify the name of this file in paper.tex via the 'biblocation'
#   tag (which needs to be commented out by a '%' in the tex file).  Two
#   possible syntaxes:
# 
#   % biblocation /path/to/your/bibliography.txt
#
#   or
# 
#   % biblocation (BIB)/otherbibfilename.txt
#
#   In the first case, the path can either be relative or absolute.  In the
#   second case, "(BIB)" gets replaced by the directory you have specified
#   in the variable $bibdirectory at the top of this file.  This is useful
#   for sharing a paper.tex file with a collaborator.  If a bibliography is
#   not specified, then reftex just assumes you don't have one and proceeds
#   (with a warning that it didn't find a file).  The format for this
#   bibliography file is a separate line for each reference (blank lines OK):
# 
#   EPR35           A. Einstein, B. Podolsky, and N. Rosen, PR 47, 777 (1935).
#   LeeRutenberg97  B.P.Lee and A.D.Rutenberg, PRL 79, 4842 (1997).
#   % for comments.  Nonbreaking space added between initials.
#
#   Here the first item in the line is the citation name, and the 
#   rest is the reference (which can contain multiple papers).  Non-journal
#   references must be in standard tex form.  Journals will automatically
#   get their volume number bold-faced if it not already, and the 
#   abbreviations PR, PRE (and A-D), JPA, EPL, RMP, and JSP are expanded.
#
# In your revtex paper:
#   You need to have the \begin{thebibliography} or \begin{references}
#   tag in the file, as well as the associated \end{} command.  Between 
#   them you can include any \bibitem entries you like, though these must
#   be tex formatted (no expansion of abbreviations like PRE).  If a citation 
#   name appears in both your bibliography file and as a \bibitem entry
#   in your paper, the latter version is used.  Only those \bibitem entries
#   that are actually \cite-ed appear (same goes for the bibliography, for
#   that matter).

# code begins here
# deal with command line inputs
my $texfile = $ARGV[0];
unless( $texfile && $texfile ne "-h" && $texfile ne "--h" ){
    print "The documentation for reftex is located within the source code\n";
    exit;
}
$texfile =~ s/\.tex$//;
$bibdirectory =~ s#/$##;

# finds all \cite{} arguments in file
open(TEXFILE,"$texfile.tex") || die "Cannot open $texfile.tex: $!";
while( <TEXFILE> ){
    if( /biblocation\s+(\S+)/ ){ 
	($biblocation) = $1;
	$biblocation =~ s/^\(BIB\)/$bibdirectory/;
    }
#    @text = join(",",/(?:\\cite\{(.*?)\})*/ );   <- not right
#    $k = join(",",@text);                           
#    @list = split(/,/,$k);
#    push(@citations,@list);

    @text = split( /\\cite\{/ );
    shift @text;
    foreach $k (@text){
	($k) = split(/\}/,$k);
	@list = split(/,/,$k);
	push(@citations,@list);
    }
}
close(TEXFILE);

# now assign refs based on their order of appearance
foreach $cite (@citations){
    $flag = 0;
    foreach $ref (@references){
	if( $ref eq $cite ){ $flag=1; last; }
    }
    if( $flag == 0 ){
	push(@references,$cite);
    }
}

# read in bibliography entries
unless( $biblocation ) { print "No biblocation specified\n"; }
open(BIB,$biblocation) || warn "Cannot open $biblocation: $!";
while(<BIB>){
    chomp;
    next unless /\S+/;
    ($line) = split(/%/);
    next unless $line =~ /\S+/;
    ($refname,@rest) = split(/\s+/,$line);
    next unless in_list($refname,@references);

    $line = join(" ",@rest) . "\n";
    $line =~ s/([A-Z])\.(\W*)/$1.~/g;   # tildify initials
    $line =~ s/(\d+)\s*,\s*(\d+)\s*\((\d+)\)/\{\\bf $1\}, $2 ($3)/g; # bf vol.
#   Journal Substitutions    
    $line =~ s/PRA/Phys.\ Rev.\ A/g;
    $line =~ s/PRB/Phys.\ Rev.\ B/g;
    $line =~ s/PRC/Phys.\ Rev.\ C/g;
    $line =~ s/PRD/Phys.\ Rev.\ D/g;
    $line =~ s/PRE/Phys.\ Rev.\ E/g;
    $line =~ s/PRL/Phys.\ Rev.\ Lett.\ /g;
    $line =~ s/JPA/J.\ Phys.\ A/g;
    $line =~ s/JSP/J.\ Stat.\ Phys.\ /g;
    $line =~ s/EPL/Europhys.\ Lett.\ /g;
    $line =~ s/RMP/Rev.\ Mod.\ Phys.\ /g;
    $refinfo{$refname} = $line;
}
close BIB;

# copy paper.tex to paper.ref.tex, and when reaching the references section,
# insert the correct \bibitem entries
open(IN,"$texfile.tex");
open(OUT,">$texfile.ref.tex");
$bibparse = 0;  $all = "";
while(<IN>){
    if( $bibparse ) { 
	if(/\\end\{thebibliography\}/ || /\\end\{references\}/){ 
	    @bibs = split(/\\bibitem\{/,$all);
	    foreach $case (@bibs){
		$case =~ /\}/;
		$refinfo{$`} = $';
	    }
	    foreach $ref (@references){
		print OUT "\\bibitem{$ref} $refinfo{$ref}\n";
	    }
	    print OUT $_;
	    $bibparse = 0;
	}
	else{    # still reading bibitems
	    chomp;
	    $all .= " $_";
	}
    }
    else { print OUT $_; }
    if(/\\begin\{thebibliography\}/ || /\\begin\{references\}/){ 
	$bibparse = 1; 
    }
}
close(IN);
close(OUT);

# now run latex on paper.ref.tex and move the result to paper.dvi
system("latex $texfile.ref.tex; mv $texfile.ref.dvi $texfile.dvi");
print "\n--- DVI output in $texfile.dvi ---\n";

sub in_list
{
    my ($check,@list) = @_;
    my ($item); 
    my ($found) = 0;
    foreach $item (@list){
	if( $item eq $check ){
	    $found=1;
	    last;
	}
    }
    return $found;
}