% version = 1.01 of openmind.sty 2002 Feb 11
% LaTeX style file for Open Mind Journals
% http://www.openmindjournals.com/
% http://www.openmindjournals.com/instructions.html

% Dr. Thomas D. Schneider
% National Cancer Institute
% Laboratory of Experimental and Computational Biology
% Frederick, Maryland  21702-1201
% toms@ncifcrf.gov
% permanent email: toms@alum.mit.edu
% http://www.lecb.ncifcrf.gov/~toms/

% from jmb.sty:
% LaTeX style file for the Journal of Molecular Biology

% 2000 Mar 15, 2.14: cite.sty is now required to get the
% semicolon between references.

% 2000 Mar 15, 2.13
% NEW AND IMROVED commands:
% \section{} Introduction, etc
% \subsection{} sub sections
% \subsubsection{} sub sub sections

% This was interestingly tricky!  If a section is immediately followed by a
% subsection the code must not add extra space above itself (it is too big).
% But a subsection should add space if there is no section above.

% history:

% 2000 Feb 2: fixed reference section to be pretty good.
%             section and subsection implemented properly.
% 2000 Jan 28: dump the junk that prevents one from having spaces
%              between \cite{} entries!!  I don't know why we care about it.
% 1998 Dec 18: make no hyphenation by using \raggedright
%              to follow author instructions... but it has no effect!
% 1996 oct 17: "References" is not centered
% 1996 oct 9: JMB no longer has numbers on sections, removed.
% 1995 Feb 18: Section and SubSection removed
% because the conflict somehow...
% 1994 November 11:
% additional definition of Section and SubSection
%
% from apalike.sty 1989 June 19
%
% apalike.sty style, used in conjunction with apalike.bst,
% will produce an apa-like bibliography style:
%
% 1) Bibliography entries formatted alphabetically, last name
%    first, each entry having a hanging indentation and no label.
% 2) References in the following formats:
%		(Author, 1986)
%		(Author and Author, 1986)
%		(Author et al., 1986).
% 3) Multiple references in the form (Author1, 1986; Author2, 1987)
%
% To be used as an optional argument to the \documentstyle command; for example
%	\documentstyle[11pt,apalike]{book}
%
% 16-Sep-86, original version by Susan King and Oren Patashnik.
% 13-Oct-87 changes:
%	Fixed bug in last line by adding the {} that disappeard when
%		the \hbox{} was removed from the pre-APALIKE definition;
%	added club and widow penalties;
%	patched the \newblock LaTeX bug from `-.07em' to simply `.07em';
%	and made this work for document styles that don't define `chapter'.

% Use parens instead of brackets for \cite, and no label in the bibliography:
% use this if natbib.sty is not implemented:
\def\@cite#1#2{(#1\if@tempswa , #2\fi)} % this works
% \def\@cite#1#2{(#1\if@tempswa ; #2\fi)} % doesn't change the ;

% \bibpunct[, ]{(}{)}{;}{a}{,}{,} % puts parens around year only.
% \bibpunct[, ]{ }{ }{;}{a}{,}{,} % no parens at all!

% for natbib.sty redefine cite:
% \renewcommand{\cite}{citep}
% fails

% \renewcommand{\@cite}[2]{BRA{#1\ifthenelse{\boolean{@tempswa}}{COM #2}{}BRAR}
% \renewcommand{\@cite}[2]{BRA{#1\ifthenelse{\boolean{@tempswa}}{COM #2}{}BRAR}
%\renewcommand{\@cite}[2]{%
%   HELO ({#1\ifthenelse{\boolean{@tempswa}}{\bibpunct #2}{})}}

% The next line removes the biblabel from the References list:
\def\@biblabel#1{}
% see p. 374 of the Companion book

% Set length of hanging indentation for bibliography entries
% currently not used
%
%\newlength{\bibhang}
%\setlength{\bibhang}{2em}

% some old junk:
% \thebibliography environment depends on whether or not `chapter's can exist
%
% \@ifundefined{chapter}{\def\thebibliography#1{\section*{
% {\large \bfseries References}
% \@mkboth
%   {REFERENCES}{REFERENCES}}\list
%   {\relax}{\setlength{\labelsep}{0em}
% 	\setlength{\itemindent}{-\bibhang}
% 	\setlength{\leftmargin}{\bibhang}}
%     \def\newblock{\hskip .11em plus .33em minus .07em}
%     \sloppy\clubpenalty4000\widowpenalty4000
%     \sfcode`\.=1000\relax}}%
% {\def\thebibliography#1{\chapter*{Bibliography\@mkboth
%   {BIBLIOGRAPHY}{BIBLIOGRAPHY}}\list
%   {\relax}{\setlength{\labelsep}{0em}
% 	\setlength{\itemindent}{-\bibhang}
% 	\setlength{\leftmargin}{\bibhang}}
%     \def\newblock{\hskip .11em plus .33em minus .07em}
%     \sloppy\clubpenalty4000\widowpenalty4000
%     \sfcode`\.=1000\relax}}

% unfortunately this doesn't work in latex2e.
% the ";" does work, but only the first reference works, the rest are "?"
% `; ' goes between cites, and there's no \hbox around individual cites
%
%\def\@citex[#1]#2{\if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi
%  \def\@citea{}\@cite{\@for\@citeb:=#2\do
%    {\@citea\def\@citea{; }\@ifundefined
%       {b@\@citeb}{{\bf ?}\@warning
%       {Citation `\@citeb' on page \thepage \space undefined}}%
%{\csname b@\@citeb\endcsname}}}{#1}}

% unfortunately this doesn't work in latex2e:
% `; ' goes between cites, and there's no \hbox around individual cites
%
%\def\@citex[#1]#2{\if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi
%  \def\@citea{}\@cite{\@for\@citeb:=#2\do
%    {\@citea\def\@citea{DUD }\@ifundefined
%       {b@\@citeb}{{\bf ?}\@warning
%       {Citation `\@citeb' on page \thepage \space undefined}}%
%{\csname b@\@citeb\endcsname}}}{#1}}

%*******************************************************************************

% Define JMB type sections

% amount of space to skip above subsections
\newcommand{\sectionskip}{\vspace{12pt}}

\renewcommand{\section}[1]{
% \vspace{12pt}
\stepcounter{section}
% \begin{centering}
% \textbf{\Large #1}
\textbf{\large #1}%
% see what the parameter is:
% ``#1''
%\arabic{section}.
%#1}
% \end{centering}
% \vspace{12pt}
% don't skip space in subsections if immediately after a section:
\renewcommand{\sectionskip}{\vspace{0pt}}%
}
% \\}

\renewcommand{\subsection}[1]{
%\vspace{12pt}
\sectionskip
% skip space in subsections if NOT immediately after a section:
\renewcommand{\sectionskip}{\vspace{12pt}}
\stepcounter{subsection}
\begin{centering}
\textbf{\large #1}
%\arabic{subsection}.
% #1}
\end{centering}
\vspace{12pt}
}

\renewcommand{\subsubsection}[1]{
%\vspace{12pt}
\sectionskip
% skip space in subsections if NOT immediately after a section:
\renewcommand{\sectionskip}{\vspace{12pt}}
\stepcounter{subsubsection}
\noindent
\emph{\large #1}
%\arabic{subsection}.
% #1}
\vspace{12pt}
}

%\newcommand{\SubSubSection}[1]
%{ {
%\vspace{12pt}
%\noindent {\it #1 } \\ \\
%} }

% This is used for the NEXT subsection in a series,
% it only differs in that it has a vspace in front
% NO GOOD - see note at top
\newcommand{\nextsubsection}[1]{
\vspace{12pt}
\subsection{#1}
}

%*******************************************************************************

% Change Reference name
% page 30-31 of the Companion says 'bibname'
% but it fails; refname works:
%\renewcommand{\bibname}{DOGWORLD}
% \renewcommand{\refname}{DOGWORLD}

\renewcommand{\refname}{References}

% from science.sty, this also works:
%\def\refname{References}

% some tests:
% \setlength{\leftmargin}{1in}
% \setlength{\labelsep}{1in} % did something
%\setlength{\labelwidth}{2in}
%\setlength{\itemindent}{1in}
% \setlength{\bibhang}{2in}

% from science.sty, but remove the "*":
\def\thebibliography#1{\section{\refname\@mkboth
  {\uppercase{\refname}}{\uppercase{\refname}}}\list
%  {\@biblabel{\arabic{enumiv}}}{\settowidth\labelwidth{\@biblabel{#1}}%
%  {BEFORE {\arabic{enumiv}} AFTER}{\settowidth\labelwidth{\@biblabel{#1}}%
   {{\arabic{enumiv}}.}{\settowidth\labelwidth{\@biblabel{#1}}%
\raggedright % allows urls to come out ok
%
% tests for setting the indents:
%\setlength{\itemindent}{-\bibhang}
%\setlength{\leftmargin}{\bibhang}
%\setlength{\itemindent}{-0.2 in}
%\setlength{\leftmargin}{1in}
% final parameters:
\setlength{\labelwidth}{2 em}
\setlength{\itemindent}{-2 em}
    \leftmargin\labelwidth
    \advance\leftmargin\labelsep
    \usecounter{enumiv}%
    \let\p@enumiv\@empty
    \def\theenumiv{\arabic{enumiv}}}%
    \def\newblock{\hskip .11em plus.33em minus.07em}%
    \sloppy\clubpenalty4000\widowpenalty4000
    \sfcode`\.=1000\relax}

% from science.sty:
% \def\thebibliography#1{\section*{\refname\@mkboth
%   {\uppercase{\refname}}{\uppercase{\refname}}}\list
% %  {\@biblabel{\arabic{enumiv}}}{\settowidth\labelwidth{\@biblabel{#1}}%
% %  {BEFORE {\arabic{enumiv}} AFTER}{\settowidth\labelwidth{\@biblabel{#1}}%
%    {{\arabic{enumiv}}.}{\settowidth\labelwidth{\@biblabel{#1}}%
%     \leftmargin\labelwidth
%     \advance\leftmargin\labelsep
%     \usecounter{enumiv}%
%     \let\p@enumiv\@empty
%     \def\theenumiv{\arabic{enumiv}}}%
%     \def\newblock{\hskip .11em plus.33em minus.07em}%
%     \sloppy\clubpenalty4000\widowpenalty4000
%     \sfcode`\.=1000\relax}

% *******************************************************************************

\usepackage{cite}
% use cite.sty to set parenthesis:
\renewcommand\citeleft{(}  % parentheses around list
\renewcommand\citeright{)} % parentheses around list
\renewcommand\citepunct{; } % use ";" breaks

% stolen from chicago - bombs
%\def\citeyear{\def\@citeseppen{-1000}%
%    \def\@cite##1##2{(##1\if@tempswa , ##2\fi)}%
%    \def\citeauthoryear##1##2##3{##3}\@citedata}

% *******************************************************************************

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
%%%%%% Old method: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5

% Define JMB type sections
% capital letter makes them different.
% I'll probably remove these later, so don't use them ...

%\newcounter{Sectioncounter}
%\newcounter{SubSectioncounter}

\newcommand{\Section}[1]
{ {
\vspace{24pt}
\noindent {\large \bfseries #1 }
} }
%\noindent {\bf #1 } \\

\newcommand{\SubSection}[1]
{ {
\vspace{12pt}
\noindent {\bf #1 } \\ \\
} }

\newcommand{\SubSubSection}[1]
{ {
\vspace{12pt}
\noindent {\it #1 } \\ \\
} }

% *******************************************************************************
% below this point is old code no longer used (all commented out):

% old section definitions with numbers
%\newcommand{\Section}[1]
%{ {
%\vspace{24pt}
%\addtocounter{Sectioncounter}{1}
%\setcounter{SubSectioncounter}{0}
%\begin{center}
%{\bf \arabic{Sectioncounter}. #1}
%\end{center}
%} }
%
%\newcommand{\SubSection}[1]
%{ {
%\addtocounter{SubSectioncounter}{1}
%\begin{center}
%{\em (\alph{SubSectioncounter}) #1}
%\end{center}
%} }

% \raggedright  this had no effect!!

% the current (2000 Feb) apalike.sty:
% /opt/local/tex/teTeX/texmf/tex/latex/misc/apalike.sty
% this fails the same way!

% \def\@cite#1#2{(#1\if@tempswa , #2\fi)}
% \def\@biblabel#1{}

% \newlength{\bibhang}
% \setlength{\bibhang}{2em}

% \def\@citex[#1]#2{\if@filesw\immediate\write\@auxout{\string\citation{#2}}\fi
%   \def\@citea{}\@cite{\@for\@citeb:=#2\do
%     {\@citea\def\@citea{DID; }\@ifundefined
%        {b@\@citeb}{{\bf ?}\@warning
%        {Citation `\@citeb' on page \thepage \space undefined}}%
% {\csname b@\@citeb\endcsname}}}{#1}}

% This fails to put a semi between references:
% \def\@citea{DID; }