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Commit b4c95ee0 authored by Jerome Mariette's avatar Jerome Mariette
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add the production tex files

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BMC_jvenn_final/1265083534131530_Formatted.tex 0 → 100644
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BMC_jvenn_final/bmc-mathtime.sty 0 → 100644
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BMC_jvenn_final/bmc_article_s50.cls 0 → 100644
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%% %
% bmc_article.cls ver: 1.03 %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%
% A Style Class based on article for %%
% formating towards BioMed Central %%
% guidelines %%
% %%
% <1 September 2003> %%
% %%
% %%
% %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% See Readme.txt for ToDo list.
%%
%
\NeedsTeXFormat{LaTeX2e}[1995/12/01]
\ProvidesClass{bmc_article}[2003/09/01 v1.01 BioMed Central article class]
\LoadClassWithOptions{article}
\renewcommand\@biblabel[1]{#1.}
\def\hi{}
\AtBeginDocument{}
\def\@abstractline{\textwidth}
\newcounter{bmc@correspondingauthor}
\setcounter{bmc@correspondingauthor}{0} %never changes
\newcounter{bmc@emailcounter} \setcounter{bmc@emailcounter}{0}
% Corresponding Authors.
% adds an asterisk * as a marker.
\def\correspondingauthor{$^*$}
\def\@corresponding{\footnotesize\correspondingauthor Corresponding author}
%%%%%%%%%%%%%% TITLE %%%%%%%%%%%%%%%%%%%%
%% Article Email
\renewcommand{\maketitle}{
\begin{flushleft}
\fontsize{20.7pt}{19.07pt}\fontfamily{ptm}\fontseries{b}
\fontshape{u}\selectfont
\@title
\end{flushleft}
}
%%%%%%%%%%%%%%%% author, email and corauthor %%%%%%%%%%%%%%%%%%%%
\renewcommand\author[2][]{\relax
{\hspace*{56pt}#2\hspace*{0pt}$^{#1}$\\}}
\newcommand\email[1]{\relax
{\hspace*{56pt}\vspace*{15pt}Email: #1\\}}
\newcommand\cor[1]{\relax
{\hspace*{56pt}$^*$Corresponding author\\}}
\newcommand\address[2][]{\relax
{\hspace*{56pt}$^#1$#2}\vspace*{7pt}\\}
% reformats abstract to BMC looks
\let\old@abstract\abstract
\renewenvironment{abstract}
{ \begin{framed}
\ifhmode\begingroup\parskip0pt\par\noindent\endgroup\fi%
% \begin{sffamily}
% use \topsep in list
{\noindent\Large\bfseries\abstractname\vspace{-0.5em}}
{\par\vbox{}}
\raggedright}{
\ifhmode\begingroup\parskip0pt\par\noindent\endgroup\fi %
% \end{sffamily}
\end{framed}
}
%% \@startsection{sec-name}{level}{indent}{pre-skip}
%% {post-skip}{style}*[srt title]{title}
\parskip = 1.2\baselineskip
\renewcommand\section{\@startsection {section}{1}{\z@}%
{-0.3cm \@plus 1ex \@minus -.2ex} {2pt\@plus.2ex} %%
{\normalfont\large\bfseries}}
\raggedright
\renewcommand\subsection{\@startsection{subsection}{2}{\z@}%
{-0.20cm \@plus -1ex \@minus -.2ex} {1pt \@plus.2ex} %%
{\normalfont\normalsize\bfseries}}
\raggedright
\renewcommand\subsubsection{\@startsection{subsubsection}{3}{\z@}%
{-0.15cm \@plus -1ex \@minus -.2ex} {.2ex \@plus.2ex} %%
{\normalfont\normalsize\bfseries\itshape}}
\raggedright
\renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}%
{12.5pt \@plus1ex \@minus.2ex}%
{-.5em}%
{\normalfont\normalsize\bfseries}}
%%\renewcommand\paragraph{\@startsection{paragraph}{4}{\z@}%
%% {-0.10cm \@plus -1ex \@minus -.2ex}{0.5pt \@plus.2ex}
%% {\normalfont\normalsize\bfseries}}
%% \raggedright
\renewcommand\subparagraph{\@startsection{subparagraph}{5}{\parindent}%
{-.2em \@plus -1ex \@minus -.2ex} {-0.5em} %%
{\normalfont\it}}
\raggedright
%%%%%%%%%%%%%%%S50 Requirements%%%%%%%%%%%%%%%%%%
\RequirePackage{times}
%\usepackage{mathtime}
%\RequirePackage[T1,mtbold]{bmc-mathtime}
\RequirePackage{setspace}
\RequirePackage[T1]{fontenc}
\RequirePackage{mathrsfs}
\RequirePackage{framed_v1}
\RequirePackage[nospace]{cite}
\renewcommand{\citedash}{\mbox{-}\penalty\citepunctpenalty}
%%%%%%%%%%%%%%%Floats %%%%%%%%%%%%%%%%%%
%%\def\tablename{\bf Table}
%%\def\figurename{\bf Figure}
%%
%%\long\def\@makecaption#1#2{%
%% \vskip\abovecaptionskip
%% \sbox\@tempboxa{#1\hspace*{4pt}\ #2}%
%% \ifdim \wd\@tempboxa >\hsize
%% #1\hspace*{4pt}\ #2\par
%% \else
%% \global \@minipagefalse
%% \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
%% \fi
%% \vskip\belowcaptionskip}
\RequirePackage{xstring}
\RequirePackage{etoolbox}
\RequirePackage{caption}
\captionsetup{labelfont=bf,labelsep=space,singlelinecheck=off}
\makeatletter
\newcommand\formatlabel[1]{%
\noexpandarg
\IfSubStr{#1}{.}{%
\StrBefore{#1}{.}[\firstcaption]%
\StrBehind{#1}{.}[\secondcaption]%
\textbf{\firstcaption.} \secondcaption}{%
#1}%
}
\patchcmd{\@caption}{#3}{\formatlabel{#3}}
\makeatother
%%%%%%%%%%%%%%%--Enunciation--%%%%%%%%%%%%%%%%%%
\RequirePackage{amsthm}
\makeatletter
\let\proof\relax
\let\endproof\relax
\newif\ifproofthm
\def\@endtheorem{\ifproofthm\qed\global\proofthmfalse\fi\endtrivlist\@endpefalse }
\makeatother
\newtheoremstyle{bmcstyleone}
{} % Space above
{} % Space below
{\normalfont} % Body font
{\parindent} % Indent amount
{\bfseries} % Theorem head font
{.} % Punctuation after theorem head
{.5em} % Space after theorem head
{} % Theorem head spec (can be left empty, meaning `normal')
\newtheoremstyle{bmcstyletwo}
{} % Space above
{} % Space below
{\normalfont} % Body font
{} % Indent amount
{\itshape} % Theorem head font
{.} % Punctuation after theorem head
{.5em} % Space after theorem head
{\thmname{#1}\thmnumber{ #2}\thmnote{. #3}} % Theorem head spec (can be left empty, meaning `normal')
\newtheoremstyle{bmcstylethree}
{} % Space above
{} % Space below
{\itshape} % Body font
{\parindent} % Indent amount
{\bfseries} % Theorem head font
{.} % Punctuation after theorem head
{.5em} % Space after theorem head
{} % Theorem head spec (can be left empty, meaning `normal')
%%%%%%%%%%%%%%%=Proof=%%%%%%%%%%%%%%%%%%
\newtheoremstyle{bmcproofone}% Proof
{12pt}% Space above
{12pt}% Space below
{\normalfont}% Body font
{\parindent}% Indent amount
{\itshape}% Theorem head font
{.}% Punctuation after theorem head
{.35em}% Space after theorem headi
{\global\proofthmtrue\thmname{#1}}% Theorem head spec (can be left empty, meaning `normal')
\newtheoremstyle{bmcprooftwo}% Proof
{12pt}% Space above
{12pt}% Space below
{\normalfont}% Body font
{\parindent}% Indent amount
{\bfseries}% Theorem head font
{.}% Punctuation after theorem head
{.35em}% Space after theorem headi
{\global\proofthmtrue\thmname{#1}}% Theorem head spec (can be left empty, meaning `normal')
%%%%%%%%%%%%%%%--Keywords--%%%%%%%%%%%%%%%%%%
\def\abshead#1{{\bfseries\large #1}\par}
\def\pacs#1{\textbf{\large Pacs}\par #1}
\def\keywords#1{\textbf{\large Keywords}\par #1}
\def\pacs#1{\textbf{\large Pacs}\par #1}
%%%%%%%%%%%%%%% Reference %%%%%%%%%%%%%%%%%%
\def\nameyear{\usepackage{natbib}\bibpunct[, ]{(}{)}{;}{a}{}{,}}
%%%%%%%%%%%%%%%--EndNotes--%%%%%%%%%%%%%%%%%%
\RequirePackage{endnotes}
\let\footnote=\endnote
\renewcommand{\notesname}{Endnotes}
\renewcommand\enoteformat{\vspace*{-12pt}\normalsize\rightskip=0pt \leftskip=0pt \parindent=0em
\leavevmode\makeenmark}
%%%%%%%%%%%%%%%--EndNotes--%%%%%%%%%%%%%%%%%%
\setlength{\paperheight}{297mm}%
\setlength{\paperwidth}{210mm}%
\setlength\topmargin{25mm}
\addtolength{\topmargin}{-1in}
\setlength\oddsidemargin{25truemm}
\addtolength{\oddsidemargin}{-1in}
\setlength{\textwidth}{159mm}
\setlength{\textheight}{246mm}%{60\baselineskip}
\addtolength\textheight{.25pt}
%%\setlength\footskip{28}
\setlength\maxdepth{0pt}
\setlength{\parskip}{12pt}
\usepackage{ragged2e}
\voffset-20mm
\endinput
%% end of bmc_article.cls
BMC_jvenn_final/framed_v1.sty 0 → 100644
View file @ b4c95ee0
% framed.sty v 0.95 2007/10/04
% Copyright (C) 1992-2007 by Donald Arseneau (asnd@triumf.ca)
% These macros may be freely transmitted, reproduced, or modified
% provided that this notice is left intact.
%
%====================== Begin Instructions =======================
%
% framed.sty
% ~~~~~~~~~~
% Create framed, shaded, or differently highlighted regions that can
% break across pages. The environments defined are
% framed -- ordinary frame box (\fbox) with edge at margin
% shaded -- shaded background (\colorbox) bleeding into margin
% snugshade -- similar
% leftbar -- thick vertical line in left margin
% to be used like
% \begin{framed}
% copious text
% \end{framed}
%
% But the more general purpose of this package is to facilitate the
% creation of environments that enable page breaking
% within arbitrary decorations using a simple new-environment definition
% incorporating \FrameCommand and
% \begin{MakeFramed}{settings} ... \end{MakeFramed}
%
% The "framed" environment uses "\fbox" as its "\FrameCommand" with
% the additional settings \fboxrule=\FrameRule and \fboxsep=\FrameSep.
% You can change these lengths (using \setlength) and you can change
% the definition of \FrameCommand to use much fancier boxes.
%
% In fact, the "shaded" environment just redefines \FrameCommand to be
% \colorbox{shadecolor} (and you have to define the color "shadecolor":
% \definecolor{shadecolor}...).
%
% A page break is allowed, and even encouraged, before the framed
% environment. If you want to attach some text (a box title) to the
% frame, then the text should be inserted by \FrameCommand.
%
% The contents of the framed regions are restricted:
% Floats, footnotes, marginpars and head-line entries will be lost.
% (Some of these may be handled in a later version.)
% This package will not work with the page breaking of multicol.sty,
% or other systems that perform column-balancing.
%
% The MakeFramed environment does the work. Its "settings" argument
% should contain any adjustments to the text width (applied to \hsize,
% and using the "\width" of the frame itself) as well as a "restore"
% command -- \@parboxrestore or \FrameRestore or something similar;
% as an example, the snugshade environment shows how to suppress excess
% spacing within the box, copying the code from minipage.
%
% Expert commands:
% \MakeFramed, \endMakeFramed: the "MakeFramed" environment
% \FrameCommand: command to draw the frame around its argument
% \FrameRestore: restore some text settings, but fewer than \@parboxrestore
% \FrameRule: length register; \fboxrule for default "framed".
% \FrameSep: length register; \fboxsep for default "framed".
% \FrameHeightAdjust: macro; height of frame above baseline at top of page
%
% This is still a `pre-production' version because I can think of many
% features/improvements that should be made. Nevertheless, starting
% with version 0.5 it should be bug-free.
%
% ToDo:
% Test more varieties of list
% Improve and correct documentation
% Propagation of \marks
% Handle footnotes (how??) floats (?) and marginpars.
% Stretchability modification.
%======================== End Instructions ========================
\ProvidesPackage{framed}[2007/10/04 v 0.95:
framed or shaded text with page breaks]
\newenvironment{framed}% using default \FrameCommand
{\MakeFramed {\advance\hsize-\width \FrameRestore}}%
{\endMakeFramed}
\newenvironment{shaded}{%
\def\FrameCommand{\fboxsep=\FrameSep \colorbox{shadecolor}}%
\MakeFramed {\FrameRestore}}%
{\endMakeFramed}
\newenvironment{leftbar}{%
\def\FrameCommand{\vrule width 3pt \hspace{10pt}}%
\MakeFramed {\advance\hsize-\width \FrameRestore}}%
{\endMakeFramed}
\newenvironment{snugshade}{%
\def\FrameCommand{\colorbox{shadecolor}}%
\MakeFramed {\FrameRestore\@setminipage}}%
{\par\unskip\endMakeFramed}
\chardef\FrameRestore=\catcode`\| % for debug
\catcode`\|=\catcode`\% % (debug: insert space after backslash)
\def\MakeFramed#1{\par
% measure added width and height; call result \width and \height
\fb@sizeofframe\FrameCommand
\let\width\fb@frw \let\height\fb@frh
% insert pre-penalties and skips
\begingroup
\skip@\lastskip
\if@nobreak\else
\penalty9999 % updates \page parameters
\ifdim\pagefilstretch=\z@ \ifdim\pagefillstretch=\z@
% not infinitely stretchable, so encourage a page break here
\edef\@tempa{\the\skip@}%
\ifx\@tempa\zero@glue \penalty-30
\else \vskip-\skip@ \penalty-30 \vskip\skip@
\fi\fi\fi
\penalty\z@
% Give a stretchy breakpoint that will always be taken in preference
% to the \penalty 9999 used to update page parameters. The cube root
% of 10000/100 indicates a multiplier of 0.21545, but the maximum
% calculated badness is really 8192, not 10000, so the multiplier
% is 0.2301.
\advance\skip@ \z@ plus-.5\baselineskip
\advance\skip@ \z@ plus-.231\height
\advance\skip@ \z@ plus-.231\skip@
\advance\skip@ \z@ plus-.231\topsep
\vskip-\skip@ \penalty 1800 \vskip\skip@
\fi
\addvspace{\topsep}%
\endgroup
% clear out pending page break
\penalty\@M \vskip 2\baselineskip \vskip\height
\penalty9999 \vskip -2\baselineskip \vskip-\height
\penalty9999 % updates \pagetotal
|\message{After clearout, \pagetotal=\the\pagetotal, \pagegoal=\the\pagegoal. }%
\fb@adjheight
\setbox\@tempboxa\vbox\bgroup
#1% Modifications to \hsize (can use \width and \height)
\textwidth\hsize \columnwidth\hsize
}
\def\endMakeFramed{\par
\kern\z@
\hrule\@width\hsize\@height\z@
\penalty-100 % put depth into height
\egroup
% {\showoutput\showbox\@tempboxa}%
\begingroup
\fb@put@frame\FrameCommand\FirstFrameCommand
\endgroup
}
% \fb@put@frame takes the contents of \@tempboxa and puts all, or a piece,
% of it on the page with a frame (\FrameCommand, \FirstFrameCommand,
% \MidFrameCommand, or \LastFrameCommand). It recurses until all of
% \@tempboxa has been used up. (\@tempboxa must have zero depth.)
% #1 = attempted framing command, if no split
% #2 = framing command if split
% First iteration: Try to fit with \FrameCommand. If it does not fit,
% split for \FirstFrameCommand.
% Later iteration: Try to fit with \LastFrameCommand. If it does not
% fit, split for \MidFrameCommand.
\def\fb@put@frame#1#2{\relax
\ifdim\pagegoal=\maxdimen \pagegoal\vsize \fi
| \message{=============== Entering putframe ====================^^J
| \pagegoal=\the\pagegoal, \pagetotal=\the\pagetotal. }%
\ifinner
\fb@putboxa#1%
\fb@afterframe
\else
\dimen@\pagegoal \advance\dimen@-\pagetotal % natural space left on page
\ifdim\dimen@<2\baselineskip % Too little room on page
| \message{Page has only \the\dimen@\space room left; eject. }%
\eject \fb@adjheight \fb@put@frame#1#2%
\else % there's appreciable room left on the page
\fb@sizeofframe#1%
| \message{\string\pagetotal=\the\pagetotal,
| \string\pagegoal=\the\pagegoal,
| \string\pagestretch=\the\pagestretch,
| \string\pageshrink=\the\pageshrink,
| \string\fb@frh=\fb@frh. \space}
| \message{Box of size \the\ht\@tempboxa\space + \fb@frh}%
\begingroup % temporarily set \dimen@ to be...
\advance\dimen@.8\pageshrink % maximum space available on page
\advance\dimen@-\fb@frh\relax % space available for frame's contents
\expandafter\endgroup
% expand \ifdim, then restore \dimen@ to real room left on page
\ifdim\dimen@>\ht\@tempboxa % whole box does fit
| \message{fits in \the\dimen@. }%
% Use vsplit anyway to capture the marks
% !!!???!!! MERGE THIS WITH THE else CLAUSE!!!
\fb@putboxa#1%
\fb@afterframe
\else % box must be split
| \message{must be split to fit in \the\dimen@. }%
% update frame measurement to use \FirstFrameCommand or \MidFrameCommand
\fb@sizeofframe#2%
\setbox\@tempboxa\vbox{% simulate frame and flexiblity of the page:
\vskip \fb@frh \@plus\pagestretch \@minus.8\pageshrink
\kern137sp\kern-137sp\penalty-30
\unvbox\@tempboxa}%
\edef\fb@resto@set{\boxmaxdepth\the\boxmaxdepth
\splittopskip\the\splittopskip}%
\boxmaxdepth\z@ \splittopskip\z@
| \message{Padded box of size \the\ht\@tempboxa\space split to \the\dimen@}%
% Split box here
\setbox\tw@\vsplit\@tempboxa to\dimen@
| \toks99\expandafter{\splitfirstmark}%
| \toks98\expandafter{\splitbotmark}%
| \message{Marks are: \the\toks99, \the\toks98. }%
\setbox\tw@\vbox{\unvbox\tw@}% natural-sized
| \message{Natural height of split box is \the\ht\tw@, leaving
| \the\ht\@tempboxa\space remainder. }%
% If the split-to size > (\vsize-\topskip), then set box to full size
\begingroup
\advance\dimen@\topskip
\expandafter\endgroup
\ifdim\dimen@>\pagegoal
| \message{Frame is big -- Use up the full column. }%
\dimen@ii\pagegoal
\advance\dimen@ii -\topskip
\advance\dimen@ii \FrameHeightAdjust\relax
\else % suspect this is wrong:
% If the split-to size > feasible room_on_page, rebox it smaller.
\advance\dimen@.8\pageshrink
\ifdim\ht\tw@>\dimen@
| \message{Box too tall; rebox it to \the\dimen@. }%
\dimen@ii\dimen@
\else % use natural size
\dimen@ii\ht\tw@
\fi
\fi
% Re-box contents to desired size \dimen@ii
\advance\dimen@ii -\fb@frh
\setbox\tw@\vbox to\dimen@ii \bgroup
% remove simulated frame and page flexibility:
\vskip -\fb@frh \@plus-\pagestretch \@minus-.8\pageshrink
\unvbox\tw@ \unpenalty\unpenalty
\ifdim\lastkern=-137sp % whole box went to next page
| \message{box split at beginning! }%
% need work here???
\egroup \fb@resto@set \eject % (\vskip for frame size was discarded)
\fb@adjheight
\fb@put@frame#1#2% INSERTED ???
\else % Got material split off at the head
\egroup \fb@resto@set
\ifvoid\@tempboxa % it all fit after all
| \message{box split at end! }%
\setbox\@tempboxa\box\tw@
\fb@putboxa#1%
\fb@afterframe
\else % it really did split
| \message{box split as expected. Its reboxed height is \the\ht\tw@. }%
\ifdim\wd\tw@>\z@
\wd\tw@\wd\@tempboxa
\centerline{#2{\box\tw@}}% ??? \centerline bad idea
\else
| \message{Zero width means likely blank. Don't frame it (guess)}%
\box\tw@
\fi
\hrule \@height\z@ \@width\hsize
\eject
\fb@adjheight
\fb@put@frame\LastFrameCommand\MidFrameCommand
\fi\fi\fi\fi\fi
}
\def\fb@putboxa#1{%
\ifvoid\@tempboxa
PackageWarning{framed}{Boxa is void -- discard it. }%
\else
| \message{Frame and place boxa. }%
| %{\showoutput\showbox\@tempboxa}%
\centerline{#1{\box\@tempboxa}}%
\fi
}
\def\fb@afterframe{%
\nointerlineskip \null %{\showoutput \showlists}
\penalty-30 \vskip\topsep \relax
}
% measure width and height added by frame (#1 = frame command)
% call results \fb@frw and \fb@frh
\newdimen\fb@frw
\newdimen\fb@frh
\def\fb@sizeofframe#1{\begingroup
\setbox\z@\vbox{\vskip-5in \hbox{\hskip-5in
#1{\hbox{\vrule \@height 4.7in \@depth.3in \@width 5in}}}%
\vskip\z@skip}%
| \message{Measuring frame addition for \string#1 in \@currenvir\space
| gives ht \the\ht\z@\space and wd \the\wd\z@. }%
%{\showoutput\showbox\z@}%
\global\fb@frw\wd\z@ \global\fb@frh\ht\z@
\endgroup
}
\def\fb@adjheight{%
\vbox to\FrameHeightAdjust{}% get proper baseline skip from above.
\penalty\@M \nointerlineskip
\vskip-\FrameHeightAdjust
\penalty\@M} % useful for tops of pages
\edef\zero@glue{\the\z@skip}
\catcode`\|=\FrameRestore
% Provide configuration commands:
\setlength{\textwidth}{162.5mm}
\providecommand\FrameCommand{%
\setlength\fboxrule{\FrameRule}\setlength\fboxsep{\FrameSep}%
\fbox}
\@ifundefined{FrameRule}{\newdimen\FrameRule \FrameRule=\fboxrule}{}
\@ifundefined{FrameSep} {\newdimen\FrameSep \FrameSep =1.5\fboxsep}{}
\providecommand\FirstFrameCommand{\FrameCommand}
\providecommand\MidFrameCommand{\FrameCommand}
\providecommand\LastFrameCommand{\FrameCommand}
% Height of frame above first baseline when frame starts a page:
\providecommand\FrameHeightAdjust{6pt}
% \FrameRestore has parts of \@parboxrestore, performing a similar but
% less complete restoration of a default layouy. See how it is used in the
% "settings" argument of \MakeFrame. Though not a parameter, \hsize
% should be set to the desired total line width available inside the
% frame before invoking \FrameRestore.
\def\FrameRestore{%
\let\if@nobreak\iffalse
\let\if@noskipsec\iffalse
\let\-\@dischyph
\let\'\@acci\let\`\@accii\let\=\@acciii
% \message{FrameRestore:
% \@totalleftmargin=\the \@totalleftmargin,
% \rightmargin=\the\rightmargin,
% \@listdepth=\the\@listdepth. }%
% Test if we are in a list (or list-like paragraph)
\ifnum \ifdim\@totalleftmargin>\z@ 1\fi
\ifdim\rightmargin>\z@ 1\fi
\ifnum\@listdepth>0 1\fi 0>\z@
% \message{In a list: \linewidth=\the\linewidth, \@totalleftmargin=\the\@totalleftmargin,
% \parshape=\the\parshape, \columnwidth=\the\columnwidth, \hsize=\the\hsize,
% \labelwidth=\the\labelwidth. }%
\@setminipage % snug fit around the item
% Now try to propageate changes of width from \hsize to list parameters.
% This is deficient, but a more advanced way to indicate modification to text
% dimensions is not (y