From 199ec164ca9149890e549797f43794c8f5730e1f Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Mon, 22 Feb 2010 20:23:50 -0500 Subject: [PATCH] Use \chapter{}, \section{}, and \ref{} in fdl.txt. Also revert bustamante08 -> betterment08 spellcheck error introduced in 96237f4dfe4fe90895e36f36199235cfb8282560 --- tex/src/fdl.tex | 178 +++++++++++++--------------------- tex/src/introduction/main.tex | 2 +- tex/src/root.bib | 1 + 3 files changed, 67 insertions(+), 114 deletions(-) diff --git a/tex/src/fdl.tex b/tex/src/fdl.tex index 6c6f909..f86055e 100644 --- a/tex/src/fdl.tex +++ b/tex/src/fdl.tex @@ -1,30 +1,22 @@ %\hfuzz = .6pt % avoid black boxes -\chapter*{\rlap{GNU Free Documentation License}} -\phantomsection % so hyperref creates bookmarks -\addcontentsline{toc}{chapter}{GNU Free Documentation License} +\chapter{GNU Free Documentation License} \label{sec:fdl} \begin{center} - Version 1.3, 3 November 2008 + Version 1.3, 3 November 2008 - - Copyright \copyright{} 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc. - - \bigskip + Copyright \copyright{} 2000, 2001, 2002, 2007, 2008 Free Software Foundation, Inc. - - - \bigskip + \url{http://fsf.org/} Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. \end{center} -\begin{center} -{\bf\large Preamble} -\end{center} +\section*{Preamble} +\label{sec:fdl:preamble} The purpose of this License is to make a manual, textbook, or other functional and useful document ``free'' in the sense of freedom: to @@ -48,11 +40,8 @@ whether it is published as a printed book. We recommend this License principally for works whose purpose is instruction or reference. -\begin{center} -{\Large\bf 1. APPLICABILITY AND DEFINITIONS\par} -\phantomsection -\addcontentsline{toc}{section}{1. APPLICABILITY AND DEFINITIONS} -\end{center} +\section{APPLICABILITY AND DEFINITIONS} +\label{sec:fdl:definitions} This License applies to any manual or other work, in any medium, that contains a notice placed by the copyright holder saying it can be @@ -143,11 +132,8 @@ implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License. -\begin{center} -{\Large\bf 2. VERBATIM COPYING\par} -\phantomsection -\addcontentsline{toc}{section}{2. VERBATIM COPYING} -\end{center} +\section{VERBATIM COPYING} +\label{sec:fdl:copying} You may copy and distribute the Document in any medium, either commercially or noncommercially, provided that this License, the @@ -157,18 +143,15 @@ conditions whatsoever to those of this License. You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute. However, you may accept compensation in exchange for copies. If you distribute a large enough -number of copies you must also follow the conditions in section~3. +number of copies you must also follow the conditions in +section~\ref{sec:fdl:quantity}. You may also lend copies, under the same conditions stated above, and you may publicly display copies. -\begin{center} -{\Large\bf 3. COPYING IN QUANTITY\par} -\phantomsection -\addcontentsline{toc}{section}{3. COPYING IN QUANTITY} -\end{center} - +\section{COPYING IN QUANTITY} +\label{sec:fdl:quantity} If you publish printed copies (or copies in media that commonly have printed covers) of the Document, numbering more than 100, and the @@ -206,18 +189,16 @@ Document well before redistributing any large number of copies, to give them a chance to provide you with an updated version of the Document. -\begin{center} -{\Large\bf 4. MODIFICATIONS\par} -\phantomsection -\addcontentsline{toc}{section}{4. MODIFICATIONS} -\end{center} +\section{MODIFICATIONS} +\label{sec:fdl:modifications} You may copy and distribute a Modified Version of the Document under -the conditions of sections 2 and 3 above, provided that you release -the Modified Version under precisely this License, with the Modified -Version filling the role of the Document, thus licensing distribution -and modification of the Modified Version to whoever possesses a copy -of it. In addition, you must do these things in the Modified Version: +the conditions of sections \ref{sec:fdl:copying} and +\ref{sec:fdl:quantity} above, provided that you release the Modified +Version under precisely this License, with the Modified Version +filling the role of the Document, thus licensing distribution and +modification of the Modified Version to whoever possesses a copy of +it. In addition, you must do these things in the Modified Version: \begin{itemize} \item[A.] @@ -326,19 +307,16 @@ give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version. -\begin{center} -{\Large\bf 5. COMBINING DOCUMENTS\par} -\phantomsection -\addcontentsline{toc}{section}{5. COMBINING DOCUMENTS} -\end{center} - +\section{COMBINING DOCUMENTS} +\label{sec:fdl:combining} You may combine the Document with other documents released under this -License, under the terms defined in section~4 above for modified -versions, provided that you include in the combination all of the -Invariant Sections of all of the original documents, unmodified, and -list them all as Invariant Sections of your combined work in its -license notice, and that you preserve all their Warranty Disclaimers. +License, under the terms defined in +section~\ref{sec:fdl:modifications} above for modified versions, +provided that you include in the combination all of the Invariant +Sections of all of the original documents, unmodified, and list them +all as Invariant Sections of your combined work in its license notice, +and that you preserve all their Warranty Disclaimers. The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single @@ -355,11 +333,8 @@ in the various original documents, forming one section Entitled and any sections Entitled ``Dedications''. You must delete all sections Entitled ``Endorsements''. -\begin{center} -{\Large\bf 6. COLLECTIONS OF DOCUMENTS\par} -\phantomsection -\addcontentsline{toc}{section}{6. COLLECTIONS OF DOCUMENTS} -\end{center} +\section{COLLECTIONS OF DOCUMENTS} +\label{sec:fdl:collections} You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this @@ -373,12 +348,8 @@ License into the extracted document, and follow this License in all other respects regarding verbatim copying of that document. -\begin{center} -{\Large\bf 7. AGGREGATION WITH INDEPENDENT WORKS\par} -\phantomsection -\addcontentsline{toc}{section}{7. AGGREGATION WITH INDEPENDENT WORKS} -\end{center} - +\section{AGGREGATION WITH INDEPENDENT WORKS} +\label{sec:fdl:aggregation} A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or @@ -389,47 +360,41 @@ When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document. -If the Cover Text requirement of section~3 is applicable to these -copies of the Document, then if the Document is less than one half of -the entire aggregate, the Document's Cover Texts may be placed on -covers that bracket the Document within the aggregate, or the -electronic equivalent of covers if the Document is in electronic form. -Otherwise they must appear on printed covers that bracket the whole -aggregate. - +If the Cover Text requirement of section~\ref{sec:fdl:quantity} is +applicable to these copies of the Document, then if the Document is +less than one half of the entire aggregate, the Document's Cover Texts +may be placed on covers that bracket the Document within the +aggregate, or the electronic equivalent of covers if the Document is +in electronic form. Otherwise they must appear on printed covers that +bracket the whole aggregate. -\begin{center} -{\Large\bf 8. TRANSLATION\par} -\phantomsection -\addcontentsline{toc}{section}{8. TRANSLATION} -\end{center} +\section{TRANSLATION} +\label{sec:fdl:translation} Translation is considered a kind of modification, so you may -distribute translations of the Document under the terms of section~4. -Replacing Invariant Sections with translations requires special -permission from their copyright holders, but you may include -translations of some or all Invariant Sections in addition to the -original versions of these Invariant Sections. You may include a -translation of this License, and all the license notices in the -Document, and any Warranty Disclaimers, provided that you also include -the original English version of this License and the original versions -of those notices and disclaimers. In case of a disagreement between -the translation and the original version of this License or a notice -or disclaimer, the original version will prevail. +distribute translations of the Document under the terms of +section~\ref{sec:fdl:modifications}. Replacing Invariant Sections +with translations requires special permission from their copyright +holders, but you may include translations of some or all Invariant +Sections in addition to the original versions of these Invariant +Sections. You may include a translation of this License, and all the +license notices in the Document, and any Warranty Disclaimers, +provided that you also include the original English version of this +License and the original versions of those notices and disclaimers. +In case of a disagreement between the translation and the original +version of this License or a notice or disclaimer, the original +version will prevail. If a section in the Document is Entitled ``Acknowledgements'', -``Dedications'', or ``History'', the requirement (section~4) to Preserve -its Title (section~1) will typically require changing the actual -title. - +``Dedications'', or ``History'', the requirement +(section~\ref{sec:fdl:modifications}) to Preserve its Title +(section~\ref{sec:fdl:definitions}) will typically require changing +the actual title. -\begin{center} -{\Large\bf 9. TERMINATION\par} -\phantomsection -\addcontentsline{toc}{section}{9. TERMINATION} -\end{center} +\section{TERMINATION} +\label{sec:fdl:termination} You may not copy, modify, sublicense, or distribute the Document except as expressly provided under this License. Any attempt @@ -457,12 +422,7 @@ reinstated, receipt of a copy of some or all of the same material does not give you any rights to use it. -\begin{center} -{\Large\bf 10. FUTURE REVISIONS OF THIS LICENSE\par} -\phantomsection -\addcontentsline{toc}{section}{10. FUTURE REVISIONS OF THIS LICENSE} -\end{center} - +\section{FUTURE REVISIONS OF THIS LICENSE} The Free Software Foundation may publish new, revised versions of the GNU Free Documentation License from time to time. Such new @@ -484,12 +444,8 @@ version permanently authorizes you to choose that version for the Document. -\begin{center} -{\Large\bf 11. RELICENSING\par} -\phantomsection -\addcontentsline{toc}{section}{11. RELICENSING} -\end{center} - +\section{RELICENSING} +\label{sec:fdl:relicensing} ``Massive Multiauthor Collaboration Site'' (or ``MMC Site'') means any World Wide Web server that publishes copyrightable works and also @@ -519,11 +475,7 @@ under CC-BY-SA on the same site at any time before August 1, 2009, provided the MMC is eligible for relicensing. -\begin{center} -{\Large\bf ADDENDUM: How to use this License for your documents\par} -\phantomsection -\addcontentsline{toc}{section}{ADDENDUM: How to use this License for your documents} -\end{center} +\section*{ADDENDUM: How to use this License for your documents} To use this License in a document you have written, include a copy of the License in the document and put the following copyright and diff --git a/tex/src/introduction/main.tex b/tex/src/introduction/main.tex index 6626ecb..a15a777 100644 --- a/tex/src/introduction/main.tex +++ b/tex/src/introduction/main.tex @@ -18,7 +18,7 @@ techniques, in which the macromolecules are studied one at a time, allow direct access to the variation within the population without averaging. This provides important and complementary information about the functional mechanisms of several biological -systems\citep{betterment08}. +systems\citep{bustamante08}. % What do genes do? Why is protein folding interesting? An organism's genetic code is stored in DNA in the cell nucleus. diff --git a/tex/src/root.bib b/tex/src/root.bib index 06f512c..0b6d288 100644 --- a/tex/src/root.bib +++ b/tex/src/root.bib @@ -4746,6 +4746,7 @@ doi = {10.1063/1.439715} url = "http://www.sciencemag.org/cgi/content/abstract/275/5304/1295", eprint = "http://www.sciencemag.org/cgi/reprint/275/5304/1295.pdf", } + @Article{bustamante08, author = CBustamante, title = "In singulo Biochemistry: When Less Is More", -- 2.26.2