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first after download template from overleaf

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
% Glossary entries are defined with the command \nomenclature{1}{2}
% 1 = Entry name, e.g. abbreviation; 2 = Explanation
% You can place all explanations in this separate file or declare them in the middle of the text. Either way they will be collected in the glossary.
% required to print nomenclature name to page header
\markboth{\MakeUppercase{\nomname}}{\MakeUppercase{\nomname}}
% ----------------------- contents from here ------------------------
%
\nomenclature{LaTeX}{Lamport TeX}

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% Thesis Abstract -----------------------------------------------------
\begin{abstracts} %creates the abstract header
The abstract will be printed on the spikblad which will be folded into the printed thesis. However, if you feel it necessary to also have the abstract in the printed document put it here.
\end{abstracts}
% ----------------------------------------------------------------------

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% Thesis Acknowledgements ------------------------------------------------
\chapter{Acknowledgements}
I would like to acknowledge...
% ------------------------------------------------------------------------

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% Author's contribution -----------------------------------------------------
\chapter{Author's contribution}
If you want to include a summary of your contributions to the presented work in the frontmatter, put it here.
% ----------------------------------------------------------------------

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% Thesis Dedictation ---------------------------------------------------
\begin{dedication}
{\fontfamily{calligra}\selectfont
{\Large
This thesis is dedicated to...
}
}
\end{dedication}
% ----------------------------------------------------------------------

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\chapter{List of Papers}
\vspace{-5pt} % Increase to have a larger space.
The following papers, referred to in the text by their Roman numerals, are included in this thesis.
\vspace{0pt} % Increase to have a larger space before the list is started.
\begin{enumerate}[P{A}PER I: ]
%\begin{enumerate}[I]
\setlength{\itemsep}{3.3mm} %Set the vertical distance between the items
% Suggested order
% Author 1 surname, Author 2 first name initial., Author 1 surname, Author 2 first name
% initial. etc. (Year of publication) Paper main title.
% Paper subtitle. Name of journal in italics, volume(number):page rage
% Example
\item\textbf{Titel}\\
Author1, Author2, \emph{paper}, \textbf{issue}, page (YEAR).\\
DOI: \href{}{}
\end{enumerate}
\noindent
\rule{\linewidth}{0.5mm}
\vspace{2mm}
\noindent
Reprints were made with permission from the publishers.

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{1_introduction/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
%: ----------------------- HELP: latex document organisation
% the commands below help you to subdivide and organise your thesis
% \chapter{} = level 1, top level
% \section{} = level 2
% \subsection{} = level 3
% \subsubsection{} = level 4
% note that everything after the percentage sign is hidden from output
\chapter{Introduction} % top level followed by section, subsection
\section{What is this?}
This is a template for producing PhD-thesis at Stockholm University (SU)\nomenclature{SU}{Stockholm University} using pdf\LaTeX. It could also, with some alterations, be used for Master thesis and Licentiat thesis. Observe that it is designed to be used with pdf\LaTeX and will not work (at least not as in the present state) with \TeX,\LaTeX or pdf\TeX.
The template produces all necessary parts such as half title page, title page, printing info and so on. Simply input the information as called for in the file \emph{thesis.tex}. It also produces a number of parts for the front matter and back matter. Some of these parts are mandatory and some are optional depending on whether the it is a monograph or a summary. Comment or uncomment these to fit your preferences. For more information see Section~\ref{layout}.
%\subsection{Name your subsection} % subsection headings are again smaller than section names
%\subsubsection{Name your subsubsection} % subsubsection headings are again smaller than subsection names
%Starch of plants and glycogen of animals consists of $\alpha$-1,4-glycosidic glucose polymers \cite{lastname07}. See figure \ref{largepotato} for a comparison of glucose polymer structure and chemistry.
%Two references can be placed separated by a comma \cite{lastname07,name06}.
%: ----------------------- HELP: references
% References can be links to figures, tables, sections, or references.
% For figures, tables, and text you define the target of the link with \label{XYZ}. Then you call cross-link with the command \ref{XYZ}, as above
% Citations are bound in a very similar way with \cite{XYZ}. You store your references in a BibTex file with a programme like BibDesk.
%\figuremacro{largepotato}{A common glucose polymers}{The figure shows starch granules in potato cells, taken from \href{http://molecularexpressions.com/micro/gallery/burgersnfries/burgersnfries4.html}{Molecular Expressions}.}
%: ----------------------- HELP: adding figures with macros
% This template provides a very convenient way to add figures with minimal code.
% \figuremacro{1}{2}{3}{4} calls up a series of commands formating your image.
% 1 = name of the file without extension; PNG, JPEG is ok; GIF doesn't work
% 2 = title of the figure AND the name of the label for cross-linking
% 3 = caption text for the figure
%: ----------------------- HELP: www links
% You can also see above how, www links are placed
% \href{http://www.something.net}{link text}
%\figuremacroW{largepotato}{Title}{Caption}{0.8}
% variation of the above macro with a width setting
% \figuremacroW{1}{2}{3}{4}
% 1-3 as above
% 4 = size relative to text width which is 1; use this to reduce figures
%: ----------------------- HELP: tables
% Directly coding tables in latex is tiresome. See below.
% I would recommend using a converter macro that allows you to make the table in Excel and convert them into latex code which you can then paste into your doc.
% This is the link: http://www.softpedia.com/get/Office-tools/Other-Office-Tools/Excel2Latex.shtml
% It's a Excel template file containing a macro for the conversion.
%\begin{table}[htdp]
%\centering
%\begin{tabular}{ccc} % ccc means 3 columns, all centered; alternatives are l, r
%{\bf Gene} & {\bf GeneID} & {\bf Length} \\
% & denotes the end of a cell/column, \\ changes to next table row
%\hline % draws a line under the column headers
%human latexin & 1234 & 14.9 kbps \\
%mouse latexin & 2345 & 10.1 kbps \\
%rat latexin & 3456 & 9.6 kbps \\
% Watch out. Every line must have 3 columns = 2x &.
% Otherwise you will get an error.
%\end{tabular}
%\caption[title of table]{\textbf{title of table} - Overview of latexin genes.}
% You only need to write the title twice if you don't want it to appear in bold in the list of tables.
%\label{latexin_genes} % label for cross-links with \ref{latexin_genes}
%\end{table}
% There you go. You already know the most important things.
% ----------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{1_introduction/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{Instructions} % top level followed by section, subsection
\section{Outline of the thesis \label{layout}}
The outline of the thesis depends on whether it is a monograph or a summary. The different parts of the two types of thesis are summarized in Table\ref{tab:outline} were the optional parts have been put in italics. In this template all parts have been included and it is up to the author to exclude (comment) the appropriate parts in the main file \emph{thesis.tex}. The different parts of the thesis are described in the following sections.
\begin{table}[htp]
\begin{tabular}{|l|l|}
\hline
\textbf{Summary} & \textbf{Monograph} \\
Title page & Half title page \\
Printing info (\emph{abstract}) & Empty page \\
\emph{Dedication page} & Title page \\
Possible empty page & Printing info (\emph{abstract}) \\
List of papers & \emph{Dedication page} \\
Possible empty page & Possible empty page \\
\emph{Authors contribution} & Table of contents \\
Possible empty page & Possible empty page \\
Table of contents & \emph{List of Abbreviations/Figures/Tables} \\
Possible empty page & Possible empty page \\
\emph{List of Abbreviations/Figures/Tables} & \emph{Acknowledgments} \\
Possible empty page & Possible empty page \\
Chapter 1 introduction & Chapter 1 introduction\\
Chapter 2...N & Chapter 2...N\\
Summary & Summary \\
\emph{Acknowledgments} & References \\
References & \\
\hline
\end{tabular}
\caption{\label{tab:outline}Outline of the two types of thesis. Parts in italics are optional.}
\end{table}
\subsection{Title page}
This should include the SU logotype, thesis title and subtitle as well as the name of the author. The page is automatically generated by the template using information supplied by the author in the file \emph{thesis.tex}.
\subsection{Half title page}
This page (smutstittelsida) is generated by the command
\begin{verbatim}
\halftitlepage
\end{verbatim}
in \emph{thesis.tex}.
\subsection{Printing info (abstract)}
The printing info should be supplied by the author in the file \emph{thesis.tex}. The abstract of the thesis will be printed on the spikblad which will be generated upon the electronic spikning. However, if the author believes it necessary to also include the abstract in the printed document this is were it should go. The body of the abstract should the be included in the file \emph{abstract.tex} in \emph{$\backslash$0\_frontmatter}.
\subsection{Dedication}
If you would like to include a dedication put the text in the file \emph{dedication.tex} in \emph{$\backslash$0\_frontmatter}. If not, comment the line
\begin{verbatim}
\include 0_frontmatter/dedication
\end{verbatim}
in \emph{thesis.tex}.
\subsection{List of papers}
Same as Dedication.
\subsection{Authors contribution}
Same as Dedication
\subsection{Table of contents}
Automatically generated by \emph{thesis.tex}.
\subsection{List of Abbreviations/Figures/Tables}
These lists can be included or excluded according to the authors wishes. List of figures and List of Tables are automatically generated by corresponding commands in \emph{thesis.tex}. The List of Abbreviations is also generated by \emph{thesis.tex} using the file \emph{thesis.nls}. This can in turn be generated by the command 'makeindex thesis.nlo -s nomencl.ist -o thesis.nls' from the file \emph{thesis.nlo} which is automatically generated by pdf\LaTeX from the entries found in the file \emph{abbreviations.tex} in \emph{$\backslash$0\_frontmatter} or in any of the included .tex-files using the syntax
\begin{verbatim}
\nomenclature{STHML}{Stockholm}.
\end{verbatim}
\nomenclature{STHML}{Stockholm} For more information see the documatation of the \emph{nomencl} package \citep{nomencl}
\subsection{Acknowledgements}
If you are writing a Monograph and would like to add acknowledgements this is were you put it. Simply make sure the line
\begin{verbatim}
\include{0_frontmatter/acknowledgement}
\end{verbatim}
in the Front matter part of \emph{thesis.tex} and edit the file \emph{acknowledgement.tex} in \emph{$\backslash$0\_frontmatter}.
\subsection{Chapter 1...N}
The chapters are included in the Main matter part of \emph{thesis.tex}. To help you organize your document it is recommended that each chapter is put in separate file in a folder of its own.
\subsection{Summary}
A short summary in Swedish should be be included if the thesis is written in a foreign language.
\subsection{Acknowledgements}
If you are writing a Summary and would like to add acknowledgements this is were you put it. Simply make sure the line
\begin{verbatim}
\include{0_backmatter/acknowledgement}
\end{verbatim}
in the Back matter part of \emph{thesis.tex} is not commented and edit the file \emph{acknowledgement.tex} in \emph{$\backslash$0\_frontmatter}.
\subsection{References}
Put you references in the Bib\TeX-file \emph{references.bib} in \emph{9\_backmatter}. A few Bib\TeX style files are included in \emph{$\backslash$Latex$\backslash$Classes} but the author a free to use the bibliographic style of her/his preference. More information on how to use Bib\TeX can be found at the Bib\TeX homepage \citep{bibtex}.
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{3/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{\label{ch3}Name of chapter 3} % top level followed by section, subsection
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
\section{\label{}Name of section}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum \ref{fig:potato}.
\begin{figure}[htbp]
\includegraphics[width=\textwidth]{conversion.eps}
\caption{\label{fig:potato}Example figure}
\end{figure}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
\subsection{\label{}Name of subsection}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
\subsubsection{\label{}Name of subsubsection}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{4/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{\label{ch4}Name of chapter 4} % top level followed by section, subsection
\section{\label{}Name of section}
\subsection{\label{}Name of subsection}
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{5/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{\label{ch5}Name of chapter 5} % top level followed by section, subsection
\section{\label{}Name of section}
\subsection{\label{}Name of subsection}
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{6/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{\label{ch6}Name of chapter 6} % top level followed by section, subsection
\section{\label{}Name of section}
\subsection{\label{}Name of subsection}
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{7/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{\label{ch7}Name of chapter 7} % top level followed by section, subsection
\section{\label{}Name of section}
\subsection{\label{}Name of subsection}
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% this file is called up by thesis.tex
% content in this file will be fed into the main document
%: ----------------------- introduction file header -----------------------
\graphicspath{{8/figures/}} % specifies where the figures are stored
% ----------------------------------------------------------------------
%: ----------------------- content -----------------------
% ----------------------------------------------------------------------
\chapter{\label{ch8}Name of chapter 8} % top level followed by section, subsection
\section{\label{}Name of section}
\subsection{\label{}Name of subsection}
% ---------------------------------------------------------------------------
%: ----------------------- end of thesis sub-document ------------------------
% ---------------------------------------------------------------------------

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% Thesis Acknowledgements ------------------------------------------------
%\begin{acknowledgementslong} %uncommenting this line, gives a different acknowledgements heading
%\begin{acknowledgements} %this creates the heading for the acknowlegments
\chapter{Acknowledgements}
I would like to acknowledge...
%\end{acknowledgements}
%\end{acknowledgmentslong}
% ------------------------------------------------------------------------

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% Thesis statement of originality -------------------------------------
% Depending on the regulations of your faculty you may need a declaration like the one below. This specific one is from the medical faculty of the university of Dresden.
\begin{declaration} %this creates the heading for the declaration page
I herewith declare that I have produced this paper without the prohibited assistance of third parties and without making use of aids other than those specified; notions taken over directly or indirectly from other sources have been identified as such. This paper has not previously been presented in identical or similar form to any other German or foreign examination board.
The thesis work was conducted from XXX to YYY under the supervision of PI at ZZZ.
\vspace{10mm}
CITY,
\end{declaration}
% ----------------------------------------------------------------------

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@article{nomencl,
Author = {Boris Veytsman, Bernd Schandl, Lee Netherton, CV Radhakrishnan},
url = "http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/nomencl.pdf",
Title = {nomencl},
Year = {2005}
}
@misc{bibtex,
url = " http://www.bibtex.org/",
Title = {http://www.bibtex.org/},
}

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% Thesis summary -------------------------------------
% Should be in swedish if thesis are in another language, otherwize in english.
\selectlanguage{swedish}
%\summarytitle{Summering}
%\begin{summary} %this creates the heading for the declaration page
\chapter{Sammanfattning}
En kort summering av avhandlingen p\r{a} svenska om avhandlingen \"ar skriven p\r{a} ett annat spr\r{a}k.
\r{a} \"a \"o
%\end{summary}
\selectlanguage{english}
% ----------------------------------------------------------------------

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../../thesis.tex

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%---------------------------------------------------------------
% PhDthesis class file by Andreas Solders 2011 based on
% PhDthesis version 2 style file by Jakob Suckale, 2007
% and CUEDthesis version 1 by Harish Bhanderi 2002
%---------------------------------------------------------------
%-------------------------- identification ---------------------
%\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{Latex/Classes/PhDthesisSU}[2011/09/23 PhD thesis class]
%:-------------------------- book style -----------------------
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{book}}
\ProcessOptions\relax
\LoadClass[pdftex, a4paper]{book}
%:-------------------------- packages for fancy things -----------------------
\usepackage{mathptmx} % Default font for dissertations is Times.
%\usepackage{fourier} % If mathematics don't display well using Times, then use Fourier.
\usepackage{geometry}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsbsy}
%\usepackage{graphics}
\usepackage[pdftex]{graphicx} % for improved inclusion of graphics
\usepackage{epstopdf} % converts eps figures to pdf
%\usepackage{wrapfig} % to include figure with text wrapping around it
\usepackage[margin=10pt,font=small,labelfont=bf]{caption} % for improved layout of figure captions with extra margin, smaller font than text
\usepackage{fancyhdr} % for better header layout
\usepackage{eucal}
\usepackage[english,swedish]{babel}
\usepackage[usenames, dvipsnames]{color}
\usepackage[perpage]{footmisc}
\usepackage{enumerate} % enumerated list for List of Papers
\usepackage[sort,compress]{natbib}
\usepackage{ifthen}
\usepackage{multicol} % for pages with multiple text columns, e.g. References
\setlength{\columnsep}{20pt} % space between columns; default 10pt quite narrow
\usepackage[nottoc]{tocbibind} % correct page numbers for bib in TOC, nottoc suppresses an entry for TOC itself
%\usepackage{nextpage}
\usepackage[T1]{fontenc}
\usepackage{calligra}
\renewcommand\boldsymbol[1]{\pmb{#1}}
\DeclareFixedFont{\timesEightteen}{\encodingdefault}{\sfdefault}{\seriesdefault}{\shapedefault}{17\p@}
% Removing the "Chapter n" text an replacing it by a single number.
\def\@makechapterhead#1{%
\vspace{0\p@}%
{\parindent \z@ \raggedright \normalfont
\ifnum \c@secnumdepth >\m@ne
% Skipping the "Chapter n" text
\if@mainmatter
\baselineskip=20pt\rightskip 2cm plus 3cm\huge\thechapter.\hspace{0.5em}%Chapterpoint added.
\fi
\fi
\huge #1\par\nobreak
\vskip 84\p@
}}
\def\@makeschapterhead#1{%
\vspace*{0\p@}%
{\parindent \z@ \raggedright
\normalfont
\interlinepenalty\@M
\huge #1\par\nobreak
\vskip 84\p@
}}
%:-------------------------- Glossary/Abbrev./Symbols -----------------------
\usepackage[intoc]{nomencl} % load nomencl extension; include in TOC
%\nomrefpage % to include page numbers after abbrevations
\renewcommand{\nomlabel}[1]{\textbf{#1}} % make abbreviations bold
\makenomenclature % used to be \makeglossary
\newcommand{\g}{\footnote{For all abbreviations see the glossary on page \pageref{nom}.}} % type "\g" to refer to glossary
% used to be for sorting into categories:
%\renewcommand\nomgroup[1]{%
% \ifthenelse{\equal{#1}{A}}{%
% \item[\textbf{Roman Symbols}] }{% A - Roman
% \ifthenelse{\equal{#1}{G}}{%
% \item[\textbf{Greek Symbols}]}{% G - Greek
% \ifthenelse{\equal{#1}{R}}{%
% \item[\textbf{Superscripts}]}{% R - Superscripts
% \ifthenelse{\equal{#1}{S}}{%
% \item[\textbf{Subscripts}]}{{% S - Subscripts
% \ifthenelse{\equal{#1}{X}}{%
% \item[\textbf{Other Symbols}]}{{% X - Other Symbols
% \ifthenelse{\equal{#1}{Z}}{%
% \item[\textbf{Acronyms}]}% Z - Acronyms
% {{}}}}}}}}}}
%:-------------------------- PDF/PS setup -----------------------
%if you use a macTeX 2008 or later, use the ifpdf package
\usepackage{ifpdf}
%-->
%--> Google.com search "hyperref options"
%-->
%--> http://www.ai.mit.edu/lab/sysadmin/latex/documentation/latex/hyperref/manual.pdf
%--> http://www.chemie.unibas.ch/~vogtp/LaTeX2PDFLaTeX.pdf
%--> http://www.uni-giessen.de/partosch/eurotex99/ oberdiek/print/sli4a4col.pdf
%--> http://me.in-berlin.de/~miwie/tex-refs/html/latex-packages.html
%-->
\usepackage[ pdftex, plainpages = false, pdfpagelabels,
pdfpagemode=UseOutlines,
bookmarks,
bookmarksopen = true,
bookmarksnumbered = true,
breaklinks = true,
linktocpage,
pagebackref,
colorlinks = false, % was true
linkcolor = blue,
urlcolor = blue,
citecolor = red,
anchorcolor = green,
hyperindex = true,
hyperfigures
]{hyperref}
\DeclareGraphicsExtensions{.png, .jpg, .jpeg, .pdf} %GIF doesn't work
\usepackage[pdftex]{graphicx}
\pdfcompresslevel=9
\graphicspath{{0_frontmatter/figures/}}
%:-------------------------- page layout -----------------------
%S5 settings (default)
\geometry{paperheight=242mm,paperwidth=165mm}
\geometry{left=22.5mm,right=22.5mm}
\geometry{top=22.5mm,bottom=22.5mm}
%Make al headlines non-fat
\def\section{\@startsection {section}{1}{\z@}{-3.5ex plus -1ex minus
-.2ex}{2.3ex plus .2ex}{\Large}}
\def\subsection{\@startsection{subsection}{2}{\z@}{-3.25ex plus -1ex minus
-.2ex}{1.5ex plus .2ex}{\large}}
\def\subsubsection{\@startsection{subsubsection}{3}{\z@}{-3.25ex plus
-1ex minus -.2ex}{1.5ex plus .2ex}{\normalsize}}
%:-------------------------- page layout -----------------------
% FRONTMATTER
% No page numbering until chapter 1
\newcommand{\frontmatterSU}{
\frontmatter
\pagestyle{empty}
\fancypagestyle{plain}{
\fancyhead{}
\fancyfoot{}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
}
% MAINMATTER
\newcommand{\mainmatterSU}{
\begingroup
\cleardoublepage
\edef\x{\endgroup
\noexpand\mainmatter
\setcounter{page}{\the\value{page}}%
}%
\x
\cleardoublepage
\fancypagestyle{plain}
{
\fancyhead{}
\fancyfoot[LE,RO]{{\fontfamily{verdana}\selectfont\thepage}}
} % re-define plain page
\pagestyle{fancy}
\fancyhf{}
\fancyfoot[LE,RO]{{\fontfamily{verdana}\selectfont\thepage}}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
% BACKMATTER
\newcommand{\backmatterSU}{
\backmatter
\renewcommand{\thepage}{\roman{page}}
%
\pagestyle{empty}
\fancypagestyle{plain}{
\fancyhead{}
\fancyfoot{}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
}
% DECLARATIONS
% These macros are used to declare arguments needed for the
% construction of the title page and other preamble.
% Subtitle
\def\subtitle#1{\gdef\@subtitle{#1}}
% Defining the crest
\def\crest#1{\gdef\@crest{#1}}
% These macros define an environment for front matter that is always
% single column even in a double-column document.
\newenvironment{alwayssingle}{%
\@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn
\else\newpage\fi}
{\if@restonecol\twocolumn\else\newpage\fi}
%Halftitlepage
\newcommand{\halftitlepage}%
{
\thispagestyle{empty}
\noindent
{\large \@title~-- \@subtitle\\}\\
\noindent
{\Large\@author}
\cleardoublepage
}
\crest{\includegraphics[width=25mm]{SU-Logga}}
%define title page layout
\renewcommand{\maketitle}{
\renewcommand{\footnotesize}{\small}
\renewcommand{\footnoterule}{\relax}
\thispagestyle{empty}
{\large \vspace*{0mm} \hspace*{90mm} {{\@crest} \par} } %Move the logo
{ \Huge \vspace*{30mm}{\noindent}{\@title} \par \vspace*{4mm}}
{\large {\noindent}{\@subtitle} \par \vspace*{8mm}}
{{\LARGE {\noindent}\@author} \par}
\null\vfill
}
% page number for cover back side should have page number blanked
%:-------------------------- front matter layout -----------------------
% ABSTRACT
%
\newenvironment{abstracts} { \pagestyle{empty}
\let\cleardoublepage\clearpage
\chapter{Abstract}
}
% DEDICATION
%
% The dedication environment makes sure the dedication gets its
% own page and is set out in verse format.
\newenvironment{dedication}
{
\phantom{.}
\vspace{13cm}
\begin{quote} \begin{flushright}}
{\end{flushright} \end{quote}}

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Latex/Classes/PhDthesisSU_A4.cls Normal file
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%---------------------------------------------------------------
% PhDthesis class file by Andreas Solders 2011 based on
% PhDthesis version 2 style file by Jakob Suckale, 2007
% and CUEDthesis version 1 by Harish Bhanderi 2002
%---------------------------------------------------------------
%-------------------------- identification ---------------------
%\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{Latex/Classes/PhDthesisSU}[2011/09/23 PhD thesis class]
%:-------------------------- book style -----------------------
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{book}}
\ProcessOptions\relax
\LoadClass[pdftex, a4paper]{book}
%:-------------------------- packages for fancy things -----------------------
\usepackage{mathptmx} % Default font for dissertations is Times.
%\usepackage{fourier} % If mathematics don't display well using Times, then use Fourier.
\usepackage{geometry}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsbsy}
%\usepackage{graphics}
\usepackage[pdftex]{graphicx} % for improved inclusion of graphics
\usepackage{epstopdf} % converts eps figures to pdf
%\usepackage{wrapfig} % to include figure with text wrapping around it
\usepackage[margin=10pt,font=small,labelfont=bf]{caption} % for improved layout of figure captions with extra margin, smaller font than text
\usepackage{fancyhdr} % for better header layout
\usepackage{eucal}
\usepackage[english,swedish]{babel}
\usepackage[usenames, dvipsnames]{color}
\usepackage[perpage]{footmisc}
\usepackage{enumerate} % enumerated list for List of Papers
\usepackage[sort,compress]{natbib}
\usepackage{ifthen}
\usepackage{multicol} % for pages with multiple text columns, e.g. References
\setlength{\columnsep}{20pt} % space between columns; default 10pt quite narrow
\usepackage[nottoc]{tocbibind} % correct page numbers for bib in TOC, nottoc suppresses an entry for TOC itself
%\usepackage{nextpage}
\usepackage[T1]{fontenc}
\usepackage{calligra}
\renewcommand\boldsymbol[1]{\pmb{#1}}
\DeclareFixedFont{\timesEightteen}{\encodingdefault}{\sfdefault}{\seriesdefault}{\shapedefault}{17\p@}
% Removing the "Chapter n" text an replacing it by a single number.
\def\@makechapterhead#1{%
\vspace{0\p@}%
{\parindent \z@ \raggedright \normalfont
\ifnum \c@secnumdepth >\m@ne
% Skipping the "Chapter n" text
\if@mainmatter
\baselineskip=20pt\rightskip 2cm plus 3cm\huge\thechapter.\hspace{0.5em}%Chapterpoint added.
\fi
\fi
\huge #1\par\nobreak
\vskip 84\p@
}}
\def\@makeschapterhead#1{%
\vspace*{0\p@}%
{\parindent \z@ \raggedright
\normalfont
\interlinepenalty\@M
\huge #1\par\nobreak
\vskip 84\p@
}}
%:-------------------------- Glossary/Abbrev./Symbols -----------------------
\usepackage[intoc]{nomencl} % load nomencl extension; include in TOC
%\nomrefpage % to include page numbers after abbrevations
\renewcommand{\nomlabel}[1]{\textbf{#1}} % make abbreviations bold
\makenomenclature % used to be \makeglossary
\newcommand{\g}{\footnote{For all abbreviations see the glossary on page \pageref{nom}.}} % type "\g" to refer to glossary
% used to be for sorting into categories:
%\renewcommand\nomgroup[1]{%
% \ifthenelse{\equal{#1}{A}}{%
% \item[\textbf{Roman Symbols}] }{% A - Roman
% \ifthenelse{\equal{#1}{G}}{%
% \item[\textbf{Greek Symbols}]}{% G - Greek
% \ifthenelse{\equal{#1}{R}}{%
% \item[\textbf{Superscripts}]}{% R - Superscripts
% \ifthenelse{\equal{#1}{S}}{%
% \item[\textbf{Subscripts}]}{{% S - Subscripts
% \ifthenelse{\equal{#1}{X}}{%
% \item[\textbf{Other Symbols}]}{{% X - Other Symbols
% \ifthenelse{\equal{#1}{Z}}{%
% \item[\textbf{Acronyms}]}% Z - Acronyms
% {{}}}}}}}}}}
%:-------------------------- PDF/PS setup -----------------------
%if you use a macTeX 2008 or later, use the ifpdf package
\usepackage{ifpdf}
%-->
%--> Google.com search "hyperref options"
%-->
%--> http://www.ai.mit.edu/lab/sysadmin/latex/documentation/latex/hyperref/manual.pdf
%--> http://www.chemie.unibas.ch/~vogtp/LaTeX2PDFLaTeX.pdf
%--> http://www.uni-giessen.de/partosch/eurotex99/ oberdiek/print/sli4a4col.pdf
%--> http://me.in-berlin.de/~miwie/tex-refs/html/latex-packages.html
%-->
\usepackage[ pdftex, plainpages = false, pdfpagelabels,
pdfpagelayout = useoutlines,
bookmarks,
bookmarksopen = true,
bookmarksnumbered = true,
breaklinks = true,
linktocpage,
pagebackref,
colorlinks = false, % was true
linkcolor = blue,
urlcolor = blue,
citecolor = red,
anchorcolor = green,
hyperindex = true,
hyperfigures
]{hyperref}
\DeclareGraphicsExtensions{.png, .jpg, .jpeg, .pdf} %GIF doesn't work
\usepackage[pdftex]{graphicx}
\pdfcompresslevel=9
\graphicspath{{0_frontmatter/figures/}}
%:-------------------------- page layout -----------------------
%S5 settings (default)
%\geometry{paperheight=242mm,paperwidth=165mm}
%\geometry{left=22.5mm,right=22.5mm}
%\geometry{top=22.5mm,bottom=22.5mm}
%Make al headlines non-fat
\def\section{\@startsection {section}{1}{\z@}{-3.5ex plus -1ex minus
-.2ex}{2.3ex plus .2ex}{\Large}}
\def\subsection{\@startsection{subsection}{2}{\z@}{-3.25ex plus -1ex minus
-.2ex}{1.5ex plus .2ex}{\large}}
\def\subsubsection{\@startsection{subsubsection}{3}{\z@}{-3.25ex plus
-1ex minus -.2ex}{1.5ex plus .2ex}{\normalsize}}
%:-------------------------- page layout -----------------------
% FRONTMATTER
% No page numbering until chapter 1
\newcommand{\frontmatterSU}{
\frontmatter
\pagestyle{empty}
\fancypagestyle{plain}{
\fancyhead{}
\fancyfoot{}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
}
% MAINMATTER
\newcommand{\mainmatterSU}{
\begingroup
\cleardoublepage
\edef\x{\endgroup
\noexpand\mainmatter
\setcounter{page}{\the\value{page}}%
}%
\x
\cleardoublepage
\fancypagestyle{plain}
{
\fancyhead{}
\fancyfoot[LE,RO]{{\fontfamily{verdana}\selectfont\thepage}}
} % re-define plain page
\pagestyle{fancy}
\fancyhf{}
\fancyfoot[LE,RO]{{\fontfamily{verdana}\selectfont\thepage}}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
% BACKMATTER
\newcommand{\backmatterSU}{
\backmatter
\renewcommand{\thepage}{\roman{page}}
%
\pagestyle{empty}
\fancypagestyle{plain}{
\fancyhead{}
\fancyfoot{}
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
}
}
% DECLARATIONS
% These macros are used to declare arguments needed for the
% construction of the title page and other preamble.
% Subtitle
\def\subtitle#1{\gdef\@subtitle{#1}}
% Defining the crest
\def\crest#1{\gdef\@crest{#1}}
% These macros define an environment for front matter that is always
% single column even in a double-column document.
\newenvironment{alwayssingle}{%
\@restonecolfalse\if@twocolumn\@restonecoltrue\onecolumn
\else\newpage\fi}
{\if@restonecol\twocolumn\else\newpage\fi}
%Halftitlepage
\newcommand{\halftitlepage}%
{
\thispagestyle{empty}
\noindent
{\large \@title~-- \@subtitle\\}\\
\noindent
{\Large\@author}
\cleardoublepage
}
\crest{\includegraphics[width=25mm]{SU-Logga}}
%define title page layout
\renewcommand{\maketitle}{
\renewcommand{\footnotesize}{\small}
\renewcommand{\footnoterule}{\relax}
\thispagestyle{empty}
{\large \vspace*{0mm} \hspace*{90mm} {{\@crest} \par} } %Move the logo
{ \Huge \vspace*{30mm}{\noindent}{\@title} \par \vspace*{4mm}}
{\large {\noindent}{\@subtitle} \par \vspace*{8mm}}
{{\LARGE {\noindent}\@author} \par}
\null\vfill
}
% page number for cover back side should have page number blanked
%:-------------------------- front matter layout -----------------------
% ABSTRACT
%
\newenvironment{abstracts} { \pagestyle{empty}
\let\cleardoublepage\clearpage
\chapter{Abstract}
}
% DEDICATION
%
% The dedication environment makes sure the dedication gets its
% own page and is set out in verse format.
\newenvironment{dedication}
{
\phantom{.}
\vspace{13cm}
\begin{quote} \begin{flushright}}
{\end{flushright} \end{quote}}

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#! /usr/bin/env perl
#
# Usage: ./urlbst.pl [--eprint] [--doi]
# [--nohyperlinks] [--inlinelinks] [--hypertex] [--hyperref]
# [input-file [output-file]]
# If either input-file or output-file is omitted, they are replaced by
# stdin or stdout respectively.
#
# See http://purl.org/nxg/dist/urlbst for documentation
#
# $Id: urlbst.in,v 1.8 2007/03/26 17:21:56 norman Exp $
$version = '0.6';
($progname = $0) =~ s/.*\///;
$mymarker = "% $progname";
$mymarkerend = "% ...$progname to here";
$myurl = 'http://purl.org/nxg/dist/urlbst';
$infile = '-';
$outfile = '-';
$addeprints = 0; # if true (nonzero) we add support for eprints
$eprintprefix = 'arXiv:'; # make these settable with --eprint? syntax?
$eprinturl = 'http://arxiv.org/abs/';
$adddoiresolver = '0';
$doiprefix = 'doi:';
$doiurl = 'http://dx.doi.org/';
$makehref = 0;
$availablestring = "Available from: ";
$inlinelinks = 0;
$Usage = "$progname [--eprint] [--doi]\n [--nohyperlinks] [--inlinelinks] [--hypertex] [--hyperref]\n [--help] [input-file [output-file]]";
while ($#ARGV >= 0) {
if ($ARGV[0] eq '--eprint') {
$addeprints = 1;
} elsif ($ARGV[0] eq '--doi') {
$adddoiresolver = 1;
} elsif ($ARGV[0] eq '--nohyperlinks') {
$makehref = 0;
} elsif ($ARGV[0] eq '--hypertex') {
$makehref = 1;
} elsif ($ARGV[0] eq '--hyperref') {
$makehref = 2;
} elsif ($ARGV[0] eq '--inlinelinks') {
$inlinelinks = 1;
} elsif ($ARGV[0] eq '--help') {
print <<EOD;
urlbst version $version
Usage: $Usage
--eprint: include support for `eprint' fields
--doi: include support for `doi' field
--nohyperlinks do not include active links anywhere
--inlinelinks add hyperlinks to entry titles
--hypertex: include HyperTeX-style hyperlink support
--hyperref: include {hyperref}-style hyperlink support
(generally better)
--help: print this help
Input and output files may be given as `-' (default) to indicate stdin/out
EOD
exit(0);
} elsif ($ARGV[0] =~ /^-/) {
die "Unrecognised option $ARGV[0]: Usage: $Usage\n";
} elsif ($infile eq '-') {
$infile = $ARGV[0];
} elsif ($outfile eq '-') {
$outfile = $ARGV[0];
} else {
die "Usage: $Usage\n";
}
shift(@ARGV);
}
if ($inlinelinks && $makehref == 0) {
print <<'EOD';
Warning: --inlinelinks and --nohyperlinks were both specified (possibly
implicitly). That combination makes no sense, so I'll ignore
--nohyperlinks and use --hyperref instead
EOD
$makehref = 2;
}
$exitstatus = 0; # success status
open (IN, "<$infile") || die "Can't open $infile to read";
open (OUT, ">$outfile") || die "Can't open $outfile to write";
# We have to make certain assumptions about the source files, in order
# to patch them at the correct places. Specifically, we assume that
#
# - there's a function init.state.consts
#
# - ...and an output.nonnull which does the actual outputting, which
# has the `usual' interface.
#
# - we can replace
# fin.entry
# by
# new.block
# output.url % the function which formats and displays any URL
# fin.entry
#
# - there is a function which handles the `article' entry type (this
# will always be true)
#
# - there is a function output.bibitem which is called at the
# beginning of each entry type
# - ...and one called fin.entry which is called at the end
#
# If the functions format.date, format.title or new.block are not defined (the
# former is not in apalike, for example, and the last is not in the
# AMS styles), then replacements are included in the output.
#
# All these assumptions are true of the standard files and, since most
# style files derive from them more or less directly, are true of most (?)
# other style files, too.
#
# There's some rather ugly Perl down here. The parsing for
# brace-matching could probably do with being rewritten in places, to
# make it less ugly, and more robust.
print OUT "%%% Modification of BibTeX style file ", ($infile eq '-' ? '<stdin>' : $infile), "\n";
print OUT "%%% ... by $progname, version $version (marked with \"$mymarker\")\n%%% See <$myurl>\n";
print OUT "%%% Added webpage entry type, and url and lastchecked fields.\n";
print OUT "%%% Added eprint support.\n" if ($addeprints);
print OUT "%%% Added DOI support.\n" if ($adddoiresolver);
print OUT "%%% Added HyperTeX support.\n" if ($makehref == 1);
print OUT "%%% Added hyperref support.\n" if ($makehref == 2);
print OUT "%%% Original headers follow...\n\n";
$found{initconsts} = 0;
$found{outputnonnull} = 0;
$found{article} = 0;
$found{outputbibitem} = 0;
$found{finentry} = 0;
$found{formatdate} = 0;
$found{formattitle} = 0;
$found{newblock} = 0;
while (<IN>) {
/^ *%/ && do {
# Pass commented lines unchanged
print OUT;
next;
};
/^ *ENTRY/ && do {
# Work through the list of entry types, finding what ones are there.
# If we find a URL entry there already, object, since these edits
# will mess things up.
$line = $_;
until ($line =~ /\{\s*(\w*)/) {
$line .= <IN>;
}
$bracematchtotal = 0; # reset
bracematcher($line);
$line =~ /\{\s*(\w*)/;
$found{'entry'.$1} = 1;
print OUT $line;
$line = <IN>;
until (bracematcher($line) == 0) {
# XXX deal with multiple entries on one line
($line =~ /^\s*(\w*)/) && ($found{'entry'.$1} = 1);
print OUT $line;
$line = <IN>;
}
if (defined($found{entryurl})) {
print STDERR "$progname: style file $infile already has URL entry!\n";
# print out the rest of the file, and give up
print OUT $line;
while (<IN>) {
print OUT;
}
$exitstatus = 1;
last;
} else {
print OUT " eprint $mymarker\n doi $mymarker\n url $mymarker\n lastchecked $mymarker\n";
}
print OUT $line;
next;
};
/^ *FUNCTION *\{init\.state\.consts\}/ && do {
# In the init.state.consts function, add an extra set of
# constants at the beginning. Also use this as the marker for
# the place to add the init strings function.
print OUT <<EOD;
STRINGS { urlintro eprinturl eprintprefix doiprefix doiurl openinlinelink closeinlinelink } $mymarker...
INTEGERS { hrefform inlinelinks makeinlinelink addeprints adddoiresolver }
% Following constants may be adjusted by hand, if desired
FUNCTION {init.urlbst.variables}
{
"$availablestring" 'urlintro := % prefix before URL
"$eprinturl" 'eprinturl := % prefix to make URL from eprint ref
"$eprintprefix" 'eprintprefix := % text prefix printed before eprint ref
"$doiurl" 'doiurl := % prefix to make URL from DOI
"$doiprefix" 'doiprefix := % text prefix printed before DOI ref
#$addeprints 'addeprints := % 0=no eprints; 1=include eprints
#$adddoiresolver 'adddoiresolver := % 0=no DOI resolver; 1=include it
#$makehref 'hrefform := % 0=no crossrefs; 1=hypertex xrefs; 2=hyperref refs
#$inlinelinks 'inlinelinks := % 0=URLs explicit; 1=URLs attached to titles
% the following are internal state variables, not config constants
#0 'makeinlinelink := % state variable managed by setup.inlinelink
"" 'openinlinelink := % ditto
"" 'closeinlinelink := % ditto
}
INTEGERS {
bracket.state
outside.brackets
open.brackets
within.brackets
close.brackets
}
$mymarkerend
EOD
$line = $_;
until ($line =~ /\{.*\}.*\{/s) {
$line .= <IN>;
}
$line =~ s/(\{.*?\}.*?\{)/$1 #0 'outside.brackets := $mymarker
#1 'open.brackets :=
#2 'within.brackets :=
#3 'close.brackets :=
/s;
print OUT $line;
$found{initconsts} = 1;
next;
};
/^ *EXECUTE *\{init\.state\.consts\}/ && do {
print OUT "EXECUTE {init.urlbst.variables}\n";
print OUT;
next;
};
/^ *FUNCTION *\{new.block\}/ && do {
$found{newblock} = 1;
};
/^ *FUNCTION *{output\.nonnull}/ && do {
print OUT "$mymarker\n";
print OUT "FUNCTION {output.nonnull.original}\n";
copy_block();
print_output_functions();
$found{outputnonnull} = 1;
next;
};
/FUNCTION *\{fin.entry\}/ && do {
# Rename fin.entry to fin.entry.original (wrapped below)
s/fin.entry/fin.entry.original/;
$found{finentry} = 1;
print OUT;
next;
};
/^ *FUNCTION *{format\.date}/ && do {
$found{formatdate} = 1;
print OUT;
next;
};
/^ *FUNCTION *{format\.title}/ && do {
# record that we found this
$found{formattitle} = 1;
print OUT;
next;
};
/^ *format\.b?title/ && do {
# interpolate a call to setup.inlinelink
print OUT " title empty\$ 'skip\$ 'setup\.inlinelink if\$ $mymarker\n";
print OUT;
next;
};
/^ *FUNCTION *\{article\}/ && do {
print_missing_functions();
print_webpage_def();
print OUT;
$found{article} = 1;
next;
};
/FUNCTION *\{output.bibitem\}/ && do {
# Rename output.bibitem to output.bibitem.original (wrapped below)
s/{output.bibitem\}/\{output.bibitem.original\}/;
$found{outputbibitem} = 1;
print OUT;
next;
};
print OUT;
};
if ($exitstatus == 0) {
# Skip this if we've already reported an error -- it'll only be confusing
foreach $k (keys %found) {
if ($found{$k} == 0) {
print STDERR "$progname: $infile: failed to find feature $k\n";
}
}
}
close (IN);
close (OUT);
exit $exitstatus;;
sub print_output_functions {
print OUT "$mymarker...\n";
print OUT <<'EOD';
% The following three functions are for handling inlinelink. They wrap
% a block of text which is potentially output with write$ by multiple
% other functions, so we don't know the content a priori.
% They communicate between each other using the variables makeinlinelink
% (which is true if a link should be made), and closeinlinelink (which holds
% the string which should close any current link. They can be called
% at any time, but start.inlinelink will be a no-op unless something has
% previously set makeinlinelink true, and the two ...end.inlinelink functions
% will only do their stuff if start.inlinelink has previously set
% closeinlinelink to be non-empty.
FUNCTION {setup.inlinelink}
{ makeinlinelink
{ hrefform #1 = % hypertex
{ "\special {html:<a href=" quote$ * url * quote$ * "> }{" * 'openinlinelink :=
"\special {html:</a>}" 'closeinlinelink :=
}
{ hrefform #2 = % hyperref
{ "\href{" url * "}{" * 'openinlinelink :=
"}" 'closeinlinelink :=
}
'skip$
if$ % hrefform #2 =
}
if$ % hrefform #1 =
#0 'makeinlinelink :=
}
'skip$
if$ % makeinlinelink
}
FUNCTION {add.inlinelink}
{ openinlinelink empty$
'skip$
{ openinlinelink swap$ * closeinlinelink *
"" 'openinlinelink :=
}
if$
}
EOD
# new.block is defined elsewhere
print OUT <<'EOD';
FUNCTION {output.nonnull}
{ % Save the thing we've been asked to output
's :=
% If the bracket-state is close.brackets, then add a close-bracket to
% what is currently at the top of the stack, and set bracket.state
% to outside.brackets
bracket.state close.brackets =
{ "]" *
outside.brackets 'bracket.state :=
}
'skip$
if$
bracket.state outside.brackets =
{ % We're outside all brackets -- this is the normal situation.
% Write out what's currently at the top of the stack, using the
% original output.nonnull function.
s
add.inlinelink
output.nonnull.original % invoke the original output.nonnull
}
{ % Still in brackets. Add open-bracket or (continuation) comma, add the
% new text (in s) to the top of the stack, and move to the close-brackets
% state, ready for next time (unless inbrackets resets it). If we come
% into this branch, then output.state is carefully undisturbed.
bracket.state open.brackets =
{ " [" * }
{ ", " * } % bracket.state will be within.brackets
if$
s *
close.brackets 'bracket.state :=
}
if$
}
% Call this function just before adding something which should be presented in
% brackets. bracket.state is handled specially within output.nonnull.
FUNCTION {inbrackets}
{ bracket.state close.brackets =
{ within.brackets 'bracket.state := } % reset the state: not open nor closed
{ open.brackets 'bracket.state := }
if$
}
FUNCTION {format.lastchecked}
{ lastchecked empty$
{ "" }
{ inbrackets "cited " lastchecked * }
if$
}
EOD
print OUT "$mymarkerend\n";
}
sub print_webpage_def {
print OUT "$mymarker...\n";
# Some of the functions below call new.block, so we need a dummy
# version, in the case where the style being edited doesn't supply
# that function.
if (! $found{newblock}) {
print OUT "FUNCTION {new.block} % dummy new.block function\n{\n % empty\n}\n\n";
$found{newblock} = 1;
}
print OUT <<'EOD';
% Functions for making hypertext links.
% In all cases, the stack has (link-text href-url)
%
% make 'null' specials
FUNCTION {make.href.null}
{
pop$
}
% make hypertex specials
FUNCTION {make.href.hypertex}
{
"\special {html:<a href=" quote$ *
swap$ * quote$ * "> }" * swap$ *
"\special {html:</a>}" *
}
% make hyperref specials
FUNCTION {make.href.hyperref}
{
"\href {" swap$ * "} {\path{" * swap$ * "}}" *
}
FUNCTION {make.href}
{ hrefform #2 =
'make.href.hyperref % hrefform = 2
{ hrefform #1 =
'make.href.hypertex % hrefform = 1
'make.href.null % hrefform = 0 (or anything else)
if$
}
if$
}
% If inlinelinks is true, then format.url should be a no-op, since it's
% (a) redundant, and (b) could end up as a link-within-a-link.
FUNCTION {format.url}
{ inlinelinks #1 = url empty$ or
{ "" }
{ hrefform #1 =
{ % special case -- add HyperTeX specials
urlintro "\url{" url * "}" * url make.href.hypertex * }
{ urlintro "\url{" * url * "}" * }
if$
}
if$
}
FUNCTION {format.eprint}
{ eprint empty$
{ "" }
{ eprintprefix eprint * eprinturl eprint * make.href }
if$
}
FUNCTION {format.doi}
{ doi empty$
{ "" }
{ doiprefix doi * doiurl doi * make.href }
if$
}
% Output a URL. We can't use the more normal idiom (something like
% `format.url output'), because the `inbrackets' within
% format.lastchecked applies to everything between calls to `output',
% so that `format.url format.lastchecked * output' ends up with both
% the URL and the lastchecked in brackets.
FUNCTION {output.url}
{ url empty$
'skip$
{ new.block
format.url output
format.lastchecked output
}
if$
}
FUNCTION {output.web.refs}
{
new.block
output.url
addeprints eprint empty$ not and
{ format.eprint output.nonnull }
'skip$
if$
adddoiresolver doi empty$ not and
{ format.doi output.nonnull }
'skip$
if$
}
% Wrapper for output.bibitem.original.
% If the URL field is not empty, set makeinlinelink to be true,
% so that an inline link will be started at the next opportunity
FUNCTION {output.bibitem}
{ outside.brackets 'bracket.state :=
output.bibitem.original
inlinelinks url empty$ not and
{ #1 'makeinlinelink := }
{ #0 'makeinlinelink := }
if$
}
% Wrapper for fin.entry.original
FUNCTION {fin.entry}
{ output.web.refs % urlbst
makeinlinelink % ooops, it appears we didn't have a title for inlinelink
{ setup.inlinelink % add some artificial link text here, as a fallback
"[link]" output.nonnull }
'skip$
if$
bracket.state close.brackets = % urlbst
{ "]" * }
'skip$
if$
fin.entry.original
}
% Webpage entry type.
% Title and url fields required;
% author, note, year, month, and lastchecked fields optional
% See references
% ISO 690-2 http://www.nlc-bnc.ca/iso/tc46sc9/standard/690-2e.htm
% http://www.classroom.net/classroom/CitingNetResources.html
% http://neal.ctstateu.edu/history/cite.html
% http://www.cas.usf.edu/english/walker/mla.html
% for citation formats for web pages.
FUNCTION {webpage}
{ output.bibitem
author empty$
{ editor empty$
'skip$ % author and editor both optional
{ format.editors output.nonnull }
if$
}
{ editor empty$
{ format.authors output.nonnull }
{ "can't use both author and editor fields in " cite$ * warning$ }
if$
}
if$
new.block
title empty$ 'skip$ 'setup.inlinelink if$
format.title "title" output.check
inbrackets "online" output
new.block
year empty$
'skip$
{ format.date "year" output.check }
if$
% We don't need to output the URL details ('lastchecked' and 'url'),
% because fin.entry does that for us, using output.web.refs. The only
% reason we would want to put them here is if we were to decide that
% they should go in front of the rather miscellaneous information in 'note'.
new.block
note output
fin.entry
}
EOD
print OUT "$mymarkerend\n\n\n";
}
sub print_missing_functions {
# We've got to the bit of the file which handles the entry
# types, so write out the webpage entry handler. This uses
# the format.date function, which which many but not all
# bst files have (for example, apalike doesn't). So
# check that we either have found this function already, or
# add it.
if (! $found{formatdate}) {
if ($found{entrymonth}) {
print OUT <<'EOD';
FUNCTION {format.date}
{ year empty$
{ month empty$
{ "" }
{ "there's a month but no year in " cite$ * warning$
month
}
if$
}
{ month empty$
'year
{ month " " * year * }
if$
}
if$
}
EOD
} else {
print OUT <<'EOD';
FUNCTION {format.date}
{ year empty$
'skip$
{ %write$
"(" year * ")" *
}
if$
}
EOD
}
$found{formatdate} = 1;
}
# If the style file didn't supply a format.title function, then supply
# one here (the {webpage} function requires it).
if (! $found{formattitle}) {
print OUT <<'EOD';
FUNCTION {format.title}
{ title empty$
{ "" }
{ title "t" change.case$ }
if$
}
EOD
$found{formattitle} = 1;
}
}
# Utility function: Keep track of open and close braces in the string argument.
# Keep state in $bracematchtotal, return the current value.
sub bracematcher {
my $s = shift;
$s =~ s/[^\{\}]//g;
#print "s=$s\n";
foreach my $c (split (//, $s)) {
$bracematchtotal += ($c eq '{' ? 1 : -1);
}
return $bracematchtotal;
}
# Utility function: use bracematcher to copy the complete block which starts
# on or after the current line.
sub copy_block {
$bracematchtotal = 0;
# copy any leading lines which don't have braces (presumably comments)
while (defined ($line = <IN>) && ($line !~ /{/)) {
print OUT $line;
}
while (defined ($line) && bracematcher($line) > 0) {
print OUT $line;
$line = <IN>;
}
print OUT "$line\n"; # print out terminating \} (assumed
# alone on the line)
}

73
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% This file contains macros that can be called up from connected TeX files
% It helps to summarise repeated code, e.g. figure insertion (see below).
% insert a centered figure with caption and description
% parameters 1:filename, 2:title, 3:description and label
\newcommand{\figuremacro}[3]{
\begin{figure}[htbp]
\centering
\includegraphics[width=1\textwidth]{#1}
\caption[#2]{\textbf{#2} - #3}
\label{#1}
\end{figure}
}
% insert a centered figure with caption and description AND WIDTH
% parameters 1:filename, 2:title, 3:description and label, 4: textwidth
% textwidth 1 means as text, 0.5 means half the width of the text
\newcommand{\figuremacroW}[4]{
\begin{figure}[htbp]
\centering
\includegraphics[width=#4\textwidth]{#1}
\caption[#2]{\textbf{#2} - #3}
\label{#1}
\end{figure}
}
% inserts a figure with wrapped around text; only suitable for NARROW figs
% o is for outside on a double paged document; others: l, r, i(inside)
% text and figure will each be half of the document width
% note: long captions often crash with adjacent content; take care
% in general: above 2 macro produce more reliable layout
\newcommand{\figuremacroN}[3]{
\begin{wrapfigure}{o}{0.5\textwidth}
\centering
\includegraphics[width=0.48\textwidth]{#1}
\caption[#2]{{\small\textbf{#2} - #3}}
\label{#1}
\end{wrapfigure}
}
% predefined commands by Harish
\newcommand{\PdfPsText}[2]{
\ifpdf
#1
\else
#2
\fi
}
\newcommand{\IncludeGraphicsH}[3]{
\PdfPsText{\includegraphics[height=#2]{#1}}{\includegraphics[bb = #3, height=#2]{#1}}
}
\newcommand{\IncludeGraphicsW}[3]{
\PdfPsText{\includegraphics[width=#2]{#1}}{\includegraphics[bb = #3, width=#2]{#1}}
}
\newcommand{\InsertFig}[3]{
\begin{figure}[!htbp]
\begin{center}
\leavevmode
#1
\caption{#2}
\label{#3}
\end{center}
\end{figure}
}
%%% Local Variables:
%%% mode: latex
%%% TeX-master: "~/Documents/LaTeX/CUEDThesisPSnPDF/thesis"
%%% End:

247
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% ----------------------------------------------------------------------
% LATEX TEMPLATE FOR PhD THESIS AT STOCKHOLM UNIVERSITY
% ----------------------------------------------------------------------
% based on Harish Bhanderi's PhD/MPhil template, then Uni Cambridge
% http://www-h.eng.cam.ac.uk/help/tpl/textprocessing/ThesisStyle/
% corrected and extended in 2007 by Jakob Suckale, then MPI-CBG PhD programme
% and made available through OpenWetWare.org - the free biology wiki
% modified for SU by Andreas Solders in 2011
%: Style file for Latex
% Most style definitions are in the external filePhDthesisSU.
% In this template package, it can be found in ./Latex/Classes/
\documentclass[twoside,11pt]{Latex/Classes/PhDthesisSU} %Default style using S5 paper
%\documentclass[twoside,11pt]{Latex/Classes/PhDthesisSU_A4} %Use this instead if you need A4 paper.
%: Macro file for Latex
% Macros help you summarize frequently repeated Latex commands.
% Here, they are placed in an external file /Latex/Macros/MacroFile1.tex
% An macro that you may use frequently is the figuremacro
\include{Latex/Macros/MacroFile1}
\setcitestyle{square,numbers} % change how references are included (see the natbib package).
%: -------------------------------------------------------------
%: TITLE PAGE
% --------------------------------------------------------------
\title{Title of your thesis}%Title of the thesis
\subtitle{Subtitle}% Subtitle of the thesis
\author{\href{mailto:email@department.su.se}{Your Name}}
%put the following in PDF header
%\pdfinfo { /Title ()
% /Creator ()
% /Producer ()
% /Author ()
% /CreationDate (D:YYYYMMDDhhmmss) %format D:YYYYMMDDhhmmss
% /ModDate (D:YYYYMMDDhhmm)
% /Subject (xyz)
% /Keywords (add, your, keywords, here) }
%\pdfcatalog { /PageMode (/UseOutlines)
% /OpenAction (fitbh) }
\pdfinfo{
/Author (Nicola Talbot)
/Title (Creating a PDF document using PDFLaTeX)
/CreationDate (D:20040502195600)
/Subject (PDFLaTeX)
/Keywords (PDF;LaTeX)
}
% ---------------------------------------------------------------
% turn of those nasty overfull and underfull hboxes
\hbadness=10000
\hfuzz=50pt
% ---------------------------------------------------------------
%: FRONT MATTER: dedications, abstract,..
% ---------------------------------------------------------------
%\includeonly{X/filename} % Uncomment to only compile the specified files.
\begin{document}
\selectlanguage{english}
\frontmatterSU
\halftitlepage
%: ----------------------- Generate cover page ------------------------
\maketitle % command to print the title page with above variables
%: ----------------------- Cover page back side ------------------------
\newpage
\thispagestyle{empty}
\input{0_frontmatter/abstract} % Uncomment to input the abstract if you want to have it printed.
\phantom{.}
\vspace{\stretch{1}}
{\fontfamily{verdana}\selectfont
{\scriptsize
\noindent
\copyright Your Name, Stockholm 20XX % Name of author, location year
\vspace{5mm}
\noindent
ISBN XXX-XX-XXXX-XXX-X % Provided by the library
\vspace{5mm}
\noindent
Printed in Sweden by XXXX, Stockholm 2011 %name of printing company
\noindent
Distributor: Department of XX, Stockholm University %name of department
}
}
\cleardoublepage
%: ----------------------- Tie in front matter ------------------------
\include{0_frontmatter/dedication} % Include a page with dedication
\include{0_frontmatter/listofpapers} % Include a list of papers
\include{0_frontmatter/contribution} % Include a page with authors contribution
%: ----------------------- Table of contents ------------------------
\setcounter{secnumdepth}{2} % organisational level that receives a numbers
\setcounter{tocdepth}{2} % print table of contents for level 2
\tableofcontents % print the table of contents
% levels are: 0 - chapter, 1 - section, 2 - subsection, 3 - subsubsection
%: ----------------------- Abbreviations ------------------------
% Tie in external source file for definitions: /0_frontmatter/abbreviations.tex
% Abbreviation entries can also be defined in the main text. See abbreviations.tex
% To create the glossary run "makeindex thesis.nlo -s nomencl.ist -o thesis.nls"
\renewcommand{\nomname}{Abbreviations} % Change title of page from Nomenclature to Abbreviations
%\nomrefpage % to include page numbers after abbrevations
% In the text type "\g" to refer to glossary
\include{0_frontmatter/abbreviations}
%\begin{multicols}{2} % uncomment to have 2 columns
\begin{footnotesize} % scriptsize(7) < footnotesize(8) < small (9) < normal (10)
\printnomenclature[2 cm] % [] = distance between entry and description
\label{nom} % target name for links to glossary
\end{footnotesize}
%\end{multicols}
%: ----------------------- list of figures/tables ------------------------
\listoffigures % print list of figures
\listoftables % print list of tables
%: ----------------------- Acknowledgements ------------------------
\include{0_frontmatter/acknowledgement} % Use this to include an acknowledgement in the frontmatter
%: --------------------------------------------------------------
%: MAIN DOCUMENT SECTION
% --------------------------------------------------------------
% the main text starts here with the introduction, 1st chapter,...
\mainmatterSU
%: ----------------------- subdocuments ------------------------
% Parts of the thesis are included below. Rename the files as required.
% But take care that the paths match. You can also change the order of appearance by moving the include commands.
\include{1_introduction/introduction}
\include{2/instructions}
\include{3/chapter3}
% Include as many chapters as you need
% --------------------------------------------------------------
%: BACK MATTER: appendices, refs,..
% --------------------------------------------------------------
\backmatterSU
% the back matter: summary and references close the thesis
\include{9_backmatter/summary}
\include{9_backmatter/acknowledgement} % Use this to include an acknowledgement in the backmatter
%: ----------------------- bibliography ------------------------
% The section below defines how references are listed and formatted.
%\begin{multicols}{2} % \begin{multicols}{ # columns}[ header text][ space] %uncomment to have 2 columns
\begin{scriptsize} % tiny(5) < scriptsize(7) < footnotesize(8) < small (9)
\bibliographystyle{Latex/Classes/PhDbiblio-url2} %Default style file. Change according to you preferences.
\renewcommand{\bibname}{References} % changes the header from Bibliography to References
\bibliography{9_backmatter/references} % adjust this to fit your BibTex file
\end{scriptsize}
%\end{multicols}
% Various bibliography styles exit. Replace above style as desired.
% in-text refs: (1) (1; 2)
% ref list: alphabetical; author(s) in small caps; initials last name; page(s)
%\bibliographystyle{Latex/Classes/PhDbiblio-case} % title forced lower case
%\bibliographystyle{Latex/Classes/PhDbiblio-bold} % title as in bibtex but bold
%\bibliographystyle{Latex/Classes/PhDbiblio-url} % bold + www link if provided
%\bibliographystyle{Latex/Classes/jmb} % calls style file jmb.bst
% in-text refs: author (year) without brackets
% ref list: alphabetical; author(s) in normal font; last name, initials; page(s)
%\bibliographystyle{plainnat} % calls style file plainnat.bst
% in-text refs: author (year) without brackets
% (this works with package natbib)
% --------------------------------------------------------------
\end{document}