uothesis (20jul11)

git-svn-id: svn://tug.org/texlive/trunk@23207 c570f23f-e606-0410-a88d-b1316a301751

1 files changed, 127 insertions, 32 deletions

diff --git a/Master/texmf-dist/source/latex/uothesis/uothesis.dtx b/Master/texmf-dist/source/latex/uothesis/uothesis.dtx
index 0fc2a8adb90..557ceda8ac7 100644
--- a/Master/texmf-dist/source/latex/uothesis/uothesis.dtx
+++ b/Master/texmf-dist/source/latex/uothesis/uothesis.dtx
@@ -106,7 +106,7 @@ uothesis.ins, and, uothesis.pdf.
 \NeedsTeXFormat{LaTeX2e}
 %</class>
 %<*driver>
-\ProvidesFile{\jobname.dtx}[2011/05/14 v2.5.2 Submission to University of Oregon Graduate School]
+\ProvidesFile{\jobname.dtx}[2011/07/19 v2.5.5 Submission to University of Oregon Graduate School]
 \documentclass[a4paper]{ltxdoc}
 \usepackage[T1]{fontenc}
 \usepackage{achemso,array,booktabs,lmodern}
@@ -306,12 +306,19 @@ uothesis.ins, and, uothesis.pdf.
 %
 %\subsection{New To This Version (2.5.1)}
 %
-%The package |natbib| is still required by the cls, but now it is loaded directly, no user input is required to load |\natbib| by itself.  Customization of the citation formatting can now be accomplished through the use the options, as described in the |natbib| documentation, included in the options for the class itself.  This change is reflected in the example header in this document.  Last, the problem requiring the |\formatbib| command has been corrected and now is not needed.  Calling the |\formatbib| command will now produce an error. 
+%The package |natbib| is still required by the cls, but now it is loaded directly, no user input is required to load |\natbib| by itself.  Customization of the citation formatting can now be accomplished through the use of the native |natbib| options, as described in the |natbib| documentation, included in the options for the class itself.  This change is reflected in the example header in this document.  Last, the problem requiring the |\formatbib| command has been corrected and now is not needed.  Calling the |\formatbib| command will now produce an error. 
 %
 %\subsection{New To This Version (2.5.2)} 
 %
 %This version corrects a page number position change that was recently put in place by the graduate school. 
 %
+%\subsection{New To This Version (2.5.3)}
+%
+%Corrected a formatting issue with the block quotes environment.  
+%
+%\subsection{New To This Version (2.5.4)}
+%Added the |nofigures| and |notables| options.  These options are used to exclude the LOF and LOT from the TOC's if no tables or figures are present in the document.  Also an issue with the TOC column labels and long section titles not wrapping were corrected.
+%
 %\section{Installation}
 %
 % The package is supplied in \file{dtx} format, running 
@@ -429,6 +436,12 @@ uothesis.ins, and, uothesis.pdf.
 %\DescribeOption{bound}
 %The |bound| option is provided strictly for personal use.  It reformats the margins and text block parameters to allow for printing and binding of finished documents.  A disclaimer is placed at the bottom of the copyright page, and the copyright notation on this page is suppressed.
 %
+%\DescribeOption{nofigures}
+%Excludes the list of figures from the table of contents section of the frontmatter in cases were there are no figures in the document.
+%
+%\DescribeOption{notables}
+%Excludes the list of tables from the table of contents section of the frontmatter in cases were there are no tables in the document.
+%
 %\section{Manuscript macros}
 %\subsection{General macros}
 %\DescribeMacro{\cleanbreak}
@@ -452,6 +465,9 @@ uothesis.ins, and, uothesis.pdf.
 %\DescribeMacro{\needref{}}
 %|\needref{}| places a diamond in the text body at the command location, and a red margin note at the same line with an arrow and a "citation." The "|{}|" can be left blank, but must be included at the moment.  Text in the braces will also appear on the notes page in the draft copy.
 %
+%\DescribeMacro{\rfmk}
+%Extensive use of the |\needref{}| macro may result in float errors in the compile.  The |\rfmk| command is provided in such cases.  It does not provide margin note, only the text marker in the document body and the entry into the list of todo's that appears in the draft mode.  |\rfmk| also functions in draft modes, inserting a dummy |\cite| command in the text which results in the default missing citation place holder for the bibtex style being used.  
+%
 %\DescribeMacro{\here}
 %|\here| places a square in the text body and a red "here" in the margin.  It is intended to mark incomplete sections and will place an "incomplete section" note in the draft copy notes page.
 %
@@ -476,6 +492,18 @@ uothesis.ins, and, uothesis.pdf.
 %	 \cmath{(\text{Fd3m, } \langle 111\rangle_{SL} )} + Se ^ }
 %\end{LaTeXdemo}
 %
+%\DescribeMacro{\chemarray}
+%The |\chemarray| environment is for multiple equations that are desired to have a single reference number as in multistep reactions.  Like |\Chem|, the |\\| argument is used to separate lines but the |&| command can also be used to define alignment points within each equation.  The |{rl}| argument indicates the alignment of each column created by the |&| commands.  In this case right justification for the left hand column and left justification for the right column.
+%\begin{LaTeXdemo}[code only]
+%	\chemarray[rxn:thirdrxn]{rl}{CuCl + 2CrCl3 + OLA \text{(excess)} 
+%	&->[\ce{Ar}][\SI{150}{\celsius}] CuCr(OLA)_x\\
+%	Se + OLA \text{(excess)} &->[\ce{Ar}][\SI{330}{\celsius}]
+%	Se(OLA)_x\reactiontag\\
+%	CuCr(OLA)_x + Se(OLA)_x &->[\ce{Ar},\ \SI{200}{\celsius},\ 
+%	\SI{2}{\hour}][\ce{Ar},\ \SI{200}{\celsius},\ \SIrange{0.5}{2}{\hour}]
+%	\spinel\ce{(OLA)_x}}
+%\end{LaTeXdemo}
+%
 %\section{Manuscript organization}
 %It is suggested that you use some scheme for breaking up your document both for ease of editing and for debugging purposes.  The method that has been suggested in the past is to break up the manuscript into a header or root file and a series of dependent tex files that contain one chapter each contained in a directory folder.  These dependent tex files can then be included or excluded by using |\include{}| commands.  |uothesis| is set up to support this method of working.  The inclusion of the "|\% !TEX root =|\meta{path to root file}" command will aid in this.  The manuscript header example provided demonstrates one possible scheme for splitting of documents.  The different components of the header and will be provided in the next section.
 %
@@ -672,7 +700,7 @@ uothesis.ins, and, uothesis.pdf.
 %
 %    \begin{macrocode}
 %<*class>
-\ProvidesClass{uothesis} [2010/04/10 v2.5.1 Submission to
+\ProvidesClass{uothesis} [2010/04/10 v2.5.5 Submission to
  University of Oregon Graduate School]
 %    \end{macrocode}
 %
@@ -714,6 +742,8 @@ uothesis.ins, and, uothesis.pdf.
 \newif\ifchem
 \newif\ifbound
 \newif\ifnatbib
+\newif\ifnotables
+\newif\ifnofigures
 \newif\if@dissertation
 \newif\if@copyright
 \newif\if@gsmodern
@@ -737,6 +767,8 @@ uothesis.ins, and, uothesis.pdf.
 \DeclareOption{chemistry}{\chemtrue\amstextrue}
 \DeclareOption{smallcaps}{\sctrue}
 \DeclareOption{justified}{\justifiedtrue}
+\DeclareOption{nofigures}{\nofigurestrue}
+\DeclareOption{notables}{\notablestrue}
 \DeclareOption{cheqns}{}
 \DeclareOption{final}{\draftcopyfalse\draftimagefalse
 	\committeedraftfalse\latedraftfalse\finaltrue}
@@ -865,6 +897,7 @@ uothesis.ins, and, uothesis.pdf.
 % Here we create the editing markup commands.  These are based off of the |\todo| command.
 %    \begin{macrocode}
 \ifdraftcopy
+	\RequirePackage[colorlinks=true]{hyperref}
 %    \end{macrocode}
 %\begin{macro}{\ednote}
 %Create |\ednote| command.
@@ -880,7 +913,7 @@ uothesis.ins, and, uothesis.pdf.
 %\begin{macro}{\here}
 %Create |\here| command.
 %    \begin{macrocode}
-	\newcommand{\here}{\textcolor{BrickRed}{$\blacksquare$}\todo[inline,color=red!40,
+	\newcommand{\here}{\textcolor{BrickRed}{$\blacksquare$}\todo[color=red!40,
 		size=\small,caption={\uppercase{Incomplete Section: Section \arabic{chapter}.
 		\arabic{section}}}]{\hfil\textbf{\uppercase{Incomplete Section}}\hfil}}
 %    \end{macrocode}
@@ -889,13 +922,22 @@ uothesis.ins, and, uothesis.pdf.
 % create |\needref| command.
 %    \begin{macrocode}
 	\newcounter{citation}
-	\@addtoreset{citation}{chapter}
-   	\newcommand{\needref}[1]{\stepcounter{citation}\todo[color=green!40,
+	\newcounter{citationbychapter}
+	\@addtoreset{citationbychapter}{chapter}
+   	\newcommand{\needref}[1]{\stepcounter{citation}\stepcounter{citationbychapter}\todo[color=green!40,
 		size=\scriptsize,caption={CITE \arabic{chapter}.\arabic{citation}: #1}]
-		{\bf\hfil N.\arabic{chapter}.\arabic{citation}\hfil}
+		{\bf C.\arabic{chapter}.\arabic{citation}}
 		{\textbf{\textcolor{ForestGreen}{[C.\arabic{chapter}.\arabic{citation}]}}}}
 %    \end{macrocode}
 %\end{macro}
+%\begin{macro}{\rfmk}
+% create |\rfmk| command.
+%    \begin{macrocode}
+   	\newcommand{\rfmk}{\stepcounter{citation}\stepcounter{citationbychapter}
+		{\addcontentsline{tdo}{todo}{\protect{\colorbox{green!40}{\textcolor{green!40}{o}}\ Missing Reference: C.\arabic{chapter}.\arabic{citationbychapter}}}}%
+		{{\textcolor{red}{\ensuremath{^\text{[REF: C.\arabic{chapter}.\arabic{citationbychapter}]}}}}}}
+%    \end{macrocode}
+%\end{macro}
 % If the draft mode is not enabled we need to remove commands so that they don't cause errors.
 % This is done by setting them to be empty if |\ifdraft| comes back as false.
 %    \begin{macrocode}
@@ -903,6 +945,8 @@ uothesis.ins, and, uothesis.pdf.
    	\newcommand{\ednote}[1]{}
 	\newcommand{\here}{}
 	\newcommand{\needref}{}
+	\newcounter{citation}
+	\newcommand{\rfmk}{\stepcounter{citation}{\textcolor{red}{\cite{dummy_\arabic{citation}}}}}
 \fi
 %    \end{macrocode}
 
@@ -941,6 +985,13 @@ uothesis.ins, and, uothesis.pdf.
 	\ifx\@empty#1\@empty\else\label{#1}\fi\reactiontag\end{equation}}
 %    \end{macrocode}
 %\end{macro}
+%\begin{macro}{\chemarray}
+%Create new chemarray environment (allows for mulitple equations with one reference and number).  Requires |\reactiontag| to be placed explicitly in the equation.
+%    \begin{macrocode}
+\newcommand{\chemarray}[3][]{\begin{equation}\begin{array}{#2}\cee{#3}%
+	\end{array}\ifx\@empty#1\@empty\else\label{#1}\fi\reactiontag\end{equation}}
+%    \end{macrocode}
+%\end{macro}
 %\begin{macro}{\Chem}
 %Create new Chem environment (enables line breaks)
 %    \begin{macrocode}
@@ -1529,8 +1580,7 @@ This \@papertype\ has been accepted and approved
 %    \begin{macrocode}
 \@committee\\
 and & \\ \\	
-\@graddean & Vice President for Research 
-and Graduate Studies/ Dean of the Graduate School
+\@graddean & Vice President for Research and Innovation/ Dean of the Graduate School
 %    \end{macrocode}
 % end tablular environment
 %    \begin{macrocode}
@@ -1971,10 +2021,13 @@ Title: \@abstracttitle\\*[\baselineskip]
 %    \end{macrocode}
 % set the page style for non-"tocheadings" style TOC, LOF, LOT figures.
 %    \begin{macrocode}
-\pagestyle{tocextraheadings}
 \@tableofcontents
+\ifnofigures\else
 \IfFileExists{\jobname.\ext@figure}{\@listoffigures}{\@starttoc{\ext@figure}}
+\fi
+\ifnotables\else
 \IfFileExists{\jobname.\ext@table}{\@listoftables}{\@starttoc{\ext@table}}
+\fi
 %    \end{macrocode}
 % create clear page
 %    \begin{macrocode}
@@ -2067,7 +2120,7 @@ Draft of \@longdraftdate\\
 %    \end{macrocode}
 % call the abstract string.
 %    \begin{macrocode}
-\par\@abstract
+{\footnotesize \par\@abstract}
 %    \end{macrocode}
 % vertical fill
 %    \begin{macrocode}
@@ -2127,10 +2180,11 @@ Draft of \@longdraftdate\\
 % page headings
 %    \begin{macrocode}
 \def\@footlines#1{\hbox to\textwidth{#1}}
-\def\@footer{\ifbound
-	\hfill\rm\thepage
-	\else
-	\hfil\rm\thepage\hfil\fi}
+\ifbound
+	\def\@footer{\hfill\rm\thepage}
+\else
+	\def\@footer{\hfil\rm\thepage\hfil}
+\fi
 %    \end{macrocode}
 %  define the toc chapter and page labels for first page
 %    \begin{macrocode}
@@ -2140,16 +2194,33 @@ Draft of \@longdraftdate\\
 	\let\@evenfoot\@oddfoot
 	\let\@evenhead\@oddhead}
 %    \end{macrocode}
-% define the toc chapter and page labels for additional pgs.
+%\changes{v2.5.4}{2011/07/14}{Corrected formatting in extra tof and lot pages}
+% define the toc, tof, and lot labels for additional pgs.
 %    \begin{macrocode}
 \def\ps@tocextraheadings{
 	\def\@oddfoot{\@footlines{\@footer}}
 	\def\@oddhead{{\hbox to\textwidth{Chapter\hfil{Page}}}}
-	\let\@evenfoot\@oddfoot
-	\let\@evenhead\@oddhead
+	\def\@evenfoot\@oddfoot
+	\def\@evenhead{{\hbox to\textwidth{Chapter\hfil{Page}}}}
+	\textheight 620pt
+	\headheight 14pt
+	\headsep 14pt}	
+\def\ps@lofextraheadings{
+	\def\@oddfoot{\@footlines{\@footer}}
+	\def\@oddhead{{\hbox to\textwidth{Figure\hfil{Page}}}}
+	\def\@evenfoot\@oddfoot
+	\def\@evenhead{{\hbox to\textwidth{Figure\hfil{Page}}}}
 	\textheight 620pt
 	\headheight 14pt
-	\headsep 14pt}						
+	\headsep 14pt}	
+\def\ps@lotextraheadings{
+	\def\@oddfoot{\@footlines{\@footer}}
+	\def\@oddhead{{\hbox to\textwidth{Table\hfil{Page}}}}
+	\def\@evenfoot\@oddfoot
+	\def\@evenhead{{\hbox to\textwidth{Table\hfil{Page}}}}
+	\textheight 620pt
+	\headheight 14pt
+	\headsep 14pt}	
 %    \end{macrocode}
 % redefine the plain page headers and footers for bound option.
 %    \begin{macrocode}
@@ -2165,21 +2236,33 @@ Draft of \@longdraftdate\\
 
 %\subsubsection{TOC,TOF, etc\ldots Headers}
 %    \begin{macrocode}
-\def\@contentspages#1#2{
+\def\@tableofcontents{%
 	\clearpage
-	\markboth{#1}{#1}
+	\markboth{Chapter}{Chapter}
 	\thispagestyle{tocheadings}
-	\@startchapter{#2}
+	\@startchapter{TABLE OF CONTENTS}
 	\vspace*{14pt}
 	\noindent
-	\makebox[\textwidth][l]{#1 \hfill Page}
-}
-\def\@tableofcontents{\@contentspages{Chapter}{TABLE OF CONTENTS}
-	\@mysingle\@starttoc{toc}\pagestyle{tocextraheadings}} 
-\def\@listoffigures{\@contentspages{Figure}{LIST OF FIGURES}
-	\@mydouble\@starttoc{\ext@figure}\pagestyle{tocextraheadings}}
-\def\@listoftables{\@contentspages{Table}{LIST OF TABLES}
-	\@mydouble\@starttoc{\ext@table}\pagestyle{tocextraheadings}}
+	\makebox[\textwidth][l]{Chapter \hfill Page}
+	\pagestyle{tocextraheadings}\@mysingle\@starttoc{toc}}
+\def\@listoffigures{%
+	\clearpage
+	\markboth{Figure}{Figure}
+	\thispagestyle{tocheadings}
+	\@startchapter{LIST OF FIGURES}
+	\vspace*{14pt}
+	\noindent
+	\makebox[\textwidth][l]{Figure \hfill Page}
+	\pagestyle{lofextraheadings}\@mydouble\@starttoc{\ext@figure}}
+\def\@listoftables{%
+	\clearpage
+	\markboth{Table}{Table}
+	\thispagestyle{tocheadings}
+	\@startchapter{LIST OF TABLES}
+	\vspace*{14pt}
+	\noindent
+	\makebox[\textwidth][l]{Table \hfill Page}
+	\pagestyle{lotextraheadings}\@mydouble\@starttoc{\ext@table}}
 %    \end{macrocode}
 
 %\subsection{Table of Contents Formatting}
@@ -2377,7 +2460,7 @@ Draft of \@longdraftdate\\
       	\ifdim \@tempskipa>\z@
         		\if@gsmodern
           		\begingroup
-            		\@hangfrom{{\bf#6\relax\hskip #3\relax\@svsec{#8}}}
+            		\@hangfrom{{\bf#6\relax\hskip #3\relax}}{\bf\@svsec{#8}}
             		\interlinepenalty \@M
           		\endgroup	
         		\else
@@ -2482,6 +2565,17 @@ Draft of \@longdraftdate\\
 	\clearpage
 	\addcontentsline{toc}{chapter}{#1}
 	\@startchapter{#1}
+		\ifnum \c@citation > 0
+				\centering
+				\setlength\fboxsep{10pt} 
+				\setlength\fboxrule{2pt}
+				\begin{center}
+					\framebox[1\columnwidth]{\parbox{0.95\columnwidth}{\textcolor{red}
+						{\centering\textbf{There are unresolved citation issues!\\*%
+						 Number of unresolved citations: \arabic{citation}.\\*%
+						}}}}
+				\end{center}
+		\fi
 	\singlespacing
 	\@mybibsingle
 	\vspace*{3ex}}
@@ -2616,6 +2710,7 @@ Draft of \@longdraftdate\\
 %\end{macro}
 
 %\subsection{Environment Refinements}
+%\changes{v2.5.3}{2011/06/08}{Corrected block quotes}
 %\begin{macro}{\@@begintheorem}
 %    \begin{macrocode}
 \def\@@begintheorem#1#2#3{\noindent
@@ -2684,7 +2779,7 @@ Draft of \@longdraftdate\\
 %\begin{environment}{quote}
 %    \begin{macrocode}
 \renewenvironment{quote}
-	{\begin{quote*}\singlespace\it\footnotesize}
+	{\begin{quote*}\setstretch{1.7}}
 	{\end{quote*}}
 %    \end{macrocode}
 %\end{environment}