From c0db8f0b8dabf239fb2b5162bb6581380fd1ba3f Mon Sep 17 00:00:00 2001
From: "W. Trevor King" <wking@drexel.edu>
Date: Tue, 9 Feb 2010 15:15:05 -0500
Subject: [PATCH] Fix linenumbers handling and use 'subfig' drexel-thesis
 option

---
 tex/src/cantilever_calib/main.tex        |  1 -
 tex/src/hyeon_temp/main.tex              |  1 -
 tex/src/packages.tex                     | 11 +++++------
 tex/src/root.tex                         |  5 +++--
 tex/src/sawsim/main.tex                  |  1 -
 tex/src/unfolding_distributions/main.tex |  1 -
 tex/src/viscocity/main.tex               |  1 -
 7 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/tex/src/cantilever_calib/main.tex b/tex/src/cantilever_calib/main.tex
index 14cab7c..5d9dd02 100644
--- a/tex/src/cantilever_calib/main.tex
+++ b/tex/src/cantilever_calib/main.tex
@@ -1,4 +1,3 @@
-\linenumbers
 \chapter{Cantilever Calibration}
 \input{cantilever_calib/overview}
 \input{cantilever_calib/setup_general}
diff --git a/tex/src/hyeon_temp/main.tex b/tex/src/hyeon_temp/main.tex
index 1426afb..430b89a 100644
--- a/tex/src/hyeon_temp/main.tex
+++ b/tex/src/hyeon_temp/main.tex
@@ -1,4 +1,3 @@
-\linenumbers
 \chapter{Temperature dependent unfolding}
 
 \section{Energy landscape roughness}
diff --git a/tex/src/packages.tex b/tex/src/packages.tex
index e7bed86..077b8ac 100644
--- a/tex/src/packages.tex
+++ b/tex/src/packages.tex
@@ -21,14 +21,13 @@
 % fonts like mathbb (blackboard)
 \usepackage{amsfonts}
 
-\usepackage{subfig}
-\usepackage{fr-subfig}
-
 \usepackage{xcolor}
 
-%% The lineno packages adds line numbers. Start line numbering with
-%% \begin{linenumbers}, end it with \end{linenumbers}. Or switch it on
-%% for the whole article with \linenumbers after \end{frontmatter}.
+% The lineno packages adds line numbers. Start line numbering with
+% \begin{linenumbers}, end it with \end{linenumbers}. Or switch it on
+% for the whole article with \linenumbers after \end{preamble}.
+% Note that line numbering messes with TOC/LOT/LOF \numberline,
+% so ensure line numbering is off for the tables.
 \usepackage{lineno}
 
 \usepackage{wtk_cmmds}  % common personal macros, in ~/texmf/tex/latex/
diff --git a/tex/src/root.tex b/tex/src/root.tex
index 5480bbd..1b501ec 100644
--- a/tex/src/root.tex
+++ b/tex/src/root.tex
@@ -1,4 +1,5 @@
-\documentclass[%
+\documentclass[subfig,%
+               indenttoc,%
 %               final%
                draft%
                ]{drexel-thesis}
@@ -19,7 +20,6 @@
 \begin{document}
 \begin{preamble}
 
-\linenumbers
 \begin{dedications}
 % Type dedications in here - OPTIONAL
 \end{dedications}
@@ -37,6 +37,7 @@ R01-GM071793.
 % Type abstract in here
 \end{abstract}
 \end{preamble}
+\linenumbers
 
 \begin{thesis}
 \pdfbookmark[-1]{Mainmatter}{Mainmatter}
diff --git a/tex/src/sawsim/main.tex b/tex/src/sawsim/main.tex
index 34ac919..28d36a8 100644
--- a/tex/src/sawsim/main.tex
+++ b/tex/src/sawsim/main.tex
@@ -1,4 +1,3 @@
-\linenumbers
 \chapter{Monte Carlo mechanical unfolding simulation}
 
 \section{Introduction}
diff --git a/tex/src/unfolding_distributions/main.tex b/tex/src/unfolding_distributions/main.tex
index e34172b..0be2e71 100644
--- a/tex/src/unfolding_distributions/main.tex
+++ b/tex/src/unfolding_distributions/main.tex
@@ -1,4 +1,3 @@
-\linenumbers
 \chapter{Theoretical unfolding force distributions}
 \input{unfolding_distributions/overview}
 \input{unfolding_distributions/review}
diff --git a/tex/src/viscocity/main.tex b/tex/src/viscocity/main.tex
index 167846d..d8d8cfb 100644
--- a/tex/src/viscocity/main.tex
+++ b/tex/src/viscocity/main.tex
@@ -1,4 +1,3 @@
-\linenumbers
 \chapter{Hydrodynamic effects in fast AFM single-molecule force measurements}
 
 \begin{center}
-- 
2.26.2