Fix linenumbers handling and use 'subfig' drexel-thesis option

diff --git a/tex/src/cantilever_calib/main.tex b/tex/src/cantilever_calib/main.tex
index 14cab7c69ae737e6786d0baae5a3addd9c94f5b8..5d9dd02179682ee44e07b6858d7eddffe0aeb931 100644 (file)
--- 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 1426afb870acae6516f6bfcd01dae1bb017735c3..430b89a9cf66df40828bda936b182b729ffb5090 100644 (file)
--- 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 e7bed86a9e0fb0f2712f30094bfcca54a5699e93..077b8ac6a01caee18deb4edeed9a3aa20da61020 100644 (file)
--- 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 5480bbd5dc390c3b1240d1ddaf0658cefa6914b9..1b501ec4991e9f351526e4475627778bb015f0be 100644 (file)
--- 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 34ac91990bf70c721f5bebe409d2ee7f5b800c20..28d36a81d60989011b29a248ad66958951517b54 100644 (file)
--- 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 e34172b309456631a55e9ac7208cf693d5dbb9dd..0be2e718f51f9ef4fa7c18fb72f7bed1884093c8 100644 (file)
--- 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 167846d8aeddc37c7cd71860e03e754a116abab8..d8d8cfbe3b3d2145e3da58b8fc600af5cb40d035 100644 (file)
--- 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}