From 2110e31754fe10091091c0aa8ed8e5e70af7db17 Mon Sep 17 00:00:00 2001
From: Samuel Ortion <samuel@ortion.fr>
Date: Thu, 18 Apr 2024 12:53:14 +0200
Subject: [PATCH] rephrase and switch back to link all toc entries, but
 uncolored

---
 report.org        | 28 ++++++++++++++--------------
 report.pdf        |  4 ++--
 sty/lamme2024.sty |  2 +-
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/report.org b/report.org
index 12bfef5..cd44802 100644
--- a/report.org
+++ b/report.org
@@ -9,13 +9,8 @@
 #+exclude_tags: noexport
 #+options: H:7
 #+options: toc:nil
-#+MACRO: conditional-header (eval (concat "#+header: :results output " (print-to-string org-export-current-backend)))
-# ref. conditional-header https://emacs.stackexchange.com/a/64340/41374
-
-
 # ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode
 
-
 #+name: acronyms
 | key        | abbreviation | full form                                  |
 |------------+--------------+--------------------------------------------|
@@ -53,9 +48,12 @@
 #+end_center
 
 #+begin_export latex
+{
+\hypersetup{linkcolor=black}
 \tableofcontents
 \listoffigures
 \listoftables
+}
 #+end_export
 
 [[printglossaries:]]
@@ -154,19 +152,21 @@ In this step, the typical tool involved is =BLAST= (Basic Local Alignment Search
 
 Several =BLAST= metrics can be used as an homology measure, such as bitscore, identity percentage, E-value or variations of these. The choice of metrics can affect the results of graph clustering in the following step, and we should therefore chose them carefully [cite:@gibbonsEvaluationBLASTbasedEdgeweighting2015].
 **** Identification of gene families
-Based on the homology links between each pair of genes, we construct a undirected weighted graph whose vertices correspond to genes and edges to homology links between them.
+Based on the homology links between each pair of genes, we construct an undirected weighted graph whose vertices correspond to genes and edges to homology links between them.
 We apply a graph clustering algorithm on the graph in order to infer the gene families corresponding to densely connected communities of vertices.
 
-FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
-**** Detection of TAGs
-The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
-For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Ref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
 #+begin_export latex
 \fladdfig{
 	\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
 	\caption[Schematic representation of TAG definitions]{\label{fig:tag-definitions} Schematic representation of TAG definitions. Several genes are represented on a linear chromosome. The red box represent a singleton gene. Orange boxes represent a TAG with two duplicate genes seperated by 7 other genes ($\mathrm{TAG}_7$). Four green boxes constitute a TAG, the gene at the extremities are seperated by three genes ($\mathrm{TAG}_3$. The two blue boxes represents a TAG with two genes next to each other $\mathrm{TAG}_0$. The bended edges represents the homology links between each pair of genes of a TAG.}}
 #+end_export
 
+
+FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
+**** Detection of TAGs
+The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
+For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Cref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
+
 * Objectives for the internship
 ** Scientific questions
 The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.
@@ -216,6 +216,10 @@ Principle: construct vertex communities based on where an agent would get stuck
 
 #  LocalWords:  speciation Subfunctionalization Neofunctionalization
 #  LocalWords:  Pseudogenization
+# Local Variables:
+# eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
+# End:
+
 * Setup :noexport:
 
 #+name: startup
@@ -225,7 +229,3 @@ Principle: construct vertex communities based on where an agent would get stuck
 
 #+RESULTS: startup
 : Loaded ./setup.el
-
-#  Local Variables:
-#  eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
-#  End:
diff --git a/report.pdf b/report.pdf
index e8b614d..446230e 100644
--- a/report.pdf
+++ b/report.pdf
@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:7e81782fdc5a634f39286860e802b7cafa7581f2db4925ff9041a3cd220f0cbc
-size 193053
+oid sha256:0aad7b5d59abf2860c3b7502c18047f29f8eb5538d4e162f30568a3d6521e5a6
+size 193201
diff --git a/sty/lamme2024.sty b/sty/lamme2024.sty
index 656d8a1..6ce047c 100644
--- a/sty/lamme2024.sty
+++ b/sty/lamme2024.sty
@@ -84,7 +84,7 @@
   linkcolor=primaryLink,
   anchorcolor=primaryLink,
   citecolor=primaryCite,
-  linktoc=page
+  %linktoc=page
 }
 \newcommand*{\glsplainhyperlink}[2]{%
     \begingroup%