From b830fded272bef0e48cfc9c75114c94dba5a5179 Mon Sep 17 00:00:00 2001
From: Samuel Ortion <samuel+git@ortion.fr>
Date: Fri, 15 Mar 2024 09:16:50 +0100
Subject: [PATCH] Add motif search automata

---
 figures/part1/motif_search_automaton.pdf     |  3 +
 figures/part1/motif_search_automaton.tex     | 42 ++++++++++++++
 figures/part1/motif_search_automaton_bis.pdf |  3 +
 figures/part1/motif_search_automaton_bis.tex | 61 ++++++++++++++++++++
 4 files changed, 109 insertions(+)
 create mode 100644 figures/part1/motif_search_automaton.pdf
 create mode 100644 figures/part1/motif_search_automaton.tex
 create mode 100644 figures/part1/motif_search_automaton_bis.pdf
 create mode 100644 figures/part1/motif_search_automaton_bis.tex

diff --git a/figures/part1/motif_search_automaton.pdf b/figures/part1/motif_search_automaton.pdf
new file mode 100644
index 0000000..d4553e5
--- /dev/null
+++ b/figures/part1/motif_search_automaton.pdf
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:53b263eacece1fa3402f78ba9157b23888fd6c91a9128bde5f71f4bceb636165
+size 20747
diff --git a/figures/part1/motif_search_automaton.tex b/figures/part1/motif_search_automaton.tex
new file mode 100644
index 0000000..399d832
--- /dev/null
+++ b/figures/part1/motif_search_automaton.tex
@@ -0,0 +1,42 @@
+\documentclass[tikz]{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+\usetikzlibrary{automata,positioning}
+
+\iffalse
+  Let $M = $ ACACT be a motif.
+  $\Sigma = \{ACT\}$
+  \fi
+\begin{tikzpicture}[shorten >=1pt,node distance=2cm,on grid, auto]
+% TODO
+  \node[state, initial] (q_0) {$q_{0}$};
+  \node[state,right=of q_0] (q_1) {$q_{1}$};
+  \node[state,right=of q_1] (q_2) {$q_{2}$};
+  \node[state,right=of q_2] (q_3) {$q_{3}$};
+   \node[state,right=of q_3] (q_4) {$q_{4}$};
+   \node[state,right=of q_4,accepting] (q_5) {$q_{5}$};
+
+  % M itself
+  \path[->] (q_0) edge node {A} (q_1)
+  (q_1) edge node {C} (q_2)
+  (q_2) edge node {A} (q_3)
+  (q_3) edge node {C} (q_4)
+  (q_4) edge node {T} (q_5);
+
+
+  % Make it complete so that it recognize all motif in the sequence
+  \path[->] (q_0) edge[loop above] node {C, T} (q_1);
+  \path[->] (q_1) edge[loop above] node {A} (q_1);
+  \path[->] (q_1) edge[bend left=30] node {T} (q_0);
+  \path[->] (q_2) edge[bend left=30] node {C, T} (q_0);
+  \path[->] (q_3) edge[bend right=30] node[above] {A} (q_1);
+  \path[->] (q_3) edge[bend left=40] node {T} (q_0);
+  \path[->] (q_4) edge[bend right=50] node[above] {A} (q_3);
+  \path[->] (q_4) edge[bend left=40] node {C} (q_0);
+  \path[->] (q_5) edge[bend right=40] node[above] {A} (q_1);
+  \path[->] (q_5) edge[bend left=50] node {C,T} (q_0);
+\end{tikzpicture}
+
+\end{document}
diff --git a/figures/part1/motif_search_automaton_bis.pdf b/figures/part1/motif_search_automaton_bis.pdf
new file mode 100644
index 0000000..599abdc
--- /dev/null
+++ b/figures/part1/motif_search_automaton_bis.pdf
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:05eb655ddded590285eb6415ddff7aa500fc6407ff93e9b2c0321349d1c2350b
+size 21431
diff --git a/figures/part1/motif_search_automaton_bis.tex b/figures/part1/motif_search_automaton_bis.tex
new file mode 100644
index 0000000..e17a508
--- /dev/null
+++ b/figures/part1/motif_search_automaton_bis.tex
@@ -0,0 +1,61 @@
+\documentclass[tikz]{standalone}
+
+\usepackage{tikz}
+
+\begin{document}
+\usetikzlibrary{automata,positioning}
+
+\iffalse
+  Let $M = $ CCATCAT be a motif.
+  $\Sigma = \{A,C,T\}$
+  \fi
+\begin{tikzpicture}[shorten >=1pt,node distance=2cm,on grid, auto]
+  \node[state, initial] (q_0) {$q_{0}$};
+  \node[state,right=of q_0] (q_1) {$q_{1}$};
+  \node[state,right=of q_1] (q_2) {$q_{2}$};
+  \node[state,right=of q_2] (q_3) {$q_{3}$};
+   \node[state,right=of q_3] (q_4) {$q_{4}$};
+   \node[state,right=of q_4] (q_5) {$q_{5}$};
+   \node[state,right=of q_5] (q_6) {$q_{6}$};
+    \node[state,right=of q_6,accepting] (q_7) {$q_{7}$};
+
+  % M itself
+  \path[->] (q_0) edge node {C} (q_1)
+  (q_1) edge node {C} (q_2)
+  (q_2) edge node {A} (q_3)
+  (q_3) edge node {T} (q_4)
+  (q_4) edge node {C} (q_5)
+  (q_5) edge node {A} (q_6)
+  (q_6) edge node {T} (q_7)
+  ;
+
+
+  % % Make it complete so that it recognize all motif in the sequence
+  % \path[->] (q_0) edge[loop above] node {C, T} (q_1);
+  % \path[->] (q_1) edge[loop above] node {A} (q_1);
+  % \path[->] (q_1) edge[bend left=30] node {T} (q_0);
+  % \path[->] (q_2) edge[bend left=30] node {C, T} (q_0);
+  % \path[->] (q_3) edge[bend right=40] node[above] {A} (q_1);
+  % \path[->] (q_3) edge[bend left=40] node {T} (q_0);
+  % \path[->] (q_4) edge[bend right=50] node[above] {A} (q_3);
+  % \path[->] (q_4) edge[bend left=40] node {C} (q_0);
+  % \path[->] (q_5) edge[bend right=40] node[above] {A} (q_1);
+  % \path[->] (q_5) edge[bend left=50] node {C,T} (q_0);
+
+
+  \path[->] (q_0) edge [loop above] node {A,T} (q_0);
+  \path[->] (q_1) edge [bend right=40] node {A, T} (q_0);
+  \path[->] (q_2) edge [bend right=40] node {C} (q_1);
+  \path[->] (q_2) edge [bend right=40] node {T} (q_0);
+  \path[->] (q_3) edge [bend right=40] node {A} (q_0);
+  \path[->] (q_3) edge [bend right=40] node {C} (q_1);
+  \path[->] (q_4) edge [bend right=40] node {A, T} (q_0);
+  \path[->] (q_5) edge [bend left=40] node[above] {C} (q_1);
+  \path[->] (q_5) edge [bend left=40] node[above] {T} (q_0);
+  \path[->] (q_6) edge [bend left=40] node[above] {A} (q_0);
+  \path[->] (q_6) edge [bend right=40] node {C} (q_1);
+  \path[->] (q_7) edge [bend right=40] node {A, C, T} (q_0);
+  
+\end{tikzpicture}
+
+\end{document}