From d9df045a86550501e7f52a4505713f665b9afd6b Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@moulon.inra.fr>
Date: Sat, 16 Nov 2013 22:16:27 +0100
Subject: [PATCH] latex images are automatically converted : png replaced by
svg tex document use image files without extensions
---
doc/images/pappso.pdf | Bin 6011 -> 0 bytes
doc/images/pappso.svg | 189 +++++++++++++++++++++++++++++++++++++++
doc/xtandem_pipeline.tex | 32 +++----
3 files changed, 205 insertions(+), 16 deletions(-)
delete mode 100755 doc/images/pappso.pdf
create mode 100755 doc/images/pappso.svg
diff --git a/doc/images/pappso.pdf b/doc/images/pappso.pdf
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diff --git a/doc/xtandem_pipeline.tex b/doc/xtandem_pipeline.tex
index f45bf4cca..915344a7f 100644
--- a/doc/xtandem_pipeline.tex
+++ b/doc/xtandem_pipeline.tex
@@ -17,7 +17,7 @@
\author{Benoit Valot and Olivier Langella\\
\texttt{valot@moulon.inra.fr; langella@moulon.inra.fr}\\
PAPPSO - \url{http://pappso.inra.fr/}\\
-\includegraphics[width=1cm]{images/pappso.pdf}
+\includegraphics[width=1cm]{images/pappso}
}
\title{$\X$\\Automated analyses, filtering and export of X!Tandem MS/MS results}
\date{22 June 2012}
@@ -29,7 +29,7 @@ PAPPSO - \url{http://pappso.inra.fr/}\\
%\fancyhead{}
\fancyfoot{}
\rfoot{\thepage}
-\lfoot{\includegraphics[width=1cm]{images/pappso.pdf}}
+\lfoot{\includegraphics[width=1cm]{images/pappso}}
\begin{document}
@@ -106,7 +106,7 @@ At the firt start, the application open the configuration path window:
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_configuration.png}
+\center \includegraphics[scale=0.5]{images/tandem_configuration}
\caption{Configuration window}
\label{configuration}
\end{figure}
@@ -124,7 +124,7 @@ Three successive graphical boxes help you select first the mzXML files or other
To perform database searching, you must create or edit a model XML file (stored in the xtandem models folder). Open the menu \textit{Option $\rightarrow$ X!Tandem preset} (Fig~\ref{xtandem_parameter}).
\begin{figure}[!ht]
-\center \includegraphics[scale=0.4]{images/tandem_parameter.png}
+\center \includegraphics[scale=0.4]{images/tandem_parameter}
\caption{X!Tandem preset window}
\label{xtandem_parameter}
\end{figure}
@@ -153,7 +153,7 @@ X!Tandem works with open peak-list files like mzXML, mgf, mzData, mzML or pkl fi
X!Tandem software uses only protein databases in fasta format. It doesn't work with EST\footnote{Expressed Sequenced tag} sequences. You can transform your database using our application \textit{Protein database manager}, available \href{http://pappso.inra.fr/bioinformatique.html}{here}, or you can directly run it \href{http://pappso.inra.fr/documents/bioinformatique/database_manager.jnlp}{here}.
\begin{figure}[!ht]
-\center \includegraphics[scale=0.4]{images/tandem_analysis.png}
+\center \includegraphics[scale=0.4]{images/tandem_analysis}
\caption{X!Tandem parameter window}
\label{xtandem_analysis}
\end{figure}
@@ -204,7 +204,7 @@ Interesting because it allows you to always include the same contaminant protein
\end{description}
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_filter.png}
+\center \includegraphics[scale=0.5]{images/tandem_filter}
\caption{Filter window}
\label{filter}
\end{figure}
@@ -229,7 +229,7 @@ After loading the results, you can select the result to view in the main window
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_principal.png}
+\center \includegraphics[scale=0.5]{images/tandem_principal}
\caption{Main window}
\label{principal}
\end{figure}
@@ -245,7 +245,7 @@ View the list of protein identified on the result. For more details on column se
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_protein.png}
+\center \includegraphics[scale=0.5]{images/window_protein}
\caption{Proteins List}
\end{figure}
@@ -254,7 +254,7 @@ View the list of protein identified on the result. For more details on column se
View the protein sequence and coverage on a identified protein. To view this window, you must open it in the menu \textit{Windows $\rightarrow$ Protein details}.
\begin{figure}[!ht]
-\center \includegraphics[scale=0.7]{images/window_protein_detail.png}
+\center \includegraphics[scale=0.7]{images/window_protein_detail}
\caption{Protein details}
\end{figure}
@@ -269,7 +269,7 @@ View the peptides identified a protein. For more details on column see Fig~\ref{
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_peptide.png}
+\center \includegraphics[scale=0.5]{images/window_peptide}
\caption{Peptides List}
\end{figure}
@@ -283,7 +283,7 @@ View the MS/MS spectra of an identified peptide.
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/window_peptide_detail.png}
+\center \includegraphics[scale=0.5]{images/window_peptide_detail}
\caption{Peptides Details}
\end{figure}
@@ -310,7 +310,7 @@ The export window (Fig~\ref{export}) shows the different types of available expo
\end{description}
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_export.png}
+\center \includegraphics[scale=0.5]{images/tandem_export}
\caption{Export window}
\label{export}
\end{figure}
@@ -344,7 +344,7 @@ The identified proteins are represented by sample (individual mode) or for all s
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_prot.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_prot}
\caption{Protein results}
\label{prot}
\end{figure}
@@ -381,7 +381,7 @@ Identified peptides are grouped by group (Fig~\ref{pep}). One line corresponds t
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_peptide}
\caption{Peptide results}
\label{pep}
\end{figure}
@@ -412,7 +412,7 @@ The list of proteins is repeated 4 times, corresponding to the 4 parameters that
\normalsize
\begin{figure}[!ht]
-\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison.pdf}
+\center \includegraphics[width=1.0\textwidth]{images/tandem_comparaison}
\caption{Comparison results}
\label{compar}
\end{figure}
@@ -427,7 +427,7 @@ In this case, the column corresponding to the normal and reverse search are indi
\end{itemize}
\begin{figure}[!ht]
-\center \includegraphics[scale=0.5]{images/tandem_fdr.png}
+\center \includegraphics[scale=0.5]{images/tandem_fdr}
\caption{FDR results}
\label{fdr2}
\end{figure}
--
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