\newcommand{\msxpsurlbase}[1][]{\url{http://www.msxpertsuite.org#1}}
\newcommand{\msxpshrefbase}[2]{\href{http://www.msxpertsuite.org/#1}{#2}}

%%% Version of the software suite
\newcommand{\ver}{5.5.3}
\newcommand{\msXpsver}{\emph{msXpertSuite} version \ver}

%%% msXpertSuite
\newcommand{\msxps}{\textsl{msxpertsuite}\xspace}
\newcommand{\msXps}{\textsl{msXpertSuite}\xspace}

%%% massXpert
\newcommand{\massxp}{\textsl{massxpert}\xspace}
\newcommand{\massXp}{\textsl{massXpert}\xspace}
\newcommand{\xpd}{\textsl{XpertDef}\xspace}
\newcommand{\xpc}{\textsl{XpertCalc}\xspace}
\newcommand{\xpe}{\textsl{XpertEdit}\xspace}
\newcommand{\xpm}{\textsl{XpertMiner}\xspace}
\newcommand{\mzl}{\textsl{mzLab}\xspace}

%%% mineXpert
\newcommand{\minexp}{\textsl{minexpert}\xspace}
\newcommand{\mineXp}{\textsl{mineXpert}\xspace}

%%% convXpert
\newcommand{\convxp}{\textsl{convxpert}\xspace}
\newcommand{\convXp}{\textsl{convXpert}\xspace}

\newcommand{\alertbox}[1]{\begin{center}\fbox{\parbox{0.9\textwidth}{\textsl{#1}}}\end{center}}

\newcommand{\prompt}{\texttt{shell-prompt \$}}
\newcommand{\promptsu}{\texttt{shell-prompt \#}}

\newcommand{\OSname}[1]{\textit{#1}}

\newcommand{\progname}[1]{\texttt{#1}}% for example Emacs
\newcommand{\libname}[1]{\progname{#1}}% for example Emacs
\newcommand{\command}[1]{\texttt{#1}} % for example % pwd
\newcommand{\filename}[1]{\texttt{#1}} % for example /usr/local
\newcommand{\fileformat}[1]{\textsl{#1}} % for example jpg

\newcommand{\kbdEnterKey}{$\looparrowleft$}
\newcommand{\kbdKey}[1]{\ovalbox{#1}}

%% Small vignettes for the mouse buttons.
\DeclareRobustCommand{\lmb}[1][1]%
{\raisebox{-0.33ex}{\mbox{\includegraphics[scale=#1]
	{figures/left-mouse-button.png}}}\xspace}

	\DeclareRobustCommand{\mmb}[1][1]%
	{\raisebox{-0.33ex}{\mbox{\includegraphics[scale=#1]
		{figures/middle-mouse-button.png}}}\xspace}

		\DeclareRobustCommand{\rmb}[1][1]%
		{\raisebox{-0.33ex}{\mbox{\includegraphics[scale=#1]%
			{figures/right-mouse-button.png}}}\xspace}

			\newcommand{\mzz}{(m/z$\,,\,$z)\xspace}
			\newcommand{\mzi}{(mz$\,,\,$i)\xspace}
			\newcommand{\mz}[1]{m/z~#1}

			\newcommand{\cfgkey}[1]{\texttt{#1}} % configuration key
			\newcommand{\cfgval}[1]{\texttt{#1}} % configuration value

			\newcommand{\guimenu}[1]{\textsl{#1}} % for example File
% for example Exit
			\newcommand{\guimenuitem}[1]{\mbox{$\longrightarrow$\textsl{#1}}} 
% for example ``Modification name''
			\newcommand{\guilabel}[1]{\textsf{#1}}
% for example ``Acetylation''
			\newcommand{\guivalue}[1]{\textsl{#1}}

			\newcommand{\sps}[1]{\raisebox{0.33ex}{\footnotesize #1}}
			\newcommand{\sbs}[1]{\raisebox{-0.33ex}{\footnotesize #1}}

			\newcommand{\ppt}{$\mathrm <$}
			\newcommand{\pgd}{$\mathrm >$}

%%% FIXME alert in ongoing text
			\newcommand{\fixme}[1]{\xspace$\blacktriangleright$ #1 %
			$\blacktriangleleft $\xspace}


	%% Needed to help typesetting the titles.
			\newcommand{\sectitle}{}


% this variable is used in mynoindent environment.
			\newlength{\tempvar}

			\newenvironment{mynoindent}
			{
				\setlength{\tempvar}{\parindent}
  \setlength{\parindent}{0pt}
  }
{
  \setlength{\parindent}{\tempvar}
  }
