<?xml version="1.0"?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN"
[
<!ENTITY progname "minexpert">
<!ENTITY progName "mineXpert">
]>

<refentry>

	<refentryinfo>
		<date> 03 july 2017</date>
	</refentryinfo>

	<refmeta>
		<refentrytitle>
			<application>&progName;</application>
		</refentrytitle>
		<manvolnum>1</manvolnum>
		<refmiscinfo>&progName; module of the msXpertSuite for mass spectrometry</refmiscinfo>
	</refmeta>

	<refnamediv>
		<refname>
			<application>&progName;</application>
		</refname>

		<refpurpose>
			Open mass spectrometric data files of a wide variety of formats and mine data graphically
		</refpurpose>
	</refnamediv>

	<refsynopsisdiv>

		<cmdsynopsis>
			<command>&progname;</command>
			<arg><option><replaceable class="parameter">options</replaceable></option></arg>
			<arg><option><replaceable class="parameter">filename ...</replaceable></option></arg>
		</cmdsynopsis>

	</refsynopsisdiv>

	<refsect1>
		<title>DESCRIPTION</title>
		<para>

			This manual page documents briefly the
			<command>&progName;</command> software shipped within the
			<filename>msXpertSuite</filename> software suite. 

			This program can be used to load mass spectrometry data files and show the
			spectral data in a plot widget for further analysis according to a variety
			of available integrations. While this program can operate integrally in a
			graphical mode, it is also widely scriptable using JavaScript as a
			scripting language. A typical data mining session would involve the
			following steps/actions:

			<itemizedlist>

				<listitem> <para> Open a mass spectrometry file and immediately compute a
						TIC chromatogram, show that chromatogram in a dedicated window. If the
						data are from an ion mobility mass spectrometry experiment, compute a
						mz = f(dt) color map. The TIC chromatogram and the color map are then
						the starting points for the mining of the data.  </para> </listitem>

				<listitem> <para> Perform a wide variety of integrations to a mass
						spectrum or a drift spectrum. Each new spectrum is displayed in its
						dedicated window (the TIC chromatogram window, the Color map window,
						the Mass spectrum window and the Drift spectrum window).  Each new
						plot (be it a TIC chromatogram, a mass spectrum or a drift spectrum)
						is potentially the start of another integration such that the
						analysis can drill at each step further in the depth of the data.
					</para> </listitem>

				<listitem> <para> Each plot has specific functions associated to it:
						export as a (x,y) file, automatic recording of the relevant data of
						signalled peaks into a file using a specific easy-to-understand
						grammar, slicing of the data file into smaller data files.  </para>
				</listitem>

				<listitem> <para> One feature of importance is the fact that a large part
						of the functionalities of the program are scriptable (JavaScript) and
						a powerful scripting console is available to elaborate scripts before
						storing them in script files to be automatically executed.  </para>
				</listitem>

			</itemizedlist>

		</para>
	</refsect1>

	<refsect1>
		<title>OPTIONS</title>
		<variablelist>

			<varlistentry>
				<term><option>-h | --help</option></term>
				<listitem>
					<para>
						Displays detailed usage information and exits.
					</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-c | --config</option></term>
				<listitem>
					<para>
						Display program configuration at build time and the Qt version used to build it.
					</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-V | --Version</option></term>
				<listitem>
					<para>
						Print the version of the software program along the with version of the Qt libraries used to build it.
					</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-l | --license</option></term>
				<listitem>
					<para>
						Print the license of this software.
					</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-s | --streamed</option></term>
				<listitem>
					<para>
						When opening one or more files in the gui, do that in streamed mode, otherwise in full.
					</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-j | --scriptFile &lt;filename&gt;</option></term>
				<listitem>
					<para>
						Start the program and immediately run the JavaScript script.
					</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><replaceable class="parameter">filename ... </replaceable></term>
				<listitem>
					<para>
						One or more names of files to be opened.
					</para>
				</listitem>      
			</varlistentry>

		</variablelist>
		</refsect1>

		<refsect1>
			<title>Bibliographic reference to be cited</title>
			<para>
				Not yet published...
			</para>
		</refsect1>

		<refsect1>
			<title>See also</title>
			<para>
				<emphasis>massxpert (1)</emphasis>,<emphasis>msxpertsuite-doc (7)</emphasis>
			</para>
		</refsect1>

		<refsect1>
			<title>Useful reading</title>
			<para>
				The program is documented fully in the <emphasis>&progName; User
					Manual</emphasis>, that is packaged in msxpertsuite-doc. That manual is
				available in the form of a PDF-formatted file
				(<filename>/usr/share/doc/msxpertsuite/&progname;-doc.pdf</filename>).
			</para>
		</refsect1>

		<refsect1>
			<title>AUTHOR</title>
			<para>
				<author>
					<firstname>Filippo</firstname>
					<surname>Rusconi &lt;lopippo@debian.org&gt;</surname>
					<authorblurb>
						<para>

							This manual page was written by Filippo Rusconi
							&lt;lopippo@debian.org&gt; (initial writing 03 july 2017).
							Permission is granted to copy, distribute and/or modify this
							document under the terms of the GNU General Public License,
							Version 3, published by the Free Software Foundation.

						</para>

						<para>
							On a Debian system the complete text of the GNU General
							Public License version 3 can be found in the file
							<filename>/usr/share/common-licenses/GPL\-3</filename>.
						</para>

					</authorblurb>
				</author>
			</para>
		</refsect1>
	</refentry>

