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  <!ENTITY legal SYSTEM "legal.xml">
  <!ENTITY appversion "0.14.0">
  <!ENTITY manrevision "0.3">
  <!ENTITY date "August 2012">
  <!ENTITY app "GSpectrum">
]>
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<!-- =============Document Header ============================= -->
<book id="index" lang="en">
  <title>&app; manual</title>
<!-- please do not change the id; for translations, change lang to -->
<!-- appropriate code -->
  <bookinfo> 
	 <title>&app; Manual V&manrevision;</title>
	 <copyright> 
       <year>2008-2012</year>
       <holder>Jean Br&#233;fort</holder>
     </copyright>

  <!-- translators: uncomment this and add lang=".." to the <book> tag:

  <copyright>
   <year>2002</year>
   <holder>ME-THE-TRANSLATOR (Latin translation)</holder>
  </copyright>

   -->

	&legal;

	<publisher role="maintainer">
		<publishername>GNOME Documentation Project</publishername>
	</publisher>

	 <authorgroup> 
		<author> 
		  <firstname>Jean</firstname>
		  <surname>Br&#233;fort</surname>
		  <affiliation> 
			 <address> <email>jean.brefort@normalesup.org</email> </address>
		  </affiliation>
		</author> 
<!-- This is appropriate place for other contributors: translators,
      maintainers,  etc. Commented out by default.
       <othercredit role="translator">
	<firstname>Latin</firstname> 
	<surname>Translator 1</surname> 
	<affiliation> 
	  <orgname>Latin Translation Team</orgname> 
	  <address> <email>translator@gnome.org</email> </address> 
	</affiliation>
	<contrib>Latin translation</contrib>
      </othercredit>
-->
	 </authorgroup>

<!-- According to GNU FDL, revision history is mandatory if you are -->
<!-- modifying/reusing someone else's document.  If not, you can omit it. -->
	 <revhistory>
<!-- Remember to remove the &manrevision; entity from the revision entries other
   than the current revision. -->
   		<revision> 
		  <revnumber>&app; Manual V&manrevision;</revnumber>
		  <date>&date;</date> 
		  <revdescription> 
			 <para role="author">Jean Br&#233;fort
				<email>jean.brefort@normalesup.org</email> </para>
			 <para role="publisher">GNOME Documentation Project</para>
		  </revdescription>
		</revision>
   		<revision> 
		  <revnumber>&app; Manual V0.2</revnumber>
		  <date>April 2010</date> 
		  <revdescription> 
			 <para role="author">Jean Br&#233;fort
				<email>jean.brefort@normalesup.org</email> </para>
			 <para role="publisher">GNOME Documentation Project</para>
		  </revdescription>
		</revision>
   		<revision> 
		  <revnumber>&app; Manual V0.1</revnumber>
		  <date>October 2008</date> 
		  <revdescription> 
			 <para role="author">Jean Br&#233;fort
				<email>jean.brefort@normalesup.org</email> </para>
			 <para role="publisher">GNOME Documentation Project</para>
		  </revdescription>
		</revision>
	 </revhistory>
	 <releaseinfo> This manual describes version &appversion; of &app;.
		</releaseinfo>
	 <legalnotice> 
		<title>Feedback</title>
		<para>To report a bug or make a suggestion regarding the &app; application or
		this manual, go to the
		<ulink url="http://savannah.nongnu.org/projects/gchemutils" type="html"><application>&app;</application> home page</ulink>. 
      </para>
<!-- Translators may also add here feedback address for translations -->
	 </legalnotice>
	<abstract role="description">
		<para>&app; is a simple spectrum viewer.</para>
	</abstract>
  </bookinfo>  

<!-- ============= Document Body ============================= -->

<!-- ============= Introduction ============================= -->
 <preface id="gspectrum-intro">
    <title>Introduction</title>
	<para>The <application>&app;</application> application is a spectrum viewer. It can
	load a variety of files in the JCAMP-DX format. It can also load NMR data from
	the NUTS format.</para>
	<para>Supported spectra include UV-visible, IR, Raman, NMR (both spectra and FIDs),
	and Mass.</para>
 </preface>

<!-- ============= Getting started ============================= -->
 <chapter id="gspectrum-getting-started">
    <title>Getting started</title>
	<sect1 id="gspectrum-to-start">
		<title>To Start &app;</title>
		<para>You can start <application>&app;</application> in the following ways:</para>
		<variablelist>
    		<varlistentry>
    		<term>Applications list</term>
    		<listitem>
    		<para>Choose 
    		<quote>Spectrum viewer</quote>. It might be listed either in the Education or
            Science category.</para>
    		</listitem>
    		</varlistentry>
    		<varlistentry>
    		<term>Command line</term>
    		<listitem>
    		<para>Type <command>gspectrum</command>, then press <keycap>Return</keycap>.
		</para>
    		</listitem>
    		</varlistentry>
    		</variablelist>
	</sect1>
	<sect1 id="gspectrum-when-you-start">
		<title>When You Start &app;</title>
		<para>When you start <application>&app;</application>, the following window is displayed:</para>
 			<figure id="gspectrum-main-window"> 
			  <title>&app; document window</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the GSpectrum document window.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/gspectrum.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
	
		<para>The <application>&app;</application> window contains the following
		  elements: </para>
		<variablelist> 
		  <varlistentry> <term>Menubar</term> 
			 <listitem> 
				<para>The menus on the menubar contain all of the commands you need
				  to work with files in <application>&app;</application>.</para>
			 </listitem>
		  </varlistentry>
		  <varlistentry> <term>Display area</term> 
			 <listitem> 
				<para> The display area contains the contents of the file that you are
				  displaying and/or editing. </para>
			 </listitem>
		  </varlistentry>
		</variablelist>
	</sect1>
	<sect1 id="gspectrum-open-file">
		<title>To Open a File</title>
		<para>To open a file, choose 
		  <menuchoice> <guimenu>File</guimenu> <guimenuitem>Open</guimenuitem>
			 </menuchoice>
		  to display the <guilabel>Open File</guilabel> dialog. Select the file
		  that you want to open, then click <guibutton>OK</guibutton>. The file is
		  displayed in a new <application>&app;</application> document window. </para>
		<para>To Open a recently opened file, choose the appropriate entry
		in <menuchoice> <guimenu>File</guimenu> <guimenuitem>Open recent</guimenuitem>
		</menuchoice></para>
		<para><application>&app;</application> can open files on a remote server.</para>
		<para>You can open multiple files in <application>&app;</application>.
		  Each file is opened in it's own top-level window.</para>
	</sect1>
	<sect1 id="gspectrum-run-from-cmd-line">
		<title>To Open Multiple Files from a Command Line</title>
		<para>You can run <application>&app;</application> from a command line
		  and open a single file or multiple files. To open multiple files from a command
		  line, type the following command, then press <keycap>Return</keycap>:</para>
		<para><command>gspectrum <replaceable>file1 file2 file2 ...</replaceable></command></para>
		<para>where file1 and others, might be relative, absolute paths or URIs.</para>
		<para>When the application starts, a <application>&app;</application> window is created
		for each file that you specified.</para>
	</sect1>
</chapter>
<chapter id="gspectrum-usage">
    <title>Usage</title>
    <!--===================Customize the chart============================== -->
	<sect1 id="gspectrum-customize">
		<title>To Customize the spectrum view</title>
		<para>The customization options depend on the spectrum type.</para>
		<para>When a spectrum is opened in a new window, the displayed data are
		those directly read from the file. The abscissa axis might be inverted in
		some cases, according to current usage.</para>
		<para>In the simplest case, the toolbar looks like:</para>
 			<figure id="gspectrum-toolbar"> 
			  <title>GSpectrum default toolbar</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the GSpectrum simplest toolbar.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/simple-toolbar.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
			<para>You can set the values of the minimum
			and maximum displayed coordinates for both axes. These limiting values are constrained to
			be within the actual data intervals.</para>
			<para>When only a part of the spectrum is displayed, the appropriate slider can
			be used to scroll through the spectrum view. The spectrum moves in the same
			direction as the horizontal slider and to the top when the Y axis slider is moved to the right.</para>
			<para>When the spectrum is a UV-Visible spectrum, additional controls are
			available:</para>
			<figure id="gspectrum-uv-toolbar"> 
			  <title>toolbar for UV-visible spectra</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the GSpectrum toolbar for uv-visible spectra.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/uv-vis-tools.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
			<para>The abscissa can be switched between wavelength in nanometers and
			wave number in cm<superscript>&#8722;1</superscript> and the axis inverted (high values at left) or not,
			and the ordinate can be either absorbance or transmittance.</para>
			<para>The toolbar is almost identical for IR spectra. The only difference
			is that wavelengths are in micrometers instead of nanometers:</para>
			<figure id="gspectrum-ir-toolbar"> 
			  <title>toolbar for IR and Raman spectra</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the GSpectrum toolbar for ir spectra.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/ir-tools.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
			<para>The abscissa units available for NMR spectra are ppm and Hz.
			The integration curve can also been displayed or hidden:</para>
			<figure id="gspectrum-nmr-toolbar"> 
			  <title>toolbar for NMR spectra</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the GSpectrum toolbar for NMR spectra.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/nmr-tools.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
			<para>An NMR FID can be transformed to the spectrum unless some parameters are missing in the source file:</para>
			<figure id="gspectrum-fid-toolbar"> 
			  <title>toolbar for NMR FID</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the GSpectrum toolbar for NMR FID.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/fid-tools.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
	</sect1>
<!-- ============= To Save as an Image============================== -->
	<sect1 id="gspectrum-save-as-image">
                <title>Export the Spectrum as an Image</title>
                <para>To export the displayed spectrum to an image, use
                  <menuchoice> <guimenu>File</guimenu> <guimenuitem>Save As Image</guimenuitem>
                         </menuchoice>.</para>
                <para>Available formats are SVG, EPS, PS, PDF, and formats that support writing in GdkPixbuf.</para>
                <para>To choose a format, you can use an appropriate file name extension,
                or explicitly select a format in the combo box.
                With the first method, if <application>&app;</application> does
                not recognize an extension, the exported file will be a SVG
                file. <application>&app;</application> will add an extension
                to the file name if needed.</para>
                <para>You might change the default width and height of the exported image
                using the appropriate entries.</para>
                <para>Postscript and PDF files can also be produced using the
                <link linkend="gspectrum-print"><menuchoice> <guimenu>File</guimenu> <guimenuitem>Print...</guimenuitem>
                         </menuchoice> command</link>.</para>
	</sect1>
<!-- ============= To Print a File============================== -->
	<sect1 id="gspectrum-print">
		<title>To Print the Spectrum</title>
		  <para>To print a spectrum, choose 
		  <menuchoice> <guimenu>File</guimenu> <guimenuitem>Print...</guimenuitem>
			 </menuchoice>.</para>
		 <para><menuchoice> <guimenu>File</guimenu> <guimenuitem>Preview</guimenuitem>
			 </menuchoice> opens a window with a preview of the printed output.</para>
		<para>To tune the printed output, choose<menuchoice>
		<guimenu>File</guimenu> <guimenuitem>Page setup...</guimenuitem>
		 </menuchoice> as explained below.</para>
		<sect2 id="gspectrum-print-setup">
		  <title>The page setup dialog.</title>
		  <para>The first tab of the dialog concerns the paper and margins setup.
		  Headers and footers are not supported in the version of <application>&app;</application></para>
		  <figure id="gspectrum-page-setup"> 
			<title>The Page Setup tab.</title>
			<screenshot> 
			  <mediaobject>
				<imageobject>
				  <objectinfo> <abstract><para>Screenshot of page setup dialog.</para></abstract>
				  </objectinfo> 
				  <imagedata fileref="figures/page-setup.png"/>
				</imageobject>
			  </mediaobject>
			</screenshot>
		  </figure>
		  <para>The second tab allows you to choose the scale of the output. With no scaling or
		  scaling at 100%, the output will have the same size in points as the size in pixels on
		  the screen. If you choose automatic scaling, you can make the output fill the available
		  space either horizontally, vertically, or both (unchecking both options is equivalent to no scaling).</para>
		  <para>Printing to more than one page is not supported in this version of <application>&app;</application></para>
		  <figure id="gspectrum-print-scale"> 
			<title>The Print Scale tab.</title>
			<screenshot> 
			  <mediaobject>
				 <imageobject>
					<objectinfo> <abstract><para>Screenshot of the printing scale page.</para></abstract>
					</objectinfo> 
					<imagedata fileref="figures/print-scale.png"/>
				 </imageobject>
			  </mediaobject>
			</screenshot>
		  </figure>
	  </sect2>
	</sect1>
</chapter>
 <chapter id="gspectrum-support">
    <title>Support.</title>
        <sect1 id="gspectrum-question">
                <title>To Ask a Question</title>
                <para>If you choose <menuchoice> <guimenu>Help</guimenu> <guimenuitem>Ask a question</guimenuitem></menuchoice>,
                your mail client should pop up with a new message to the <ulink type="mail" url="mailto:gchemutils-main@nongnu.org">Gnome Chemistry Utils
                mailing list</ulink>.</para>
                <para>Another way to get some help is to connect on the <ulink url="irc://irc.gimp.net/gchemutils">#gchemutils</ulink> IRC channel
                on the irc.gimp.net network and ask your question there (if you are not alone on the channel).</para>
        </sect1>
        <sect1 id="gspectrum-web">
                <title>To Find the Gnome Chemistry Utils on the Web.</title>
                <para>If you choose <menuchoice> <guimenu>Help</guimenu> <guimenuitem>Gnome Chemistry Utils on the web</guimenuitem></menuchoice>,
                the default web browser should pop up and display the main page for the Gnome Chemsitry Utils.</para>
                <para>The main page is
                <ulink type="http" url="http://gchemutils.nongnu.org">http://gchemutils.nongnu.org</ulink> and the project
                page at Savannah <ulink type="http" url="http://savannah.nongnu.org/projects/gchemutils">http://savannah.nongnu.org/projects/gchemutils</ulink>.</para>
        </sect1>
        <sect1 id="gspectrum-bug">
                <title>To Report a Bug</title>
                <para>To report a bug, you must use the bug page for the Gnome Chemistry
                Utils at Savannah. You can access it by choosing
                <menuchoice> <guimenu>Help</guimenu> <guimenuitem>Report Bugs</guimenuitem></menuchoice>
                (hopefully you'll have only one at a time to report).</para>
                <para>You can also use a web browser to go to the bug report page address directly. The bug repository is at
                <ulink type="http" url="https://savannah.nongnu.org/bugs/?group=gchemutils">https://savannah.nongnu.org/bugs/?group=gchemutils</ulink></para>
        </sect1>
</chapter>

<!-- ============= Application License ============================= -->

 <chapter id="license">
  <title>License</title>
  <para>
   This program is free software; you can redistribute it and/or
   modify it under the terms of the  <ulink type="help" url="ghelp:gpl">GNU
   General Public License</ulink> as
   published by the Free Software Foundation; 
   either version 3 of the License, or (at your option) any later
   version.
  </para>
  <para>
   This program is distributed in the hope that it will be useful, but
   WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   <citetitle>GNU General Public License</citetitle> for more details.
  </para>
  <para>
   A copy of the <citetitle>GNU General Public License</citetitle> is
   included as an appendix to the <citetitle>GNOME Users
   Guide</citetitle>.  You may also obtain a copy of the
   <citetitle>GNU General Public License</citetitle> from the Free
   Software Foundation by visiting <ulink type="http"
   url="http://www.fsf.org">their Web site</ulink> or by writing to
   <address>
    Free Software Foundation, Inc.
    <street>51 Franklin St</street> - Fifth Floor
    <city>Boston</city>, <state>MA</state> <postcode>02111-1307</postcode>
    <country>USA</country>
   </address>
  </para>
 </chapter>

</book>
