<?xml version='1.0' encoding='ISO-8859-1'?>
<!--
  #%L
  S2P
  %%
  Copyright (C) 2016 - 2017 José Luis Capelo Martínez, José Eduardo Araújo, Florentino Fdez-Riverola, Miguel
  			Reboiro-Jato, Hugo López-Fernández, and Daniel Glez-Peña
  %%
  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as
  published by the Free Software Foundation, either version 3 of the
  License, or (at your option) any later version.
  
  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
  GNU General Public License for more details.
  
  You should have received a copy of the GNU General Public
  License along with this program.  If not, see
  <http://www.gnu.org/licenses/gpl-3.0.html>.
  #L%
  -->

<!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 2.0//EN"
		"http://java.sun.com/products/javahelp/toc_2_0.dtd">

<toc version="1.0">
	<tocitem text="S2P Help">
		<tocitem target="top" text="Welcome to the S2P Help!" />
		
		<tocitem text="S2P basics">
			<tocitem
				text="Application workflow"
				target="basics.workflow"
			/>
			<tocitem
				text="Main user interface"
				target="basics.mainGUI"
			/>
		</tocitem>

		<tocitem text="Operations">
			<tocitem text="The File menu">
				<tocitem
					text="Open recent"
					target="file.openrecent"
				/>
				<tocitem
					text="New plate"
					target="file.newplate"
				/>
				<tocitem
					text="New Venn Diagram Design"
					target="file.newvenndiagramdesign"
				/>
				<tocitem
					text="Clear clipboard"
					target="file.clearclipboard"
				/>
			</tocitem>

			<tocitem text="The Import menu">
				<tocitem
					text="Import Mascot identifications"
					target="import.mascot"
				/>
				<tocitem
					text="Import Mascot quantifications"
					target="import.mascot.quantifications"
				/>
				<tocitem
					text="Import plate"
					target="import.plate"
				/>
				<tocitem
					text="SameSpots">
					<tocitem
						text="Report from HTM files"
						target="import.samespots.report"
					/>
					<tocitem
						text="Single HTM report"
						target="import.samespots.singlereport"
					/>
					<tocitem
						text="Spots from CSV files"
						target="import.samespots.csv"
					/>
				</tocitem>				
			</tocitem>

			<tocitem text="The Load Menu">
				<tocitem
					text="Load spots"
					target="load.spots"
				/>
				<tocitem
					text="Load identifications"
					target="load.identifications"
				/>
				<tocitem
					text="Load spot identifications"
					target="load.spotidentifications"
				/>
				<tocitem
					text="Load plate"
					target="load.plate"/>
				<tocitem
					text="Load Venn Diagram design"
					target="load.venndiagramdesign"
				/>
			</tocitem>

			<tocitem text="The Operations menu">
				<tocitem
					text="Fill plate"
					target="operations.fillplate"
				/>
				<tocitem
					text="Associate Mascot identifications from a CSV file"
					target="operations.associatemascotidentifications.csv"
				/>
				<tocitem
					text="Associate Mascot identifications from a HTM Mascot report file"
					target="operations.associatemascotidentifications.report"
				/>
			</tocitem>
		</tocitem>

		<tocitem text="Datatypes">
			<tocitem
				text="Maldi plate"
				target="datatype.maldiplate"
			/>
			<tocitem
				text="Venn Diagram design"
				target="datatype.venndiagramdesign"
			/>
			<tocitem
				text="Mascot identifications"
				target="datatype.mascotidentifications"
			/>
			<tocitem
				text="Spot Mascot identifications"
				target="datatype.spotmascotidentifications"
			/>
			<tocitem
				text="Mascot quantifications"
				target="datatype.mascotquantifications"
			/>
			<tocitem
				text="SameSpots analysis"
				target="datatype.samespotsanalysis"
			/>
			<tocitem
				text="Spots data"
				target="datatype.spotsdata"
			/>			
		</tocitem>

		<tocitem text="S2P Advanced">
			<tocitem
				text="Fill SameSpots report"
				target="advanced.fillsamespotsreport"
			/>
		</tocitem>

		<tocitem
			text="About"
			target="about"
		/>
	</tocitem>
</toc>
