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‎.gitignore‎

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.classpath
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.project
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.settings
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/distrib
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/lib
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/bin
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**/.DS_Store

‎LICENSE.txt‎

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‎NOTICE.txt‎

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This product includes software developed by:
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The Plealog Team (http://www.plealog.com)
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Plealog license is here: http://www.apache.org/licenses/LICENSE-2.0
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It targets: jgaf
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Plealog license is here: https://www.gnu.org/licenses/agpl-3.0.txt
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It targets: pb-core, pb-ui, pb-filter, pb-filter-ui, pb-seqvertor, hge
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The Apache Software Foundation (http://www.apache.org/)
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Apache license is here: http://www.apache.org/licenses/LICENSE-2.0
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It targets: commons-io, commons-lang, commons-logging, xerces, xmlParser
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The Castor Framework Team (http://castor-data-binding.github.io/castor)
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Castor license is here: http://castor-data-binding.github.io/castor/about/licenses.html
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It targets: castor-xml
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The XStream Framework Team (http://x-stream.github.io/):
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XStream License is here: http://x-stream.github.io/license.html
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It targets: xstream
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The JGoodies Forms Framework Team (http://www.jgoodies.com/freeware/libraries/forms/).
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JGoodies license is here: https://opensource.org/licenses/bsd-license.html
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It targets: forms
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The Biojava Team (http://biojava.org)
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Biojava license is here: http://www.gnu.org/copyleft/lesser.html
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It targets: biojava
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The JMol Team (http://jmol.sourceforge.net/)
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JMol license is here: https://opensource.org/licenses/LGPL-2.1
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It targets: JMol

‎README.md‎

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#BioDocumentViewer
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[![License](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt)
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##Introduction
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BioDocumentViewer is a software enabling to query, browse, fetch and retrieve sequences from NCBI and EBI public servers.
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The software has been made to facilitate the use of public web services so that it is easy to retrieve set of sequences in batch mode.
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BioDocumentViewer also provides you with viewing capabilities to display annotated sequences and 3D structures.
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##Requirements
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Use a [Java Virtual Machine](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 1.7 (or above) from Oracle.
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*Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.*
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##Working with the binary release
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The most easy way to use BioDocViewer Tool consists in downloading an official release. It is made of a single Java binary archive file:
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biodocviewer-x.y.z.jar
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It is available from this Github page: check [Releases] tab and download the latest release.
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We invite all users to start working with that tool, as explained in the next section.
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*Notice for developers:* this unique JAR file is absolutely not intended to be embedded within any other applications since it contains all the dependencies (third-party libraries) into a single large file. So, if you want to include BioDocViewer into some other softwares, start from its source code (git clone).
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##User manual
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###Start the graphical interface
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After retrieving an official release of the BioDocumentViewer (BDV) software (see above section), you can start it quite easily:
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java -jar biodocviewer-x.y.z.jar
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By default, BDV uses [NCBI Entrez eUtils services](https://www.ncbi.nlm.nih.gov/books/NBK25499/) (NCBI, Bethesda, USA) to let you query and retrieve protein and nucleotide sequences, 3D structures and taxonomy information.
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However, you can also ask BDV to use [EB-eye Search services](https://www.ebi.ac.uk/ebisearch/) (EBI, Hinxton, UK) as follows:
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java -DV_PROVIDER=EBI -jar biodocviewer-x.y.z.jar
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JVM argument "V_PROVIDER" accepts one of: NCBI (default) or EBI.
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###Make and run a query
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Whatever the data provider you use, NCBI or EBI, the software is quite easy to use:
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* select a bank to query
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* click on the [Go...] button
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* setup the criteria in the query dialogue box
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* click on the [Ok] button... and wait a little bit to get an answer from the provider
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The DocumentNavigator is displayed as soon as you get a valid answer from the bank provider, i.e. your query matches some entries.
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Use the DocumentNavigator:
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* to navigate through entries; use [<] [>] buttons the the top right corner
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* to display an entry in the Sequence or 3D Structure viewer
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* to fetch entries as Fasta of plain format (e.g. Genbk, EMBL, Uniprot, etc.)
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###NCBI/EBI recommendations
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**BDV strictly respects the recommendations of NCBI and EBI for the use or their public resources**, especially when retrieving sequences in batch mode.
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Basically:
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* keep in mind that you are using resources that are shared by many users around the world
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* do not overload NCBI/EBI remote serves
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* retrieve sequences in batch mode using timers
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* provide your email address: NCBI or EBI can get in touch with you in case they consider your are querying too much remote services.
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More about these recommendations: [here for NCBI](https://www.ncbi.nlm.nih.gov/home/about/policies.shtml#scripting), [here for EBI](http://www.ebi.ac.uk/Tools/webservices/help/faq).
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###Extended configuration
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BDV accepts the following optional JVM arguments on the command line:
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* V_DEBUG. Accepts one of: true, false. Default is false.
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* V_PROVIDER. Accepts one of: NCBI, EBI. Default is NCBI.
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* V_EMAIL. Your email address; see "NCBI/EBI recommendations" section, above. Default is none, so BDV will ask you that information at runtime, the first time you use the software.
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You use all these arguments as follows:
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java -DV_PROVIDER=EBI -DV_DEBUG=true ... -jar biodocviewer-x.y.z.jar
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###Log viewer
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BDV uses a logging framework to monitor the software... this can be quite useful when you experience NCBI/EBI connections failure.
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To access the log messages, simply click on the little icon located on the top right corner of BDV main frame, next to [Documents] pulldown menu.
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By default, BDV uses "info" log level, which does not provide much messages. However, you are advised to start BDV with "-DV_DEBUG=true" to get more log messages, which can help to diagnose problems.
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##License and dependencies
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BioDocViewer itself is released under the GNU Affero General Public License, Version 3.0. [AGPL](https://www.gnu.org/licenses/agpl-3.0.txt)
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BioDocViewer depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.
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--
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(c) 2007-2016 - Patrick G. Durand

‎build.xml‎

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<?xml version="1.0" encoding="utf-8"?>
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<!-- ============================================================= -->
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<project name="Document Viewer Tool" default="help" basedir=".">
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<property file="${basedir}/src/bzh/plealog/bioinfo/docviewer/ui/version.properties"/>
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<property name="pbc.libName" value="${prg.name}" />
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<property name="pbc.LibVersion" value="${prg.version}" />
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<property name="compile.optimize" value="on" />
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<property name="compile.debug" value="off" />
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<property name="src" value="${basedir}/src" />
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<property name="jar" value="${basedir}/jar" />
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<property name="distrib" value="${basedir}/distrib" />
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<property name="Dlib" value="${distrib}/lib" />
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<property name="Dsrc" value="${distrib}/src" />
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<property name="Ddoc" value="${distrib}/doc" />
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<property name="Ddoc.api" value="${Ddoc}/api" />
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<property name="pbc.libJar" value="${distrib}/${pbc.libName}-${pbc.LibVersion}.jar"/>
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<path id="class.path">
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<pathelement path="${classpath}"/>
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<fileset dir="${jar}">
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<include name="**/*.jar"/>
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</fileset>
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<pathelement location="${Dlib}"/>
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</path>
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<!-- ============================================================= -->
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<target name="help">
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<echo>Ant task to handle Document Viewer Tool project.</echo>
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<echo/>
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<echo> compile: compile the code.</echo>
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<echo> makedistrib: compile and make release JAR of the DocViewer system.</echo>
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</target>
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<!-- ============================================================= -->
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<target name="prepare">
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<delete dir="${distrib}"/>
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<mkdir dir="${Dlib}"/>
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<mkdir dir="${Dsrc}"/>
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<mkdir dir="${Ddoc.api}"/>
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</target>
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<!-- ============================================================= -->
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<target name="compile" depends="prepare">
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<copy todir="${Dsrc}">
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<fileset dir="${src}">
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<include name="bzh/plealog/bioinfo/**"/>
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</fileset>
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</copy>
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<javac srcdir="${Dsrc}"
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destdir="${Dlib}"
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classpathref="class.path"
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debug="${compile.debug}"
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optimize="${compile.optimize}"
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>
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</javac>
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<copy todir="${Dlib}/bzh/plealog/bioinfo/">
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<fileset dir="${Dsrc}/bzh/plealog/bioinfo/">
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<include name="**/*properties"/>
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<include name="**/*messages"/>
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<include name="**/*cfg"/>
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<include name="**/*gif"/>
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<include name="**/*png"/>
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</fileset>
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</copy>
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</target>
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<!-- ============================================================= -->
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<target name="makedistrib" depends="compile" >
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<jar destfile="${pbc.libJar}">
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<fileset dir="${Dlib}">
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<include name="bzh/plealog/bioinfo/**"/>
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</fileset>
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<restrict>
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<name name="**/*"/>
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<archives>
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<zips>
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<fileset dir="jar" includes="**/*.jar"/>
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</zips>
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</archives>
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</restrict>
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<manifest>
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<attribute name="Main-Class" value="bzh.plealog.bioinfo.docviewer.DocumentViewer"/>
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<attribute name="Built-By" value="Patrick G. Durand"/>
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<attribute name="Title" value="${prg.name}"/>
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<attribute name="Version" value="${prg.version}"/>
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</manifest>
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</jar>
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<jar destfile="${pbc.libJar}" update="true">
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<zipfileset dir="${basedir}" includes="*.txt"/>
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</jar>
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</target>
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</project>

‎conf/README.txt‎

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You can place here ncbiQuery.cfg and/or ebiQuery.cfg.
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Then start application using JVM argument: -DDV_CONF=./conf

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