initial commit as open-source software

.gitignore

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

NOTICE.txt

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

README.md

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+#BioDocumentViewer
+
+[![License](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt)
+
+##Introduction
+
+BioDocumentViewer is a software enabling to query, browse, fetch and retrieve sequences from NCBI and EBI public servers.
+
+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. 
+
+BioDocumentViewer also provides you with viewing capabilities to display annotated sequences and 3D structures.
+
+##Requirements
+
+Use a [Java Virtual Machine](http://www.oracle.com/technetwork/java/javase/downloads/index.html) 1.7 (or above) from Oracle. 
+
+*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.*
+
+##Working with the binary release
+
+The most easy way to use BioDocViewer Tool consists in downloading an official release. It is made of a single Java binary archive file:
+
+    biodocviewer-x.y.z.jar
+
+It is available from this Github page: check [Releases] tab and download the latest release.
+
+We invite all users to start working with that tool, as explained in the next section. 
+
+*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).
+
+##User manual
+
+###Start the graphical interface
+
+After retrieving an official release of the BioDocumentViewer (BDV) software (see above section), you can start it quite easily:
+
+    java -jar biodocviewer-x.y.z.jar
+
+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. 
+
+However, you can also ask BDV to use [EB-eye Search services](https://www.ebi.ac.uk/ebisearch/) (EBI, Hinxton, UK) as follows:
+
+    java -DV_PROVIDER=EBI -jar biodocviewer-x.y.z.jar
+
+JVM argument "V_PROVIDER" accepts one of: NCBI (default) or EBI.
+
+###Make and run a query
+
+Whatever the data provider you use, NCBI or EBI, the software is quite easy to use:
+
+* select a bank to query
+* click on the [Go...] button
+* setup the criteria in the query dialogue box
+* click on the [Ok] button... and wait a little bit to get an answer from the provider
+
+The DocumentNavigator is displayed as soon as you get a valid answer from the bank provider, i.e. your query matches some entries.
+
+Use the DocumentNavigator:
+
+* to navigate through entries; use [<] [>] buttons the the top right corner
+* to display an entry in the Sequence or 3D Structure viewer
+* to fetch entries as Fasta of plain format (e.g. Genbk, EMBL, Uniprot, etc.)
+
+###NCBI/EBI recommendations
+
+**BDV strictly respects the recommendations of NCBI and EBI for the use or their public resources**, especially when retrieving sequences in batch mode.
+
+Basically:
+
+* keep in mind that you are using resources that are shared by many users around the world 
+* do not overload NCBI/EBI remote serves
+* retrieve sequences in batch mode using timers
+* provide your email address: NCBI or EBI can get in touch with you in case they consider your are querying too much remote services. 
+
+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).
+
+###Extended configuration
+
+BDV accepts the following optional JVM arguments on the command line:
+
+* V_DEBUG. Accepts one of: true, false. Default is false.
+* V_PROVIDER. Accepts one of: NCBI, EBI. Default is NCBI.
+* 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.
+
+You use all these arguments as follows:
+
+    java -DV_PROVIDER=EBI -DV_DEBUG=true ... -jar biodocviewer-x.y.z.jar
+
+###Log viewer
+
+BDV uses a logging framework to monitor the software... this can be quite useful when you experience NCBI/EBI connections failure. 
+
+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.
+
+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.
+
+##License and dependencies
+
+BioDocViewer itself is released under the GNU Affero General Public License, Version 3.0. [AGPL](https://www.gnu.org/licenses/agpl-3.0.txt)
+
+BioDocViewer depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.
+
+--
+(c) 2007-2016 - Patrick G. Durand

build.xml

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

conf/README.txt

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