first open-source release of BlastViewer

.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
+
+ The Apache Software Foundation (http://www.apache.org/)
+ Apache license is here: http://www.apache.org/licenses/LICENSE-2.0
+ It targets: commons-xxx, 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
+

README.md

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+#BlastViewer
+
+[![License](https://img.shields.io/badge/license-Affero%20GPL%203.0-blue.svg)](https://www.gnu.org/licenses/agpl-3.0.txt)
+
+##Introduction
+
+This is the BlastViewer Tool. It aims at displaying in a graphical way results from the NCBI BLAST software.
+
+![BlastViewer](doc/BlastViewer.png)
+
+##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.*
+
+##Software use
+
+
+See the Wiki page of this project.
+
+
+##License and dependencies
+
+BlastViewer itself is released under the GNU Affero General Public License, Version 3.0. [AGPL](https://www.gnu.org/licenses/agpl-3.0.txt)
+
+It depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.
+
+##Once upon a time was: VisualBlast / KoriBlast
+
+During Summer 2004 I was asking myself how easy it could be to rewrite in Java the original [VisualBlast software](http://www.ncbi.nlm.nih.gov/pubmed/9283755) written in C for the MS-Windows platform.
+
+Actually, the answer was quite immediate: it took me a few days to fully rewrite Visual Blast, thanks to the many libraries available, mostly from Sun MicroSystems and the Apache Software Foundation.
+
+So, during my holidays on Summer 2004, I started a wonderful story: the creation of what would eventually become the [KoriBlast/ngKLAST suite of softwares](http://plealog.com/korilog/product-sheets/ngKLAST.pdf), the founding software of my company, Korilog.
+
+Korilog ceased its activities on June 2015, therefore I decided to release these UI components to the open source community... just in time for Christmas 2016! ;-) 
+
+--
+(c) 2003-2016 - Patrick G. Durand

build.xml

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+<?xml version="1.0" encoding="utf-8"?>
+
+<!-- ============================================================= -->
+<project name="BLAST Viewer Tool" default="help" basedir=".">
+
+<property file="${basedir}/src/bzh/plealog/blastviewer/version.properties"/>
+
+<property name="pbc.libName" value="${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 BLAST Viewer Tool project.</echo>
+ <echo/>
+ <echo> compile: compile the code.</echo>
+ <echo> makedistrib: compile and make release JAR of the BLAST 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/blastviewer/**"/>
+ </fileset>
+ </copy>
+ <javac srcdir="${Dsrc}"
+ destdir="${Dlib}"
+ classpathref="class.path"
+ debug="${compile.debug}"
+ optimize="${compile.optimize}"
+ >
+ </javac>
+ <copy todir="${Dlib}/bzh/plealog/blastviewer/">
+ <fileset dir="${Dsrc}/bzh/plealog/blastviewer/">
+ <include name="**/*properties"/>
+ <include name="**/*messages"/>
+ <include name="**/*cfg"/>
+ <include name="**/*gif"/>
+ <include name="**/*png"/>
+ </fileset>
+ </copy>
+</target>
+
+<!-- ============================================================= -->
+<target name="makejar" depends="compile" >
+ <jar destfile="${pbc.libJar}">
+ <fileset dir="${Dlib}">
+ <include name="bzh/plealog/blastviewer/**"/>
+ </fileset>
+ <manifest>
+ <attribute name="Main-Class" value="bzh.plealog.blastviewer.BlastViewer"/>
+ <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>
+
+ <!-- ============================================================= -->
+ <target name="makedistrib" depends="compile" >
+ <jar destfile="${pbc.libJar}">
+ <fileset dir="${Dlib}">
+ <include name="bzh/plealog/blastviewer/**"/>
+ </fileset>
+ <restrict>
+ <name name="**/*"/>
+ <archives>
+ <zips>
+ <fileset dir="jar" includes="**/*.jar"/>
+ </zips>
+ </archives>
+ </restrict>
+ <manifest>
+ <attribute name="Main-Class" value="bzh.plealog.blastviewer.BlastViewer"/>
+ <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>