Merge remote-tracking branch 'origin/master' into development

Conflicts: src/main/java/de/sbtab/view/SBTabMenuController.java
draeger-lab · Aug 9, 2018 · 62d9e86 · 62d9e86
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diff --git a/README.md b/README.md
@@ -1,9 +1,7 @@
-# SBTabEditor<sup>0.1.4</sup>
-[![License (MIT)](https://img.shields.io/badge/license-MIT-blue.svg?style=plastic)](http://opensource.org/licenses/MIT)
+# SBTabEditor
+![Version](https://img.shields.io/badge/version-0.1.4-yellow.svg) [![License (MIT)](https://img.shields.io/github/license/mashape/apistatus.svg)](http://opensource.org/licenses/MIT) [![Build Status](https://travis-ci.com/draeger-lab/SBTabEditor.svg?token=ByDn1ybpoXpKvMHXpZD4&branch=master)](https://travis-ci.com/draeger-lab/SBTabEditor)
 <img align="right" src="src/main/resources/de/sbtab/view/Icon_256.png"/>
 
-[![Build Status](https://travis-ci.com/draeger-lab/SBTabEditor.svg?token=ByDn1ybpoXpKvMHXpZD4&branch=master)](https://travis-ci.com/draeger-lab/SBTabEditor)
-
 **Free, open-source application to help you read, write, manipulate and validate SBML files**
 
 The available information about biological systems increased strongly in the last decade and will
@@ -15,7 +13,6 @@ amounts of data. For this reason the table based data<br> format SBtab was devel
 there is no proper editor designed explicitly for SBtab, the aim of this project solves this problem
 by developing an extensible editor which can read, write and save SBtab and SBML data
 and display them in table form.
-___________________________________________________________________________________________________________
 
 ## Authors
 [Franziska Daumueller](https://github.com/FranziskaDaumueller),
@@ -31,21 +28,26 @@ Supervisor:
 ## How to start
 In order to run JavaFX application, a valid JRE 8+ needed.
 
-**Packaging into an executable Jar file**
+_Packaging into an executable Jar file:_
 
 To create executable jar, call `mvn jfx:jar`. Target jar-file will be placed at: target/jfx/app.
 
 To run: `java -jar sbmltab-x.x.x-jfx.jar`
 
 
-**Assembling into platform-specific bundle**
+_Assembling into platform-specific bundle:_
 
 To create os-specific launcher/installer, call `mvn jfx:native`. Target folder: target/jfx/native
 
 Running process is platform specific. Example `./sbmltab-x.x.x` (running on Unix-like system)
 
+## Documentation
+All relevant information you can find on GitHub [Wiki](https://github.com/draeger-lab/SBTabEditor/wiki).
+
+## Third-party libraries, which we are using
 
-## Third-party libraries, which we are using:
+[JSBML](https://github.com/sbmlteam/jsbml): Pure Java library for reading, writing, and manipulating SBML files and data streams.
 
-[JSBML](https://github.com/sbmlteam/jsbml)
+[JUnit](https://github.com/junit-team/junit5/): Test framework which uses annotations to identify methods that specify a test. 
 
+[Log4j](https://logging.apache.org/log4j/2.x/): Java-based logging utility.
diff --git a/docs/dependencies.html b/docs/dependencies.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<!-- Generated by Apache Maven Doxia Site Renderer 1.8.1 from org.apache.maven.plugins:maven-project-info-reports-plugin:3.0.0:dependencies at 2018-07-23 -->
+<!-- Generated by Apache Maven Doxia Site Renderer 1.8.1 from org.apache.maven.plugins:maven-project-info-reports-plugin:3.0.0:dependencies at 2018-08-02 -->
 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -172,10 +172,10 @@ <h3><a name="compile"></a>compile</h3>
 <td><a class="externalLink" href="http://www.eclipse.org/legal/epl-v10.html">Eclipse Public License 1.0</a></td></tr>
 <tr class="a">
 <td>net.sf.jtidy</td>
-<td>jtidy</td>
+<td><a class="externalLink" href="http://jtidy.sourceforge.net">jtidy</a></td>
 <td>r938</td>
 <td>jar</td>
-<td>-</td></tr>
+<td><a class="externalLink" href="http://jtidy.svn.sourceforge.net/viewvc/jtidy/trunk/jtidy/LICENSE.txt?revision=95">Java HTML Tidy License</a></td></tr>
 <tr class="b">
 <td>org.apache.logging.log4j</td>
 <td><a class="externalLink" href="http://logging.apache.org/log4j/2.x/log4j-1.2-api/">log4j-1.2-api</a></td>
@@ -268,10 +268,10 @@ <h3><a name="compile"></a>compile</h3>
 <td><a class="externalLink" href="http://opensource.org/licenses/LGPL-2.1">LGPL License</a><a class="externalLink" href="http://sbml.org/Software/JSBML/License">Licensing and Distribution Terms for JSBML</a></td></tr>
 <tr class="a">
 <td>org.sbml.jsbml.ext</td>
-<td>jsbml-req</td>
+<td><a class="externalLink" href="http://www.sbml.org/Software/JSBML/ext/jsbml-req">jsbml-req</a></td>
 <td>1.2</td>
 <td>jar</td>
-<td>-</td></tr>
+<td><a class="externalLink" href="http://opensource.org/licenses/LGPL-2.1">LGPL License</a><a class="externalLink" href="http://sbml.org/Software/JSBML/License">Licensing and Distribution Terms for JSBML</a></td></tr>
 <tr class="b">
 <td>org.sbml.jsbml.ext</td>
 <td><a class="externalLink" href="http://www.sbml.org/Software/JSBML/ext/jsbml-spatial">jsbml-spatial</a></td>
@@ -722,7 +722,15 @@ <h3><a name="Dependency_Tree"></a>Dependency Tree</h3>
 <p><b>Description: </b>JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams.</p>
 <p><b>URL: </b><a class="externalLink" href="http://www.sbml.org/Software/JSBML/ext/jsbml-render">http://www.sbml.org/Software/JSBML/ext/jsbml-render</a></p>
 <p><b>Project Licenses: </b><a class="externalLink" href="http://opensource.org/licenses/LGPL-2.1">LGPL License</a>, <a class="externalLink" href="http://sbml.org/Software/JSBML/License">Licensing and Distribution Terms for JSBML</a></p></td></tr></table></div></li>
-<li>org.sbml.jsbml.ext:jsbml-req:jar:1.2 (compile) <img id="_img73" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep72', '_img73' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep72" style="display:none"></td></tr></table></div></li>
+<li>org.sbml.jsbml.ext:jsbml-req:jar:1.2 (compile) <img id="_img73" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep72', '_img73' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep72" style="display:none">
+<table border="0" class="bodyTable">
+<tr class="a">
+<th>jsbml-req</th></tr>
+<tr class="b">
+<td>
+<p><b>Description: </b>JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams.</p>
+<p><b>URL: </b><a class="externalLink" href="http://www.sbml.org/Software/JSBML/ext/jsbml-req">http://www.sbml.org/Software/JSBML/ext/jsbml-req</a></p>
+<p><b>Project Licenses: </b><a class="externalLink" href="http://opensource.org/licenses/LGPL-2.1">LGPL License</a>, <a class="externalLink" href="http://sbml.org/Software/JSBML/License">Licensing and Distribution Terms for JSBML</a></p></td></tr></table></div></li>
 <li>org.sbml.jsbml.ext:jsbml-spatial:jar:1.2 (compile) <img id="_img75" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep74', '_img75' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep74" style="display:none">
 <table border="0" class="bodyTable">
 <tr class="a">
@@ -742,7 +750,17 @@ <h3><a name="Dependency_Tree"></a>Dependency Tree</h3>
 <p><b>URL: </b><a class="externalLink" href="http://www.sbml.org/Software/JSBML/modules/jsbml-tidy">http://www.sbml.org/Software/JSBML/modules/jsbml-tidy</a></p>
 <p><b>Project Licenses: </b><a class="externalLink" href="http://opensource.org/licenses/LGPL-2.1">LGPL License</a>, <a class="externalLink" href="http://sbml.org/Software/JSBML/License">Licensing and Distribution Terms for JSBML</a></p></td></tr></table></div>
 <ul>
-<li>net.sf.jtidy:jtidy:jar:r938 (compile) <img id="_img79" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep78', '_img79' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep78" style="display:none"></td></tr></table></div></li></ul></li></ul></li>
+<li>net.sf.jtidy:jtidy:jar:r938 (compile) <img id="_img79" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep78', '_img79' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep78" style="display:none">
+<table border="0" class="bodyTable">
+<tr class="a">
+<th>JTidy</th></tr>
+<tr class="b">
+<td>
+<p><b>Description: </b>JTidy is a Java port of HTML Tidy, a HTML syntax checker and pretty printer. Like its non-Java cousin, JTidy can be
+    used as a tool for cleaning up malformed and faulty HTML. In addition, JTidy provides a DOM interface to the
+    document that is being processed, which effectively makes you able to use JTidy as a DOM parser for real-world HTML.</p>
+<p><b>URL: </b><a class="externalLink" href="http://jtidy.sourceforge.net">http://jtidy.sourceforge.net</a></p>
+<p><b>Project Licenses: </b><a class="externalLink" href="http://jtidy.svn.sourceforge.net/viewvc/jtidy/trunk/jtidy/LICENSE.txt?revision=95">Java HTML Tidy License</a></p></td></tr></table></div></li></ul></li></ul></li>
 <li>org.apache.logging.log4j:log4j-api:jar:2.1 (compile) <img id="_img81" src="./images/icon_info_sml.gif" alt="[Information]" onclick="toggleDependencyDetails( '_dep80', '_img81' );" style="cursor: pointer; vertical-align: text-bottom;"></img><div id="_dep80" style="display:none">
 <table border="0" class="bodyTable">
 <tr class="a">
@@ -775,19 +793,20 @@ <h2><a name="Licenses"></a>Licenses</h2>
 <p><b>W3C Software License: </b>W3C Jigsaw</p>
 <p><b>The Apache License, Version 2.0: </b>Woodstox, org.apiguardian:apiguardian-api, org.opentest4j:opentest4j</p>
 <p><b>Eclipse Public License 1.0: </b>JUnit</p>
-<p><b>LGPL License: </b>JSBML, jsbml-arrays, jsbml-comp, jsbml-core, jsbml-distrib, jsbml-dyn, jsbml-fbc, jsbml-groups, jsbml-layout, jsbml-multi, jsbml-qual, jsbml-render, jsbml-spatial, jsbml-tidy</p>
+<p><b>LGPL License: </b>JSBML, jsbml-arrays, jsbml-comp, jsbml-core, jsbml-distrib, jsbml-dyn, jsbml-fbc, jsbml-groups, jsbml-layout, jsbml-multi, jsbml-qual, jsbml-render, jsbml-req, jsbml-spatial, jsbml-tidy</p>
 <p><b>The BSD License: </b>Stax2 API</p>
 <p><b>The 3-Clause BSD License: </b>ControlsFX</p>
 <p><b>MIT License: </b>SLF4J API Module</p>
 <p><b>Eclipse Public License v2.0: </b>org.junit.jupiter:junit-jupiter-api, org.junit.jupiter:junit-jupiter-engine, org.junit.platform:junit-platform-commons, org.junit.platform:junit-platform-engine, org.junit.platform:junit-platform-launcher, org.junit.platform:junit-platform-runner, org.junit.platform:junit-platform-suite-api, org.junit.vintage:junit-vintage-engine</p>
+<p><b>Java HTML Tidy License: </b>JTidy</p>
 <p><b>Indiana University Extreme! Lab Software License, vesion 1.1.1: </b>MXP1: Xml Pull Parser 3rd Edition (XPP3)</p>
 <p><b>GNU LGPL v2: </b>biojava-ontology</p>
 <p><b>Public Domain: </b>MXP1: Xml Pull Parser 3rd Edition (XPP3)</p>
 <p><b>New BSD License: </b>Hamcrest Core</p>
 <p><b>BSD style: </b>XStream Core</p>
 <p><b>BSD: </b>StaxMate</p>
 <p><b>Unknown: </b>SBTabEditor</p>
-<p><b>Licensing and Distribution Terms for JSBML: </b>JSBML, jsbml-arrays, jsbml-comp, jsbml-core, jsbml-distrib, jsbml-dyn, jsbml-fbc, jsbml-groups, jsbml-layout, jsbml-multi, jsbml-qual, jsbml-render, jsbml-spatial, jsbml-tidy</p>
+<p><b>Licensing and Distribution Terms for JSBML: </b>JSBML, jsbml-arrays, jsbml-comp, jsbml-core, jsbml-distrib, jsbml-dyn, jsbml-fbc, jsbml-groups, jsbml-layout, jsbml-multi, jsbml-qual, jsbml-render, jsbml-req, jsbml-spatial, jsbml-tidy</p>
 <p><b>The Apache Software License, Version 2.0: </b>Apache Log4j 1.x Compatibility API, Apache Log4j API, Apache Log4j Core, Apache Log4j SLF4J Binding, JSON.simple</p></div><a name="Dependency_File_Details"></a>
 <div class="section">
 <h2><a name="Dependency_File_Details"></a>Dependency File Details</h2>
@@ -1189,4 +1208,4 @@ <h2><a name="Dependency_File_Details"></a>Dependency File Details</h2>
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/dependency-info.html b/docs/dependency-info.html
@@ -1,5 +1,5 @@
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@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -101,4 +101,4 @@ <h3><a name="Leiningen"></a>Leiningen</h3><a name="Leiningen"></a>
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/index.html b/docs/index.html
@@ -1,5 +1,5 @@
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@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -66,4 +66,4 @@ <h2><a name="About_SBTabEditor"></a>About SBTabEditor</h2><a name="About_SBTabEd
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/plugin-management.html b/docs/plugin-management.html
@@ -1,5 +1,5 @@
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   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -86,4 +86,4 @@ <h2><a name="Project_Plugin_Management"></a>Project Plugin Management</h2><a nam
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/plugins.html b/docs/plugins.html
@@ -1,5 +1,5 @@
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@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -121,4 +121,4 @@ <h2><a name="Project_Report_Plugins"></a>Project Report Plugins</h2><a name="Pro
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/project-info.html b/docs/project-info.html
@@ -1,5 +1,5 @@
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@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -93,4 +93,4 @@ <h3><a name="Overview"></a>Overview</h3>
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/summary.html b/docs/summary.html
@@ -1,5 +1,5 @@
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@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -104,4 +104,4 @@ <h3><a name="Build_Information"></a>Build Information</h3><a name="Build_Informa
       </div>
     </div>
   </body>
-</html>
+</html>
diff --git a/docs/team.html b/docs/team.html
@@ -1,5 +1,5 @@
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@@ -27,7 +27,7 @@
     </div>
     <div id="breadcrumbs">
       <div class="xleft">
-        <span id="publishDate">Last Published: 2018-07-23</span>
+        <span id="publishDate">Last Published: 2018-08-02</span>
           &nbsp;| <span id="projectVersion">Version: 0.1.4</span>
       </div>
       <div class="xright">      </div>
@@ -114,4 +114,4 @@ <h3><a name="Contributors"></a>Contributors</h3><a name="Contributors"></a>
       </div>
     </div>
   </body>
-</html>
+</html>