Merged develop

matthiaskoenig · Nov 3, 2015 · c6f0db1 · c6f0db1
2 parents 8297b1d + 66faf2f
commit c6f0db1
Show file tree

Hide file tree

Showing 47 changed files with 1,148 additions and 123 deletions.
diff --git a/.classpath b/.classpath
@@ -10,7 +10,7 @@
 	<classpathentry kind="lib" path="lib/sbml/jsbml-qual-2.1-b1.jar"/>
 	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/cytoscape.jar"/>
 	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/plugins/advanced-network-merge-2.8.3-jar-with-dependencies.jar"/>
-	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/plugins/attribute-browser-2.8.3-jar-with-dependencies.jar"/>
+	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/plugins/attribute-browser-2.8.3-jar-with-dependencies.jar" sourcepath="/home/mkoenig/Programs/cytoscape2-parent-2.8.3-fixed"/>
 	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/plugins/automatic-layout-2.8.3-jar-with-dependencies.jar"/>
 	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/plugins/biomart-client-2.8.3-jar-with-dependencies.jar"/>
 	<classpathentry kind="lib" path="/home/mkoenig/git/cy2fluxviz/lib/cytoscape-2.8.3/plugins/biopax-2.8.3-jar-with-dependencies.jar"/>

diff --git a/.gitignore b/.gitignore
@@ -9,3 +9,4 @@ build/*
 .classpath
 .settings/*
 /bin/
+jsbml.log
diff --git a/.jekyll-metadata b/.jekyll-metadata
diff --git a/.sass-cache/2b7df6a9f8af49940c15a89d9b5a1149392c868b/_base.scssc b/.sass-cache/2b7df6a9f8af49940c15a89d9b5a1149392c868b/_base.scssc
diff --git a/.sass-cache/2b7df6a9f8af49940c15a89d9b5a1149392c868b/_layout.scssc b/.sass-cache/2b7df6a9f8af49940c15a89d9b5a1149392c868b/_layout.scssc
diff --git a/.sass-cache/2b7df6a9f8af49940c15a89d9b5a1149392c868b/_syntax-highlighting.scssc b/.sass-cache/2b7df6a9f8af49940c15a89d9b5a1149392c868b/_syntax-highlighting.scssc
diff --git a/README.md b/README.md
@@ -52,6 +52,12 @@ ant cy2fluxviz
 ```
 
 # Changelog
+=======
+## Changelog
+**v1.0.0** [2015-11-03]
+- fixes empty FluxDistribution bug after loading #1
+- updated logging
+
 **v0.95** [2015-10-26]
 - small bug fix release and rebuild with java 8
 - sourceforge to github migration

diff --git a/_site/about.html b/_site/about.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<html>
+
+  <head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+
+  <title>About</title>
+  <meta name="description" content="cy2fluxviz: Cytoscape 2 plugin for visualization of flux distributions.
+">
+
+  <link rel="stylesheet" href="/cy2fluxviz/css/main.css">
+  <link rel="stylesheet" href="/cy2fluxviz/css/core.css">
+  <link rel="canonical" href="http://matthiaskoenig.github.io/cy2fluxviz/about.html">
+  <link rel="alternate" type="application/rss+xml" title="cy2fluxviz" href="http://matthiaskoenig.github.io/cy2fluxviz/feed.xml">
+</head>
+
+
+  <body>
+
+    <header class="site-header">
+
+  <div class="wrapper">
+
+    <a class="site-title" href="/cy2fluxviz/">cy2fluxviz</a>
+
+    <nav class="site-nav">
+      <a href="#" class="menu-icon">
+        <svg viewBox="0 0 18 15">
+          <path fill="#424242" d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.031C17.335,0,18,0.665,18,1.484L18,1.484z"/>
+          <path fill="#424242" d="M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0c0-0.82,0.665-1.484,1.484-1.484 h15.031C17.335,6.031,18,6.696,18,7.516L18,7.516z"/>
+          <path fill="#424242" d="M18,13.516C18,14.335,17.335,15,16.516,15H1.484C0.665,15,0,14.335,0,13.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.031C17.335,12.031,18,12.696,18,13.516L18,13.516z"/>
+        </svg>
+      </a>
+
+      <div class="trigger">
+
+
+          <a class="page-link" href="/cy2fluxviz/about.html">About</a>
+
+
+
+
+
+          <a class="page-link" href="/cy2fluxviz/">cy2fluxviz</a>
+
+
+
+
+      </div>
+    </nav>
+
+  </div>
+
+</header>
+
+
+    <div class="page-content">
+      <div class="wrapper">
+        <article class="post">
+
+  <header class="post-header">
+    <h1 class="post-title">About</h1>
+  </header>
+
+  <div class="post-content">
+    <p>This is a an open source project by 
+<a href="https://github.com/matthiaskoenig"><span class="icon icon--github"><svg viewBox="0 0 16 16"><path fill="#828282" d="M7.999,0.431c-4.285,0-7.76,3.474-7.76,7.761 c0,3.428,2.223,6.337,5.307,7.363c0.388,0.071,0.53-0.168,0.53-0.374c0-0.184-0.007-0.672-0.01-1.32 c-2.159,0.469-2.614-1.04-2.614-1.04c-0.353-0.896-0.862-1.135-0.862-1.135c-0.705-0.481,0.053-0.472,0.053-0.472 c0.779,0.055,1.189,0.8,1.189,0.8c0.692,1.186,1.816,0.843,2.258,0.645c0.071-0.502,0.271-0.843,0.493-1.037 C4.86,11.425,3.049,10.76,3.049,7.786c0-0.847,0.302-1.54,0.799-2.082C3.768,5.507,3.501,4.718,3.924,3.65 c0,0,0.652-0.209,2.134,0.796C6.677,4.273,7.34,4.187,8,4.184c0.659,0.003,1.323,0.089,1.943,0.261 c1.482-1.004,2.132-0.796,2.132-0.796c0.423,1.068,0.157,1.857,0.077,2.054c0.497,0.542,0.798,1.235,0.798,2.082 c0,2.981-1.814,3.637-3.543,3.829c0.279,0.24,0.527,0.713,0.527,1.437c0,1.037-0.01,1.874-0.01,2.129 c0,0.208,0.14,0.449,0.534,0.373c3.081-1.028,5.302-3.935,5.302-7.362C15.76,3.906,12.285,0.431,7.999,0.431z"/></svg>
+</span><span class="username">matthiaskoenig</span></a></p>
+
+  </div>
+
+</article>
+
+      </div>
+    </div>
+
+    <footer class="site-footer">
+
+  <div class="wrapper">
+
+    <h2 class="footer-heading">cy2fluxviz</h2>
+
+    <div class="footer-col-wrapper">
+      <div class="footer-col footer-col-1">
+        <ul class="contact-list">
+          <li>cy2fluxviz</li>
+          <li><a href="mailto:konigmatt@googlemail.com">konigmatt@googlemail.com</a></li>
+        </ul>
+      </div>
+
+      <div class="footer-col footer-col-2">
+        <ul class="social-media-list">
+
+          <li>
+            <a href="https://github.com/matthiaskoenig"><span class="icon icon--github"><svg viewBox="0 0 16 16"><path fill="#828282" d="M7.999,0.431c-4.285,0-7.76,3.474-7.76,7.761 c0,3.428,2.223,6.337,5.307,7.363c0.388,0.071,0.53-0.168,0.53-0.374c0-0.184-0.007-0.672-0.01-1.32 c-2.159,0.469-2.614-1.04-2.614-1.04c-0.353-0.896-0.862-1.135-0.862-1.135c-0.705-0.481,0.053-0.472,0.053-0.472 c0.779,0.055,1.189,0.8,1.189,0.8c0.692,1.186,1.816,0.843,2.258,0.645c0.071-0.502,0.271-0.843,0.493-1.037 C4.86,11.425,3.049,10.76,3.049,7.786c0-0.847,0.302-1.54,0.799-2.082C3.768,5.507,3.501,4.718,3.924,3.65 c0,0,0.652-0.209,2.134,0.796C6.677,4.273,7.34,4.187,8,4.184c0.659,0.003,1.323,0.089,1.943,0.261 c1.482-1.004,2.132-0.796,2.132-0.796c0.423,1.068,0.157,1.857,0.077,2.054c0.497,0.542,0.798,1.235,0.798,2.082 c0,2.981-1.814,3.637-3.543,3.829c0.279,0.24,0.527,0.713,0.527,1.437c0,1.037-0.01,1.874-0.01,2.129 c0,0.208,0.14,0.449,0.534,0.373c3.081-1.028,5.302-3.935,5.302-7.362C15.76,3.906,12.285,0.431,7.999,0.431z"/></svg>
+</span><span class="username">matthiaskoenig</span></a>
+
+          </li>
+
+
+
+          <li>
+            <a href="https://twitter.com/konigmatt"><span class="icon icon--twitter"><svg viewBox="0 0 16 16"><path fill="#828282" d="M15.969,3.058c-0.586,0.26-1.217,0.436-1.878,0.515c0.675-0.405,1.194-1.045,1.438-1.809c-0.632,0.375-1.332,0.647-2.076,0.793c-0.596-0.636-1.446-1.033-2.387-1.033c-1.806,0-3.27,1.464-3.27,3.27 c0,0.256,0.029,0.506,0.085,0.745C5.163,5.404,2.753,4.102,1.14,2.124C0.859,2.607,0.698,3.168,0.698,3.767 c0,1.134,0.577,2.135,1.455,2.722C1.616,6.472,1.112,6.325,0.671,6.08c0,0.014,0,0.027,0,0.041c0,1.584,1.127,2.906,2.623,3.206 C3.02,9.402,2.731,9.442,2.433,9.442c-0.211,0-0.416-0.021-0.615-0.059c0.416,1.299,1.624,2.245,3.055,2.271 c-1.119,0.877-2.529,1.4-4.061,1.4c-0.264,0-0.524-0.015-0.78-0.046c1.447,0.928,3.166,1.469,5.013,1.469 c6.015,0,9.304-4.983,9.304-9.304c0-0.142-0.003-0.283-0.009-0.423C14.976,4.29,15.531,3.714,15.969,3.058z"/></svg>
+</span><span class="username">konigmatt</span></a>
+
+          </li>
+
+	  <li>
+	  <a href="https://livermetabolism.com">
+<span class="icon icon--github"><img src=/cy2fluxviz/images/icon-livermetabolism.png></img></span><span class="username"> livermetabolism </span></a>
+
+
+	  </li>
+        </ul>
+      </div>
+
+      <div class="footer-col footer-col-3">
+        <p>cy2fluxviz: Cytoscape 2 plugin for visualization of flux distributions.
+</p>
+      </div>
+    </div>
+
+  </div>
+
+</footer>
+
+
+  </body>
+
+</html>
diff --git a/_site/css/core.css b/_site/css/core.css
@@ -0,0 +1,4 @@
+.caption {
+	font-size:smaller;	
+	text-align:justify;
+}