Updating javadoc sections

Author: josemduarte

index.html

@@ -44,7 +44,7 @@ <h2>Protein Structure Modules<br />
 								  <li>Perform standard analysis such as sequence and structure alignments</li>
 								  <li>Visualize structures</li>
 								</ul>
-								    
+
 							</div>
 						</section>
 						<section class="spotlight">
@@ -79,7 +79,7 @@ <h2>Please cite<br />
 							  <h2>Mailing lists</h2>
 							  <p>
 
-							    BioJava has two main mailing lists. 
+							    BioJava has two main mailing lists.
 							    </p>
 							</header>
 							  <ul class="icons major">
@@ -89,14 +89,14 @@ <h2>Mailing lists</h2>
 							        </a>  general discussion list
 							    </li>
 							    <li><span class="icon fa-envelope-o major style2">
-								
+
 							      </span>
 <a href="/wiki/BioJava:MailingLists/">
 								  <span class="label">biojava-dev</span>
 								</a> developers list
 							    </li>
 							  </ul>
-							  
+
 
 						</div>
 						</section>
@@ -116,10 +116,9 @@ <h3>Cookbook</h3>
 								</li>
 								<li class="icon fa-code">
 									<h3>Javadoc API</h3>
-									<p>Read the</p>
-									<a href="http://www.biojava.org/docs/api4.2.1/index.html" class="button">Javadoc API</a></br>
-									<a href="http://www.biojava.org/docs/api1.9.1/index.html" >legacy 1.9.1 API</a>
-									
+									<p>The Javadocs for the current BioJava release</p>
+									<a href="docs/api4.2.1/" class="button">Javadoc API</a></br>
+
 								</li>
 								<li class="icon fa-globe">
 									<h3>Current release: {{ site.release.version }}</h3>
@@ -131,9 +130,9 @@ <h3>Wiki</h3>
 									<a href="wiki.html" class="button">View wiki</a>
 								</li>
 								<li class="icon fa-flag-o">
-									<h3>Javadoc API</h3>
-									<p>We are hosting a copy of the javadocs.</p>
-									<a href="docs/api4.2.1/" class="button">View javadocs</a>
+									<h3>Legacy Javadoc API</h3>
+									<p>The Javadocs for legacy 1.x BioJava.</p>
+									<a href="docs/api1.9.1/" class="button">View 1.9.1 API</a>
 								</li>
 							</ul>
 						</div>