JAL-2119 updates to invalid / obsolete help links

diff --git a/help/html/features/dasfeatures.html b/help/html/features/dasfeatures.html
index c0c888a..90958ae 100644 (file)
--- a/help/html/features/dasfeatures.html
+++ b/help/html/features/dasfeatures.html
@@ -29,8 +29,7 @@
   </p>
   <p>
     Jalview includes a client for retrieving sequences and their
-    features via the <a href="http://www.biodas.org">Distributed
-      Annotation System</a>.
+    features via the Distributed Annotation System.
   </p>
   <ol>
     <li>Open the Feature Settings panel by selecting &quot;View
@@ -69,6 +68,10 @@
   <p>
     <em>DAS support was introduced in Jalview Version 2.1.</em>
   </p>
+  <br/>
+  <p>
+    <em>The DAS registry at http://www.dasregistry.org was decommissioned early in 2015. An unmaintained mirror is currently hosted at http://www.ebi.ac.uk/das-srv/registry/.</em>
+  </p>
   <p>&nbsp;
 </body>
 </html>

diff --git a/help/html/features/varna.html b/help/html/features/varna.html
index 029edce..ce446f3 100644 (file)
--- a/help/html/features/varna.html
+++ b/help/html/features/varna.html
@@ -27,7 +27,7 @@
     <strong>The VARNA RNA Viewer</strong>
   </p>
   <p>
-    <a href="http://varna.lri.fr/index.html">VARNA</a> was integrated
+    <a href="http://varna.lri.fr">VARNA</a> was integrated
     into Jalview 2.8 to allow interactive viewing of RNA secondary
     structure annotation. It is opened by selecting the <strong>&quot;Structure&#8594;View
       Structure:&quot;</strong> option in the <a href="../menus/popupMenu.html">sequence

diff --git a/help/html/io/index.html b/help/html/io/index.html
index c0a89cf..d2196c1 100755 (executable)
--- a/help/html/io/index.html
+++ b/help/html/io/index.html
@@ -33,10 +33,6 @@
       NBRF/PIR (including MODELLER variant), Pfam/Stockholm</em>
   </p>
   <p>
-    The EBI has <a href="http://www.ebi.ac.uk/help/formats.html">examples</a>
-    of these file formats.
-  </p>
-  <p>
     Additionally, whole sets of coloured and annotated alignments and
     trees can be read from a <a href="../features/jalarchive.html">Jalview
       (jar) format</a> file using <strong>Desktop&#8594;Load

diff --git a/help/html/na/index.html b/help/html/na/index.html
index ae4c1c6..de2741b 100644 (file)
--- a/help/html/na/index.html
+++ b/help/html/na/index.html
@@ -65,7 +65,7 @@ td {
       annotation.</li>
     <li><em>Clustal files</em> - certain RNA alignment programs,
       such as <a
-      href="http://rna.informatik.uni-freiburg.de:8080/LocARNA.jsp"
+      href="http://rna.informatik.uni-freiburg.de/LocARNA"
     >LocaRNA</a> output consensus RNA secondary structure lines in the
       line normally reserved for the Clustal consensus line in a clustal
       file.</li>

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index b03bb9d..1463554 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -90,7 +90,7 @@
     services were maintained by the Barton group at the University of
     Dundee, and ran programs on the Life Sciences High-performance
     Computing Cluster. With the advent of <a
-      href="http://www.compbio.dundee.ac.uk/JABAWS"
+      href="http://www.compbio.dundee.ac.uk/jabaws"
     >JABAWS</a>, however, it is possible for anyone to host Jalview web
     services.
   </p>

diff --git a/utils/HelpLinksChecker.java b/utils/HelpLinksChecker.java
index 1f666a4..1ad5322 100644 (file)
--- a/utils/HelpLinksChecker.java
+++ b/utils/HelpLinksChecker.java
@@ -90,7 +90,7 @@ public class HelpLinksChecker
       return;
     }
 
-    internetAvailable &= connectToUrl("http://www.example.com");
+    internetAvailable &= connectToUrl("http://www.example.org");
 
     Map<String, String> tocTargets = checkHelpMappings(helpFolder);