JAL-2418 JAL-2549 JABAWS 2.2 release notes

diff --git a/help/html/releases.html b/help/html/releases.html
index 1fe2602..01fd6c2 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -90,7 +90,7 @@ li:before {
             <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
           <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>  
           <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>
             <li><!-- JAL-1476 -->Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera</li>
           <li><!-- JAL-1596 -->Faster Chimera/Jalview communication by file-based command exchange</li>  
           <li><!-- JAL-2316, -->URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB</li>

-          
+          <li><!-- JAL-2549 -->Updated JABAWS client to v2.2</li>

           </ul>
           <em>Experimental features</em>
           <ul>
           </ul>
           <em>Experimental features</em>
           <ul>

diff --git a/help/html/webServices/JABAWS.html b/help/html/webServices/JABAWS.html
index f74e4c4..84b2b86 100644 (file)
--- a/help/html/webServices/JABAWS.html
+++ b/help/html/webServices/JABAWS.html
@@ -28,10 +28,10 @@
     <strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
     <strong>system</strong> (<strong>JABAWS</strong>)<br> Jalview
     includes a client for interacting with programmatic (SOAP) web
     <strong><em>A</em></strong>nalysis <strong><em>W</em></strong>eb <strong><em>S</em></strong>ervices
     <strong>system</strong> (<strong>JABAWS</strong>)<br> Jalview
     includes a client for interacting with programmatic (SOAP) web

-    services for the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
-    service model, developed at the University of Dundee by Peter
-    Troshin and Geoff Barton. This is an open source system that
-    provides a framework for wrapping command line bioinformatics
+    services provided by the <a href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
+    system, developed at the University of Dundee by Peter
+    Troshin, Sasha Sherstnev, Dan Barton, Fabio Madeira-Marquez, Jim Procter and Geoff Barton.
+    This is an open source system that provides a framework for wrapping command line bioinformatics

     analysis programs that enables them to be executed locally or on a
     cluster using data and analysis parameters provided by a program
     linked with the JABA engine directly or accessing it remotely <em>via</em>
     analysis programs that enables them to be executed locally or on a
     cluster using data and analysis parameters provided by a program
     linked with the JABA engine directly or accessing it remotely <em>via</em>

@@ -69,12 +69,15 @@
     each new server.
   </p>
   <p>
     each new server.
   </p>
   <p>

-    <em>Support for accessing JABAWS servers was introduced in
-      Jalview 2.6.</em>
+    <em>JABAWS Client updated to version 2.2 in Jalview 2.10.2</em>

   </p>
   <p>
     <em>Option for adding JABAWS servers which fails validation was
       introduced from version 2.8.2 </em>
   </p>
   </p>
   <p>
     <em>Option for adding JABAWS servers which fails validation was
       introduced from version 2.8.2 </em>
   </p>

+  <p>
+    <em>Support for accessing JABAWS servers was introduced in
+      Jalview 2.6.</em>
+  </p>

 </body>
 </html>
 </body>
 </html>

diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html
index 2fbbdbc..d627c66 100644 (file)
--- a/help/html/webServices/msaclient.html
+++ b/help/html/webServices/msaclient.html
@@ -52,21 +52,18 @@
   </p>
   <p>
     <strong>Alignment programs supported by JABAWS</strong>. <br />Versions
   </p>
   <p>
     <strong>Alignment programs supported by JABAWS</strong>. <br />Versions

-    shown are those bundled with JABAWS 2.01 - if you are using a
+    shown are those bundled with JABAWS 2.2 - if you are using a

     different server, check its home page to find out which versions are
     provided.
     different server, check its home page to find out which versions are
     provided.

-  <ul>
-    <li><a href="http://www.clustal.org/">Clustal Omega and
-        Clustal W</a> (version 2.0.12)</li>
-    <li><a href="http://mafft.cbrc.jp/alignment/software/">Mafft</a>
-      (version 6.8.57b)</li>
-    <li><a href="http://www.drive5.com/muscle">Muscle</a> (version
-      3.8.31)</li>
-    <li><a
-      href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a>
-      (version 8.99)</li>
-    <li><a href="http://probcons.stanford.edu/">Probcons</a>
-      (version 1.12)</li>
+    <ul>
+      <li><a href="http://www.clustal.org/omega">Clustal Omega</a> (version 1.2.4)</li>
+      <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.1)</li>
+      <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 7.310)</li>
+      <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31)</li>
+      <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-coffee</a> (version 11.00.8cbe486)</li>
+      <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>
+      <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>
+      <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>

   </ul>
   </p>
 
   </ul>
   </p>
 

diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html
index 1c35bf3..a06b3a9 100644 (file)
--- a/help/html/webServices/proteinDisorder.html
+++ b/help/html/webServices/proteinDisorder.html
@@ -48,7 +48,7 @@
       By Annotation</a> dialog box to colour sequences according to the
     results of predictors shown as annotation rows.
   </p>
       By Annotation</a> dialog box to colour sequences according to the
     results of predictors shown as annotation rows.
   </p>

-  <p>JABAWS 2.0 provides four disorder predictors which are
+  <p>JABAWS 2.2 provides four disorder predictors which are

     described below:</p>
   <ul>
     <li><a href="#disembl">DisEMBL</a></li>
     described below:</p>
   <ul>
     <li><a href="#disembl">DisEMBL</a></li>

@@ -146,7 +146,7 @@
   </p>
   <p>
     <strong><a name="iupred"></a><a
   </p>
   <p>
     <strong><a name="iupred"></a><a

-      href="http://iupred.enzim.hu/Help.php">IUPred</a></strong><br />
+      href="http://iupred.enzim.hu/">IUPred</a></strong><br />

     IUPred employs an empirical model to estimate likely regions of
     disorder. There are three different prediction types offered, each
     using different parameters optimized for slightly different
     IUPred employs an empirical model to estimate likely regions of
     disorder. There are three different prediction types offered, each
     using different parameters optimized for slightly different