patch name, reference and URL for Multi-Harmony : JAL-724

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 2bc4187..926a710 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -21,7 +21,7 @@
 <tocitem text="Jalview Documentation" target="home" expand="true" >
        <tocitem text="What's new" target="new" expand="true">
       <tocitem text="Enhanced Jmol/Jalview interaction" target="pdbjmol"/>
-          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+          <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
           <tocitem text="Jalview News Reader" target="newsreader"/>
           <tocitem text="Sort alignments associated with tree" target="treeviewer"/>
       <tocitem text="Default Annotation preferences" target="colours.annotation"/>
@@ -53,7 +53,7 @@
                 <tocitem text="Multiple Alignment Subjobs" target="msaservice"/>
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
-          <tocitem text="Sequence Harmony Multi-Relief Analysis" target="shmrws"/>
+          <tocitem text="Multi-Harmony Alignment Analysis" target="shmrws"/>
                <tocitem text="Sequence Retrieval" target="seqfetch"/>
                <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
                <tocitem text="DAS Feature Retrieval" target="das.viewing"/>

diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index d6bd77e..ff74139 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -553,10 +553,10 @@
                                        </ul></li>
                                <li><strong>Analysis</strong><br />
                                        <ul>
-                                               <li><strong>Sequence Harmony Multi-Relief</strong><br> <em>Performs
+                                               <li><strong>Multi-Harmony</strong><br> <em>Performs
                                                                functional residue analysis on a protein family alignment with
                                                                sub-families defined on it. See the <a
-                                                               href="../webServices/shmr.html">SHMR client</a> entry for more
+                                                               href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
                                                                information.</em>
                                                </li>
                                        </ul></li>

diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html
index a0449ad..fb16551 100755 (executable)
--- a/help/html/menus/wsmenu.html
+++ b/help/html/menus/wsmenu.html
@@ -78,10 +78,10 @@
                                        </ul></li>
                                <li><strong>Analysis</strong><br />
                                        <ul>
-                                               <li><strong>Sequence Harmony Multi-Relief</strong><br> <em>Performs
+                                               <li><strong>Multi-Harmony</strong><br> <em>Performs
                                                                functional residue analysis on a protein family alignment with
                                                                sub-families defined on it. See the <a
-                                                               href="../webServices/shmr.html">SHMR client</a> entry for more
+                                                               href="../webServices/shmr.html">Multi-Harmony service</a> entry for more
                                                                information.</em>
                                                </li>
                                        </ul></li>

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 820d90b..21bceca 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -48,7 +48,7 @@
                                <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
                                                structure prediction</a> based at the University of Dundee.</li>
                                <li>Services for alignment analysis, such as <a
-                                       href="shmr.html">Sequence Harmony Multi Relief</a>.
+                                       href="shmr.html">Multi-Harmony</a>.
                                <li>Services for submitting IDs and sequences to external
                                        bioinformatics services such as Envision2 (see <a href="#envision2">below</a>).</li>
                        </ul>

diff --git a/help/html/webServices/shmr.html b/help/html/webServices/shmr.html
index 58bacd9..73ab6d6 100755 (executable)
--- a/help/html/webServices/shmr.html
+++ b/help/html/webServices/shmr.html
@@ -23,7 +23,7 @@
        <strong>Functional residue analysis with Sequence Harmony and
                Multi-Relief</strong>
        <p>
-               The Sequence Harmony and Multi-Relief (SHMR) service (<a
+               The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (<a
                        href="#shmrref">Brandt, Feenstra and Heringa, 2010</a>) available
                from the <em>Analysis</em> sub-menu of the alignment window's web
                services menu provides a method for the identification of significant
@@ -44,7 +44,7 @@
                of the alignment. Once submitted, a job progress window will display
                status information about your job, including a URL which allows you to
                visit the status page on the
-               <a href="http://www.ibi.vu.nl/programs/shmrwww/">IBIVU SHMR server</a>.
+               <a href="http://zeus.few.vu.nl/programs/shmrwww/">IBIVU SHMR server</a>.
        </p>
        <p>When the job is complete, Jalview will automatically open a new
                window containing the alignment and groups that were submitted for
@@ -57,8 +57,8 @@
                        href="http://nar.oxfordjournals.org/cgi/content/abstract/gkq415">Nucleic
                        Acids Res. 38: W35-W40.</a> (<em>* joint first authors</em>)
        <p>
-       <strong><em>Note:</em></strong> The SHMR service is implemented with Jalview's RESTful
-               web service client, first introduced in Jalview 2.7.
+       <strong><em>Note:</em></strong> The Multi-Harmony service is implemented with a prototype of Jalview's RESTful
+               web service client introduced in Jalview 2.7. A few bugs remain in this prototye, which we intend to fixed in version 2.7.1.
        </ul>
        </p>
 </body>

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index e618c3f..f42c0c4 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -304,7 +304,7 @@ public class RestClient extends WSClient implements WSClientI,
 
   public static RestClient makeShmmrRestClient()
   {
-    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (UNSTABLE!)", name = "Sequence Harmony";
+    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = "Multi-Harmony";
     Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
     jalview.ws.rest.params.JobConstant toolp;
     //toolp = new jalview.ws.rest.JobConstant("tool","jalview");
@@ -334,7 +334,7 @@ public class RestClient extends WSClient implements WSClientI,
             action,
             description,
             name,
-            "http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
+            "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
             "?tool=jalview", iparams, true, false, '-');
     // a priori knowledge of the data returned from the service
     shmrService.addResultDatatype(JvDataType.ANNOTATION);