From: jprocter Date: Tue, 27 Sep 2011 13:30:57 +0000 (+0100) Subject: patch name, reference and URL for Multi-Harmony : JAL-724 X-Git-Tag: Release_2_7~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1984126973e19bd10f39bb516d728c9226f2ba71;p=jalview.git patch name, reference and URL for Multi-Harmony : JAL-724 --- diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 2bc4187..926a710 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -21,7 +21,7 @@ - + @@ -53,7 +53,7 @@ - + diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html index d6bd77e..ff74139 100755 --- a/help/html/menus/alignmentMenu.html +++ b/help/html/menus/alignmentMenu.html @@ -553,10 +553,10 @@
  • Analysis
      -
    • Sequence Harmony Multi-Relief
      Performs +
    • Multi-Harmony
      Performs functional residue analysis on a protein family alignment with sub-families defined on it. See the SHMR client entry for more + href="../webServices/shmr.html">Multi-Harmony service entry for more information.
    • diff --git a/help/html/menus/wsmenu.html b/help/html/menus/wsmenu.html index a0449ad..fb16551 100755 --- a/help/html/menus/wsmenu.html +++ b/help/html/menus/wsmenu.html @@ -78,10 +78,10 @@
  • Analysis
      -
    • Sequence Harmony Multi-Relief
      Performs +
    • Multi-Harmony
      Performs functional residue analysis on a protein family alignment with sub-families defined on it. See the SHMR client entry for more + href="../webServices/shmr.html">Multi-Harmony service entry for more information.
    • diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 820d90b..21bceca 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -48,7 +48,7 @@
  • Jalview SOAP Web Services for secondary structure prediction based at the University of Dundee.
  • Services for alignment analysis, such as Sequence Harmony Multi Relief. + href="shmr.html">Multi-Harmony.
  • Services for submitting IDs and sequences to external bioinformatics services such as Envision2 (see below).
    • diff --git a/help/html/webServices/shmr.html b/help/html/webServices/shmr.html index 58bacd9..73ab6d6 100755 --- a/help/html/webServices/shmr.html +++ b/help/html/webServices/shmr.html @@ -23,7 +23,7 @@ Functional residue analysis with Sequence Harmony and Multi-Relief

    - The Sequence Harmony and Multi-Relief (SHMR) service (Brandt, Feenstra and Heringa, 2010) available from the Analysis 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 - IBIVU SHMR server. + IBIVU SHMR server.

    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. (* joint first authors)

    - Note: The SHMR service is implemented with Jalview's RESTful - web service client, first introduced in Jalview 2.7. + Note: 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.

    diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java index e618c3f..f42c0c4 100644 --- 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 iparams = new Hashtable(); 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);