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<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
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- <td style="width:150px;height:80px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:150px;height:80px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
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</div>
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- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<table>
<tr class="mid">
- <td class="mid"><a href="http://www.bbsrc.ac.uk/home/home.aspx"><img src="images/bbsrc_flat.png" width="190" height="51" alt="UK BBSRC" class="logo" title="UK BBSRC"/></a></td>
- <td class="mid"><a href="http://www.enfin.org"><img src="images/enfin.jpeg" width="210" height="60" alt="ENFIN" title="ENFIN"/></a></td>
- <td class="mid"><a href="http://www.wellcome.ac.uk"><img src="images/wellcome.jpeg" width="240" height="60" alt="Wellcome Trust" title="Wellcome Trust"/></a></td>
- <td class="mid"><a href="http://www.sulsa.ac.uk"><img src="images/sulsalogo.jpg" width="222" height="60" alt="SULSA" title="SULSA"/></a></td>
+ <td class="mid"><a href="http://www.bbsrc.ac.uk/home/home.aspx"><img src="../images/bbsrc_flat.png" width="190" height="51" alt="UK BBSRC" class="logo" title="UK BBSRC"/></a></td>
+ <td class="mid"><a href="http://www.enfin.org"><img src="../images/enfin.jpeg" width="210" height="60" alt="ENFIN" title="ENFIN"/></a></td>
+ <td class="mid"><a href="http://www.wellcome.ac.uk"><img src="../images/wellcome.jpeg" width="240" height="60" alt="Wellcome Trust" title="Wellcome Trust"/></a></td>
+ <td class="mid"><a href="http://www.sulsa.ac.uk"><img src="../images/sulsalogo.jpg" width="222" height="60" alt="SULSA" title="SULSA"/></a></td>
</tr>
</table>
<br></br>
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<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS.
This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which
is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify
- working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
+ working with JABAWS. For more information please refer to the <a href="../dm_javadoc/index.html">data model javadoc</a>.
</p>
</div><!-- content end-->
<div id="copyright">Last update: 30 April 2014<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>.
</li>
<li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console</a> and switch to AWS Elastic Beanstalk view.
- <img src="images/aws_bs_launch.gif" alt="Elastic Beanstalk launch JABAWS war step 1" width="852" height="418" />
+ <img src="../images/aws_bs_launch.gif" alt="Elastic Beanstalk launch JABAWS war step 1" width="852" height="418" />
</li>
<li>Create a new Beanstalk application by uploading JABAWS war file:
- <img src="images/aws_bs_launch1.gif" alt="Elastic Beanstalk launch JABAWS war step 2" width="532" height="388" />
+ <img src="../images/aws_bs_launch1.gif" alt="Elastic Beanstalk launch JABAWS war step 2" width="532" height="388" />
</li>
<li>Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS.
- <img src="images/aws_bs_launch2.gif" alt="Elastic Beanstalk launch JABAWS war step 3" width="530" height="492" />
+ <img src="../images/aws_bs_launch2.gif" alt="Elastic Beanstalk launch JABAWS war step 3" width="530" height="492" />
</li>
<li>Choose the type of hardware you want to run JABAWS on.
- <img src="images/aws_bs_launch3.gif" alt="Elastic Beanstalk launch JABAWS war step 4" />
+ <img src="../images/aws_bs_launch3.gif" alt="Elastic Beanstalk launch JABAWS war step 4" />
</li>
<li>If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com
- <img src="images/aws_bs_done.gif" alt="Elastic Beanstalk launch JABAWS war " width="682" height="422" />
+ <img src="../images/aws_bs_done.gif" alt="Elastic Beanstalk launch JABAWS war " width="682" height="422" />
</li>
</ol>
<p> </p>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>
<li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console.</a> Make sure you are in the EU West (Ireland) region. JABAWS image is not available in other regions as yet. See marker 1. </li>
<li>Click on "Launch Instance" button marker 2.
- <img src="images/aws_console_launch.gif" alt="AWS console" width="687" height="704" />
+ <img src="../images/aws_console_launch.gif" alt="AWS console" width="687" height="704" />
</li>
<li>Go to the "Community AMI" tab and search for JABAWS, then click select.
- <img src="images/aws_launch.gif" alt="select AMI" width="864" height="262" /></li>
+ <img src="../images/aws_launch.gif" alt="select AMI" width="864" height="262" /></li>
<li>Choose the "hardware" for your JABAWS server instance. "Large" instance should be sufficient for a single user needs.
If you are planning to use this instance as a server for the lab, you may want to select a more powerful machine. Once you have chosen
the hardware click continue.
- <img src="images/aws_launch_instance.gif" alt="select hardware" width="872" height="590" />
+ <img src="../images/aws_launch_instance.gif" alt="select hardware" width="872" height="590" />
</li>
<li>You should not need to customize anything on this page, continue to the next page.
- <img src="images/aws_launch_instance2.gif" alt="keys" width="872" height="592" />
+ <img src="../images/aws_launch_instance2.gif" alt="keys" width="872" height="592" />
</li>
<li> At the "Create a key pair" step, choose "Proceed without a key pair" unless you want to access JABAWS server via SSH.
- <img src="images/aws_launch_instance3.gif" width="872" height="592" />
+ <img src="../images/aws_launch_instance3.gif" width="872" height="592" />
</li>
<li>Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if
you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance, SSH is not necessary,
you can do this from the Amazon Webservices Console (AWS).
- <img src="images/aws_launch_instance_sec_group.gif" alt="ese" width="856" height="588" />
+ <img src="../images/aws_launch_instance_sec_group.gif" alt="ese" width="856" height="588" />
</li>
<li>Review the configuration and launch the instance, then click "view your instances on the Instances page".
- <img src="images/aws_launch_instance5.gif" width="870" height="430" />
+ <img src="../images/aws_launch_instance5.gif" width="870" height="430" />
</li>
<li>At this point you should have JABAWS instance up and running. Your AWS console should look something like this:
- <img src="images/aws_launch_instance_done.gif" width="812" height="848" />
+ <img src="../images/aws_launch_instance_done.gif" width="812" height="848" />
</li>
<li>Now you can run JABAWS web services by accessing the public DNS address of your JABAWS server instance.
For instance, to register it with Jalview, just add the new JABAWS web server. Prefix your instance public
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<p>
The command line client comes as a part of <a href="http://www.compbio.dundee.ac.uk/download"> client package</a> which you are welcome to download.
The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of
-the functions which can be accessed programmatically via <a href="dm_javadoc/index.html">JABAWS API</a>. Using this client you could align sequences
+the functions which can be accessed programmatically via <a href="../dm_javadoc/index.html">JABAWS API</a>. Using this client you could align sequences
using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.
</p>
<span class="code"><strong>Usage:</strong><br/> java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS]<br />
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
Limit limit = getLimit(String name)<br />
LimitsManager lm = getLimits()<br />
PresetManager pm = getPresets()</span></p>
-<p>Please refer to a <a href="dm_javadoc/compbio/data/msa/MsaWS.html">data model javadoc</a> for a detailed description of each methods. </p>
+<p>Please refer to a <a href="../dm_javadoc/compbio/data/msa/MsaWS.html">data model javadoc</a> for a detailed description of each methods. </p>
<h3><a name="templatestr" id="templatestr"></a>Structure of the template command line client</h3>
<table width="100%" border="1">
<tr>
</tr>
</table>
<p>Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />
- Please refer to a <a href="dm_javadoc/index.html">data model javadoc</a> for a detailed description of each class and its methods. </p>
+ Please refer to a <a href="../dm_javadoc/index.html">data model javadoc</a> for a detailed description of each class and its methods. </p>
<h3><a name="connectto" id="connectto"></a>Connecting to JABAWS</h3>
<p>
Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to
MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS
- interface. The full documentation of MsaWS functions is available from the <a href="dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>.
+ interface. The full documentation of MsaWS functions is available from the <a href="../dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>.
</p>
The names of all the parameters supported by a web service e.g. "PAM300" can be obtained
using <span class="hightlight">options.getArguments() </span>method. Further details on the methods
available from <span class="hightlight">RunnerConfig</span> object are available from the
- <a href="dm_javadoc/index.html">javadoc</a>. </p>
+ <a href="../dm_javadoc/index.html">javadoc</a>. </p>
<h3><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h3>
<p>There is a utility method in the client library that does exactly that. </p>
<p> <span class="code">Alignment alignment = align(...) <br />
}
}
</pre>
-For a more detailed description of all available types and their functions please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.
+For a more detailed description of all available types and their functions please refer to the <a href="../dm_javadoc/index.html">data model javadoc</a>.
<h3><a name="buildart" id="buildart"></a>Building web services artifacts</h3>
<p>
JABAWS are the standard <a href="http://jax-ws.java.net/">JAX-WS</a> SOAP web services, which are <a href="http://www.ws-i.org/">WS-I</a>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
</ul>
<h4><a name="api" id="api"></a>The API </h4>
- <p><a href="dm_javadoc/index.html">Data model</a> javadoc- read this if your are coding against JABA Web Services</p>
- <p><a href="full_javadoc/index.html">Complete</a> javadoc - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
+ <p><a href="../dm_javadoc/index.html">Data model</a> javadoc- read this if your are coding against JABA Web Services</p>
+ <p><a href="../full_javadoc/index.html">Complete</a> javadoc - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
<h4><a name="thesrc" id="thesrc"></a>The source code</h4>
<p><a name="svn">Publicly available Git repository:</a><a href="http://source.jalview.org/gitweb/?p=jabaws.git;a=summary">http://source.jalview.org/gitweb/?p=jabaws.git;a=summary</a></p>
<p>Another publicly available JABAWS repository, containing the code for each JABAWS public release, is located at <a href="https://jabaws.googlecode.com">jabaws.googlecode.com</a></p>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<h3><a name="jabawsAppliance" id="jabawsAppliance"/>JABAWS Appliance details</h3>
<p>By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.</p>
<p>The VMware Player screen shot below displays JABAWS VM CPU settings. </p>
-<p><img src="images/VMware_cpu.png" alt="vmware cpu settings" width="708" height="267" style="border: solid black 1px" /></p>
+<p><img src="../images/VMware_cpu.png" alt="vmware cpu settings" width="708" height="267" style="border: solid black 1px" /></p>
<p><strong>JABAWS Virtual Appliance Configuration: </strong></p>
<p><strong>VMware info</strong></p>
New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview
<a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>.
</p>
-<p><img src="images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>
+<p><img src="../images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>
<p>If you click on Advanced Menu, you will see the configuration console, similar to the one below. </p>
-<p><img src="images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>
+<p><img src="../images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>
<p>If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.</p>
<h3><a name="vmiaccess" id="vmiaccess"/>VM Network Settings </h3>
<p>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<div id="banner">
<table>
<tr>
- <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
- <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
- <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+ <td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+ <td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+ <td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div>
<p>JABAWS comes with a web application for visualizing usage statistics. The screenshot below shows the main page of this application. The individual month is linked to detailed usage statistics (described later). Please note, that the links to the detailed monthly statistics are only available for authenticated users in the role <span class="hightlight">admin</span>. There is a link at the bottom of the page that lets you login, if you have not done so. </p>
<p>If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, i.e. empty. </p>
<p>If you have deployed a JABAWS WAR file, then please see the <a href="#conf_tomcat_user">configuring privileged access for Tomcat web application server</a> section for further details. </p>
-<p><img src="images/usage_statistics_main.gif" alt="JABAWS usage statistics" width="608" height="318" /></p>
+<p><img src="../images/usage_statistics_main.gif" alt="JABAWS usage statistics" width="608" height="318" /></p>
<p>The table contains the number of jobs processed by JABAWS per month, for the whole period when the statistics was collected</p>
<p>For each month the table contains the following information.</p>
<ul>
<p>Authentication lets you see the detailed usage statistics. If you are using JABAWS VA (Virtual Appliance) then the username is <span class="hightlight">jabaws</span> and password is not defined, i.e. empty. In other cases you need to ask your system administrator for it. </p>
<h3><a name="detailed_usage"></a>Detailed Usage Statistic </h3>
<p>Detailed execution statistics for each month is available for authenticated users only. </p>
-<p><img src="images/usage_statistics_month.gif" alt="JABAWS one month usage statistics" width="670" height="902" /></p>
+<p><img src="../images/usage_statistics_month.gif" alt="JABAWS one month usage statistics" width="670" height="902" /></p>
<p>Each table contains the number of jobs processed by JABAWS during the period of time specified in the title:</p>
<ul>
<li>The "All Jobs" table contains the summary of all jobs</li>
</ul>
<h3><a name="job_list"></a>Job List </h3>
<p>Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see <a href="#exec_stat_conf">Configuring JABAWS execution statistics</a> section for further details. </p>
-<p><img src="images/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198" /> </p>
+<p><img src="../images/usage_statistics_details.gif" alt="JABAWS - job list" width="917" height="198" /> </p>
<p>Columns: </p>
<ul>
<li>JobID - the JABAWS job id, unique for every job</li>
<li>isFinished - whether the job has finished. This does not necessarily mean that the job has produced the result. The job can sometime finish in failure</li>
</ul>
<h3><a name="job_dir"></a>JABAWS Job Directory Content </h3>
-<p><img src="images/usage_statistics_job_details.gif" alt="JABAWS- job details" width="716" height="420" /></p>
+<p><img src="../images/usage_statistics_job_details.gif" alt="JABAWS- job details" width="716" height="420" /></p>
<p>STARTED and FINISHED files contain Unix timestamp - when the job was started and completed respectively. STARTED is replaced by SUBMITTED if the job has been submitted to the cluster, as opposed to executed locally, on the server. </p>
<p>COLLECTED file is empty and indicates that the job results were collected by the user. Due to asynchronous nature of the job it is possible that the job was started and finished, but the results has never been requested. </p>
<p>RunnerConfig.xml file contains a complete description of the job and JABAWS can restart the job based on this description. </p>
<div id="banner">
<table>
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
-<td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+<td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+<td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div><!-- banner end-->
<div id="banner">
<table>
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
-<td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+<td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+<td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div><!-- banner end-->
<div id="banner">
<table>
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
-<td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+<td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+<td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div><!-- banner end-->
<div id="banner">
<table>
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
-<td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+<td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+<td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div><!-- banner end-->
span.directory {
-background: transparent url(images/dir.gif) no-repeat scroll left center;
+background: transparent url(../images/dir.gif) no-repeat scroll left center;
color:#666666;
font-family:"Courier New",Courier,monospace;
font-style:normal;
}
.source .header {
- background:#E9EAEC url(images/minus.png) no-repeat scroll 98% center;
+ background:#E9EAEC url(../images/minus.png) no-repeat scroll 98% center;
color:#3B3D3F;
cursor:pointer;
font-weight:bold;
}
.source .header.collapsed {
- background:#E9EAEC url(images/plus.png) no-repeat scroll 98% center;
+ background:#E9EAEC url(../images/plus.png) no-repeat scroll 98% center;
padding:0 15px 0 15px;
}
<div id="banner">
<table>
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
-<td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="../images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>
+<td class="bg"><img src="../images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>
+<td class="bg"><img src="../images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
</tr>
</table>
</div><!-- banner end-->
}
#wrapper #choicematrix th {
- background-image:url(images/brickhead2.jpg);
+ background-image:url(../images/brickhead2.jpg);
background-repeat:repeat-x;
}
-webkit-border-radius:10px;
-moz-border-radius:10px;
border-radius: 20px;
- background-image:url(images/brickhead2_line.jpg);
+ background-image:url(../images/brickhead2_line.jpg);
background-repeat:repeat-x;
}
}
#wrapper {
- background:url("images/panel_bg_long.png") repeat-y left top;
+ background:url("../images/panel_bg_long.png") repeat-y left top;
margin:0;
padding:0;
}
}
span.directory {
- background: transparent url(images/dir.gif) no-repeat scroll left center;
+ background: transparent url(../images/dir.gif) no-repeat scroll left center;
color:#666666;
font-family:"Courier New",Courier,monospace;
font-style:normal;
}
.source .header {
- background:#E9EAEC url(images/minus.png) no-repeat scroll 98% center;
+ background:#E9EAEC url(../images/minus.png) no-repeat scroll 98% center;
color:#3B3D3F;
cursor:pointer;
font-weight:bold;
}
.source .header.collapsed {
- background:#E9EAEC url(images/plus.png) no-repeat scroll 98% center;
+ background:#E9EAEC url(../images/plus.png) no-repeat scroll 98% center;
padding:0 15px 0 15px;
}
body {
font-family:Arial, Helvetica, sans-serif;
font: 12px/170% Verdana;
- background-image:url(images/matrix_bg6.jpg);
+ background-image:url(../images/matrix_bg6.jpg);
background-repeat:repeat;
line-height: 2em;
min-width: 760px;
#banner td.bg {
border-collapse: collapse;
- background-image:url("images/banner_bg.gif");
+ background-image:url("../images/banner_bg.gif");
background-repeat: repeat-x;
background-color:transparent;
background-position:inherit;
#panel {
width:160px;
/* margin-left: -150px;*/
- background:url("images/panel_bg_long.png") repeat-y ;
+ background:url("../images/panel_bg_long.png") repeat-y ;
float:left;
font-family:Verdana, Arial, Helvetica, sans-serif;
padding-top:1em;
color: #888888;
text-decoration: none;
background-color: rgba(219,87,5,1);
- background-image:url("images/banner_bg.gif");
+ background-image:url("../images/banner_bg.gif");
font-family: 'Yanone Kaffeesatz';
font-weight: 400;
display: block;
#panel a.newpressed {
color: #FFFFFF;
text-decoration: none;
- background-image:url("images/banner_bg.gif");
+ background-image:url("../images/banner_bg.gif");
background-color: #F5F5F5;
font-family: 'Yanone Kaffeesatz';
font-weight: 700;
git://source.jalview.org / jabaws.git / commitdiff