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<div id="content">\r
-<h2 align="center">JABAWS Manual</h2>\r
-\r
-<h3>Table of content</h3>\r
-<h4>JABAWS Virtual Appliance \r
-</h4>\r
-<ul>\r
- <li><a href="#whenvm">When to use virtual appliance</a> </li>\r
- <li><a href="#virtualbox">VirtualBox appliance configuration</a></li>\r
- <li><a href="#vmplayer">VMware Player appliance configuration </a></li>\r
- <li><a href="#jabawsAppliance">JABAWS Appliance details </a></li>\r
- <li><a href="#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a> </li>\r
-</ul>\r
-\r
-<h4>JABAWS Installation</h4>\r
-<ul>\r
- <li><a href="#sysreq">System Requirements</a></li>\r
- <li><a href="#instwar">Installing the JABAWS WAR file</a></li>\r
- <li><a href="#prepexec">Preparing executables for use with JABAWS</a></li>\r
- <li><a href="#useprebin">Using the pre-compiled i386 binaries on Linux</a></li>\r
- <li><a href="#recompbinaries">Recompiling the bundled\r
- programs for your system</a></li>\r
- <li><a href="#haveexec">Reuse the binaries that are\r
- already in your system</a></li>\r
- <li><a href="#obtainexec">Obtaining alignment\r
- programs for your operation system from elsewhere</a></li>\r
-</ul>\r
-<h4>Configuring JABAWS</h4>\r
-<ul>\r
- <li><a href="#defjabaconf">Default JABA Web Services Configuration</a></li>\r
- <li><a href="#locEngConf">Local Engine Configuration</a></li>\r
- <li><a href="#clustEngConf">Cluster Engine Configuration</a></li>\r
- <li><a href="#setexecenv">Defining Environment Variables for\r
- Executables</a></li>\r
-</ul>\r
-<h4>Using JABAWS in your program </h4>\r
-<ul>\r
- <li><a href="#wsfunctions">Web services functions overview </a></li>\r
- <li><a href="#templatestr">The template client structure</a></li>\r
- <li><a href="#connectto">Connecting to JABAWS</a></li>\r
- <li><a href="#validnames">Valid JABAWS service names and WSDL files</a></li>\r
- <li><a href="#defalign">Aligning sequences</a></li>\r
- <li><a href="#checkresults">Checking the status of the calculation </a></li>\r
- <li><a href="#presetalign">Aligning with presets</a></li>\r
- <li><a href="#customalign">Aligning with custom parameters</a></li>\r
- <li><a href="#writingaltofile">Writing alignments to a file</a></li>\r
- <li><a href="#compex">A complete client example </a></li>\r
- <li><a href="#buildart">Building web services artifacts</a></li>\r
-</ul>\r
-<h4>JABA Web Services Internals </h4>\r
-<ul>\r
- <li><a href="#testingJaba">Testing JABA Web Services</a></li>\r
- <li><a href="#logfiles">JABAWS Log Files</a></li>\r
- <li><a href="#warfile">JABAWS War File Content</a></li>\r
-</ul>\r
-<h3>JABAWS Virtual Appliance </h3>\r
-<h4><a name="whenvm" id="whenvm"/></a>When to use the virtual appliance </h4>\r
-<p>The appliance best suits for individual users who want to use the JABA web services locally, without Internet connection, want to keep their data private and uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users but they can always deploy a <a href="#instwar">war distribution</a> instead. <br />\r
-To run the appliance you would need to have relatively powerful computer. The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M. </p>\r
-<h4><a name="virtualbox" id="virtualbox"/>VirtualBox appliance configuration</h4>\r
-<p>VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operating systems. Use the VitualBox "Import Appliance" option to import the JABAWS. Please bear in mind that to benefit from multiple CPU support under the VirtualBox software you need to enable<a href="http://en.wikipedia.org/wiki/X86_virtualization"> hardware virtualization extensions</a>, such as Intel Virtualization VT-x or AMD-V support in the BIOS of your computer. Unfortunately, we were unable to find a reliable way to do it on Mac, so some Macs running VirtualBox will be limited to one CPU only, irrespective of the number of CPUs of the host machine. </p>\r
-<p>We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the <a href="howto.html#vmbexc"></a><a href="howto.html#vmbexc">VERR_VMX_MSR_LOCKED_OR_DISABLED</a> exception if your computer does not support the extensions or their support is disabled. Just deselect the checkboxes shown on the screen shot below to solve the problem. </p>\r
-<p>VirtualBox JABAWS VM configuration screen shot displaying virtualization settings.</p>\r
-<p><img src="images/vmb_virtual.png" alt="VT-x extension on VirtualBox" width="669" height="535" /></p>\r
-<h4><a name="vmplayer" id="vmplayer"/>VMware Player appliance configuration </h4>\r
-<p>The free <a href="http://downloads.vmware.com/d/info/desktop_downloads/vmware_player/3_0">VMware Player</a> can be used to run the JABAWS services from the Windows and Linux host operating systems, there is no support for Mac in time of writing. However, <a href="https://www.vmware.com/vmwarestore/buyfusion.html">VMware Fusion</a>, a commercial VMware product, offers virtual machine support for Mac computers too. </p>\r
-<p>To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the JABAWS.vmx file to open an appliance. </p>\r
-<p>When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all. </p>\r
-<h4><a name="jabawsAppliance" id="jabawsAppliance"/>JABAWS Appliance details</h4>\r
-<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>\r
-<p>The VMware Player screen shot below displays JABAWS VM CPU settings. </p>\r
-<p><img src="images/VMware_cpu.png" alt="vmware cpu settings" width="852" height="267" border="1" /></p>\r
-<p><strong>JABAWS appliance configuration: </strong></p>\r
-<p><strong>VMware info</strong><br />\r
- - Date of creation: 8 October 2010<br />\r
- - CPUs : 1<br />\r
- - RAM : 512 MB<br />\r
- - Networking : Host only (the VM has no access to the outside network, nothing from the outside network can access the VM)<br />\r
- - Hard disk : 20 GB (expanding)<br />\r
- - VMware tools : Installed</p>\r
-<p><strong>OS info</strong><br />\r
- - OS : TurnKey Linux, based on Ubuntu 8.0.4 JEOS (Just-Enough-Operation-System)<br />\r
- - Installation : Oracle Java 6, Tomcat 6, JABAWS v. 1.0 <br />\r
- - Hostname : tomcat <br />\r
- - Patches : till date of creation<br />\r
- - IPv4 address : dhcp<br />\r
- - IPv6 address : auto<br />\r
- - DNS name : none<br />\r
- - Name server : dhcp<br />\r
- - Route : dhcp<br />\r
- - Keyboard : US_intl</p>\r
-<p><strong>Login credentials</strong><br />\r
- - Root password: jabaws</p>\r
-<p> <strong>Services</strong></p>\r
-<ul>\r
- <li>Default virtual console Alt+F7 </li>\r
- <li>Tomcat web server. <br />\r
- <em>Access:</em> http://VM_IP</li>\r
- <li>JABAWS URL: http://VM_IP/jabaws</li>\r
- <li>Web Shell<br />\r
- <em>Access:</em> https://VM_IP:12320/</li>\r
- <li>Webmean<br />\r
- <em>Access:</em> https://VM_IP:12321/</li>\r
- <li>SSH/SFTP<br />\r
- <em>Access:</em> root@VM_IP</li>\r
- </ul>\r
-<p>Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. Under VirtualBox host only networking, first VM may have 192.168.56.101 IP address.</p>\r
-<h4><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</a> </h4>\r
-<p>After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> 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>\r
-<p><img src="images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>\r
-<p>If you click on Advanced Menu, you will see the configuration console, similar to the one below. </p>\r
-<p><img src="images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>\r
-<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>\r
-<h3>JABAWS Installation</h3>\r
-<h4><a name="sysreq" id="sysreq"></a>System Requirements</h4>\r
-\r
-<p>JABAWS requires a Java web application server compliant with\r
-version 2.4 of the Java Servlet specification, and a Java 6 runtime\r
-environment. We recommend using an official Oracle Java 6 runtime\r
-environment, and <a\r
-href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a> web application server version 6, but other versions may work as well.</p>\r
-\r
-<!-- todo: link to help about obtaining and installing tomcat -->\r
-<h4><a name="instwar" id="instwar"></a>Installing the JABAWS WAR file</h4>\r
-\r
-<p>JABAWS is distributed as a web application archive (WAR). To\r
-deploy JABAWS in Apache-Tomcat - simply drop the war file into the\r
-<span class="highlight">webapps</span> directory of a running\r
-Tomcat, and it will do the rest. For any other web application\r
-server, please follow your server's specific deployment procedure\r
-for 'WAR' files. If you are installing on a windows machine, then\r
-at this point your JABAWS installation will already be up and\r
-running, and you can try its services out using the <a href=\r
-"howto.html#usingWsTester">JABAWS test client</a>, but\r
-installations on other operating systems will require a final step\r
-to ensure JABAWS can locate and execute the binary programs it\r
-needs.</p>\r
-\r
-<h4><a name="prepexec" id="prepexec"></a>Preparing executables for use with JABAWS</h4>\r
-\r
-<p>JABAWS's web services use command line programs to do\r
-the actual analysis, so it must have access to programs\r
-which can be executed on your platform. The native executables\r
-bundled with JABAWS for Windows (32-bit) and Linux (i386) should be\r
-OK for those systems. However, the source code for these \r
-programs is also provided so you can recompile for your own\r
-architecture and exploit any optimizations that your system can\r
-provide. Alternately, if you have already got binaries on your\r
-system, then you can simply change the paths in JABAWS's\r
-configuration files so these are used instead.</p>\r
-\r
-<h4><a name="useprebin" id="useprebin"></a>Using the pre-compiled i386 binaries on Linux</h4>\r
\r
-<p>Before the binaries that are bundled with JABAWS can be used,\r
-they must first be made executable using the provided <a name=\r
-"setexecflag" id="setexecflag">'setexecflag.sh'</a> script:</p>\r
+<h2 id="headtitle">JABAWS MANUAL</h2>\r
+<h2>Quick Start Guide</h2>\r
\r
+<h3><a name="whichjaba" id="whichjaba"></a>Choose JABAWS distribution</h3>\r
+<p>There are three main packages you could use</p>\r
<ol>\r
-<li>cd to <span class=\r
-"hightlight"><webapplicationpath>/binaries/src</span></li>\r
-\r
-<li>run <span class="hightlight">sh setexecflag.sh</span></li>\r
-\r
-<li>Make sure binaries supplied work under your OS.<br />\r
- For this run each binary, without any command line options or\r
-input files. If you see an error message complaining about missing\r
-libraries or other problems, then you probably need to <a href=\r
-"#recompbinaries">recompile the binaries</a>. with</li>\r
-\r
-<li>Restart the Tomcat.</li>\r
+ <li>A JABAWS Server Virtual Appliance (or Virtual Machine) - for anyone who wants to run JABAWS locally for themselves </li>\r
+ <li>A JABAWS Server Web Application Archive (WAR) package - for anyone who wants to run JABAWS for their group, lab or organization. Wants to use the cluster or perform very large tasks </li>\r
+ <li>A client package - for anyone who wants to use JABAWS from their own code, without Jalview, scripting against local or public version of JABAWS Server. </li>\r
</ol>\r
-\r
-That's it! JABAWS should work at this point. Try it out using the JABAWS<a\r
-href="howto.html#usingWsTester"> test client</a>. If not,\r
-read on... or have a look at <a href=\r
-"howto.html#usingtomcat">deploying on Tomcat</a> tips.<br />\r
- <em>Note: You may want to enable logging, <a href="#logfiles">see\r
-below for instructions on how to do that</a>.</em><br />\r
- \r
-\r
-<h4><a name="recompbinaries">Recompiling the bundled\r
-programs for your system</a></h4>\r
-\r
-<p>If you have a fully equipped build environment on your\r
-(POSIX-like) system, then you should be able to recompile the\r
-programs from the source distributions which are included\r
-in the JABAWS war file. A script called 'compilebin.sh' is provided\r
-to automate this task.</p>\r
-\r
+<p>Virtual Appliance (VA) package (1) contains TurnKey Linux with JABAWS installed. JABAWS VA contains JABAWS WAR deployed on the Apache Tomcat 6 web application server. If you use MS Windows read no further - the VA is the way to go. You would need to install <a href="http://www.vmware.com/products/player">VMWare Player</a> or <a href="http://www.virtualbox.org/wiki/Downloads">Oracle VirtualBox</a> (both are free) on your computer to use this package. More details about JABAWS virtual appliance is available from the <a href="man_servervm.html">Server VA</a> section of the manual. </p>\r
+<p>Option 2, Web Application Archive package contains JABAWS ready to be deployed on the Servlet 2.4 compatible web application server such as Apache Tomcat version 6. To make this version work you would need </p>\r
<ol>\r
-<li>In a terminal window, change the working directory to <span\r
-class="hightlight">binaries/src</span></li>\r
-\r
-<li>execute the <span class="highlight">compilebin.sh</span>\r
-script,<br />\r
- either use: <span class="hightlight">chmod +x compilebin.sh;\r
-compilebin.sh > compilebin.out;</span><br />\r
- or: <span class="hightlight">sh compilebin.sh >\r
-compilebin.out</span></li>\r
-\r
-<li>Now run <span class="hightlight">sh setexecflag.sh</span><br />\r
- If any of the binaries was not recompiled, then a 'file not found'\r
-error will be raised.</li>\r
-\r
-<li>Finally, restart your tomcat (or servlet container), and use\r
-the <a href="howto.html#usingWsTester">JABAWS test client</a> to\r
-check that JABAWS can use the new binaries.</li>\r
+ <li>Install Apache-Tomcat or similar web application server. </li>\r
+ <li>If you are not on Linux, you would have to make binaries for your system available to JABAWS. </li>\r
+ </ol>\r
+<p>Read more on <a href="man_serverwar.html">JABAWS WAR in the manual</a>. </p>\r
+<p>A client only package (3) contains the JABAWS command line client. It functionality is equivalent to that of Jalview . This is the package for anyone who wants to connect to and to use JABAWS from their own software. Read more about how to use command line client <a href="#cmdclient">in the CMD Client</a> section of the manual. Also, JABA Web Services are fully WS-I compliant, so one could use any language to access them. </p>\r
+<p><strong>If you chose option 1 </strong></p>\r
+<p>and you work on Windows or Linux or Unix </p>\r
+<ul>\r
+ <li>download and install VMWare Player </li>\r
+ <li>Download JABAWS Virtual Appliance </li>\r
+ <li>Unpack JABAWS virtual appliance and open it with VMware Player. </li>\r
+ </ul>\r
+<p>otherwise </p>\r
+<ul>\r
+ <li>download and install Virtual Box. </li>\r
+ <li>Download JABAWS Virtual Appliance </li>\r
+ <li>Unpack JABAWS virtual appliance, import it into VirtualBox and then start the appliance. </li>\r
+ </ul>\r
+<p><strong>If you chose option 2 </strong></p>\r
+<p>If you are on Linux or Windows </p>\r
+<ol><li>Download JABAWS WAR </li>\r
+ <li>Download and install <a href="http://tomcat.apache.org/download-60.cgi">Apache-Tomcat</a> </li>\r
+ <li>Drop the JABAWS war file into<span class="hightlight"> tomcat/webapps</span> directory. </li>\r
+ <li>If you are on Linux, <span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./setexecflag.sh </span> script to set an executable flag for JABAWS binaries. </li>\r
+ <li>Restart the Tomcat </li>\r
</ol>\r
-\r
-<p>If you couldn't compile everything, then it may be that your system does\r
-not have all the tools required for compiling the programs. At the very\r
-least check that you have gcc, g++ and make installed in your\r
-system. If not install these packages and repeat the compilation\r
-steps again. You should also review the compilebin.sh output -\r
-which was redirected to compilebin.out, and any errors output to\r
-the terminal. Finally, try obtaining the <a href="#obtainexec">pre\r
-compiled binaries</a> for your OS.</p>\r
-\r
-<h4><a name="haveexec" id="haveexec">Reuse the binaries that are\r
-already in your system</a></h4>\r
-\r
-<p>If you would like to use the binaries you already have then you\r
-just need to let JABAWS know there they are. To do this, edit:\r
-<span class="code">conf/Executable.properties</span>\r
-<p>When specifying paths to executables that already exist on your system, make sure you provide an absolute path, or one relative to the JABAWS directory inside <span class="highlight">webapps</span>. For example, the default path for clustalw is defined\r
-as<span class=\r
-"code">local.clustalw.bin=binaries/src/clustalw/src/clustalw2</span>\r
-Alternatively, instead of changing <span class=\r
-"hightlight">Executable.properties</span> you could also replace\r
-the executables bundled with JABAWS with the ones that you have, or make symlinks to them.\r
-Then the default configuration will work for you. More information\r
-about <a href="#exec"><span class="hightlight">the\r
-Executable.properties</span> file is given below</a>.</p>\r
-\r
-<h4><a name="obtainexec" id="obtainexec">Obtaining alignment\r
-programs for your operation system from elsewhere</a></h4>\r
-\r
-<p>You could search for pre-packaged compiled executable in your\r
-system package repository or alternately, download pre-compiled\r
-binaries from each alignment program's home page. Then, either\r
-replace the executables supplied with the downloaded ones, or\r
-modify the paths in <span class=\r
-"hightlight">executable.properties</span> as described above.</p>\r
-\r
-<h3>Configuring JABAWS</h3>\r
-<p>There are three parts of the system you can configure. The local\r
-and cluster engines, and the paths to individual executables for\r
-each engine. These settings are stored in configuration files\r
-within the web application directory (for an overview, then take a\r
-look at the <a href="#warfile">war file content table</a>).</p>\r
-\r
-<h4><a name="defjabaconf" id="defjabaconf"></a>Default JABA Web Services Configuration</h4>\r
-\r
-<p>Initially, JABAWS is configured with only the local engine\r
-enabled, with job output written to directory called "jobsout"\r
-within the web application itself. This means that JABAWS will work\r
-out of the box, but may not be suitable for serving a whole lab or\r
-a university.</p>\r
-\r
-<h4><a name="locEngConf" id="locEngConf"></a>Local Engine Configuration</h4>\r
-\r
-<p>The Local execution engine configuration is defined in the\r
-properties file conf/Engine.local.properties. The supported\r
-configuration settings are:<br />\r
- <span class="hightlight">engine.local.enable=true</span> - #\r
-enable or disable local engine, valid values true | false<br />\r
- <span class=\r
-"hightlight">local.tmp.directory=D:\\clusterengine\\testoutput</span>\r
-- a directory to use for temporary files storage, optional,\r
-defaults to java temporary directory<br />\r
- <span class="hightlight">engine.local.thread.number=4</span> -\r
-Number of threads for tasks execution (valid values between 1 and\r
-2x cpu. Where x is a number of cores available in the system).\r
-Optional defaults to the number of cores for core number <=4 and\r
-number of cores-1 for greater core numbers.</p>\r
-\r
-<p>If you are planning to heavily use the local engine (which you\r
-have to if you do not have a cluster) it is a good idea to increase\r
-the amount of memory available for the web application server. If\r
-you are using Apache-Tomcat, then you can define its memory\r
-settings in the JAVA_OPTS environment variable. To specify which\r
-JVM to use for Apache-Tomcat, put the full path to the JRE\r
-installation in the JAVA_HOME environment variable (We would\r
-recommend using Sun Java Virtual Machine (JVM) in preference to\r
-Open JDK). Below is an example of code which can be added to <span\r
-class="hightlight"><tomcat_dir>/bin/setenv.sh</span> script\r
-to define which JVM to use and a memory settings for Tomcat server.\r
-Tomcat server startup script (<span class=\r
-"hightlight">catalina.sh</span>) will execute <span class=\r
-"hightlight">setenv.sh</span> on each server start\r
-automatically.<br />\r
- <span class="code">export\r
-JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/<br />\r
- export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"</span></p>\r
-\r
-<h4><a name="clustEngConf" id="clustEngConf"></a>Cluster Engine Configuration</h4>\r
-\r
-<p>Supported configuration settings:<br />\r
- <span class="hightlight">engine.cluster.enable=true</span> - #\r
-enable or disable local engine true | false, defaults to\r
-false<br />\r
- <span class=\r
-"hightlight">cluster.tmp.directory=/homes/clustengine/testoutput-</span>\r
-a directory to use for temporary files storage. The value must be\r
-an absolute path to the temporary directory. Required. The value\r
-must be different from what is defined for local engine. This\r
-directory must be accessible from all cluster nodes.<br />\r
- For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH\r
-environment variables have to be defined. They tell the cluster\r
-engine where to find DRMAA libraries. These variables\r
-should be defined when the web application server starts up, e.g.</p>\r
-\r
-<p><span class="code">SGE_ROOT=/gridware/sge<br />\r
- LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64</span></p>\r
-\r
-<p>Finally, do not forget to configure executables for the cluster\r
-execution, they may be the same as for the local execution but may\r
-be different. Please refer to the executable configuration section\r
-for further details.</p>\r
-\r
-<h4><a name="exec" id="exec"></a>Executable Configuration</h4>\r
-\r
-<p>All the executable programs\r
-are configured in conf/Executable.properties file. Each executable\r
-is configured with a number of options. They are: <span class=\r
-"code">local.X.bin.windows=<path to executable under windows\r
-system, optional><br />\r
- local.X.bin=<path to the executable under non-windows system,\r
-optional><br />\r
- cluster.X.bin=<path to the executable on the cluster, all\r
-cluster nodes must see it, optional><br />\r
- X.bin.env=<semicolon separated list of environment variables\r
-for executable, use hash symbol as name value separator,\r
-optional><br />\r
- X.--aamatrix.path=<path to the directory containing\r
-substitution matrices, optional><br />\r
- X.presets.file=<path to the preset configuration file, optional\r
-><br />\r
- X.parameters.file=<path to the parameters configuration file,\r
-optional><br />\r
- X.limits.file=<path to the limits configuration file,\r
-optional><br />\r
- X.cluster.settings=<list of the cluster specific options,\r
-optional></span></p>\r
-\r
-<p>Where X is a short executable wrapper class name.</p>\r
-\r
-<p>Default JABAWS configuration includes path to local executables\r
-to be run by the local engine only, all cluster related settings\r
-are commented out, but they are there for you as example. Cluster\r
-engine is disabled by default. To configure executable for cluster\r
-execution un comment the X.cluster settings and change them\r
-appropriately. </p>\r
-<p>By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing <span class="hightlight">conf/settings/<X>Limit.xml</span> files.<br />\r
- After you have completed the editing your configuration may look like\r
- this:<span class="code">local.mafft.bin.windows=<br />\r
- local.mafft.bin=binaries/mafft<br />\r
- cluster.mafft.bin=/homes/cengine/mafft<br />\r
- mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;<br />\r
- mafft.--aamatrix.path=binaries/matrices<br />\r
- mafft.presets.file=conf/settings/MafftPresets.xml<br />\r
- mafft.parameters.file=conf/settings/MafftParameters.xml<br />\r
- mafft.limits.file=conf/settings/MafftLimits.xml<br />\r
- mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l\r
- h_vmem=6000M -l ram=6000M</span></p>\r
-<p>Please not that relative paths must only be specified for the\r
-files that reside inside web application directory, all other paths\r
-must be supplied as absolute!</p>\r
-\r
-<p>Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly\r
-specify the absolute path to anything\r
-normally evaluated from an environment variable at execution time.</p>\r
-\r
-<p>If you are using JABAWS to submit jobs to the cluster (with\r
-cluster engine enabled), executables must be available from all\r
-cluster nodes the task can be sent to, also paths to the\r
-executables on the cluster e.g. <span class=\r
-"hightlight">cluster.<exec_name>.bin</span> must be\r
-absolute.</p>\r
-\r
-<p>Executables can be located anywhere in your system, they do not\r
-have to reside on the server as long as the web application server\r
-can access and execute them.</p>\r
-\r
-<p>Cluster settings are treated as a black box, the system will\r
-just pass whatever is specified in this line directly to the\r
-cluster submission library. This is how DRMAA itself treats this\r
-settings. More exactly DRMAA JobTemplate.setNativeSpecification()\r
-function will be called.</p>\r
-\r
-<h4><a name="setexecenv" />Defining Environment Variables for\r
-Executables</h4>\r
-\r
-<p>Environment variables can be defined in property <span class=\r
-"code">x.bin.env</span> Where <span class="hightlight">x</span> is\r
-one of five executables supported by JABAWS. Several environment\r
-variables can be specified in the same line. For example.<br />\r
- <span class=\r
-"code">mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;</span></p>\r
-\r
-<p>The example above defines two environment variables with names\r
-MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft\r
-and /bin/fasta34 respectively. Semicolon is used as a separator\r
-between different environment variables whereas hash is used as a\r
-separator for name and value of the variable.</p>\r
-\r
-<h4><a name="mafftconf" id="mafftconf"></a>Configure JABAWS to Work\r
-with Mafft</h4>\r
-\r
-<p>If you use default configuration you do not need to read any\r
-further. The default configuration will work for you without any\r
-changes, however, if you want to install Mafft yourself then there\r
-is a couple of more steps to do.</p>\r
-\r
-<p>Mafft executable needs to know the location of other files\r
-supplied with Mafft. In addition some Mafft functions depends on\r
-the fasta executable, which is not supplied with Mafft, but is a\r
-separate package. Mafft needs to know the location of fasta34\r
-executable.</p>\r
-\r
-<p>To let Mafft know where the other files from its package are\r
-change the value of MAFFT-BINARIES environment variables. To let\r
-Mafft know where is the fasta34 executable set the value of\r
-FASTA_4_MAFFT environment variable to point to a location of\r
-fasta34 program. The latter can be added to the PATH variable\r
-instead. If you are using executables supplied with JABAWS, the\r
-path to Mafft binaries would be like <span class=\r
-"hightlight"><relative path to web application\r
-directory>/binaries/src/mafft/binaries</span> and the path to\r
-fasta34 binary would be <span class="hightlight"><relative path\r
-to web application\r
-directory>/binaries/src/fasta34/fasta34</span>. You can specify\r
-the location of Mafft binaries as well as fasta34 program elsewhere\r
-by providing an absolute path to them. All these settings are\r
-defined in <span class=\r
-"hightlight">conf/Executable.properties</span> file.</p>\r
-\r
-<h3>Using JABAWS in your program </h3>\r
-<h4><a name="wsfunctions" id="wsfunctions"></a>Web services functions overview </h4>\r
-<p>All JABA multiple sequence alignment web services comply to the same interface, thus the function described below are available from all the services. </p>\r
-<p><strong>Functions for initiating the alignment </strong><span class="code"> String id = align(List<FastaSequence> list)<br />\r
- String id = customAlign(List<FastaSequence> sequenceList, List<Option> optionList)<br />\r
- String id = presetAlign(List<FastaSequence> sequenceList, Preset preset)</span></p>\r
-<p><strong>Functions pertaining to job monitoring and control</strong><br />\r
- <span class="code">JobStatus status = getJobStatus(String id)<br />\r
- Alignment al = getResult(String id)<br />\r
- boolean cancelled = cancelJob(String id)<br />\r
- ChunkHolder chunk = pullExecStatistics(String id, long marker)</span></p>\r
-<p><strong>Functions relating to service features discovery</strong><br />\r
- <span class="code">RunnerConfig rc = getRunnerOptions()<br />\r
- Limit limit = getLimit(String name)<br />\r
- LimitsManager lm = getLimits()<br />\r
- PresetManager pm = getPresets()</span></p>\r
-<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>\r
-<h4><a name="templatestr" id="templatestr"></a>Structure of the template command line client</h4>\r
-<table width="100%" border="1">\r
- <tr>\r
- <td width="18%"><strong>Packages</strong></td>\r
- <td width="82%"><strong>Classes and Interfaces </strong></td>\r
- </tr>\r
- <tr>\r
- <td>compbio.data.msa </td>\r
- <td>MsaWS the interface for all multiple sequence alignment web services </td>\r
- </tr>\r
- <tr>\r
- <td>compbio.data.sequence</td>\r
- <td>JABAWS data types </td>\r
- </tr>\r
- <tr>\r
- <td>compbio.metadata</td>\r
- <td>JABAWS meta data types </td>\r
- </tr>\r
- <tr>\r
- <td>compbio.ws.client</td>\r
- <td>JABAWS command line client </td>\r
- </tr>\r
-</table>\r
-<p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />\r
- 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>\r
-<h4><a name="connectto" id="connectto"></a>Connecting to JABAWS</h4>\r
-<p class="attention">For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the <a href="download.html">download page</a>. Please note that for now all the examples are in Java other languages will follow given a sufficient demand. </p>\r
-<p>Download a binary JABAWS <a href="download.html">client</a>. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee. </p>\r
-<p class="code"> import java.net.URL;<br />\r
- import javax.xml.namespace.QName;<br />\r
- import javax.xml.ws.Service;<br />\r
- ...............<br />\r
- 1) String qualifiedName = "http://msa.data.compbio/01/01/2010/";<br />\r
- 2) URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");<br />\r
- 3) QName qname = new QName(, "ClustalWS");<br />\r
- 4) Service serv = Service.create(url, qname);<br />\r
- 5) MsaWS msaws = serv.getPort(new QName(qualifiedName, "ClustalWSPort"),\r
- MsaWS.class);</p>\r
-<p>Line 1 makes a qualified name for JABA web services.<br />\r
- Line 2 \r
- constructs the URL to the web services WSDL. <br />\r
- Line 3 makes a qualified name instance for Clustal JABA web service. <br />\r
- Line 4 creates a service instance.<br />\r
- Line 5 makes a connection to the server. </p>\r
-<p>A more generic connection method would look like this </p>\r
-<p class="code"> import java.net.URL;<br />\r
- import javax.xml.namespace.QName;<br />\r
- import javax.xml.ws.Service;<br />\r
- import compbio.ws.client.Services<br />\r
- .............. <br />\r
- String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";<br />\r
- String host = "http://www.compbio.dundee.ac.uk/jabaws";<br />\r
- // In real life the service name can come from args<br />\r
- Services clustal = Services.ClustalWS;<br />\r
- URL url = new URL(host + "/" + clustal.toString() + "?wsdl");<br />\r
- QName qname = new QName(qualifiedServiceName, clustal.toString());<br />\r
- Service serv = Service.create(url, qname);<br />\r
- MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal<br />\r
- + "Port"), MsaWS.class);</p>\r
-<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="file:///D:/workspace/JWS2/website/dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>. </p>\r
-<h4><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h4>\r
+<p>otherwise</p>\r
<ul>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl) </li>\r
- <li><a href="http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl) </li>\r
+ <li>Complete steps 1-3 from the above.</li>\r
+ <li> <span class="hightlight">cd</span> to <span class="hightlight">webapps/jabaws/binaries/src/</span> and execute <span class="hightlight">./compilebin.sh </span> script to compile all binaries JABAWS depends on. </li>\r
+ <li><span class="hightlight">cd</span> to <span class="hightlight"> webapps/jabaws/binaries/src/ </span>and execute <span class="hightlight">./setexecflag.sh </span> script. </li>\r
+ <li>Restart the Tomcat </li>\r
</ul>\r
-<h4><a name="defalign" id="defalign"></a>Aligning sequences </h4>\r
-<p>Given that <span class="hightlight">msaws</span> is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows: </p>\r
-<p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
- 2) String jobId = msaws.align(fastalist); <br />\r
- 3) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one loads FASTA sequence from the file<br />\r
- Line two submits them to web service represented by msaws proxy <br />\r
- Line three retrieves the alignment from a web service. This line will block the execution until the result is available. Use this with caution. In general, you should make sure that the calculation has been completed before attempting retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. While this may be ok with your local server, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) will not let you hold the connection for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check the status of the calculation.<br />\r
- Methods and classes mentioned in the excerpt are available from the JABAWS client library. </p>\r
-<h4><a name="checkresults" id="checkresults"></a>Checking the status of the calculation </h4>\r
-<p> You may have noticed that there was no pause between submitting the job and retrieving of the results. This is because <span class="hightlight">getResult(jobId)</span> method block the processing until the calculation is completed. However, taking into account that the connection holds server resources, our public server (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) is configured to reset the connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the calculation has been completed before accessing the results. You can do it like this: </p>\r
-<p> <span class="code">while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {<br />\r
- Thread.sleep(2000); // wait two seconds, then recheck the status <br />\r
- }</span></p>\r
-<h4><a name="presetalign" id="presetalign"></a>Aligning with presets</h4>\r
-<p class="code">1) PresetManager presetman = msaws.getPresets();<br />\r
- 2) Preset preset = presetman.getPresetByName(presetName);<br />\r
- 3) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
- 4) String jobId = msaws.presetAlign(fastalist, preset);<br />\r
- 5) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one obtains the lists of presets supported by a web service.<br />\r
- Line two return a particular Preset \r
- by its name<br />\r
- Lines three to five are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>\r
-<h4><a name="customalign" id="customalign"></a>Aligning with custom parameters</h4>\r
-<p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />\r
- 2) Argument matrix = options.getArgument("MATRIX");<br />\r
- 3) matrix.setValue("PAM300");<br />\r
- 4) Argument gapopenpenalty = options.getArgument("GAPOPEN");<br />\r
- 5) gapopenpenalty.setValue("20");<br />\r
- 6) List<Argument> arguments = new ArrayList<Argument>(); <br />\r
- 7) arguments.add(matrix);\r
- arguments.add(gapopenpenalty);<br />\r
- 8) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
- 9) String jobId = msaws.customAlign(fastalist, arguments);<br />\r
- 10) Alignment alignment = msaws.getResult(jobId);</p>\r
-<p>Line one obtains the RunnerConfig object that holds information on supported parameters and their values<br />\r
- Line two retrieve a particular parameter from the holder by its name<br />\r
- Lines three sets a value to this parameter which will be used in the calculation. <br />\r
- Line four and five do the same but for another parameter<br />\r
- Line 6 makes a List to hold the parameters <br />\r
- Line seven puts the parameters into that list<br />\r
- Line eight \r
- and ten is the same as in previous examples<br />\r
- Line nine submit an alignment request with the sequences and the parameters <br />\r
- The names of all the parameters supported by a web service e.g. "PAM300" can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the <a href="dm_javadoc/index.html">javadoc</a>. </p>\r
-<h4><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h4>\r
-<p>There is a utility method in the client library that does exactly that. </p>\r
-<p> <span class="code">Alignment alignment = align(...) <br />\r
- FileOutputStream outStream = new FileOutputStream(file);<br />\r
- ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>\r
-<h4><a name="compex" id="compex"></a>A complete client example </h4>\r
-<p>Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a <a href="download.html">JABAWS binary client</a>. Please make sure that the client is in the Java class path before running this example.</p>\r
-<pre class="code" style="line-height:1em;">\r
-import java.io.ByteArrayInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.net.URL;\r
-import java.util.List;\r
-\r
-import javax.xml.namespace.QName;\r
-import javax.xml.ws.Service;\r
-\r
-import compbio.data.msa.MsaWS;\r
-import compbio.data.sequence.Alignment;\r
-import compbio.data.sequence.FastaSequence;\r
-import compbio.data.sequence.SequenceUtil;\r
-import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.LimitExceededException;\r
-import compbio.metadata.Preset;\r
-import compbio.metadata.PresetManager;\r
-import compbio.metadata.ResultNotAvailableException;\r
-import compbio.metadata.UnsupportedRuntimeException;\r
-import compbio.metadata.WrongParameterException;\r
-\r
-public class Example {\r
-\r
- /*\r
- * Input sequences for alignment\r
- */\r
- static final String input = ">Foo\r\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR"\r
- + "VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ"\r
- + "LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL"\r
- + "APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA"\r
- + "STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD"\r
- + "YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN"\r
- + "PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD"\r
- + "LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS"\r
- + "DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n"\r
- + "\r\n"\r
- + ">Bar\r\n"\r
- + "MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH"\r
- + "QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA"\r
- + "HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG"\r
- + "IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL"\r
- + "RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL"\r
- + "SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC"\r
- + "PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV"\r
- + "FEMDGFADDFGALLQALARRHGWLGI\r\n"\r
- + "\r\n"\r
- + ">Friends\r\n"\r
- + "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV"\r
- + "RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG"\r
- + "VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL"\r
- + "TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD"\r
- + "LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF"\r
- + "QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA"\r
- + "DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP"\r
- + "GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI";\r
-\r
- public static void main(String[] args) throws UnsupportedRuntimeException,\r
- LimitExceededException, JobSubmissionException,\r
- WrongParameterException, FileNotFoundException, IOException,\r
- ResultNotAvailableException, InterruptedException {\r
-\r
- String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";\r
-\r
- /* Make a URL pointing to web service WSDL */\r
- URL url = new URL(\r
- "http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");\r
-\r
- /*\r
- * If you are making a client that connects to different web services\r
- * you can use something like this:\r
- */\r
- // URL url = new URL(host + "/" + Services.ClustalWS.toString() +\r
- // "?wsdl");\r
-\r
- QName qname = new QName(qualifiedServiceName, "ClustalWS");\r
- Service serv = Service.create(url, qname);\r
- /*\r
- * Multiple sequence alignment interface for Clustal web service\r
- * instance\r
- */\r
- MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, "ClustalWS"\r
- + "Port"), MsaWS.class);\r
-\r
- /* Get the list of available presets */\r
- PresetManager presetman = msaws.getPresets();\r
-\r
- /* Get the Preset object by preset name */\r
- Preset preset = presetman\r
- .getPresetByName("Disable gap weighting (Speed-oriented)");\r
-\r
- /*\r
- * Load sequences in FASTA format from the file You can use something\r
- * like new FileInputStream(<filename>) to load sequence from the file\r
- */\r
- List<FastaSequence> fastalist = SequenceUtil\r
- .readFasta(new ByteArrayInputStream(input.getBytes()));\r
-\r
- /*\r
- * Submit loaded sequences for an alignment using preset. The job\r
- * identifier is returned by this method, you can retrieve the results\r
- * with it sometime later.\r
- */\r
- String jobId = msaws.presetAlign(fastalist, preset);\r
-\r
- /* This method will block for the duration of the calculation */\r
- Alignment alignment = msaws.getResult(jobId);\r
-\r
- /*\r
- * This is a better way of obtaining results, it does not involve\r
- * holding the connection open for the duration of the calculation,\r
- * Besides, as the University of Dundee public server will reset the\r
- * connection after 10 minutes of idling, this is the only way to obtain\r
- * the results of long running task from our public server.\r
- */\r
- // while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {\r
- // Thread.sleep(1000); // wait a second, then recheck the status\r
- // }\r
-\r
- /* Output the alignment to standard out */\r
- System.out.println(alignment);\r
-\r
- // Alternatively, you can record retrieved alignment into the file in\r
- // ClustalW format\r
-\r
- // ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(\r
- // "output.al"), alignment);\r
-\r
- }\r
-}\r
-</pre>\r
-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>.\r
-<h4><a name="buildart" id="buildart"></a>Building web services artifacts</h4>\r
-<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> basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our <a href="#connectto"> client library</a> as it provides a handful of useful methods in addition to plain data types. </p>\r
-<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
-<p> </p>\r
-<h3>JABA Web Services Internals </h3>\r
-<h4><a name="testingJaba" id="testingJaba"></a>Testing JABA Web Services</h4>\r
-<p>You can use a command line client (part of the client only\r
-package) to test you JABAWS installation as described <a href=\r
-"howto.html#usingcclient">here</a>. If you downloaded a JABAWS\r
-server package, you can use <span class=\r
-"hightlight"><your_jaba_context_name>/WEB-INF/lib/jaba-client.jar</span>\r
-to test JABAWS installation as described in <a href=\r
-"howto.html#usingWsTester">how-to</a>. If you downloaded the source\r
-code, then you could run a number of test suits defined in the\r
-build.xml ant build file.</p>\r
-\r
-<h4><a name="logfiles" id="logfiles"></a>JABAWS Log Files</h4>\r
-\r
-<p>JABAWS can be configured to log what it is doing. This comes\r
-handy if you would like to see who is using your web services or\r
-need to chase some problems. JABAWS uses <a href=\r
-"http://logging.apache.org/log4j/1.2/">log4j</a> to do the logging,\r
-the example of log4j configuration is bundled with JABAWS war file.\r
-You will find it in the <span class=\r
-"hightlight">/WEB-INF/classes/log4j.properties</span> file. All the\r
-lines in this file are commented out. The reason why the logging is\r
-disabled by default it simple, log4j have to know the exact\r
-location where the log files should be stored. This is not known up\r
-until the deployment time. To enable the logging you need to\r
-define<span class="hightlight"> logDir</span> property in the <span\r
-class="hightlight">log4j.properties</span> and uncomment section of\r
-the file which corresponds to your need. More information is given\r
-in the <span class="hightlight">log4j.properties</span> file\r
-itself. Restart the tomcat or the JABAWS web application to apply\r
-the settings.</p>\r
-\r
-<p>After you have done this, assuming that you did not change the\r
-log4j.properties file yourself, you should see the application log\r
-file called <span class="hightlight">activity.log</span>. The\r
-amount of information logged can be adjusted using different\r
-logging levels, it is reduced in the following order of log levels\r
-TRACE, DEBUG, INFO, WARN, ERROR, FATAL.</p>\r
-\r
-<p>If you would like to know who is using your services, you might\r
-want to <a href="howto.html#logs">enable tomcat access\r
-logging</a>.</p>\r
-\r
-<h4><a name="warfile" id="warfile"></a>JABAWS War File Content</h4>\r
-\r
-<table width="100%">\r
-<tr>\r
-<th width="19%">Directory</th>\r
-<th width="81%">Content description</th>\r
-</tr>\r
-\r
-<tr>\r
-<td>conf/</td>\r
-<td>contains configuration files such as Executable.properties,\r
-Engine.local.properties, Engine.cluster.properties</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>conf/settings</td>\r
-<td>Contains individual executable description files. In particular\r
-XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the\r
-name of the executable</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>jobsout/</td>\r
-<td>Contains directories generated when running an individual executable. E.g. input and output files and some other task\r
-related data. (optional)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>binaries/</td>\r
-<td>Directory contains native executables - programs,\r
-windows binaries (optional)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>binaries/src</td>\r
-<td>Contains source of native executables and Linux i386\r
-binaries.</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>binaries/matrices</td>\r
-<td>Substitution matrices <!-- what format ? --></td>\r
-</tr>\r
-\r
-<tr>\r
-<td>WEB-INF</td>\r
-<td>Web application descriptor</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>WEB-INF/lib</td>\r
-<td>Web application libraries</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>WEB-INF/classes</td>\r
-<td>log4j.properties - log configuration file (optional)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td colspan="2"><strong>Help Pages</strong> </td>\r
-</tr>\r
-\r
-<tr>\r
-<td>/</td>\r
-<td>help pages, index.html is the starting page</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>dm_javadoc</td>\r
-<td>javadoc for JABAWS client (the link is available from How To\r
-pages)</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>prog_docs</td>\r
-<td>documentation for programs that JABAWS uses</td>\r
-</tr>\r
-\r
-<tr>\r
-<td>images</td>\r
-<td>images referenced by html pages</td>\r
-</tr>\r
-</table>\r
-\r
-<p> </p>\r
-</div>\r
-\r
-<!-- content end-->\r
-<div id="copyright">Last update: 17 November 2010<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\r
-<!-- wrapper end-->\r
+<p>Once you have JABAWS working you can point the Jalview to your local JABAWS. </p>\r
+<ul>\r
+ <li>Download and start the desktop version of <a href="http://www.jalview.org/Web_Installers/install.htm">Jalview</a> </li>\r
+ <li>Go to Jalview->Tools->Preferences->Webservices->New Service URL and enter the JABAWS URL which you can see one your appliance is booted up. </li>\r
+</ul>\r
+<p><strong>if you chose option 3</strong> </p>\r
+<p>You can use the client straight out of the box. </p>\r
+</div> \r
+<!-- about end-->\r
</div>\r
-<!-- page end-->\r
+<!-- content end--> \r
+<div id="copyright">Last update: 7 January 2011<br/>\r
+Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+</div><!-- wrapper end-->\r
+</div> <!-- page end-->\r
\r
<!-- Google analitics -->\r
<script type="text/javascript">\r
git://source.jalview.org / jabaws.git / blobdiff