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7 <title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>
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20 <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>
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21 <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>
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22 <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>
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31 <div id="supermenu">
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32 <a class="newa" href="index.html">Home</a>
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33 <a class="newa" href="quick_start.html">Getting Started</a>
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34 <a class="newpressed" href="man_about.html">Manual</a>
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37 <a class="newa" href="man_about.html">About</a>
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38 <a class="newa" href="man_servervm.html" title="JABAWS Server as Virtual Appliance">Server VA</a>
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39 <a class="newa" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>
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40 <a class="newa" href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>
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41 <a class="newa" href="man_configuration.html" >Configure JABAWS</a>
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42 <a class="newa" href="man_client.html" title="JABAWS Command Line Client">Command Client</a>
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43 <a class="newa" href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>
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44 <a class="newpressed" href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>
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45 <a class="newa" href="man_server_dev.html" >Develop JABAWS</a>
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52 <h2 id="headtitle">JABAWS MANUAL</h2>
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54 <h2>Using JABAWS From Your Program </h2>
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56 <li><a href="#wsfunctions">Web services functions overview </a></li>
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57 <li><a href="#templatestr">The template client structure</a></li>
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58 <li><a href="#connectto">Connecting to JABAWS</a></li>
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59 <li><a href="#validnames">Valid JABAWS service names and WSDL files</a></li>
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60 <li><a href="#defalign">Aligning sequences</a></li>
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61 <li><a href="#checkresults">Checking the status of the calculation </a></li>
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62 <li><a href="#presetalign">Aligning with presets</a></li>
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63 <li><a href="#customalign">Aligning with custom parameters</a></li>
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64 <li><a href="#writingaltofile">Writing alignments to a file</a></li>
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65 <li><a href="#compex">A complete client example </a></li>
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66 <li><a href="#buildart">Building web services artifacts</a></li>
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68 <h3><a name="wsfunctions" id="wsfunctions"></a>Web services functions overview </h3>
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69 <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>
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70 <p><strong>Functions for initiating the alignment </strong><span class="code"> String id = align(List<FastaSequence> list)<br />
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71 String id = customAlign(List<FastaSequence> sequenceList, List<Option> optionList)<br />
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72 String id = presetAlign(List<FastaSequence> sequenceList, Preset preset)</span></p>
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73 <p><strong>Functions pertaining to job monitoring and control</strong><br />
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74 <span class="code">JobStatus status = getJobStatus(String id)<br />
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75 Alignment al = getResult(String id)<br />
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76 boolean cancelled = cancelJob(String id)<br />
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77 ChunkHolder chunk = pullExecStatistics(String id, long marker)</span></p>
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78 <p><strong>Functions relating to service features discovery</strong><br />
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79 <span class="code">RunnerConfig rc = getRunnerOptions()<br />
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80 Limit limit = getLimit(String name)<br />
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81 LimitsManager lm = getLimits()<br />
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82 PresetManager pm = getPresets()</span></p>
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83 <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>
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84 <h3><a name="templatestr" id="templatestr"></a>Structure of the template command line client</h3>
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85 <table width="100%" border="1">
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87 <td style="width:19%"><strong>Packages</strong></td>
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88 <td style="width:81%"><strong>Classes and Interfaces </strong></td>
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91 <td>compbio.data.msa </td>
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92 <td>MsaWS the interface for all multiple sequence alignment web services </td>
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95 <td>compbio.data.sequence</td>
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96 <td>JABAWS data types </td>
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99 <td>compbio.metadata</td>
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100 <td>JABAWS meta data types </td>
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103 <td>compbio.ws.client</td>
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104 <td>JABAWS command line client </td>
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107 <p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />
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108 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>
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111 <h3><a name="connectto" id="connectto"></a>Connecting to JABAWS</h3>
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112 <p class="attention">
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113 For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client
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114 source code is available from the <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev">download page</a>. Please note that for now all
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115 the examples are in Java other languages will follow given a sufficient demand. </p>
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117 Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal
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118 web service deployed in the University of Dundee. </p>
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119 <p class="code"> import java.net.URL;<br />
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120 import javax.xml.namespace.QName;<br />
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121 import javax.xml.ws.Service;<br />
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122 ...............<br />
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123 1) String qualifiedName = "http://msa.data.compbio/01/01/2010/";<br />
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124 2) URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");<br />
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125 3) QName qname = new QName(, "ClustalWS");<br />
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126 4) Service serv = Service.create(url, qname);<br />
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127 5) MsaWS msaws = serv.getPort(new QName(qualifiedName, "ClustalWSPort"),
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131 Line 1 makes a qualified name for JABA web services.<br />
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132 Line 2 constructs the URL to the web services WSDL. <br />
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133 Line 3 makes a qualified name instance for Clustal JABA web service. <br />
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134 Line 4 creates a service instance.<br />
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135 Line 5 makes a connection to the server.
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138 A more generic connection method would look like this
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140 <p class="code"> import java.net.URL;<br />
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141 import javax.xml.namespace.QName;<br />
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142 import javax.xml.ws.Service;<br />
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143 import compbio.ws.client.Services<br />
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144 .............. <br />
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145 String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";<br />
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146 String host = "http://www.compbio.dundee.ac.uk/jabaws";<br />
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147 // In real life the service name can come from args<br />
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148 Services clustal = Services.ClustalWS;<br />
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149 URL url = new URL(host + "/" + clustal.toString() + "?wsdl");<br />
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150 QName qname = new QName(qualifiedServiceName, clustal.toString());<br />
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151 Service serv = Service.create(url, qname);<br />
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152 MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal<br />
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153 + "Port"), MsaWS.class);
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156 Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to
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157 MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS
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158 interface. The full documentation of MsaWS functions is available from the <a href="dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>.
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162 <h3><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h3>
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163 <p>Multiple sequence alignment services </p>
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164 <ul><li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalOWS?wsdl">ClustalOWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalOWS?wsdl) </li>
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165 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalWS?wsdl">ClustalWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ClustalWS?wsdl) </li>
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166 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/MuscleWS?wsdl">MuscleWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MuscleWS?wsdl) </li>
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167 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/MafftWS?wsdl">MafftWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MafftWS?wsdl) </li>
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168 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/TcoffeeWS?wsdl">TcoffeeWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/TcoffeeWS?wsdl) </li>
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169 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/ProbconsWS?wsdl">ProbconsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/ProbconsWS?wsdl) </li>
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170 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/MSAprobsWS?wsdl">MSAprobsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/MSAprobsWS?wsdl) </li>
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171 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/GLprobsWS?wsdl">GLprobsWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/GLprobsWS?wsdl) </li>
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173 <p>Protein disorder prediction services </p>
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175 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/IUPredWS?wsdl">IUPredWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/IUPredWS?wsdl) </li>
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176 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/GlobPlotWS?wsdl">GlobPlotWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/GlobPlotWS?wsdl) </li>
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177 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/DisemblWS?wsdl">DisemblWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/DisemblWS?wsdl) </li>
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178 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/JronnWS?wsdl">JronnWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/JronnWS?wsdl) </li>
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180 <p>Amino acid conservation service</p>
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182 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/AAConWS?wsdl">AAConWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/AAConWS?wsdl) </li>
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184 <p>Protein and RNA Secondary Structure Prediction</p>
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186 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/JpredWS?wsdl">JpredWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/JpredWS?wsdl) </li>
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187 <li><a href="http://www.compbio.dundee.ac.uk/jabaws-dev/RNAalifoldWS?wsdl">RNAalifoldWS</a> (http://www.compbio.dundee.ac.uk/jabaws-dev/RNAalifoldWS?wsdl) </li>
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190 Please replace <span class="hightlight">http://www.compbio.dundee.ac.uk/</span> with your JABAWS instance host name, and
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191 <span class="hightlight">jabaws</span> with your JABAWS context name to access your local version of JABAWS web services.
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192 For example <span class="hightlight">http://localhost:8080/jabaws</span> would be a valid URL for the default Apache-Tomcat
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193 installation and jabaws.war file deployment. </p>
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196 <h3><a name="defalign" id="defalign"></a>Aligning sequences </h3>
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198 Given that <span class="hightlight">msaws</span> is web service proxy, created as described in "Connecting to JABAWS"
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199 section, the actual alignment can be obtained as follows: </p>
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200 <p class="code">1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
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201 2) String jobId = msaws.align(fastalist); <br />
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202 3) Alignment alignment = msaws.getResult(jobId);</p>
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203 <p>Line one loads FASTA sequence from the file<br />
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204 Line two submits them to web service represented by msaws proxy <br />
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205 Line three retrieves the alignment from a web service. This line will block the execution until the result is available.
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206 Use this with caution. In general, you should make sure that the calculation has been completed before attempting
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207 retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time.
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208 While this may be ok with your local server, our public server
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209 (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) will not let you hold the connection
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210 for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check
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211 the status of the calculation.<br />
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212 Methods and classes mentioned in the excerpt are available from the JABAWS client library. </p>
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213 <h3><a name="checkresults" id="checkresults"></a>Checking the status of the calculation </h3>
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214 <p> You may have noticed that there was no pause between submitting the job and retrieving of the results. This is
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215 because <span class="hightlight">getResult(jobId)</span> method block the processing until the calculation is completed.
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216 However, taking into account that the connection holds server resources, our public server
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217 (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) is configured to reset the
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218 connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the
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219 calculation has been completed before accessing the results. You can do it like this: </p>
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220 <p> <span class="code">while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {<br />
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221 Thread.sleep(2000); // wait two seconds, then recheck the status <br />
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223 <h3><a name="presetalign" id="presetalign"></a>Aligning with presets</h3>
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224 <p class="code">1) PresetManager presetman = msaws.getPresets();<br />
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225 2) Preset preset = presetman.getPresetByName(presetName);<br />
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226 3) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
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227 4) String jobId = msaws.presetAlign(fastalist, preset);<br />
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228 5) Alignment alignment = msaws.getResult(jobId);</p>
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229 <p>Line one obtains the lists of presets supported by a web service.<br />
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230 Line two return a particular Preset
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232 Lines three to five are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>
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233 <h3><a name="customalign" id="customalign"></a>Aligning with custom parameters</h3>
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234 <p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />
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235 2) Argument matrix = options.getArgument("MATRIX");<br />
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236 3) matrix.setValue("PAM300");<br />
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237 4) Argument gapopenpenalty = options.getArgument("GAPOPEN");<br />
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238 5) gapopenpenalty.setValue("20");<br />
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239 6) List<Argument> arguments = new ArrayList<Argument>(); <br />
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240 7) arguments.add(matrix);
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241 arguments.add(gapopenpenalty);<br />
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242 8) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />
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243 9) String jobId = msaws.customAlign(fastalist, arguments);<br />
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244 10) Alignment alignment = msaws.getResult(jobId);</p>
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245 <p>Line one obtains the <span class="hightlight">RunnerConfig</span> object that holds information on supported parameters and their values<br />
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246 Line two retrieve a particular parameter from the holder by its name<br />
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247 Lines three sets a value to this parameter which will be used in the calculation. <br />
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248 Line four and five do the same but for another parameter<br />
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249 Line 6 makes a List to hold the parameters <br />
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250 Line seven puts the parameters into that list<br />
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252 and ten is the same as in previous examples<br />
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253 Line nine submit an alignment request with the sequences and the parameters <br />
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254 The names of all the parameters supported by a web service e.g. "PAM300" can be obtained
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255 using <span class="hightlight">options.getArguments() </span>method. Further details on the methods
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256 available from <span class="hightlight">RunnerConfig</span> object are available from the
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257 <a href="dm_javadoc/index.html">javadoc</a>. </p>
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258 <h3><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h3>
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259 <p>There is a utility method in the client library that does exactly that. </p>
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260 <p> <span class="code">Alignment alignment = align(...) <br />
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261 FileOutputStream outStream = new FileOutputStream(file);<br />
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262 ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>
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263 <h3><a name="compex" id="compex"></a>A complete client example </h3>
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265 Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using
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266 one of the Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of
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267 this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */,
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268 the alternatives given in the code are line commented // comment. You may want to remove line style comments to
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269 test alternatives of the functions. All you need for this to work is a
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270 <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=min-jaba-client-2.0.jar">JABAWS binary client</a>.
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271 Please make sure that the client is in the Java class path before running this example.</p>
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272 <pre class="code" style="line-height:1em;">
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273 import java.io.ByteArrayInputStream;
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274 import java.io.FileNotFoundException;
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275 import java.io.IOException;
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276 import java.net.URL;
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277 import java.util.List;
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279 import javax.xml.namespace.QName;
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280 import javax.xml.ws.Service;
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282 import compbio.data.msa.MsaWS;
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283 import compbio.data.sequence.Alignment;
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284 import compbio.data.sequence.FastaSequence;
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285 import compbio.data.sequence.SequenceUtil;
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286 import compbio.metadata.JobSubmissionException;
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287 import compbio.metadata.LimitExceededException;
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288 import compbio.metadata.Preset;
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289 import compbio.metadata.PresetManager;
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290 import compbio.metadata.ResultNotAvailableException;
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291 import compbio.metadata.UnsupportedRuntimeException;
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292 import compbio.metadata.WrongParameterException;
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294 public class Example {
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297 * Input sequences for alignment
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299 static final String input = ">Foo\r\n"
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300 + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR"
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301 + "VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ"
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302 + "LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL"
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303 + "APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA"
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304 + "STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD"
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305 + "YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN"
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306 + "PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD"
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307 + "LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS"
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308 + "DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n"
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310 + ">Bar\r\n"
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311 + "MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH"
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312 + "QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA"
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313 + "HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG"
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314 + "IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL"
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315 + "RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL"
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316 + "SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC"
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317 + "PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV"
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318 + "FEMDGFADDFGALLQALARRHGWLGI\r\n"
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320 + ">Friends\r\n"
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321 + "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV"
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322 + "RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG"
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323 + "VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL"
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324 + "TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD"
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325 + "LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF"
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326 + "QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA"
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327 + "DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP"
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328 + "GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI";
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330 public static void main(String[] args) throws UnsupportedRuntimeException,
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331 LimitExceededException, JobSubmissionException,
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332 WrongParameterException, FileNotFoundException, IOException,
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333 ResultNotAvailableException, InterruptedException {
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335 String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";
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337 /* Make a URL pointing to web service WSDL */
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338 URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");
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341 * If you are making a client that connects to different web services
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342 * you can use something like this:
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344 // URL url = new URL(host + "/" + Services.ClustalWS.toString() +
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345 // "?wsdl");
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347 QName qname = new QName(qualifiedServiceName, "ClustalWS");
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348 Service serv = Service.create(url, qname);
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350 * Multiple sequence alignment interface for Clustal web service
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353 MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, "ClustalWS"
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354 + "Port"), MsaWS.class);
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356 /* Get the list of available presets */
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357 PresetManager presetman = msaws.getPresets();
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359 /* Get the Preset object by preset name */
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360 Preset preset = presetman
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361 .getPresetByName("Disable gap weighting (Speed-oriented)");
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364 * Load sequences in FASTA format from the file You can use something
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365 * like new FileInputStream(<filename>) to load sequence from the file
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367 List<FastaSequence> fastalist = SequenceUtil
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368 .readFasta(new ByteArrayInputStream(input.getBytes()));
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371 * Submit loaded sequences for an alignment using preset. The job
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372 * identifier is returned by this method, you can retrieve the results
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373 * with it sometime later.
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375 String jobId = msaws.presetAlign(fastalist, preset);
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377 /* This method will block for the duration of the calculation */
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378 Alignment alignment = msaws.getResult(jobId);
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381 * This is a better way of obtaining results, it does not involve
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382 * holding the connection open for the duration of the calculation,
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383 * Besides, as the University of Dundee public server will reset the
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384 * connection after 10 minutes of idling, this is the only way to obtain
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385 * the results of long running task from our public server.
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387 // while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
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388 // Thread.sleep(1000); // wait a second, then recheck the status
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391 /* Output the alignment to standard out */
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392 System.out.println(alignment);
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394 // Alternatively, you can record retrieved alignment into the file in
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397 // ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(
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398 // "output.al"), alignment);
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403 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>.
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404 <h3><a name="buildart" id="buildart"></a>Building web services artifacts</h3>
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406 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>
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407 basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can
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408 generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as
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409 it provides a handful of useful methods in addition to plain data types. </p>
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410 <p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>
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411 </div><!-- content end-->
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412 <div id="copyright">Last update: 14 October 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>
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413 </div><!-- wrapper end-->
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414 </div><!-- page end-->
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