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  52 <h2 id="headtitle">JABAWS MANUAL</h2>\r
  53 \r
  54 <h2>Using JABAWS From Your Program </h2>\r
  55 <ul>\r
  56   <li><a href="#wsfunctions">Web services functions overview </a></li>\r
  57   <li><a href="#templatestr">The template client structure</a></li>\r
  58   <li><a href="#connectto">Connecting to JABAWS</a></li>\r
  59   <li><a href="#validnames">Valid JABAWS service names and WSDL files</a></li>\r
  60   <li><a href="#defalign">Aligning sequences</a></li>\r
  61   <li><a href="#checkresults">Checking the status of the calculation </a></li>\r
  62   <li><a href="#presetalign">Aligning with presets</a></li>\r
  63   <li><a href="#customalign">Aligning with custom parameters</a></li>\r
  64   <li><a href="#writingaltofile">Writing alignments to a file</a></li>\r
  65   <li><a href="#compex">A complete client example </a></li>\r
  66   <li><a href="#buildart">Building web services artifacts</a></li>\r
  67 </ul>\r
  68 <h3><a name="wsfunctions" id="wsfunctions"></a>Web services functions overview </h3>\r
  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>\r
  70 <p><strong>Functions for initiating the alignment </strong><span class="code">  String id = align(List&lt;FastaSequence&gt; list)<br />\r
  71   String id = customAlign(List&lt;FastaSequence&gt; sequenceList, List&lt;Option&gt; optionList)<br />\r
  72   String id = presetAlign(List&lt;FastaSequence&gt; sequenceList, Preset preset)</span></p>\r
  73 <p><strong>Functions pertaining to job monitoring and control</strong><br />\r
  74   <span class="code">JobStatus status = getJobStatus(String id)<br />\r
  75   Alignment al = getResult(String id)<br />\r
  76   boolean cancelled = cancelJob(String id)<br />\r
  77   ChunkHolder chunk = pullExecStatistics(String id, long marker)</span></p>\r
  78 <p><strong>Functions relating to service features discovery</strong><br />\r
  79   <span class="code">RunnerConfig rc = getRunnerOptions()<br />\r
  80   Limit limit = getLimit(String name)<br />\r
  81   LimitsManager lm = getLimits()<br />\r
  82   PresetManager pm = getPresets()</span></p>\r
  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>\r
  84 <h3><a name="templatestr" id="templatestr"></a>Structure of the template command line client</h3>\r
  85 <table width="100%" border="1">\r
  86   <tr>\r
  87     <td style="width:19%"><strong>Packages</strong></td>\r
  88     <td style="width:81%"><strong>Classes and Interfaces </strong></td>\r
  89   </tr>\r
  90   <tr>\r
  91     <td>compbio.data.msa </td>\r
  92     <td>MsaWS the interface for all multiple sequence alignment web services </td>\r
  93   </tr>\r
  94   <tr>\r
  95     <td>compbio.data.sequence</td>\r
  96     <td>JABAWS data types </td>\r
  97   </tr>\r
  98   <tr>\r
  99     <td>compbio.metadata</td>\r
 100     <td>JABAWS meta data types </td>\r
 101   </tr>\r
 102   <tr>\r
 103     <td>compbio.ws.client</td>\r
 104     <td>JABAWS command line client </td>\r
 105   </tr>\r
 106 </table>\r
 107 <p>Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar. <br />\r
 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>\r
 109 \r
 110 \r
 111 <h3><a name="connectto" id="connectto"></a>Connecting to JABAWS</h3>\r
 112 <p class="attention">\r
 113 For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client \r
 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 \r
 115 the examples are in Java other languages will follow given a sufficient demand. </p>\r
 116 <p>\r
 117 Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal \r
 118 web service deployed in the University of Dundee. </p>\r
 119 <p class="code"> import java.net.URL;<br />\r
 120   import javax.xml.namespace.QName;<br />\r
 121   import javax.xml.ws.Service;<br />\r
 122   ...............<br />\r
 123   1) String qualifiedName = &quot;http://msa.data.compbio/01/01/2010/&quot;;<br />\r
 124   2) URL url = new URL(&quot;http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl&quot;);<br />\r
 125   3) QName qname = new QName(, &quot;ClustalWS&quot;);<br />\r
 126   4) Service serv = Service.create(url, qname);<br />\r
 127   5) MsaWS msaws = serv.getPort(new QName(qualifiedName, &quot;ClustalWSPort&quot;),\r
 128   MsaWS.class);\r
 129 </p>\r
 130 <p>\r
 131         Line 1 makes a qualified name for JABA web services.<br />\r
 132         Line 2 constructs the URL to the web services WSDL. <br />\r
 133         Line 3 makes a qualified name instance for Clustal JABA web service. <br />\r
 134         Line 4 creates a service instance.<br />\r
 135         Line 5 makes a connection to the server.\r
 136 </p>\r
 137 <p>\r
 138         A more generic connection method would look like this\r
 139 </p>\r
 140 <p class="code"> import java.net.URL;<br />\r
 141   import javax.xml.namespace.QName;<br />\r
 142   import javax.xml.ws.Service;<br />\r
 143   import compbio.ws.client.Services<br />\r
 144   .............. <br />\r
 145   String qualifiedServiceName = &quot;http://msa.data.compbio/01/01/2010/&quot;;<br />\r
 146   String host = &quot;http://www.compbio.dundee.ac.uk/jabaws&quot;;<br />\r
 147   // In real life the service name can come from args<br />\r
 148   Services clustal = Services.ClustalWS;<br />\r
 149   URL url = new URL(host + &quot;/&quot; + clustal.toString() + &quot;?wsdl&quot;);<br />\r
 150   QName qname = new QName(qualifiedServiceName, clustal.toString());<br />\r
 151   Service serv = Service.create(url, qname);<br />\r
 152   MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal<br />\r
 153   + &quot;Port&quot;), MsaWS.class);\r
 154 </p>\r
 155 <p>\r
 156         Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to \r
 157         MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS \r
 158         interface. The full documentation of MsaWS functions is available from the <a href="dm_javadoc/compbio/data/msa/MsaWS.html">javadoc</a>.\r
 159 </p>\r
 160 \r
 161 \r
 162 <h3><a name="validnames" id="validnames"></a>Valid JABAWS service names and WSDL files </h3>\r
 163 <p>Multiple sequence alignment services </p>\r
 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>\r
 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>\r
 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>\r
 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>\r
 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>\r
 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>\r
 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>\r
 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>\r
 172 </ul>\r
 173 <p>Protein disorder prediction services </p>\r
 174 <ul>\r
 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>\r
 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>\r
 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>\r
 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>\r
 179 </ul>\r
 180 <p>Amino acid conservation service</p>\r
 181 <ul>\r
 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>\r
 183 </ul>\r
 184 <p>Protein and RNA Secondary Structure Prediction</p>\r
 185 <ul>\r
 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>\r
 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>\r
 188 </ul>\r
 189 <p>\r
 190 Please replace <span class="hightlight">http://www.compbio.dundee.ac.uk/</span> with your JABAWS instance host name, and \r
 191 <span class="hightlight">jabaws</span> with your JABAWS context name to access your local version of JABAWS web services. \r
 192 For example <span class="hightlight">http://localhost:8080/jabaws</span> would be a valid URL for the default Apache-Tomcat \r
 193 installation and jabaws.war file deployment. </p>\r
 194 \r
 195 \r
 196 <h3><a name="defalign" id="defalign"></a>Aligning sequences </h3>\r
 197 <p>\r
 198 Given that <span class="hightlight">msaws</span> is web service proxy, created as described in &quot;Connecting to JABAWS&quot; \r
 199 section, the actual alignment can be obtained as follows: </p>\r
 200 <p class="code">1) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
 201   2) String jobId = msaws.align(fastalist); <br />\r
 202   3) Alignment alignment = msaws.getResult(jobId);</p>\r
 203 <p>Line  one loads FASTA sequence from the file<br />\r
 204   Line two submits them to web service represented by msaws proxy <br />\r
 205   Line three retrieves the alignment from a web service. This line will block the execution until the result is available. \r
 206   Use this with caution. In general, you should make sure that the calculation has been completed before attempting \r
 207   retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. \r
 208   While this may be ok with your local server, our public server \r
 209   (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) will not let you hold the connection \r
 210   for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check \r
 211   the status of the calculation.<br />\r
 212   Methods and classes mentioned in the excerpt are available from the JABAWS client library. </p>\r
 213 <h3><a name="checkresults" id="checkresults"></a>Checking the status of the calculation </h3>\r
 214 <p> You may have noticed that there was no pause between submitting the job and retrieving of the results. This is \r
 215 because <span class="hightlight">getResult(jobId)</span> method block the processing until the calculation is completed. \r
 216 However, taking into account that the connection holds server resources, our public server \r
 217 (<a href="http://www.compbio.dundee.ac.uk/jabaws">www.compbio.dundee.ac.uk/jabaws</a>) is configured to reset the \r
 218 connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the \r
 219 calculation has been completed before accessing the results.    You can do it like this: </p>\r
 220 <p> <span class="code">while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {<br />\r
 221   &nbsp;&nbsp;&nbsp;&nbsp;Thread.sleep(2000); // wait two  seconds, then recheck the status <br />\r
 222   }</span></p>\r
 223 <h3><a name="presetalign" id="presetalign"></a>Aligning with presets</h3>\r
 224 <p class="code">1) PresetManager presetman = msaws.getPresets();<br />\r
 225   2) Preset preset = presetman.getPresetByName(presetName);<br />\r
 226   3) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
 227   4) String jobId = msaws.presetAlign(fastalist, preset);<br />\r
 228   5) Alignment alignment = msaws.getResult(jobId);</p>\r
 229 <p>Line one obtains the lists of presets supported by a web service.<br />\r
 230   Line two return a particular Preset \r
 231   by its name<br />\r
 232   Lines three to five  are doing the same job as in the first <a href="#defalign"> aligning sequences example</a>.</p>\r
 233 <h3><a name="customalign" id="customalign"></a>Aligning with  custom parameters</h3>\r
 234 <p class="code"> 1) RunnerConfig options = msaws.getRunnerOptions();<br />\r
 235   2) Argument matrix = options.getArgument(&quot;MATRIX&quot;);<br />\r
 236   3) matrix.setValue(&quot;PAM300&quot;);<br />\r
 237   4) Argument gapopenpenalty = options.getArgument(&quot;GAPOPEN&quot;);<br />\r
 238   5) gapopenpenalty.setValue(&quot;20&quot;);<br />\r
 239   6) List&lt;Argument&gt; arguments = new ArrayList&lt;Argument&gt;(); <br />\r
 240   7) arguments.add(matrix);\r
 241   arguments.add(gapopenpenalty);<br />\r
 242   8) List&lt;FastaSequence&gt; fastalist = SequenceUtil.readFasta(new FileInputStream(file));<br />\r
 243   9) String jobId = msaws.customAlign(fastalist, arguments);<br />\r
 244   10) Alignment alignment = msaws.getResult(jobId);</p>\r
 245 <p>Line one obtains the <span class="hightlight">RunnerConfig</span> object that holds information on supported parameters and their values<br />\r
 246   Line two retrieve a particular parameter from the holder by its name<br />\r
 247   Lines three sets a value to this parameter which will be used in the calculation. <br />\r
 248   Line four and five do the same but for another parameter<br />\r
 249   Line 6 makes a List to hold the parameters <br />\r
 250   Line seven puts the parameters into that list<br />\r
 251   Line eight \r
 252   and ten is the same as in previous examples<br />\r
 253   Line nine submit an alignment request with the sequences and the parameters <br />\r
 254   The names of all the parameters supported by a web service e.g. &quot;PAM300&quot; can be obtained \r
 255   using <span class="hightlight">options.getArguments() </span>method. Further details on the methods \r
 256   available from <span class="hightlight">RunnerConfig</span> object are available from the \r
 257   <a href="dm_javadoc/index.html">javadoc</a>. </p>\r
 258 <h3><a name="writingaltofile" id="writingaltofile"></a>Writing alignments to a file</h3>\r
 259 <p>There is a utility method in the client library that does exactly that. </p>\r
 260 <p> <span class="code">Alignment alignment = align(...) <br />\r
 261   FileOutputStream outStream = new FileOutputStream(file);<br />\r
 262   ClustalAlignmentUtil.writeClustalAlignment(outStream, align);</span></p>\r
 263 <h3><a name="compex" id="compex"></a>A complete client example </h3>\r
 264 <p>\r
 265 Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using \r
 266 one of the  Clustal web service preset. Three is also a <a href="Example_template.pdf">PDF version</a> of \r
 267 this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, \r
 268 the alternatives given in the code are line commented // comment. You may want to remove line style comments to \r
 269 test alternatives of the functions. All you need for this to work is a \r
 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>. \r
 271 Please make sure that the client is in the Java class path before running this example.</p>\r
 272 <pre class="code" style="line-height:1em;">\r
 273 import java.io.ByteArrayInputStream;\r
 274 import java.io.FileNotFoundException;\r
 275 import java.io.IOException;\r
 276 import java.net.URL;\r
 277 import java.util.List;\r
 278 \r
 279 import javax.xml.namespace.QName;\r
 280 import javax.xml.ws.Service;\r
 281 \r
 282 import compbio.data.msa.MsaWS;\r
 283 import compbio.data.sequence.Alignment;\r
 284 import compbio.data.sequence.FastaSequence;\r
 285 import compbio.data.sequence.SequenceUtil;\r
 286 import compbio.metadata.JobSubmissionException;\r
 287 import compbio.metadata.LimitExceededException;\r
 288 import compbio.metadata.Preset;\r
 289 import compbio.metadata.PresetManager;\r
 290 import compbio.metadata.ResultNotAvailableException;\r
 291 import compbio.metadata.UnsupportedRuntimeException;\r
 292 import compbio.metadata.WrongParameterException;\r
 293 \r
 294 public class Example {\r
 295 \r
 296         /*\r
 297          * Input sequences for alignment\r
 298          */\r
 299         static final String input = &quot;&gt;Foo\r\n&quot;\r
 300                         + &quot;MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR&quot;\r
 301                         + &quot;VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ&quot;\r
 302                         + &quot;LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL&quot;\r
 303                         + &quot;APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA&quot;\r
 304                         + &quot;STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD&quot;\r
 305                         + &quot;YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN&quot;\r
 306                         + &quot;PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD&quot;\r
 307                         + &quot;LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS&quot;\r
 308                         + &quot;DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n&quot;\r
 309                         + &quot;\r\n&quot;\r
 310                         + &quot;&gt;Bar\r\n&quot;\r
 311                         + &quot;MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH&quot;\r
 312                         + &quot;QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA&quot;\r
 313                         + &quot;HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG&quot;\r
 314                         + &quot;IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL&quot;\r
 315                         + &quot;RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL&quot;\r
 316                         + &quot;SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC&quot;\r
 317                         + &quot;PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV&quot;\r
 318                         + &quot;FEMDGFADDFGALLQALARRHGWLGI\r\n&quot;\r
 319                         + &quot;\r\n&quot;\r
 320                         + &quot;&gt;Friends\r\n&quot;\r
 321                         + &quot;MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV&quot;\r
 322                         + &quot;RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG&quot;\r
 323                         + &quot;VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL&quot;\r
 324                         + &quot;TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD&quot;\r
 325                         + &quot;LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF&quot;\r
 326                         + &quot;QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA&quot;\r
 327                         + &quot;DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP&quot;\r
 328                         + &quot;GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI&quot;;\r
 329 \r
 330         public static void main(String[] args) throws UnsupportedRuntimeException,\r
 331                         LimitExceededException, JobSubmissionException,\r
 332                         WrongParameterException, FileNotFoundException, IOException,\r
 333                         ResultNotAvailableException, InterruptedException {\r
 334 \r
 335                 String qualifiedServiceName = &quot;http://msa.data.compbio/01/01/2010/&quot;;\r
 336 \r
 337                 /* Make a URL pointing to web service WSDL */\r
 338                 URL url = new URL(&quot;http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl&quot;);\r
 339 \r
 340                 /*\r
 341                  * If you are making a client that connects to different web services\r
 342                  * you can use something like this:\r
 343                  */\r
 344                 // URL url = new URL(host + &quot;/&quot; + Services.ClustalWS.toString() +\r
 345                 // &quot;?wsdl&quot;);\r
 346 \r
 347                 QName qname = new QName(qualifiedServiceName, &quot;ClustalWS&quot;);\r
 348                 Service serv = Service.create(url, qname);\r
 349                 /*\r
 350                  * Multiple sequence alignment interface for Clustal web service\r
 351                  * instance\r
 352                  */\r
 353                 MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, &quot;ClustalWS&quot;\r
 354                                 + &quot;Port&quot;), MsaWS.class);\r
 355 \r
 356                 /* Get the list of available presets */\r
 357                 PresetManager presetman = msaws.getPresets();\r
 358 \r
 359                 /* Get the Preset object by preset name */\r
 360                 Preset preset = presetman\r
 361                                 .getPresetByName(&quot;Disable gap weighting (Speed-oriented)&quot;);\r
 362 \r
 363                 /*\r
 364                  * Load sequences in FASTA format from the file You can use something\r
 365                  * like new FileInputStream(&lt;filename&gt;) to load sequence from the file\r
 366                  */\r
 367                 List&lt;FastaSequence&gt; fastalist = SequenceUtil\r
 368                                 .readFasta(new ByteArrayInputStream(input.getBytes()));\r
 369 \r
 370                 /*\r
 371                  * Submit loaded sequences for an alignment using preset. The job\r
 372                  * identifier is returned by this method, you can retrieve the results\r
 373                  * with it sometime later.\r
 374                  */\r
 375                 String jobId = msaws.presetAlign(fastalist, preset);\r
 376 \r
 377                 /* This method will block for the duration of the calculation */\r
 378                 Alignment alignment = msaws.getResult(jobId);\r
 379 \r
 380                 /*\r
 381                  * This is a better way of obtaining results, it does not involve\r
 382                  * holding the connection open for the duration of the calculation,\r
 383                  * Besides, as the University of Dundee public server will reset the\r
 384                  * connection after 10 minutes of idling, this is the only way to obtain\r
 385                  * the results of long running task from our public server.\r
 386                  */\r
 387                 // while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {\r
 388                 // Thread.sleep(1000); // wait a second, then recheck the status\r
 389                 // }\r
 390 \r
 391                 /* Output the alignment to standard out */\r
 392                 System.out.println(alignment);\r
 393 \r
 394                 // Alternatively, you can record retrieved alignment into the file in\r
 395                 // ClustalW format\r
 396 \r
 397                 // ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(\r
 398                 // &quot;output.al&quot;), alignment);\r
 399 \r
 400         }\r
 401 }\r
 402 </pre>\r
 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>.\r
 404 <h3><a name="buildart" id="buildart"></a>Building web services artifacts</h3>\r
 405 <p>\r
 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> \r
 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 \r
 408 generate portable artifacts to work with JABAWS from Java. However,  if programming in Java we recommend using our  client library as \r
 409 it provides a handful of useful methods in addition to plain data types. </p>\r
 410 <p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
 411 </div><!-- content end-->\r
 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>\r
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