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  76 <li>Summary:&nbsp;</li>
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  95 <div class="subTitle">compbio.data.msa</div>
  96 <h2 title="Interface MsaWS" class="title">Interface MsaWS&lt;T&gt;</h2>
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  99 <div class="description">
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 102 <dl>
 103 <dt><span class="paramLabel">Type Parameters:</span></dt>
 104 <dd><code>T</code> - executable type / web service type</dd>
 105 </dl>
 106 <dl>
 107 <dt>All Superinterfaces:</dt>
 108 <dd><a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a>, <a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a>, <a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;T&gt;</dd>
 109 </dl>
 110 <dl>
 111 <dt>All Known Implementing Classes:</dt>
 112 <dd><a href="../../../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</a>, <a href="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</a>, <a href="../../../compbio/ws/server/GLprobsWS.html" title="class in compbio.ws.server">GLprobsWS</a>, <a href="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</a>, <a href="../../../compbio/ws/server/MSAprobsWS.html" title="class in compbio.ws.server">MSAprobsWS</a>, <a href="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</a>, <a href="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</a>, <a href="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</a></dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>public interface <span class="typeNameLabel">MsaWS&lt;T&gt;</span>
 117 extends <a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a>, <a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a>, <a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;T&gt;</pre>
 118 <div class="block">Multiple Sequence Alignment (MSA) Web Services Interface</div>
 119 <dl>
 120 <dt><span class="simpleTagLabel">Author:</span></dt>
 121 <dd>pvtroshin
 122
 123          Date November 2010</dd>
 124 </dl>
 125 </li>
 126 </ul>
 127 </div>
 128 <div class="summary">
 129 <ul class="blockList">
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 131 <!-- =========== FIELD SUMMARY =========== -->
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 134 <!--   -->
 135 </a>
 136 <h3>Field Summary</h3>
 137 <ul class="blockList">
 138 <li class="blockList"><a name="fields.inherited.from.class.compbio.data.msa.JABAService">
 139 <!--   -->
 140 </a>
 141 <h3>Fields inherited from interface&nbsp;compbio.data.msa.<a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a></h3>
 142 <code><a href="../../../compbio/data/msa/JABAService.html#JABAWS_VERSION">JABAWS_VERSION</a>, <a href="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</a>, <a href="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</a>, <a href="../../../compbio/data/msa/JABAService.html#V3_SERVICE_NAMESPACE">V3_SERVICE_NAMESPACE</a></code></li>
 143 </ul>
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 146 <!-- ========== METHOD SUMMARY =========== -->
 147 <ul class="blockList">
 148 <li class="blockList"><a name="method.summary">
 149 <!--   -->
 150 </a>
 151 <h3>Method Summary</h3>
 152 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 153 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t3" class="tableTab"><span><a href="javascript:show(4);">Abstract Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 154 <tr>
 155 <th class="colFirst" scope="col">Modifier and Type</th>
 156 <th class="colLast" scope="col">Method and Description</th>
 157 </tr>
 158 <tr id="i0" class="altColor">
 159 <td class="colFirst"><code>java.lang.String</code></td>
 160 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/msa/MsaWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>
 161 <div class="block">Align a list of sequences with default settings.</div>
 162 </td>
 163 </tr>
 164 <tr id="i1" class="rowColor">
 165 <td class="colFirst"><code>java.lang.String</code></td>
 166 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 167            java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt;&gt;&nbsp;options)</code>
 168 <div class="block">Align a list of sequences with options.</div>
 169 </td>
 170 </tr>
 171 <tr id="i2" class="altColor">
 172 <td class="colFirst"><code><a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 173 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>
 174 <div class="block">Return the result of the job.</div>
 175 </td>
 176 </tr>
 177 <tr id="i3" class="rowColor">
 178 <td class="colFirst"><code>java.lang.String</code></td>
 179 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 180            <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt;&nbsp;preset)</code>
 181 <div class="block">Align a list of sequences with preset.</div>
 182 </td>
 183 </tr>
 184 </table>
 185 <ul class="blockList">
 186 <li class="blockList"><a name="methods.inherited.from.class.compbio.data.msa.JManagement">
 187 <!--   -->
 188 </a>
 189 <h3>Methods inherited from interface&nbsp;compbio.data.msa.<a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></h3>
 190 <code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">cancelJob</a>, <a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">getJobStatus</a>, <a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></code></li>
 191 </ul>
 192 <ul class="blockList">
 193 <li class="blockList"><a name="methods.inherited.from.class.compbio.data.msa.Metadata">
 194 <!--   -->
 195 </a>
 196 <h3>Methods inherited from interface&nbsp;compbio.data.msa.<a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a></h3>
 197 <code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">getLimit</a>, <a href="../../../compbio/data/msa/Metadata.html#getLimits--">getLimits</a>, <a href="../../../compbio/data/msa/Metadata.html#getPresets--">getPresets</a>, <a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">getRunnerOptions</a></code></li>
 198 </ul>
 199 </li>
 200 </ul>
 201 </li>
 202 </ul>
 203 </div>
 204 <div class="details">
 205 <ul class="blockList">
 206 <li class="blockList">
 207 <!-- ============ METHOD DETAIL ========== -->
 208 <ul class="blockList">
 209 <li class="blockList"><a name="method.detail">
 210 <!--   -->
 211 </a>
 212 <h3>Method Detail</h3>
 213 <a name="align-java.util.List-">
 214 <!--   -->
 215 </a>
 216 <ul class="blockList">
 217 <li class="blockList">
 218 <h4>align</h4>
 219 <pre>java.lang.String&nbsp;align(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)
 220                 throws <a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a>,
 221                        <a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a>,
 222                        <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 223 <div class="block">Align a list of sequences with default settings.
 224
 225  Any dataset containing a greater number of sequences or when the average
 226  length of the sequences are greater then defined in the default Limit,
 227  will not be accepted for an alignment operation and
 228  JobSubmissionException will be thrown.</div>
 229 <dl>
 230 <dt><span class="paramLabel">Parameters:</span></dt>
 231 <dd><code>sequences</code> - List of FastaSequence objects. The program does not perform
 232             any sequence validity checks. Nor does it checks whether the
 233             sequences names are unique. It is responsibility of the caller
 234             to make sure of this</dd>
 235 <dt><span class="returnLabel">Returns:</span></dt>
 236 <dd>jobId - unique identifier for the job</dd>
 237 <dt><span class="throwsLabel">Throws:</span></dt>
 238 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 239              following reasons: 1) The number of sequences in the
 240              submission or their average length is greater then defined by
 241              the default Limit. 2) Any problems on the server side e.g. it
 242              is misconfigured or malfunction, is reported via this
 243              exception. In the first case the information on the limit
 244              could be obtained from an exception.</dd>
 245 <dd><code>java.security.InvalidParameterException</code> - thrown if input list of FASTA sequences is null or empty</dd>
 246 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 247              given web service, e.g. JABAWS is deployed on Windows and
 248              Mafft service is called</dd>
 249 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or their average
 250              length exceeds what is defined by the limit</dd>
 251 </dl>
 252 </li>
 253 </ul>
 254 <a name="customAlign-java.util.List-java.util.List-">
 255 <!--   -->
 256 </a>
 257 <ul class="blockList">
 258 <li class="blockList">
 259 <h4>customAlign</h4>
 260 <pre>java.lang.String&nbsp;customAlign(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 261                              java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt;&gt;&nbsp;options)
 262                       throws <a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a>,
 263                              <a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a>,
 264                              <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
 265                              <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 266 <div class="block">Align a list of sequences with options.</div>
 267 <dl>
 268 <dt><span class="paramLabel">Parameters:</span></dt>
 269 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
 270             any sequence validity checks. Nor does it checks whether the
 271             sequences names are unique. It is responsibility of the caller
 272             to validate this information</dd>
 273 <dd><code>options</code> - A list of Options</dd>
 274 <dt><span class="returnLabel">Returns:</span></dt>
 275 <dd>jobId - unique identifier for the job</dd>
 276 <dt><span class="throwsLabel">Throws:</span></dt>
 277 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 278              following reasons: 1) The number of sequences in the
 279              submission or their average length is greater then defined by
 280              the default Limit. 2) Any problems on the server side e.g. it
 281              is misconfigured or malfunction, is reported via this
 282              exception. In the first case the information on the limit
 283              could be obtained from an exception.</dd>
 284 <dd><code><a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is throws when 1) One of the Options provided is not
 285              supported, 2) The value of the option is defined outside the
 286              boundaries. In both cases exception object contain the
 287              information on the violating Option.</dd>
 288 <dd><code>java.security.InvalidParameterException</code> - thrown if input list of FASTA sequence is null or empty</dd>
 289 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 290              given web service, e.g. JABAWS is deployed on Windows and
 291              Mafft service is called</dd>
 292 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or their average
 293              length exceeds what is defined by the limit</dd>
 294 <dt><span class="seeLabel">See Also:</span></dt>
 295 <dd><a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><code>Default Limit is used to decide whether the calculation will be
 296       permitted or denied</code></a></dd>
 297 </dl>
 298 </li>
 299 </ul>
 300 <a name="presetAlign-java.util.List-compbio.metadata.Preset-">
 301 <!--   -->
 302 </a>
 303 <ul class="blockList">
 304 <li class="blockList">
 305 <h4>presetAlign</h4>
 306 <pre>java.lang.String&nbsp;presetAlign(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 307                              <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</a>&gt;&nbsp;preset)
 308                       throws <a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a>,
 309                              <a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a>,
 310                              <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
 311                              <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 312 <div class="block">Align a list of sequences with preset.
 313
 314  Limit for a presetName is used whether the calculation will be permitted
 315  or denied. If no Limit was defined for a presetName, than default limit
 316  is used.</div>
 317 <dl>
 318 <dt><span class="paramLabel">Parameters:</span></dt>
 319 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
 320             any sequence validity checks. Nor does it checks whether the
 321             sequences names are unique. It is responsibility of the caller
 322             to validate this information</dd>
 323 <dd><code>preset</code> - A list of Options</dd>
 324 <dt><span class="returnLabel">Returns:</span></dt>
 325 <dd>String - jobId - unique identifier for the job</dd>
 326 <dt><span class="throwsLabel">Throws:</span></dt>
 327 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 328              following reasons: 1) The number of sequences in the
 329              submission or their average length is greater then defined by
 330              the default Limit. 2) Any problems on the server side e.g. it
 331              is misconfigured or malfunction, is reported via this
 332              exception. In the first case the information on the limit
 333              could be obtained from an exception.</dd>
 334 <dd><code><a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is throws when 1) One of the Options provided is not
 335              supported, 2) The value of the option is defined outside the
 336              boundaries. In both cases exception object contain the
 337              information on the violating Option.</dd>
 338 <dd><code>java.security.InvalidParameterException</code> - thrown if input list of FASTA sequence is null or empty</dd>
 339 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 340              given web service, e.g. JABAWS is deployed on Windows and
 341              Mafft service is called</dd>
 342 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or average length
 343              exceeds what is defined by the limit</dd>
 344 <dt><span class="seeLabel">See Also:</span></dt>
 345 <dd><a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><code>Preset</code></a></dd>
 346 </dl>
 347 </li>
 348 </ul>
 349 <a name="getResult-java.lang.String-">
 350 <!--   -->
 351 </a>
 352 <ul class="blockListLast">
 353 <li class="blockList">
 354 <h4>getResult</h4>
 355 <pre><a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;getResult(java.lang.String&nbsp;jobId)
 356              throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 357 <div class="block">Return the result of the job. This method waits for the job
 358  <code>jobId</code> to complete before return.</div>
 359 <dl>
 360 <dt><span class="paramLabel">Parameters:</span></dt>
 361 <dd><code>jobId</code> - a unique job identifier</dd>
 362 <dt><span class="returnLabel">Returns:</span></dt>
 363 <dd>Alignment</dd>
 364 <dt><span class="throwsLabel">Throws:</span></dt>
 365 <dd><code><a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code> - this exception is throw if the job execution was not
 366              successful or the result of the execution could not be found.
 367              (e.g. removed). Exception could also be thrown due to the
 368              lower level problems on the server i.e. IOException,
 369              FileNotFoundException problems as well as
 370              UnknownFileFormatException.</dd>
 371 <dd><code>java.security.InvalidParameterException</code> - thrown if jobId is empty or is not recognised e.g. in invalid
 372              format</dd>
 373 </dl>
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