website/docs/full_javadoc/compbio/data/sequence/class-use/Alignment.html

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   6 <title>Uses of Class compbio.data.sequence.Alignment</title>
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  72 <div class="header">
  73 <h2 title="Uses of Class compbio.data.sequence.Alignment" class="title">Uses of Class<br>compbio.data.sequence.Alignment</h2>
  74 </div>
  75 <div class="classUseContainer">
  76 <ul class="blockList">
  77 <li class="blockList">
  78 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
  79 <caption><span>Packages that use <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
  80 <tr>
  81 <th class="colFirst" scope="col">Package</th>
  82 <th class="colLast" scope="col">Description</th>
  83 </tr>
  84 <tbody>
  85 <tr class="altColor">
  86 <td class="colFirst"><a href="#compbio.data.msa">compbio.data.msa</a></td>
  87 <td class="colLast">
  88 <div class="block">Web Service interfaces for JAva Bioinformatics Analysis Web Services.</div>
  89 </td>
  90 </tr>
  91 <tr class="rowColor">
  92 <td class="colFirst"><a href="#compbio.data.msa.jaxws">compbio.data.msa.jaxws</a></td>
  93 <td class="colLast">&nbsp;</td>
  94 </tr>
  95 <tr class="altColor">
  96 <td class="colFirst"><a href="#compbio.data.sequence">compbio.data.sequence</a></td>
  97 <td class="colLast">
  98 <div class="block">A data model for multiple sequence alignment web services and utility methods
  99  that work on the objects of this model.</div>
 100 </td>
 101 </tr>
 102 <tr class="rowColor">
 103 <td class="colFirst"><a href="#compbio.runner">compbio.runner</a></td>
 104 <td class="colLast">
 105 <div class="block">Utilities commonly used by all runners.</div>
 106 </td>
 107 </tr>
 108 <tr class="altColor">
 109 <td class="colFirst"><a href="#compbio.runner.msa">compbio.runner.msa</a></td>
 110 <td class="colLast">
 111 <div class="block">Wrappers for native executables for multiple sequence alignment (msa)</div>
 112 </td>
 113 </tr>
 114 <tr class="rowColor">
 115 <td class="colFirst"><a href="#compbio.ws.client">compbio.ws.client</a></td>
 116 <td class="colLast">
 117 <div class="block">A command line client and web services testing client for
 118  JAva Bioinformatics Analysis Web Services.</div>
 119 </td>
 120 </tr>
 121 <tr class="altColor">
 122 <td class="colFirst"><a href="#compbio.ws.server">compbio.ws.server</a></td>
 123 <td class="colLast">&nbsp;</td>
 124 </tr>
 125 </tbody>
 126 </table>
 127 </li>
 128 <li class="blockList">
 129 <ul class="blockList">
 130 <li class="blockList"><a name="compbio.data.msa">
 131 <!--   -->
 132 </a>
 133 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</a></h3>
 134 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 135 <caption><span>Methods in <a href="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 136 <tr>
 137 <th class="colFirst" scope="col">Modifier and Type</th>
 138 <th class="colLast" scope="col">Method and Description</th>
 139 </tr>
 140 <tbody>
 141 <tr class="altColor">
 142 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 143 <td class="colLast"><span class="typeNameLabel">MsaWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>
 144 <div class="block">Return the result of the job.</div>
 145 </td>
 146 </tr>
 147 </tbody>
 148 </table>
 149 </li>
 150 <li class="blockList"><a name="compbio.data.msa.jaxws">
 151 <!--   -->
 152 </a>
 153 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></h3>
 154 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing fields, and an explanation">
 155 <caption><span>Fields in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> declared as <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 156 <tr>
 157 <th class="colFirst" scope="col">Modifier and Type</th>
 158 <th class="colLast" scope="col">Field and Description</th>
 159 </tr>
 160 <tbody>
 161 <tr class="altColor">
 162 <td class="colFirst"><code>private <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 163 <td class="colLast"><span class="typeNameLabel">GetResultResponse.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/GetResultResponse.html#Z:Z_return">_return</a></span></code>&nbsp;</td>
 164 </tr>
 165 <tr class="rowColor">
 166 <td class="colFirst"><code>private <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 167 <td class="colLast"><span class="typeNameLabel">PresetFold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetFold.html#alignment">alignment</a></span></code>&nbsp;</td>
 168 </tr>
 169 <tr class="altColor">
 170 <td class="colFirst"><code>private <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 171 <td class="colLast"><span class="typeNameLabel">Fold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Fold.html#alignment">alignment</a></span></code>&nbsp;</td>
 172 </tr>
 173 <tr class="rowColor">
 174 <td class="colFirst"><code>private <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 175 <td class="colLast"><span class="typeNameLabel">CustomFold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomFold.html#alignment">alignment</a></span></code>&nbsp;</td>
 176 </tr>
 177 </tbody>
 178 </table>
 179 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 180 <caption><span>Methods in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 181 <tr>
 182 <th class="colFirst" scope="col">Modifier and Type</th>
 183 <th class="colLast" scope="col">Method and Description</th>
 184 </tr>
 185 <tbody>
 186 <tr class="altColor">
 187 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 188 <td class="colLast"><span class="typeNameLabel">PresetFold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetFold.html#getAlignment--">getAlignment</a></span>()</code>&nbsp;</td>
 189 </tr>
 190 <tr class="rowColor">
 191 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 192 <td class="colLast"><span class="typeNameLabel">Fold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Fold.html#getAlignment--">getAlignment</a></span>()</code>&nbsp;</td>
 193 </tr>
 194 <tr class="altColor">
 195 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 196 <td class="colLast"><span class="typeNameLabel">CustomFold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomFold.html#getAlignment--">getAlignment</a></span>()</code>&nbsp;</td>
 197 </tr>
 198 <tr class="rowColor">
 199 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 200 <td class="colLast"><span class="typeNameLabel">GetResultResponse.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/GetResultResponse.html#getReturn--">getReturn</a></span>()</code>&nbsp;</td>
 201 </tr>
 202 </tbody>
 203 </table>
 204 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 205 <caption><span>Methods in <a href="../../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a> with parameters of type <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 206 <tr>
 207 <th class="colFirst" scope="col">Modifier and Type</th>
 208 <th class="colLast" scope="col">Method and Description</th>
 209 </tr>
 210 <tbody>
 211 <tr class="altColor">
 212 <td class="colFirst"><code>void</code></td>
 213 <td class="colLast"><span class="typeNameLabel">PresetFold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/PresetFold.html#setAlignment-compbio.data.sequence.Alignment-">setAlignment</a></span>(<a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;alignment)</code>&nbsp;</td>
 214 </tr>
 215 <tr class="rowColor">
 216 <td class="colFirst"><code>void</code></td>
 217 <td class="colLast"><span class="typeNameLabel">Fold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/Fold.html#setAlignment-compbio.data.sequence.Alignment-">setAlignment</a></span>(<a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;alignment)</code>&nbsp;</td>
 218 </tr>
 219 <tr class="altColor">
 220 <td class="colFirst"><code>void</code></td>
 221 <td class="colLast"><span class="typeNameLabel">CustomFold.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/CustomFold.html#setAlignment-compbio.data.sequence.Alignment-">setAlignment</a></span>(<a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;alignment)</code>&nbsp;</td>
 222 </tr>
 223 <tr class="rowColor">
 224 <td class="colFirst"><code>void</code></td>
 225 <td class="colLast"><span class="typeNameLabel">GetResultResponse.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/msa/jaxws/GetResultResponse.html#setReturn-compbio.data.sequence.Alignment-">setReturn</a></span>(<a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;_return)</code>&nbsp;</td>
 226 </tr>
 227 </tbody>
 228 </table>
 229 </li>
 230 <li class="blockList"><a name="compbio.data.sequence">
 231 <!--   -->
 232 </a>
 233 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></h3>
 234 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 235 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 236 <tr>
 237 <th class="colFirst" scope="col">Modifier and Type</th>
 238 <th class="colLast" scope="col">Method and Description</th>
 239 </tr>
 240 <tbody>
 241 <tr class="altColor">
 242 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 243 <td class="colLast"><span class="typeNameLabel">ClustalAlignmentUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.File-">readClustalFile</a></span>(java.io.File&nbsp;file)</code>&nbsp;</td>
 244 </tr>
 245 <tr class="rowColor">
 246 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 247 <td class="colLast"><span class="typeNameLabel">ClustalAlignmentUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.InputStream-">readClustalFile</a></span>(java.io.InputStream&nbsp;instream)</code>
 248 <div class="block">Read Clustal formatted alignment.</div>
 249 </td>
 250 </tr>
 251 </tbody>
 252 </table>
 253 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 254 <caption><span>Methods in <a href="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> with parameters of type <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 255 <tr>
 256 <th class="colFirst" scope="col">Modifier and Type</th>
 257 <th class="colLast" scope="col">Method and Description</th>
 258 </tr>
 259 <tbody>
 260 <tr class="altColor">
 261 <td class="colFirst"><code>static void</code></td>
 262 <td class="colLast"><span class="typeNameLabel">ClustalAlignmentUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment-java.io.Writer-compbio.data.sequence.Alignment-">writeClustalAlignment</a></span>(java.io.Writer&nbsp;out,
 263                      <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;alignment)</code>
 264 <div class="block">Write Clustal formatted alignment Limitations: does not record the
 265  consensus.</div>
 266 </td>
 267 </tr>
 268 </tbody>
 269 </table>
 270 </li>
 271 <li class="blockList"><a name="compbio.runner">
 272 <!--   -->
 273 </a>
 274 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a></h3>
 275 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 276 <caption><span>Methods in <a href="../../../../compbio/runner/package-summary.html">compbio.runner</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 277 <tr>
 278 <th class="colFirst" scope="col">Modifier and Type</th>
 279 <th class="colLast" scope="col">Method and Description</th>
 280 </tr>
 281 <tbody>
 282 <tr class="altColor">
 283 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 284 <td class="colLast"><span class="typeNameLabel">Util.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/Util.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile</a></span>(java.lang.String&nbsp;workDirectory,
 285                java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 286 </tr>
 287 <tr class="rowColor">
 288 <td class="colFirst"><code>static <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 289 <td class="colLast"><span class="typeNameLabel">RunnerUtil.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/RunnerUtil.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile</a></span>(java.lang.String&nbsp;workDirectory,
 290                java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 291 </tr>
 292 </tbody>
 293 </table>
 294 </li>
 295 <li class="blockList"><a name="compbio.runner.msa">
 296 <!--   -->
 297 </a>
 298 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></h3>
 299 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 300 <caption><span>Methods in <a href="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 301 <tr>
 302 <th class="colFirst" scope="col">Modifier and Type</th>
 303 <th class="colLast" scope="col">Method and Description</th>
 304 </tr>
 305 <tbody>
 306 <tr class="altColor">
 307 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 308 <td class="colLast"><span class="typeNameLabel">Probcons.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/Probcons.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 309 </tr>
 310 <tr class="rowColor">
 311 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 312 <td class="colLast"><span class="typeNameLabel">Tcoffee.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/Tcoffee.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 313 </tr>
 314 <tr class="altColor">
 315 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 316 <td class="colLast"><span class="typeNameLabel">Mafft.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/Mafft.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 317 </tr>
 318 <tr class="rowColor">
 319 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 320 <td class="colLast"><span class="typeNameLabel">Muscle.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/Muscle.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 321 </tr>
 322 <tr class="altColor">
 323 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 324 <td class="colLast"><span class="typeNameLabel">MSAprobs.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/MSAprobs.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 325 </tr>
 326 <tr class="rowColor">
 327 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 328 <td class="colLast"><span class="typeNameLabel">ClustalO.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/ClustalO.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 329 </tr>
 330 <tr class="altColor">
 331 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 332 <td class="colLast"><span class="typeNameLabel">ClustalW.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/ClustalW.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 333 </tr>
 334 <tr class="rowColor">
 335 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 336 <td class="colLast"><span class="typeNameLabel">GLprobs.</span><code><span class="memberNameLink"><a href="../../../../compbio/runner/msa/GLprobs.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 337 </tr>
 338 </tbody>
 339 </table>
 340 </li>
 341 <li class="blockList"><a name="compbio.ws.client">
 342 <!--   -->
 343 </a>
 344 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</a></h3>
 345 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 346 <caption><span>Methods in <a href="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 347 <tr>
 348 <th class="colFirst" scope="col">Modifier and Type</th>
 349 <th class="colLast" scope="col">Method and Description</th>
 350 </tr>
 351 <tbody>
 352 <tr class="altColor">
 353 <td class="colFirst"><code>(package private) static &lt;T&gt;&nbsp;<a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 354 <td class="colLast"><span class="typeNameLabel">Jws2Client.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/client/Jws2Client.html#align-java.io.File-compbio.data.msa.MsaWS-compbio.metadata.Preset-java.util.List-">align</a></span>(java.io.File&nbsp;file,
 355      <a href="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;T&gt;&nbsp;msaws,
 356      <a href="../../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;T&gt;&nbsp;preset,
 357      java.util.List&lt;<a href="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;T&gt;&gt;&nbsp;customOptions)</code>
 358 <div class="block">Align sequences from the file using MsaWS</div>
 359 </td>
 360 </tr>
 361 </tbody>
 362 </table>
 363 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 364 <caption><span>Methods in <a href="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</a> with parameters of type <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 365 <tr>
 366 <th class="colFirst" scope="col">Modifier and Type</th>
 367 <th class="colLast" scope="col">Method and Description</th>
 368 </tr>
 369 <tbody>
 370 <tr class="altColor">
 371 <td class="colFirst"><code>(package private) static void</code></td>
 372 <td class="colLast"><span class="typeNameLabel">IOHelper.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/client/IOHelper.html#writeOut-java.io.Writer-compbio.data.sequence.Alignment-">writeOut</a></span>(java.io.Writer&nbsp;writer,
 373         <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;align)</code>
 374 <div class="block">Outputs clustal formatted alignment into the file represented by the
 375  outStream</div>
 376 </td>
 377 </tr>
 378 </tbody>
 379 </table>
 380 </li>
 381 <li class="blockList"><a name="compbio.ws.server">
 382 <!--   -->
 383 </a>
 384 <h3>Uses of <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a></h3>
 385 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing methods, and an explanation">
 386 <caption><span>Methods in <a href="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</a> that return <a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></span><span class="tabEnd">&nbsp;</span></caption>
 387 <tr>
 388 <th class="colFirst" scope="col">Modifier and Type</th>
 389 <th class="colLast" scope="col">Method and Description</th>
 390 </tr>
 391 <tbody>
 392 <tr class="altColor">
 393 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 394 <td class="colLast"><span class="typeNameLabel">GLprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/GLprobsWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 395 </tr>
 396 <tr class="rowColor">
 397 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 398 <td class="colLast"><span class="typeNameLabel">MafftWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MafftWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 399 </tr>
 400 <tr class="altColor">
 401 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 402 <td class="colLast"><span class="typeNameLabel">ClustalOWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalOWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 403 </tr>
 404 <tr class="rowColor">
 405 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 406 <td class="colLast"><span class="typeNameLabel">MSAprobsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MSAprobsWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 407 </tr>
 408 <tr class="altColor">
 409 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 410 <td class="colLast"><span class="typeNameLabel">MuscleWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/MuscleWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 411 </tr>
 412 <tr class="rowColor">
 413 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 414 <td class="colLast"><span class="typeNameLabel">ClustalWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ClustalWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 415 </tr>
 416 <tr class="altColor">
 417 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 418 <td class="colLast"><span class="typeNameLabel">TcoffeeWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/TcoffeeWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 419 </tr>
 420 <tr class="rowColor">
 421 <td class="colFirst"><code><a href="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 422 <td class="colLast"><span class="typeNameLabel">ProbconsWS.</span><code><span class="memberNameLink"><a href="../../../../compbio/ws/server/ProbconsWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>&nbsp;</td>
 423 </tr>
 424 </tbody>
 425 </table>
 426 </li>
 427 </ul>
 428 </li>
 429 </ul>
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