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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class ClustalAlignmentUtil" class="title">Class ClustalAlignmentUtil</h2>
  97 </div>
  98 <div class="contentContainer">
  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
 101 <li>
 102 <ul class="inheritance">
 103 <li>compbio.data.sequence.ClustalAlignmentUtil</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <hr>
 111 <br>
 112 <pre>public final class <span class="typeNameLabel">ClustalAlignmentUtil</span>
 113 extends java.lang.Object</pre>
 114 <div class="block">Tools to read and write clustal formated files</div>
 115 <dl>
 116 <dt><span class="simpleTagLabel">Version:</span></dt>
 117 <dd>1.0 September 2009</dd>
 118 <dt><span class="simpleTagLabel">Author:</span></dt>
 119 <dd>Petr Troshin based on jimp class</dd>
 120 </dl>
 121 </li>
 122 </ul>
 123 </div>
 124 <div class="summary">
 125 <ul class="blockList">
 126 <li class="blockList">
 127 <!-- =========== FIELD SUMMARY =========== -->
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 131 </a>
 132 <h3>Field Summary</h3>
 133 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 134 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 135 <tr>
 136 <th class="colFirst" scope="col">Modifier and Type</th>
 137 <th class="colLast" scope="col">Field and Description</th>
 138 </tr>
 139 <tr class="altColor">
 140 <td class="colFirst"><code>static char</code></td>
 141 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</a></span></code>
 142 <div class="block">Dash char to be used as gap char in the alignments</div>
 143 </td>
 144 </tr>
 145 <tr class="rowColor">
 146 <td class="colFirst"><code>private static java.util.logging.Logger</code></td>
 147 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#log">log</a></span></code>&nbsp;</td>
 148 </tr>
 149 <tr class="altColor">
 150 <td class="colFirst"><code>private static int</code></td>
 151 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#maxNameLength">maxNameLength</a></span></code>&nbsp;</td>
 152 </tr>
 153 <tr class="rowColor">
 154 <td class="colFirst"><code>private static int</code></td>
 155 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#minNameHolderLength">minNameHolderLength</a></span></code>&nbsp;</td>
 156 </tr>
 157 <tr class="altColor">
 158 <td class="colFirst"><code>private static int</code></td>
 159 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#oneLineAlignmentLength">oneLineAlignmentLength</a></span></code>&nbsp;</td>
 160 </tr>
 161 <tr class="rowColor">
 162 <td class="colFirst"><code>private static java.lang.String</code></td>
 163 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#spacer">spacer</a></span></code>&nbsp;</td>
 164 </tr>
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 176 <tr>
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 178 </tr>
 179 <tr class="altColor">
 180 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil--">ClustalAlignmentUtil</a></span>()</code>&nbsp;</td>
 181 </tr>
 182 </table>
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 197 <tr id="i0" class="altColor">
 198 <td class="colFirst"><code>static boolean</code></td>
 199 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile-java.io.InputStream-">isValidClustalFile</a></span>(java.io.InputStream&nbsp;input)</code>
 200 <div class="block">Please note this method closes the input stream provided as a parameter</div>
 201 </td>
 202 </tr>
 203 <tr id="i1" class="rowColor">
 204 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 205 <td class="colLast"><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>
 206 </tr>
 207 <tr id="i2" class="altColor">
 208 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 209 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile-java.io.InputStream-">readClustalFile</a></span>(java.io.InputStream&nbsp;instream)</code>
 210 <div class="block">Read Clustal formatted alignment.</div>
 211 </td>
 212 </tr>
 213 <tr id="i3" class="rowColor">
 214 <td class="colFirst"><code>static void</code></td>
 215 <td class="colLast"><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,
 216                      <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;alignment)</code>
 217 <div class="block">Write Clustal formatted alignment Limitations: does not record the
 218  consensus.</div>
 219 </td>
 220 </tr>
 221 </table>
 222 <ul class="blockList">
 223 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 224 <!--   -->
 225 </a>
 226 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 227 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 228 </ul>
 229 </li>
 230 </ul>
 231 </li>
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 237 <!-- ============ FIELD DETAIL =========== -->
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 240 <!--   -->
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 242 <h3>Field Detail</h3>
 243 <a name="log">
 244 <!--   -->
 245 </a>
 246 <ul class="blockList">
 247 <li class="blockList">
 248 <h4>log</h4>
 249 <pre>private static final&nbsp;java.util.logging.Logger log</pre>
 250 </li>
 251 </ul>
 252 <a name="gapchar">
 253 <!--   -->
 254 </a>
 255 <ul class="blockList">
 256 <li class="blockList">
 257 <h4>gapchar</h4>
 258 <pre>public static final&nbsp;char gapchar</pre>
 259 <div class="block">Dash char to be used as gap char in the alignments</div>
 260 <dl>
 261 <dt><span class="seeLabel">See Also:</span></dt>
 262 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.gapchar">Constant Field Values</a></dd>
 263 </dl>
 264 </li>
 265 </ul>
 266 <a name="spacer">
 267 <!--   -->
 268 </a>
 269 <ul class="blockList">
 270 <li class="blockList">
 271 <h4>spacer</h4>
 272 <pre>private static final&nbsp;java.lang.String spacer</pre>
 273 <dl>
 274 <dt><span class="seeLabel">See Also:</span></dt>
 275 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.spacer">Constant Field Values</a></dd>
 276 </dl>
 277 </li>
 278 </ul>
 279 <a name="maxNameLength">
 280 <!--   -->
 281 </a>
 282 <ul class="blockList">
 283 <li class="blockList">
 284 <h4>maxNameLength</h4>
 285 <pre>private static final&nbsp;int maxNameLength</pre>
 286 <dl>
 287 <dt><span class="seeLabel">See Also:</span></dt>
 288 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.maxNameLength">Constant Field Values</a></dd>
 289 </dl>
 290 </li>
 291 </ul>
 292 <a name="minNameHolderLength">
 293 <!--   -->
 294 </a>
 295 <ul class="blockList">
 296 <li class="blockList">
 297 <h4>minNameHolderLength</h4>
 298 <pre>private static final&nbsp;int minNameHolderLength</pre>
 299 <dl>
 300 <dt><span class="seeLabel">See Also:</span></dt>
 301 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.minNameHolderLength">Constant Field Values</a></dd>
 302 </dl>
 303 </li>
 304 </ul>
 305 <a name="oneLineAlignmentLength">
 306 <!--   -->
 307 </a>
 308 <ul class="blockListLast">
 309 <li class="blockList">
 310 <h4>oneLineAlignmentLength</h4>
 311 <pre>private static final&nbsp;int oneLineAlignmentLength</pre>
 312 <dl>
 313 <dt><span class="seeLabel">See Also:</span></dt>
 314 <dd><a href="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.oneLineAlignmentLength">Constant Field Values</a></dd>
 315 </dl>
 316 </li>
 317 </ul>
 318 </li>
 319 </ul>
 320 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 321 <ul class="blockList">
 322 <li class="blockList"><a name="constructor.detail">
 323 <!--   -->
 324 </a>
 325 <h3>Constructor Detail</h3>
 326 <a name="ClustalAlignmentUtil--">
 327 <!--   -->
 328 </a>
 329 <ul class="blockListLast">
 330 <li class="blockList">
 331 <h4>ClustalAlignmentUtil</h4>
 332 <pre>public&nbsp;ClustalAlignmentUtil()</pre>
 333 </li>
 334 </ul>
 335 </li>
 336 </ul>
 337 <!-- ============ METHOD DETAIL ========== -->
 338 <ul class="blockList">
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 340 <!--   -->
 341 </a>
 342 <h3>Method Detail</h3>
 343 <a name="readClustalFile-java.io.InputStream-">
 344 <!--   -->
 345 </a>
 346 <ul class="blockList">
 347 <li class="blockList">
 348 <h4>readClustalFile</h4>
 349 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;readClustalFile(java.io.InputStream&nbsp;instream)
 350                                  throws java.io.IOException,
 351                                         <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 352 <div class="block">Read Clustal formatted alignment. Limitations: Does not read consensus
 353
 354  Sequence names as well as the sequences are not guaranteed to be unique!</div>
 355 <dl>
 356 <dt><span class="throwsLabel">Throws:</span></dt>
 357 <dd><code>{@link</code> - IOException}</dd>
 358 <dd><code>{@link</code> - UnknownFileFormatException}</dd>
 359 <dd><code>java.io.IOException</code></dd>
 360 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 361 </dl>
 362 </li>
 363 </ul>
 364 <a name="isValidClustalFile-java.io.InputStream-">
 365 <!--   -->
 366 </a>
 367 <ul class="blockList">
 368 <li class="blockList">
 369 <h4>isValidClustalFile</h4>
 370 <pre>public static&nbsp;boolean&nbsp;isValidClustalFile(java.io.InputStream&nbsp;input)</pre>
 371 <div class="block">Please note this method closes the input stream provided as a parameter</div>
 372 <dl>
 373 <dt><span class="paramLabel">Parameters:</span></dt>
 374 <dd><code>input</code> - </dd>
 375 <dt><span class="returnLabel">Returns:</span></dt>
 376 <dd>true if the file is recognised as Clustal formatted alignment,
 377          false otherwise</dd>
 378 </dl>
 379 </li>
 380 </ul>
 381 <a name="writeClustalAlignment-java.io.Writer-compbio.data.sequence.Alignment-">
 382 <!--   -->
 383 </a>
 384 <ul class="blockList">
 385 <li class="blockList">
 386 <h4>writeClustalAlignment</h4>
 387 <pre>public static&nbsp;void&nbsp;writeClustalAlignment(java.io.Writer&nbsp;out,
 388                                          <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;alignment)
 389                                   throws java.io.IOException</pre>
 390 <div class="block">Write Clustal formatted alignment Limitations: does not record the
 391  consensus. Potential bug - records 60 chars length alignment where
 392  Clustal would have recorded 50 chars.</div>
 393 <dl>
 394 <dt><span class="paramLabel">Parameters:</span></dt>
 395 <dd><code>out</code> - </dd>
 396 <dd><code>alignment</code> - </dd>
 397 <dt><span class="throwsLabel">Throws:</span></dt>
 398 <dd><code>java.io.IOException</code></dd>
 399 </dl>
 400 </li>
 401 </ul>
 402 <a name="readClustalFile-java.io.File-">
 403 <!--   -->
 404 </a>
 405 <ul class="blockListLast">
 406 <li class="blockList">
 407 <h4>readClustalFile</h4>
 408 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;readClustalFile(java.io.File&nbsp;file)
 409                                  throws <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a>,
 410                                         java.io.IOException</pre>
 411 <dl>
 412 <dt><span class="throwsLabel">Throws:</span></dt>
 413 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 414 <dd><code>java.io.IOException</code></dd>
 415 </dl>
 416 </li>
 417 </ul>
 418 </li>
 419 </ul>
 420 </li>
 421 </ul>
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 482 </div>
 483 <a name="skip.navbar.bottom">
 484 <!--   -->
 485 </a></div>
 486 <!-- ======== END OF BOTTOM NAVBAR ======= -->
 487 </body>
 488 </html>