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  76 <li>Summary:&nbsp;</li>
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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class FastaSequence" class="title">Class FastaSequence</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.FastaSequence</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>@Immutable
 113 public class <span class="typeNameLabel">FastaSequence</span>
 114 extends java.lang.Object</pre>
 115 <div class="block">A FASTA formatted sequence. Please note that this class does not make any
 116  assumptions as to what sequence it stores e.g. it could be nucleotide,
 117  protein or even gapped alignment sequence! The only guarantee it makes is
 118  that the sequence does not contain white space characters e.g. spaces, new
 119  lines etc</div>
 120 <dl>
 121 <dt><span class="simpleTagLabel">Version:</span></dt>
 122 <dd>1.0 September 2009</dd>
 123 <dt><span class="simpleTagLabel">Author:</span></dt>
 124 <dd>pvtroshin</dd>
 125 </dl>
 126 </li>
 127 </ul>
 128 </div>
 129 <div class="summary">
 130 <ul class="blockList">
 131 <li class="blockList">
 132 <!-- =========== FIELD SUMMARY =========== -->
 133 <ul class="blockList">
 134 <li class="blockList"><a name="field.summary">
 135 <!--   -->
 136 </a>
 137 <h3>Field Summary</h3>
 138 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 139 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 140 <tr>
 141 <th class="colFirst" scope="col">Modifier and Type</th>
 142 <th class="colLast" scope="col">Field and Description</th>
 143 </tr>
 144 <tr class="altColor">
 145 <td class="colFirst"><code>private java.lang.String</code></td>
 146 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#id">id</a></span></code>
 147 <div class="block">Sequence id</div>
 148 </td>
 149 </tr>
 150 <tr class="rowColor">
 151 <td class="colFirst"><code>private java.lang.String</code></td>
 152 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#sequence">sequence</a></span></code>
 153 <div class="block">Returns the string representation of sequence</div>
 154 </td>
 155 </tr>
 156 </table>
 157 </li>
 158 </ul>
 159 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 160 <ul class="blockList">
 161 <li class="blockList"><a name="constructor.summary">
 162 <!--   -->
 163 </a>
 164 <h3>Constructor Summary</h3>
 165 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 166 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 167 <tr>
 168 <th class="colOne" scope="col">Constructor and Description</th>
 169 </tr>
 170 <tr class="altColor">
 171 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#FastaSequence--">FastaSequence</a></span>()</code>&nbsp;</td>
 172 </tr>
 173 <tr class="rowColor">
 174 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#FastaSequence-java.lang.String-java.lang.String-">FastaSequence</a></span>(java.lang.String&nbsp;id,
 175              java.lang.String&nbsp;sequence)</code>
 176 <div class="block">Upon construction the any whitespace characters are removed from the
 177  sequence</div>
 178 </td>
 179 </tr>
 180 </table>
 181 </li>
 182 </ul>
 183 <!-- ========== METHOD SUMMARY =========== -->
 184 <ul class="blockList">
 185 <li class="blockList"><a name="method.summary">
 186 <!--   -->
 187 </a>
 188 <h3>Method Summary</h3>
 189 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 190 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></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="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 191 <tr>
 192 <th class="colFirst" scope="col">Modifier and Type</th>
 193 <th class="colLast" scope="col">Method and Description</th>
 194 </tr>
 195 <tr id="i0" class="altColor">
 196 <td class="colFirst"><code>static int</code></td>
 197 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence-java.lang.String-java.lang.String-">countMatchesInSequence</a></span>(java.lang.String&nbsp;theString,
 198                       java.lang.String&nbsp;theRegExp)</code>&nbsp;</td>
 199 </tr>
 200 <tr id="i1" class="rowColor">
 201 <td class="colFirst"><code>boolean</code></td>
 202 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#equals-java.lang.Object-">equals</a></span>(java.lang.Object&nbsp;obj)</code>&nbsp;</td>
 203 </tr>
 204 <tr id="i2" class="altColor">
 205 <td class="colFirst"><code>java.lang.String</code></td>
 206 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence-int-">getFormatedSequence</a></span>(int&nbsp;width)</code>
 207 <div class="block">Format sequence per width letter in one string.</div>
 208 </td>
 209 </tr>
 210 <tr id="i3" class="rowColor">
 211 <td class="colFirst"><code>java.lang.String</code></td>
 212 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta--">getFormattedFasta</a></span>()</code>&nbsp;</td>
 213 </tr>
 214 <tr id="i4" class="altColor">
 215 <td class="colFirst"><code>java.lang.String</code></td>
 216 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#getId--">getId</a></span>()</code>
 217 <div class="block">Gets the value of id</div>
 218 </td>
 219 </tr>
 220 <tr id="i5" class="rowColor">
 221 <td class="colFirst"><code>int</code></td>
 222 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#getLength--">getLength</a></span>()</code>&nbsp;</td>
 223 </tr>
 224 <tr id="i6" class="altColor">
 225 <td class="colFirst"><code>java.lang.String</code></td>
 226 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta--">getOnelineFasta</a></span>()</code>&nbsp;</td>
 227 </tr>
 228 <tr id="i7" class="rowColor">
 229 <td class="colFirst"><code>java.lang.String</code></td>
 230 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#getSequence--">getSequence</a></span>()</code>
 231 <div class="block">Gets the value of sequence</div>
 232 </td>
 233 </tr>
 234 <tr id="i8" class="altColor">
 235 <td class="colFirst"><code>int</code></td>
 236 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#hashCode--">hashCode</a></span>()</code>&nbsp;</td>
 237 </tr>
 238 <tr id="i9" class="rowColor">
 239 <td class="colFirst"><code>java.lang.String</code></td>
 240 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaSequence.html#toString--">toString</a></span>()</code>
 241 <div class="block">Same as oneLineFasta</div>
 242 </td>
 243 </tr>
 244 </table>
 245 <ul class="blockList">
 246 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 247 <!--   -->
 248 </a>
 249 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 250 <code>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</code></li>
 251 </ul>
 252 </li>
 253 </ul>
 254 </li>
 255 </ul>
 256 </div>
 257 <div class="details">
 258 <ul class="blockList">
 259 <li class="blockList">
 260 <!-- ============ FIELD DETAIL =========== -->
 261 <ul class="blockList">
 262 <li class="blockList"><a name="field.detail">
 263 <!--   -->
 264 </a>
 265 <h3>Field Detail</h3>
 266 <a name="id">
 267 <!--   -->
 268 </a>
 269 <ul class="blockList">
 270 <li class="blockList">
 271 <h4>id</h4>
 272 <pre>private&nbsp;java.lang.String id</pre>
 273 <div class="block">Sequence id</div>
 274 </li>
 275 </ul>
 276 <a name="sequence">
 277 <!--   -->
 278 </a>
 279 <ul class="blockListLast">
 280 <li class="blockList">
 281 <h4>sequence</h4>
 282 <pre>private&nbsp;java.lang.String sequence</pre>
 283 <div class="block">Returns the string representation of sequence</div>
 284 </li>
 285 </ul>
 286 </li>
 287 </ul>
 288 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 289 <ul class="blockList">
 290 <li class="blockList"><a name="constructor.detail">
 291 <!--   -->
 292 </a>
 293 <h3>Constructor Detail</h3>
 294 <a name="FastaSequence--">
 295 <!--   -->
 296 </a>
 297 <ul class="blockList">
 298 <li class="blockList">
 299 <h4>FastaSequence</h4>
 300 <pre>FastaSequence()</pre>
 301 </li>
 302 </ul>
 303 <a name="FastaSequence-java.lang.String-java.lang.String-">
 304 <!--   -->
 305 </a>
 306 <ul class="blockListLast">
 307 <li class="blockList">
 308 <h4>FastaSequence</h4>
 309 <pre>public&nbsp;FastaSequence(java.lang.String&nbsp;id,
 310                      java.lang.String&nbsp;sequence)</pre>
 311 <div class="block">Upon construction the any whitespace characters are removed from the
 312  sequence</div>
 313 <dl>
 314 <dt><span class="paramLabel">Parameters:</span></dt>
 315 <dd><code>id</code> - </dd>
 316 <dd><code>sequence</code> - </dd>
 317 </dl>
 318 </li>
 319 </ul>
 320 </li>
 321 </ul>
 322 <!-- ============ METHOD DETAIL ========== -->
 323 <ul class="blockList">
 324 <li class="blockList"><a name="method.detail">
 325 <!--   -->
 326 </a>
 327 <h3>Method Detail</h3>
 328 <a name="getId--">
 329 <!--   -->
 330 </a>
 331 <ul class="blockList">
 332 <li class="blockList">
 333 <h4>getId</h4>
 334 <pre>public&nbsp;java.lang.String&nbsp;getId()</pre>
 335 <div class="block">Gets the value of id</div>
 336 <dl>
 337 <dt><span class="returnLabel">Returns:</span></dt>
 338 <dd>the value of id</dd>
 339 </dl>
 340 </li>
 341 </ul>
 342 <a name="getSequence--">
 343 <!--   -->
 344 </a>
 345 <ul class="blockList">
 346 <li class="blockList">
 347 <h4>getSequence</h4>
 348 <pre>public&nbsp;java.lang.String&nbsp;getSequence()</pre>
 349 <div class="block">Gets the value of sequence</div>
 350 <dl>
 351 <dt><span class="returnLabel">Returns:</span></dt>
 352 <dd>the value of sequence</dd>
 353 </dl>
 354 </li>
 355 </ul>
 356 <a name="countMatchesInSequence-java.lang.String-java.lang.String-">
 357 <!--   -->
 358 </a>
 359 <ul class="blockList">
 360 <li class="blockList">
 361 <h4>countMatchesInSequence</h4>
 362 <pre>public static&nbsp;int&nbsp;countMatchesInSequence(java.lang.String&nbsp;theString,
 363                                          java.lang.String&nbsp;theRegExp)</pre>
 364 </li>
 365 </ul>
 366 <a name="getFormattedFasta--">
 367 <!--   -->
 368 </a>
 369 <ul class="blockList">
 370 <li class="blockList">
 371 <h4>getFormattedFasta</h4>
 372 <pre>public&nbsp;java.lang.String&nbsp;getFormattedFasta()</pre>
 373 </li>
 374 </ul>
 375 <a name="getOnelineFasta--">
 376 <!--   -->
 377 </a>
 378 <ul class="blockList">
 379 <li class="blockList">
 380 <h4>getOnelineFasta</h4>
 381 <pre>public&nbsp;java.lang.String&nbsp;getOnelineFasta()</pre>
 382 <dl>
 383 <dt><span class="returnLabel">Returns:</span></dt>
 384 <dd>one line name, next line sequence, no matter what the sequence
 385          length is</dd>
 386 </dl>
 387 </li>
 388 </ul>
 389 <a name="getFormatedSequence-int-">
 390 <!--   -->
 391 </a>
 392 <ul class="blockList">
 393 <li class="blockList">
 394 <h4>getFormatedSequence</h4>
 395 <pre>public&nbsp;java.lang.String&nbsp;getFormatedSequence(int&nbsp;width)</pre>
 396 <div class="block">Format sequence per width letter in one string. Without spaces.</div>
 397 <dl>
 398 <dt><span class="returnLabel">Returns:</span></dt>
 399 <dd>multiple line formated sequence, one line width letters length</dd>
 400 </dl>
 401 </li>
 402 </ul>
 403 <a name="getLength--">
 404 <!--   -->
 405 </a>
 406 <ul class="blockList">
 407 <li class="blockList">
 408 <h4>getLength</h4>
 409 <pre>public&nbsp;int&nbsp;getLength()</pre>
 410 <dl>
 411 <dt><span class="returnLabel">Returns:</span></dt>
 412 <dd>sequence length</dd>
 413 </dl>
 414 </li>
 415 </ul>
 416 <a name="toString--">
 417 <!--   -->
 418 </a>
 419 <ul class="blockList">
 420 <li class="blockList">
 421 <h4>toString</h4>
 422 <pre>public&nbsp;java.lang.String&nbsp;toString()</pre>
 423 <div class="block">Same as oneLineFasta</div>
 424 <dl>
 425 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 426 <dd><code>toString</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 427 </dl>
 428 </li>
 429 </ul>
 430 <a name="hashCode--">
 431 <!--   -->
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 436 <pre>public&nbsp;int&nbsp;hashCode()</pre>
 437 <dl>
 438 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 439 <dd><code>hashCode</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 440 </dl>
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 442 </ul>
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 444 <!--   -->
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 446 <ul class="blockListLast">
 447 <li class="blockList">
 448 <h4>equals</h4>
 449 <pre>public&nbsp;boolean&nbsp;equals(java.lang.Object&nbsp;obj)</pre>
 450 <dl>
 451 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 452 <dd><code>equals</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 453 </dl>
 454 </li>
 455 </ul>
 456 </li>
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 473 <li><a href="package-summary.html">Package</a></li>
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 518 <li><a href="#method.detail">Method</a></li>
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