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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 FastaReader" class="title">Class FastaReader</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.FastaReader</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <dl>
 111 <dt>All Implemented Interfaces:</dt>
 112 <dd>java.util.Iterator&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>public class <span class="typeNameLabel">FastaReader</span>
 117 extends java.lang.Object
 118 implements java.util.Iterator&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</pre>
 119 <div class="block">Reads files with FASTA formatted sequences. All the information in the FASTA
 120  header is preserved including trailing white spaces. All the white spaces are
 121  removed from the sequence.
 122
 123  Examples of the correct input:
 124
 125  <pre>
 126
 127  >zedpshvyzg
 128  GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
 129
 130  >xovkactesa
 131  CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
 132  FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
 133  FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
 134  DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
 135
 136  >ntazzewyvv
 137  CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
 138  EASINM AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG
 139  EFITEA WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW
 140    RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN
 141    W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF
 142    FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
 143
 144     > 12 d t y wi               k       jbke
 145    KLSHHDCD
 146     N
 147      H
 148      HSKCTEPHCGNSHQMLHRDP
 149      CCDQCQSWEAENWCASMRKAILF
 150
 151  </pre></div>
 152 <dl>
 153 <dt><span class="simpleTagLabel">Version:</span></dt>
 154 <dd>1.0 April 2011</dd>
 155 <dt><span class="simpleTagLabel">Author:</span></dt>
 156 <dd>Peter Troshin</dd>
 157 </dl>
 158 </li>
 159 </ul>
 160 </div>
 161 <div class="summary">
 162 <ul class="blockList">
 163 <li class="blockList">
 164 <!-- =========== FIELD SUMMARY =========== -->
 165 <ul class="blockList">
 166 <li class="blockList"><a name="field.summary">
 167 <!--   -->
 168 </a>
 169 <h3>Field Summary</h3>
 170 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 171 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 172 <tr>
 173 <th class="colFirst" scope="col">Modifier and Type</th>
 174 <th class="colLast" scope="col">Field and Description</th>
 175 </tr>
 176 <tr class="altColor">
 177 <td class="colFirst"><code>private java.lang.String</code></td>
 178 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#DELIM">DELIM</a></span></code>
 179 <div class="block">Delimiter for the scanner</div>
 180 </td>
 181 </tr>
 182 <tr class="rowColor">
 183 <td class="colFirst"><code>private java.util.Scanner</code></td>
 184 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#input">input</a></span></code>&nbsp;</td>
 185 </tr>
 186 </table>
 187 </li>
 188 </ul>
 189 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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 191 <li class="blockList"><a name="constructor.summary">
 192 <!--   -->
 193 </a>
 194 <h3>Constructor Summary</h3>
 195 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 196 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 197 <tr>
 198 <th class="colOne" scope="col">Constructor and Description</th>
 199 </tr>
 200 <tr class="altColor">
 201 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#FastaReader-java.io.InputStream-">FastaReader</a></span>(java.io.InputStream&nbsp;inputStream)</code>
 202 <div class="block">This class will not close the incoming stream! So the client should do
 203  so.</div>
 204 </td>
 205 </tr>
 206 <tr class="rowColor">
 207 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#FastaReader-java.lang.String-">FastaReader</a></span>(java.lang.String&nbsp;inputFile)</code>
 208 <div class="block">Header data can contain non-ASCII symbols and read in UTF8</div>
 209 </td>
 210 </tr>
 211 </table>
 212 </li>
 213 </ul>
 214 <!-- ========== METHOD SUMMARY =========== -->
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 217 <!--   -->
 218 </a>
 219 <h3>Method Summary</h3>
 220 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 221 <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>
 222 <tr>
 223 <th class="colFirst" scope="col">Modifier and Type</th>
 224 <th class="colLast" scope="col">Method and Description</th>
 225 </tr>
 226 <tr id="i0" class="altColor">
 227 <td class="colFirst"><code>void</code></td>
 228 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#close--">close</a></span>()</code>
 229 <div class="block">Call this method to close the connection to the input file if you want to
 230  free up the resources.</div>
 231 </td>
 232 </tr>
 233 <tr id="i1" class="rowColor">
 234 <td class="colFirst"><code>boolean</code></td>
 235 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#hasNext--">hasNext</a></span>()</code></td>
 236 </tr>
 237 <tr id="i2" class="altColor">
 238 <td class="colFirst"><code><a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></code></td>
 239 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#next--">next</a></span>()</code>
 240 <div class="block">Reads the next FastaSequence from the input</div>
 241 </td>
 242 </tr>
 243 <tr id="i3" class="rowColor">
 244 <td class="colFirst"><code>void</code></td>
 245 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#remove--">remove</a></span>()</code>
 246 <div class="block">Not implemented</div>
 247 </td>
 248 </tr>
 249 <tr id="i4" class="altColor">
 250 <td class="colFirst"><code>private static <a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></code></td>
 251 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/FastaReader.html#toFastaSequence-java.lang.String-">toFastaSequence</a></span>(java.lang.String&nbsp;singleFastaEntry)</code>&nbsp;</td>
 252 </tr>
 253 </table>
 254 <ul class="blockList">
 255 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 256 <!--   -->
 257 </a>
 258 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 259 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 260 </ul>
 261 <ul class="blockList">
 262 <li class="blockList"><a name="methods.inherited.from.class.java.util.Iterator">
 263 <!--   -->
 264 </a>
 265 <h3>Methods inherited from interface&nbsp;java.util.Iterator</h3>
 266 <code>forEachRemaining</code></li>
 267 </ul>
 268 </li>
 269 </ul>
 270 </li>
 271 </ul>
 272 </div>
 273 <div class="details">
 274 <ul class="blockList">
 275 <li class="blockList">
 276 <!-- ============ FIELD DETAIL =========== -->
 277 <ul class="blockList">
 278 <li class="blockList"><a name="field.detail">
 279 <!--   -->
 280 </a>
 281 <h3>Field Detail</h3>
 282 <a name="input">
 283 <!--   -->
 284 </a>
 285 <ul class="blockList">
 286 <li class="blockList">
 287 <h4>input</h4>
 288 <pre>private final&nbsp;java.util.Scanner input</pre>
 289 </li>
 290 </ul>
 291 <a name="DELIM">
 292 <!--   -->
 293 </a>
 294 <ul class="blockListLast">
 295 <li class="blockList">
 296 <h4>DELIM</h4>
 297 <pre>private final&nbsp;java.lang.String DELIM</pre>
 298 <div class="block">Delimiter for the scanner</div>
 299 <dl>
 300 <dt><span class="seeLabel">See Also:</span></dt>
 301 <dd><a href="../../../constant-values.html#compbio.data.sequence.FastaReader.DELIM">Constant Field Values</a></dd>
 302 </dl>
 303 </li>
 304 </ul>
 305 </li>
 306 </ul>
 307 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 308 <ul class="blockList">
 309 <li class="blockList"><a name="constructor.detail">
 310 <!--   -->
 311 </a>
 312 <h3>Constructor Detail</h3>
 313 <a name="FastaReader-java.lang.String-">
 314 <!--   -->
 315 </a>
 316 <ul class="blockList">
 317 <li class="blockList">
 318 <h4>FastaReader</h4>
 319 <pre>public&nbsp;FastaReader(java.lang.String&nbsp;inputFile)
 320             throws java.io.FileNotFoundException</pre>
 321 <div class="block">Header data can contain non-ASCII symbols and read in UTF8</div>
 322 <dl>
 323 <dt><span class="paramLabel">Parameters:</span></dt>
 324 <dd><code>inputFile</code> - the file containing the list of FASTA formatted sequences to
 325             read from</dd>
 326 <dt><span class="throwsLabel">Throws:</span></dt>
 327 <dd><code>java.io.FileNotFoundException</code> - if the input file is not found</dd>
 328 <dd><code>java.lang.IllegalStateException</code> - if the close method was called on this instance</dd>
 329 </dl>
 330 </li>
 331 </ul>
 332 <a name="FastaReader-java.io.InputStream-">
 333 <!--   -->
 334 </a>
 335 <ul class="blockListLast">
 336 <li class="blockList">
 337 <h4>FastaReader</h4>
 338 <pre>public&nbsp;FastaReader(java.io.InputStream&nbsp;inputStream)
 339             throws java.io.FileNotFoundException</pre>
 340 <div class="block">This class will not close the incoming stream! So the client should do
 341  so.</div>
 342 <dl>
 343 <dt><span class="paramLabel">Parameters:</span></dt>
 344 <dd><code>inputStream</code> - </dd>
 345 <dt><span class="throwsLabel">Throws:</span></dt>
 346 <dd><code>java.io.FileNotFoundException</code></dd>
 347 </dl>
 348 </li>
 349 </ul>
 350 </li>
 351 </ul>
 352 <!-- ============ METHOD DETAIL ========== -->
 353 <ul class="blockList">
 354 <li class="blockList"><a name="method.detail">
 355 <!--   -->
 356 </a>
 357 <h3>Method Detail</h3>
 358 <a name="hasNext--">
 359 <!--   -->
 360 </a>
 361 <ul class="blockList">
 362 <li class="blockList">
 363 <h4>hasNext</h4>
 364 <pre>public&nbsp;boolean&nbsp;hasNext()</pre>
 365 <dl>
 366 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 367 <dd><code>hasNext</code>&nbsp;in interface&nbsp;<code>java.util.Iterator&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></dd>
 368 <dt><span class="throwsLabel">Throws:</span></dt>
 369 <dd><code>java.lang.IllegalStateException</code> - if the close method was called on this instance</dd>
 370 </dl>
 371 </li>
 372 </ul>
 373 <a name="next--">
 374 <!--   -->
 375 </a>
 376 <ul class="blockList">
 377 <li class="blockList">
 378 <h4>next</h4>
 379 <pre>public&nbsp;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&nbsp;next()</pre>
 380 <div class="block">Reads the next FastaSequence from the input</div>
 381 <dl>
 382 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 383 <dd><code>next</code>&nbsp;in interface&nbsp;<code>java.util.Iterator&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></dd>
 384 <dt><span class="throwsLabel">Throws:</span></dt>
 385 <dd><code>java.lang.AssertionError</code> - if the header or the sequence is missing</dd>
 386 <dd><code>java.lang.IllegalStateException</code> - if the close method was called on this instance</dd>
 387 <dd><code>MismatchException</code> - - if there were no more FastaSequence's.</dd>
 388 </dl>
 389 </li>
 390 </ul>
 391 <a name="remove--">
 392 <!--   -->
 393 </a>
 394 <ul class="blockList">
 395 <li class="blockList">
 396 <h4>remove</h4>
 397 <pre>public&nbsp;void&nbsp;remove()</pre>
 398 <div class="block">Not implemented</div>
 399 <dl>
 400 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 401 <dd><code>remove</code>&nbsp;in interface&nbsp;<code>java.util.Iterator&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></dd>
 402 </dl>
 403 </li>
 404 </ul>
 405 <a name="close--">
 406 <!--   -->
 407 </a>
 408 <ul class="blockList">
 409 <li class="blockList">
 410 <h4>close</h4>
 411 <pre>public&nbsp;void&nbsp;close()</pre>
 412 <div class="block">Call this method to close the connection to the input file if you want to
 413  free up the resources. The connection will be closed on the JVM shutdown
 414  if this method was not called explicitly. No further reading on this
 415  instance of the FastaReader will be possible after calling this method.</div>
 416 </li>
 417 </ul>
 418 <a name="toFastaSequence-java.lang.String-">
 419 <!--   -->
 420 </a>
 421 <ul class="blockListLast">
 422 <li class="blockList">
 423 <h4>toFastaSequence</h4>
 424 <pre>private static&nbsp;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&nbsp;toFastaSequence(java.lang.String&nbsp;singleFastaEntry)</pre>
 425 </li>
 426 </ul>
 427 </li>
 428 </ul>
 429 </li>
 430 </ul>
 431 </div>
 432 </div>
 433 <!-- ========= END OF CLASS DATA ========= -->
 434 <!-- ======= START OF BOTTOM NAVBAR ====== -->
 435 <div class="bottomNav"><a name="navbar.bottom">
 436 <!--   -->
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 438 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
 439 <a name="navbar.bottom.firstrow">
 440 <!--   -->
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 442 <ul class="navList" title="Navigation">
 443 <li><a href="../../../overview-summary.html">Overview</a></li>
 444 <li><a href="package-summary.html">Package</a></li>
 445 <li class="navBarCell1Rev">Class</li>
 446 <li><a href="class-use/FastaReader.html">Use</a></li>
 447 <li><a href="package-tree.html">Tree</a></li>
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