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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class SequenceUtil" class="title">Class SequenceUtil</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.SequenceUtil</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">SequenceUtil</span>
 113 extends java.lang.Object</pre>
 114 <div class="block">Utility class for operations on sequences</div>
 115 <dl>
 116 <dt><span class="simpleTagLabel">Since:</span></dt>
 117 <dd>1.0</dd>
 118 <dt><span class="simpleTagLabel">Version:</span></dt>
 119 <dd>2.0 June 2011</dd>
 120 <dt><span class="simpleTagLabel">Author:</span></dt>
 121 <dd>Peter Troshin</dd>
 122 </dl>
 123 </li>
 124 </ul>
 125 </div>
 126 <div class="summary">
 127 <ul class="blockList">
 128 <li class="blockList">
 129 <!-- =========== FIELD SUMMARY =========== -->
 130 <ul class="blockList">
 131 <li class="blockList"><a name="field.summary">
 132 <!--   -->
 133 </a>
 134 <h3>Field Summary</h3>
 135 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 136 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 137 <tr>
 138 <th class="colFirst" scope="col">Modifier and Type</th>
 139 <th class="colLast" scope="col">Field and Description</th>
 140 </tr>
 141 <tr class="altColor">
 142 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 143 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</a></span></code>
 144 <div class="block">Valid Amino acids</div>
 145 </td>
 146 </tr>
 147 <tr class="rowColor">
 148 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 149 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</a></span></code>
 150 <div class="block">Same as AA pattern but with two additional letters - XU</div>
 151 </td>
 152 </tr>
 153 <tr class="altColor">
 154 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 155 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</a></span></code>
 156 <div class="block">Ambiguous nucleotide</div>
 157 </td>
 158 </tr>
 159 <tr class="rowColor">
 160 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 161 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</a></span></code>
 162 <div class="block">A digit</div>
 163 </td>
 164 </tr>
 165 <tr class="altColor">
 166 <td class="colFirst"><code>private static java.lang.String</code></td>
 167 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#JRONN_WRONG_FORMAT_MESSAGE">JRONN_WRONG_FORMAT_MESSAGE</a></span></code>&nbsp;</td>
 168 </tr>
 169 <tr class="rowColor">
 170 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 171 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</a></span></code>
 172 <div class="block">inversion of AA pattern</div>
 173 </td>
 174 </tr>
 175 <tr class="altColor">
 176 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 177 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</a></span></code>
 178 <div class="block">Non nucleotide</div>
 179 </td>
 180 </tr>
 181 <tr class="rowColor">
 182 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 183 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</a></span></code>
 184 <div class="block">Non word</div>
 185 </td>
 186 </tr>
 187 <tr class="altColor">
 188 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 189 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</a></span></code>
 190 <div class="block">Nucleotides a, t, g, c, u</div>
 191 </td>
 192 </tr>
 193 <tr class="rowColor">
 194 <td class="colFirst"><code>static java.util.regex.Pattern</code></td>
 195 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</a></span></code>
 196 <div class="block">A whitespace character: [\t\n\x0B\f\r]</div>
 197 </td>
 198 </tr>
 199 </table>
 200 </li>
 201 </ul>
 202 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 203 <ul class="blockList">
 204 <li class="blockList"><a name="constructor.summary">
 205 <!--   -->
 206 </a>
 207 <h3>Constructor Summary</h3>
 208 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 209 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 210 <tr>
 211 <th class="colFirst" scope="col">Modifier</th>
 212 <th class="colLast" scope="col">Constructor and Description</th>
 213 </tr>
 214 <tr class="altColor">
 215 <td class="colFirst"><code>private </code></td>
 216 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#SequenceUtil--">SequenceUtil</a></span>()</code>&nbsp;</td>
 217 </tr>
 218 </table>
 219 </li>
 220 </ul>
 221 <!-- ========== METHOD SUMMARY =========== -->
 222 <ul class="blockList">
 223 <li class="blockList"><a name="method.summary">
 224 <!--   -->
 225 </a>
 226 <h3>Method Summary</h3>
 227 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 228 <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="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 229 <tr>
 230 <th class="colFirst" scope="col">Modifier and Type</th>
 231 <th class="colLast" scope="col">Method and Description</th>
 232 </tr>
 233 <tr id="i0" class="altColor">
 234 <td class="colFirst"><code>static java.lang.String</code></td>
 235 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#cleanProteinSequence-java.lang.String-">cleanProteinSequence</a></span>(java.lang.String&nbsp;sequence)</code>
 236 <div class="block">Remove all non AA chars from the sequence</div>
 237 </td>
 238 </tr>
 239 <tr id="i1" class="rowColor">
 240 <td class="colFirst"><code>static java.lang.String</code></td>
 241 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#cleanSequence-java.lang.String-">cleanSequence</a></span>(java.lang.String&nbsp;sequence)</code>
 242 <div class="block">Removes all whitespace chars in the sequence string</div>
 243 </td>
 244 </tr>
 245 <tr id="i2" class="altColor">
 246 <td class="colFirst"><code>static void</code></td>
 247 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#closeSilently-java.util.logging.Logger-java.io.Closeable-">closeSilently</a></span>(java.util.logging.Logger&nbsp;log,
 248              java.io.Closeable&nbsp;stream)</code>
 249 <div class="block">Closes the Closable and logs the exception if any</div>
 250 </td>
 251 </tr>
 252 <tr id="i3" class="rowColor">
 253 <td class="colFirst"><code>private static float[]</code></td>
 254 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#convertToNumber-java.lang.String:A-">convertToNumber</a></span>(java.lang.String[]&nbsp;annotValues)</code>&nbsp;</td>
 255 </tr>
 256 <tr id="i4" class="altColor">
 257 <td class="colFirst"><code>static java.lang.String</code></td>
 258 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#deepCleanSequence-java.lang.String-">deepCleanSequence</a></span>(java.lang.String&nbsp;sequence)</code>
 259 <div class="block">Removes all special characters and digits as well as whitespace chars
 260  from the sequence</div>
 261 </td>
 262 </tr>
 263 <tr id="i5" class="rowColor">
 264 <td class="colFirst"><code>static boolean</code></td>
 265 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein-java.lang.String-">isAmbiguosProtein</a></span>(java.lang.String&nbsp;sequence)</code>
 266 <div class="block">Check whether the sequence confirms to amboguous protein sequence</div>
 267 </td>
 268 </tr>
 269 <tr id="i6" class="altColor">
 270 <td class="colFirst"><code>static boolean</code></td>
 271 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence-java.lang.String-">isNonAmbNucleotideSequence</a></span>(java.lang.String&nbsp;sequence)</code>
 272 <div class="block">Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 273  (!) - B char</div>
 274 </td>
 275 </tr>
 276 <tr id="i7" class="rowColor">
 277 <td class="colFirst"><code>static boolean</code></td>
 278 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence-compbio.data.sequence.FastaSequence-">isNucleotideSequence</a></span>(<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&nbsp;s)</code>&nbsp;</td>
 279 </tr>
 280 <tr id="i8" class="altColor">
 281 <td class="colFirst"><code>static boolean</code></td>
 282 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence-java.lang.String-">isProteinSequence</a></span>(java.lang.String&nbsp;sequence)</code>&nbsp;</td>
 283 </tr>
 284 <tr id="i9" class="rowColor">
 285 <td class="colFirst"><code>static java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 286 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#openInputStream-java.lang.String-">openInputStream</a></span>(java.lang.String&nbsp;inFilePath)</code>
 287 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
 288  FastaSequence objects</div>
 289 </td>
 290 </tr>
 291 <tr id="i10" class="altColor">
 292 <td class="colFirst"><code>private static java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;</code></td>
 293 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#parseIUPredDomains-java.util.Scanner-">parseIUPredDomains</a></span>(java.util.Scanner&nbsp;scan)</code>
 294 <div class="block"># P53_HUMA
 295
 296  Number of globular domains: 2
 297
 298  globular domain 1.</div>
 299 </td>
 300 </tr>
 301 <tr id="i11" class="rowColor">
 302 <td class="colFirst"><code>private static float[]</code></td>
 303 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#parseIUPredScores-java.util.Scanner-">parseIUPredScores</a></span>(java.util.Scanner&nbsp;scan)</code>&nbsp;</td>
 304 </tr>
 305 <tr id="i12" class="altColor">
 306 <td class="colFirst"><code>private static java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;</code></td>
 307 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#parseRanges-java.lang.Enum-java.lang.String-">parseRanges</a></span>(java.lang.Enum&nbsp;resultType,
 308            java.lang.String&nbsp;lines)</code>
 309 <div class="block">Parsing:
 310
 311  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343,
 312  350-391, 429-485, 497-506, 539-547
 313
 314  # REM465 355-368
 315
 316  # HOTLOOPS 190-204</div>
 317 </td>
 318 </tr>
 319 <tr id="i13" class="rowColor">
 320 <td class="colFirst"><code>static java.util.HashSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 321 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readAAConResults-java.io.InputStream-">readAAConResults</a></span>(java.io.InputStream&nbsp;results)</code>
 322 <div class="block">Read AACon result with no alignment files.</div>
 323 </td>
 324 </tr>
 325 <tr id="i14" class="altColor">
 326 <td class="colFirst"><code>static java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 327 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readDisembl-java.io.InputStream-">readDisembl</a></span>(java.io.InputStream&nbsp;input)</code>
 328 <div class="block">> Foobar_dundeefriends
 329
 330  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 331
 332  # REM465 355-368
 333
 334  # HOTLOOPS 190-204
 335
 336  # RESIDUE COILS REM465 HOTLOOPS
 337
 338  M 0.86010 0.88512 0.37094
 339
 340  T 0.79983 0.85864 0.44331
 341
 342  >Next Sequence name</div>
 343 </td>
 344 </tr>
 345 <tr id="i15" class="rowColor">
 346 <td class="colFirst"><code>static java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;</code></td>
 347 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readFasta-java.io.InputStream-">readFasta</a></span>(java.io.InputStream&nbsp;inStream)</code>
 348 <div class="block">Reads fasta sequences from inStream into the list of FastaSequence
 349  objects</div>
 350 </td>
 351 </tr>
 352 <tr id="i16" class="altColor">
 353 <td class="colFirst"><code>static java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 354 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot-java.io.InputStream-">readGlobPlot</a></span>(java.io.InputStream&nbsp;input)</code>
 355 <div class="block">> Foobar_dundeefriends
 356
 357  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 358
 359  # REM465 355-368
 360
 361  # HOTLOOPS 190-204
 362
 363  # RESIDUE COILS REM465 HOTLOOPS
 364
 365  M 0.86010 0.88512 0.37094
 366
 367  T 0.79983 0.85864 0.44331
 368
 369  >Next Sequence name</div>
 370 </td>
 371 </tr>
 372 <tr id="i17" class="rowColor">
 373 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 374 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readIUPred-java.io.File-">readIUPred</a></span>(java.io.File&nbsp;result)</code>
 375 <div class="block">Read IUPred output</div>
 376 </td>
 377 </tr>
 378 <tr id="i18" class="altColor">
 379 <td class="colFirst"><code>private static java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 380 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readIUPred-java.io.InputStream-compbio.data.sequence.IUPredResult-">readIUPred</a></span>(java.io.InputStream&nbsp;input,
 381           <a href="../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a>&nbsp;type)</code>
 382 <div class="block">## Long Disorder
 383
 384  # P53_HUMAN
 385
 386  1 M 0.9943
 387
 388  2 E 0.9917
 389
 390  3 E 0.9879
 391
 392  (every line)</div>
 393 </td>
 394 </tr>
 395 <tr id="i19" class="rowColor">
 396 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 397 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readJRonn-java.io.File-">readJRonn</a></span>(java.io.File&nbsp;result)</code>&nbsp;</td>
 398 </tr>
 399 <tr id="i20" class="altColor">
 400 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 401 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#readJRonn-java.io.InputStream-">readJRonn</a></span>(java.io.InputStream&nbsp;inStream)</code>
 402 <div class="block">Reader for JRonn horizontal file format</div>
 403 </td>
 404 </tr>
 405 <tr id="i21" class="rowColor">
 406 <td class="colFirst"><code>static void</code></td>
 407 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#writeClustal-java.io.OutputStream-java.util.List-char-">writeClustal</a></span>(java.io.OutputStream&nbsp;outStream,
 408             java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 409             char&nbsp;gapChar)</code>&nbsp;</td>
 410 </tr>
 411 <tr id="i22" class="altColor">
 412 <td class="colFirst"><code>static void</code></td>
 413 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#writeFasta-java.io.OutputStream-java.util.List-">writeFasta</a></span>(java.io.OutputStream&nbsp;os,
 414           java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>
 415 <div class="block">Writes FastaSequence in the file, each sequence will take one line only</div>
 416 </td>
 417 </tr>
 418 <tr id="i23" class="rowColor">
 419 <td class="colFirst"><code>static void</code></td>
 420 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#writeFasta-java.io.OutputStream-java.util.List-int-">writeFasta</a></span>(java.io.OutputStream&nbsp;outstream,
 421           java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 422           int&nbsp;width)</code>
 423 <div class="block">Writes list of FastaSequeces into the outstream formatting the sequence
 424  so that it contains width chars on each line</div>
 425 </td>
 426 </tr>
 427 <tr id="i24" class="altColor">
 428 <td class="colFirst"><code>static void</code></td>
 429 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream-java.io.OutputStream-java.util.List-int-">writeFastaKeepTheStream</a></span>(java.io.OutputStream&nbsp;outstream,
 430                        java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 431                        int&nbsp;width)</code>&nbsp;</td>
 432 </tr>
 433 </table>
 434 <ul class="blockList">
 435 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 436 <!--   -->
 437 </a>
 438 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 439 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 440 </ul>
 441 </li>
 442 </ul>
 443 </li>
 444 </ul>
 445 </div>
 446 <div class="details">
 447 <ul class="blockList">
 448 <li class="blockList">
 449 <!-- ============ FIELD DETAIL =========== -->
 450 <ul class="blockList">
 451 <li class="blockList"><a name="field.detail">
 452 <!--   -->
 453 </a>
 454 <h3>Field Detail</h3>
 455 <a name="WHITE_SPACE">
 456 <!--   -->
 457 </a>
 458 <ul class="blockList">
 459 <li class="blockList">
 460 <h4>WHITE_SPACE</h4>
 461 <pre>public static final&nbsp;java.util.regex.Pattern WHITE_SPACE</pre>
 462 <div class="block">A whitespace character: [\t\n\x0B\f\r]</div>
 463 </li>
 464 </ul>
 465 <a name="DIGIT">
 466 <!--   -->
 467 </a>
 468 <ul class="blockList">
 469 <li class="blockList">
 470 <h4>DIGIT</h4>
 471 <pre>public static final&nbsp;java.util.regex.Pattern DIGIT</pre>
 472 <div class="block">A digit</div>
 473 </li>
 474 </ul>
 475 <a name="NONWORD">
 476 <!--   -->
 477 </a>
 478 <ul class="blockList">
 479 <li class="blockList">
 480 <h4>NONWORD</h4>
 481 <pre>public static final&nbsp;java.util.regex.Pattern NONWORD</pre>
 482 <div class="block">Non word</div>
 483 </li>
 484 </ul>
 485 <a name="AA">
 486 <!--   -->
 487 </a>
 488 <ul class="blockList">
 489 <li class="blockList">
 490 <h4>AA</h4>
 491 <pre>public static final&nbsp;java.util.regex.Pattern AA</pre>
 492 <div class="block">Valid Amino acids</div>
 493 </li>
 494 </ul>
 495 <a name="NON_AA">
 496 <!--   -->
 497 </a>
 498 <ul class="blockList">
 499 <li class="blockList">
 500 <h4>NON_AA</h4>
 501 <pre>public static final&nbsp;java.util.regex.Pattern NON_AA</pre>
 502 <div class="block">inversion of AA pattern</div>
 503 </li>
 504 </ul>
 505 <a name="AMBIGUOUS_AA">
 506 <!--   -->
 507 </a>
 508 <ul class="blockList">
 509 <li class="blockList">
 510 <h4>AMBIGUOUS_AA</h4>
 511 <pre>public static final&nbsp;java.util.regex.Pattern AMBIGUOUS_AA</pre>
 512 <div class="block">Same as AA pattern but with two additional letters - XU</div>
 513 </li>
 514 </ul>
 515 <a name="NUCLEOTIDE">
 516 <!--   -->
 517 </a>
 518 <ul class="blockList">
 519 <li class="blockList">
 520 <h4>NUCLEOTIDE</h4>
 521 <pre>public static final&nbsp;java.util.regex.Pattern NUCLEOTIDE</pre>
 522 <div class="block">Nucleotides a, t, g, c, u</div>
 523 </li>
 524 </ul>
 525 <a name="AMBIGUOUS_NUCLEOTIDE">
 526 <!--   -->
 527 </a>
 528 <ul class="blockList">
 529 <li class="blockList">
 530 <h4>AMBIGUOUS_NUCLEOTIDE</h4>
 531 <pre>public static final&nbsp;java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE</pre>
 532 <div class="block">Ambiguous nucleotide</div>
 533 </li>
 534 </ul>
 535 <a name="NON_NUCLEOTIDE">
 536 <!--   -->
 537 </a>
 538 <ul class="blockList">
 539 <li class="blockList">
 540 <h4>NON_NUCLEOTIDE</h4>
 541 <pre>public static final&nbsp;java.util.regex.Pattern NON_NUCLEOTIDE</pre>
 542 <div class="block">Non nucleotide</div>
 543 </li>
 544 </ul>
 545 <a name="JRONN_WRONG_FORMAT_MESSAGE">
 546 <!--   -->
 547 </a>
 548 <ul class="blockListLast">
 549 <li class="blockList">
 550 <h4>JRONN_WRONG_FORMAT_MESSAGE</h4>
 551 <pre>private static final&nbsp;java.lang.String JRONN_WRONG_FORMAT_MESSAGE</pre>
 552 <dl>
 553 <dt><span class="seeLabel">See Also:</span></dt>
 554 <dd><a href="../../../constant-values.html#compbio.data.sequence.SequenceUtil.JRONN_WRONG_FORMAT_MESSAGE">Constant Field Values</a></dd>
 555 </dl>
 556 </li>
 557 </ul>
 558 </li>
 559 </ul>
 560 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 561 <ul class="blockList">
 562 <li class="blockList"><a name="constructor.detail">
 563 <!--   -->
 564 </a>
 565 <h3>Constructor Detail</h3>
 566 <a name="SequenceUtil--">
 567 <!--   -->
 568 </a>
 569 <ul class="blockListLast">
 570 <li class="blockList">
 571 <h4>SequenceUtil</h4>
 572 <pre>private&nbsp;SequenceUtil()</pre>
 573 </li>
 574 </ul>
 575 </li>
 576 </ul>
 577 <!-- ============ METHOD DETAIL ========== -->
 578 <ul class="blockList">
 579 <li class="blockList"><a name="method.detail">
 580 <!--   -->
 581 </a>
 582 <h3>Method Detail</h3>
 583 <a name="isNucleotideSequence-compbio.data.sequence.FastaSequence-">
 584 <!--   -->
 585 </a>
 586 <ul class="blockList">
 587 <li class="blockList">
 588 <h4>isNucleotideSequence</h4>
 589 <pre>public static&nbsp;boolean&nbsp;isNucleotideSequence(<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&nbsp;s)</pre>
 590 <dl>
 591 <dt><span class="returnLabel">Returns:</span></dt>
 592 <dd>true is the sequence contains only letters a,c, t, g, u</dd>
 593 </dl>
 594 </li>
 595 </ul>
 596 <a name="isNonAmbNucleotideSequence-java.lang.String-">
 597 <!--   -->
 598 </a>
 599 <ul class="blockList">
 600 <li class="blockList">
 601 <h4>isNonAmbNucleotideSequence</h4>
 602 <pre>public static&nbsp;boolean&nbsp;isNonAmbNucleotideSequence(java.lang.String&nbsp;sequence)</pre>
 603 <div class="block">Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 604  (!) - B char</div>
 605 </li>
 606 </ul>
 607 <a name="cleanSequence-java.lang.String-">
 608 <!--   -->
 609 </a>
 610 <ul class="blockList">
 611 <li class="blockList">
 612 <h4>cleanSequence</h4>
 613 <pre>public static&nbsp;java.lang.String&nbsp;cleanSequence(java.lang.String&nbsp;sequence)</pre>
 614 <div class="block">Removes all whitespace chars in the sequence string</div>
 615 <dl>
 616 <dt><span class="paramLabel">Parameters:</span></dt>
 617 <dd><code>sequence</code> - </dd>
 618 <dt><span class="returnLabel">Returns:</span></dt>
 619 <dd>cleaned up sequence</dd>
 620 </dl>
 621 </li>
 622 </ul>
 623 <a name="deepCleanSequence-java.lang.String-">
 624 <!--   -->
 625 </a>
 626 <ul class="blockList">
 627 <li class="blockList">
 628 <h4>deepCleanSequence</h4>
 629 <pre>public static&nbsp;java.lang.String&nbsp;deepCleanSequence(java.lang.String&nbsp;sequence)</pre>
 630 <div class="block">Removes all special characters and digits as well as whitespace chars
 631  from the sequence</div>
 632 <dl>
 633 <dt><span class="paramLabel">Parameters:</span></dt>
 634 <dd><code>sequence</code> - </dd>
 635 <dt><span class="returnLabel">Returns:</span></dt>
 636 <dd>cleaned up sequence</dd>
 637 </dl>
 638 </li>
 639 </ul>
 640 <a name="cleanProteinSequence-java.lang.String-">
 641 <!--   -->
 642 </a>
 643 <ul class="blockList">
 644 <li class="blockList">
 645 <h4>cleanProteinSequence</h4>
 646 <pre>public static&nbsp;java.lang.String&nbsp;cleanProteinSequence(java.lang.String&nbsp;sequence)</pre>
 647 <div class="block">Remove all non AA chars from the sequence</div>
 648 <dl>
 649 <dt><span class="paramLabel">Parameters:</span></dt>
 650 <dd><code>sequence</code> - the sequence to clean</dd>
 651 <dt><span class="returnLabel">Returns:</span></dt>
 652 <dd>cleaned sequence</dd>
 653 </dl>
 654 </li>
 655 </ul>
 656 <a name="isProteinSequence-java.lang.String-">
 657 <!--   -->
 658 </a>
 659 <ul class="blockList">
 660 <li class="blockList">
 661 <h4>isProteinSequence</h4>
 662 <pre>public static&nbsp;boolean&nbsp;isProteinSequence(java.lang.String&nbsp;sequence)</pre>
 663 <dl>
 664 <dt><span class="paramLabel">Parameters:</span></dt>
 665 <dd><code>sequence</code> - </dd>
 666 <dt><span class="returnLabel">Returns:</span></dt>
 667 <dd>true is the sequence is a protein sequence, false overwise</dd>
 668 </dl>
 669 </li>
 670 </ul>
 671 <a name="isAmbiguosProtein-java.lang.String-">
 672 <!--   -->
 673 </a>
 674 <ul class="blockList">
 675 <li class="blockList">
 676 <h4>isAmbiguosProtein</h4>
 677 <pre>public static&nbsp;boolean&nbsp;isAmbiguosProtein(java.lang.String&nbsp;sequence)</pre>
 678 <div class="block">Check whether the sequence confirms to amboguous protein sequence</div>
 679 <dl>
 680 <dt><span class="paramLabel">Parameters:</span></dt>
 681 <dd><code>sequence</code> - </dd>
 682 <dt><span class="returnLabel">Returns:</span></dt>
 683 <dd>return true only if the sequence if ambiguous protein sequence
 684          Return false otherwise. e.g. if the sequence is non-ambiguous
 685          protein or DNA</dd>
 686 </dl>
 687 </li>
 688 </ul>
 689 <a name="writeFasta-java.io.OutputStream-java.util.List-int-">
 690 <!--   -->
 691 </a>
 692 <ul class="blockList">
 693 <li class="blockList">
 694 <h4>writeFasta</h4>
 695 <pre>public static&nbsp;void&nbsp;writeFasta(java.io.OutputStream&nbsp;outstream,
 696                               java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 697                               int&nbsp;width)
 698                        throws java.io.IOException</pre>
 699 <div class="block">Writes list of FastaSequeces into the outstream formatting the sequence
 700  so that it contains width chars on each line</div>
 701 <dl>
 702 <dt><span class="paramLabel">Parameters:</span></dt>
 703 <dd><code>outstream</code> - </dd>
 704 <dd><code>sequences</code> - </dd>
 705 <dd><code>width</code> - - the maximum number of characters to write in one line</dd>
 706 <dt><span class="throwsLabel">Throws:</span></dt>
 707 <dd><code>java.io.IOException</code></dd>
 708 </dl>
 709 </li>
 710 </ul>
 711 <a name="writeFastaKeepTheStream-java.io.OutputStream-java.util.List-int-">
 712 <!--   -->
 713 </a>
 714 <ul class="blockList">
 715 <li class="blockList">
 716 <h4>writeFastaKeepTheStream</h4>
 717 <pre>public static&nbsp;void&nbsp;writeFastaKeepTheStream(java.io.OutputStream&nbsp;outstream,
 718                                            java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 719                                            int&nbsp;width)
 720                                     throws java.io.IOException</pre>
 721 <dl>
 722 <dt><span class="throwsLabel">Throws:</span></dt>
 723 <dd><code>java.io.IOException</code></dd>
 724 </dl>
 725 </li>
 726 </ul>
 727 <a name="readFasta-java.io.InputStream-">
 728 <!--   -->
 729 </a>
 730 <ul class="blockList">
 731 <li class="blockList">
 732 <h4>readFasta</h4>
 733 <pre>public static&nbsp;java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;readFasta(java.io.InputStream&nbsp;inStream)
 734                                                throws java.io.IOException</pre>
 735 <div class="block">Reads fasta sequences from inStream into the list of FastaSequence
 736  objects</div>
 737 <dl>
 738 <dt><span class="paramLabel">Parameters:</span></dt>
 739 <dd><code>inStream</code> - from</dd>
 740 <dt><span class="returnLabel">Returns:</span></dt>
 741 <dd>list of FastaSequence objects</dd>
 742 <dt><span class="throwsLabel">Throws:</span></dt>
 743 <dd><code>java.io.IOException</code></dd>
 744 </dl>
 745 </li>
 746 </ul>
 747 <a name="writeFasta-java.io.OutputStream-java.util.List-">
 748 <!--   -->
 749 </a>
 750 <ul class="blockList">
 751 <li class="blockList">
 752 <h4>writeFasta</h4>
 753 <pre>public static&nbsp;void&nbsp;writeFasta(java.io.OutputStream&nbsp;os,
 754                               java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)
 755                        throws java.io.IOException</pre>
 756 <div class="block">Writes FastaSequence in the file, each sequence will take one line only</div>
 757 <dl>
 758 <dt><span class="paramLabel">Parameters:</span></dt>
 759 <dd><code>os</code> - </dd>
 760 <dd><code>sequences</code> - </dd>
 761 <dt><span class="throwsLabel">Throws:</span></dt>
 762 <dd><code>java.io.IOException</code></dd>
 763 </dl>
 764 </li>
 765 </ul>
 766 <a name="readIUPred-java.io.File-">
 767 <!--   -->
 768 </a>
 769 <ul class="blockList">
 770 <li class="blockList">
 771 <h4>readIUPred</h4>
 772 <pre>public static&nbsp;java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;readIUPred(java.io.File&nbsp;result)
 773                                                         throws java.io.IOException,
 774                                                                <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 775 <div class="block">Read IUPred output</div>
 776 <dl>
 777 <dt><span class="paramLabel">Parameters:</span></dt>
 778 <dd><code>result</code> - </dd>
 779 <dt><span class="returnLabel">Returns:</span></dt>
 780 <dd>Map key->sequence name, value->Score</dd>
 781 <dt><span class="throwsLabel">Throws:</span></dt>
 782 <dd><code>java.io.IOException</code></dd>
 783 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 784 </dl>
 785 </li>
 786 </ul>
 787 <a name="readIUPred-java.io.InputStream-compbio.data.sequence.IUPredResult-">
 788 <!--   -->
 789 </a>
 790 <ul class="blockList">
 791 <li class="blockList">
 792 <h4>readIUPred</h4>
 793 <pre>private static&nbsp;java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;readIUPred(java.io.InputStream&nbsp;input,
 794                                                                 <a href="../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a>&nbsp;type)
 795                                                          throws java.io.IOException,
 796                                                                 <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 797 <div class="block">## Long Disorder
 798
 799  # P53_HUMAN
 800
 801  1 M 0.9943
 802
 803  2 E 0.9917
 804
 805  3 E 0.9879
 806
 807  (every line)</div>
 808 <dl>
 809 <dt><span class="throwsLabel">Throws:</span></dt>
 810 <dd><code>java.io.IOException</code></dd>
 811 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 812 </dl>
 813 </li>
 814 </ul>
 815 <a name="parseIUPredDomains-java.util.Scanner-">
 816 <!--   -->
 817 </a>
 818 <ul class="blockList">
 819 <li class="blockList">
 820 <h4>parseIUPredDomains</h4>
 821 <pre>private static&nbsp;java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;parseIUPredDomains(java.util.Scanner&nbsp;scan)</pre>
 822 <div class="block"># P53_HUMA
 823
 824  Number of globular domains: 2
 825
 826  globular domain 1. 98 - 269
 827
 828  globular domain 2. 431 - 482
 829
 830  >P53_HUMA
 831
 832  meepqsdpsv epplsqetfs dlwkllpenn vlsplpsqam ddlmlspddi eqwftedpgp</div>
 833 <dl>
 834 <dt><span class="paramLabel">Parameters:</span></dt>
 835 <dd><code>scan</code> - </dd>
 836 </dl>
 837 </li>
 838 </ul>
 839 <a name="parseIUPredScores-java.util.Scanner-">
 840 <!--   -->
 841 </a>
 842 <ul class="blockList">
 843 <li class="blockList">
 844 <h4>parseIUPredScores</h4>
 845 <pre>private static&nbsp;float[]&nbsp;parseIUPredScores(java.util.Scanner&nbsp;scan)
 846                                   throws <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 847 <dl>
 848 <dt><span class="throwsLabel">Throws:</span></dt>
 849 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 850 </dl>
 851 </li>
 852 </ul>
 853 <a name="readJRonn-java.io.File-">
 854 <!--   -->
 855 </a>
 856 <ul class="blockList">
 857 <li class="blockList">
 858 <h4>readJRonn</h4>
 859 <pre>public static&nbsp;java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;readJRonn(java.io.File&nbsp;result)
 860                                                        throws java.io.IOException,
 861                                                               <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 862 <dl>
 863 <dt><span class="throwsLabel">Throws:</span></dt>
 864 <dd><code>java.io.IOException</code></dd>
 865 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 866 </dl>
 867 </li>
 868 </ul>
 869 <a name="readJRonn-java.io.InputStream-">
 870 <!--   -->
 871 </a>
 872 <ul class="blockList">
 873 <li class="blockList">
 874 <h4>readJRonn</h4>
 875 <pre>public static&nbsp;java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;readJRonn(java.io.InputStream&nbsp;inStream)
 876                                                        throws java.io.IOException,
 877                                                               <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 878 <div class="block">Reader for JRonn horizontal file format
 879
 880  <pre>
 881  &gtFoobar M G D T T A G 0.48 0.42
 882  0.42 0.48 0.52 0.53 0.54
 883
 884  <pre>
 885  Where all values are tab delimited</div>
 886 <dl>
 887 <dt><span class="paramLabel">Parameters:</span></dt>
 888 <dd><code>inStream</code> - the InputStream connected to the JRonn output file</dd>
 889 <dt><span class="returnLabel">Returns:</span></dt>
 890 <dd>Map key=sequence name value=Score</dd>
 891 <dt><span class="throwsLabel">Throws:</span></dt>
 892 <dd><code>java.io.IOException</code> - is thrown if the inStream has problems accessing the data</dd>
 893 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code> - is thrown if the inStream represents an unknown source of
 894  data, i.e. not a JRonn output</dd>
 895 </dl>
 896 </li>
 897 </ul>
 898 <a name="convertToNumber-java.lang.String:A-">
 899 <!--   -->
 900 </a>
 901 <ul class="blockList">
 902 <li class="blockList">
 903 <h4>convertToNumber</h4>
 904 <pre>private static&nbsp;float[]&nbsp;convertToNumber(java.lang.String[]&nbsp;annotValues)
 905                                 throws <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 906 <dl>
 907 <dt><span class="throwsLabel">Throws:</span></dt>
 908 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 909 </dl>
 910 </li>
 911 </ul>
 912 <a name="closeSilently-java.util.logging.Logger-java.io.Closeable-">
 913 <!--   -->
 914 </a>
 915 <ul class="blockList">
 916 <li class="blockList">
 917 <h4>closeSilently</h4>
 918 <pre>public static final&nbsp;void&nbsp;closeSilently(java.util.logging.Logger&nbsp;log,
 919                                        java.io.Closeable&nbsp;stream)</pre>
 920 <div class="block">Closes the Closable and logs the exception if any</div>
 921 <dl>
 922 <dt><span class="paramLabel">Parameters:</span></dt>
 923 <dd><code>log</code> - </dd>
 924 <dd><code>stream</code> - </dd>
 925 </dl>
 926 </li>
 927 </ul>
 928 <a name="readDisembl-java.io.InputStream-">
 929 <!--   -->
 930 </a>
 931 <ul class="blockList">
 932 <li class="blockList">
 933 <h4>readDisembl</h4>
 934 <pre>public static&nbsp;java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;readDisembl(java.io.InputStream&nbsp;input)
 935                                                                             throws java.io.IOException,
 936                                                                                    <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 937 <div class="block">> Foobar_dundeefriends
 938
 939  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 940
 941  # REM465 355-368
 942
 943  # HOTLOOPS 190-204
 944
 945  # RESIDUE COILS REM465 HOTLOOPS
 946
 947  M 0.86010 0.88512 0.37094
 948
 949  T 0.79983 0.85864 0.44331
 950
 951  >Next Sequence name</div>
 952 <dl>
 953 <dt><span class="paramLabel">Parameters:</span></dt>
 954 <dd><code>input</code> - the InputStream</dd>
 955 <dt><span class="returnLabel">Returns:</span></dt>
 956 <dd>Map key=sequence name, value=set of score</dd>
 957 <dt><span class="throwsLabel">Throws:</span></dt>
 958 <dd><code>java.io.IOException</code></dd>
 959 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 960 </dl>
 961 </li>
 962 </ul>
 963 <a name="parseRanges-java.lang.Enum-java.lang.String-">
 964 <!--   -->
 965 </a>
 966 <ul class="blockList">
 967 <li class="blockList">
 968 <h4>parseRanges</h4>
 969 <pre>private static&nbsp;java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;parseRanges(java.lang.Enum&nbsp;resultType,
 970                                                     java.lang.String&nbsp;lines)</pre>
 971 <div class="block">Parsing:
 972
 973  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343,
 974  350-391, 429-485, 497-506, 539-547
 975
 976  # REM465 355-368
 977
 978  # HOTLOOPS 190-204</div>
 979 <dl>
 980 <dt><span class="paramLabel">Parameters:</span></dt>
 981 <dd><code>lines</code> - </dd>
 982 <dt><span class="returnLabel">Returns:</span></dt>
 983 </dl>
 984 </li>
 985 </ul>
 986 <a name="readGlobPlot-java.io.InputStream-">
 987 <!--   -->
 988 </a>
 989 <ul class="blockList">
 990 <li class="blockList">
 991 <h4>readGlobPlot</h4>
 992 <pre>public static&nbsp;java.util.HashMap&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;readGlobPlot(java.io.InputStream&nbsp;input)
 993                                                                              throws java.io.IOException,
 994                                                                                     <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
 995 <div class="block">> Foobar_dundeefriends
 996
 997  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 998
 999  # REM465 355-368
1000
1001  # HOTLOOPS 190-204
1002
1003  # RESIDUE COILS REM465 HOTLOOPS
1004
1005  M 0.86010 0.88512 0.37094
1006
1007  T 0.79983 0.85864 0.44331
1008
1009  >Next Sequence name</div>
1010 <dl>
1011 <dt><span class="paramLabel">Parameters:</span></dt>
1012 <dd><code>input</code> - </dd>
1013 <dt><span class="returnLabel">Returns:</span></dt>
1014 <dd>Map key=sequence name, value=set of score</dd>
1015 <dt><span class="throwsLabel">Throws:</span></dt>
1016 <dd><code>java.io.IOException</code></dd>
1017 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
1018 </dl>
1019 </li>
1020 </ul>
1021 <a name="readAAConResults-java.io.InputStream-">
1022 <!--   -->
1023 </a>
1024 <ul class="blockList">
1025 <li class="blockList">
1026 <h4>readAAConResults</h4>
1027 <pre>public static&nbsp;java.util.HashSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;readAAConResults(java.io.InputStream&nbsp;results)</pre>
1028 <div class="block">Read AACon result with no alignment files. This method leaves incoming
1029  InputStream open!</div>
1030 <dl>
1031 <dt><span class="paramLabel">Parameters:</span></dt>
1032 <dd><code>results</code> - output file of AAConservation</dd>
1033 <dt><span class="returnLabel">Returns:</span></dt>
1034 <dd>Map with keys <a href="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><code>ConservationMethod</code></a> -> float[]</dd>
1035 </dl>
1036 </li>
1037 </ul>
1038 <a name="openInputStream-java.lang.String-">
1039 <!--   -->
1040 </a>
1041 <ul class="blockList">
1042 <li class="blockList">
1043 <h4>openInputStream</h4>
1044 <pre>public static&nbsp;java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;openInputStream(java.lang.String&nbsp;inFilePath)
1045                                                      throws java.io.IOException,
1046                                                             <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
1047 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
1048  FastaSequence objects</div>
1049 <dl>
1050 <dt><span class="paramLabel">Parameters:</span></dt>
1051 <dd><code>inFilePath</code> - the path to the input file</dd>
1052 <dt><span class="returnLabel">Returns:</span></dt>
1053 <dd>the List of FastaSequence objects</dd>
1054 <dt><span class="throwsLabel">Throws:</span></dt>
1055 <dd><code>java.io.IOException</code> - if the file denoted by inFilePath cannot be read</dd>
1056 <dd><code><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code> - if the inFilePath points to the file which format cannot be
1057              recognised</dd>
1058 </dl>
1059 </li>
1060 </ul>
1061 <a name="writeClustal-java.io.OutputStream-java.util.List-char-">
1062 <!--   -->
1063 </a>
1064 <ul class="blockListLast">
1065 <li class="blockList">
1066 <h4>writeClustal</h4>
1067 <pre>public static&nbsp;void&nbsp;writeClustal(java.io.OutputStream&nbsp;outStream,
1068                                 java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
1069                                 char&nbsp;gapChar)
1070                          throws java.io.IOException</pre>
1071 <dl>
1072 <dt><span class="throwsLabel">Throws:</span></dt>
1073 <dd><code>java.io.IOException</code></dd>
1074 </dl>
1075 </li>
1076 </ul>
1077 </li>
1078 </ul>
1079 </li>
1080 </ul>
1081 </div>
1082 </div>
1083 <!-- ========= END OF CLASS DATA ========= -->
1084 <!-- ======= START OF BOTTOM NAVBAR ====== -->
1085 <div class="bottomNav"><a name="navbar.bottom">
1086 <!--   -->
1087 </a>
1088 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
1089 <a name="navbar.bottom.firstrow">
1090 <!--   -->
1091 </a>
1092 <ul class="navList" title="Navigation">
1093 <li><a href="../../../overview-summary.html">Overview</a></li>
1094 <li><a href="package-summary.html">Package</a></li>
1095 <li class="navBarCell1Rev">Class</li>
1096 <li><a href="class-use/SequenceUtil.html">Use</a></li>
1097 <li><a href="package-tree.html">Tree</a></li>
1098 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
1099 <li><a href="../../../index-files/index-1.html">Index</a></li>
1100 <li><a href="../../../help-doc.html">Help</a></li>
1101 </ul>
1102 </div>
1103 <div class="subNav">
1104 <ul class="navList">
1105 <li><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><span class="typeNameLink">Prev&nbsp;Class</span></a></li>
1106 <li><a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
1107 </ul>
1108 <ul class="navList">
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1127 <div>
1128 <ul class="subNavList">
1129 <li>Summary:&nbsp;</li>
1130 <li>Nested&nbsp;|&nbsp;</li>
1131 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
1132 <li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
1133 <li><a href="#method.summary">Method</a></li>
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1136 <li>Detail:&nbsp;</li>
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1139 <li><a href="#method.detail">Method</a></li>
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