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76 <li>Summary: </li>
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95 <div class="subTitle">compbio.data.sequence</div>
96 <h2 title="Class SequenceUtil" class="title">Class SequenceUtil</h2>
98 <div class="contentContainer">
99 <ul class="inheritance">
100 <li>java.lang.Object</li>
102 <ul class="inheritance">
103 <li>compbio.data.sequence.SequenceUtil</li>
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109 <li class="blockList">
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>
116 <dt><span class="simpleTagLabel">Since:</span></dt>
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>
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">
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"> </span></caption>
138 <th class="colFirst" scope="col">Modifier and Type</th>
139 <th class="colLast" scope="col">Field and Description</th>
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>
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>
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>
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>
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> </td>
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>
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>
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>
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>
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>
202 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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209 <caption><span>Constructors</span><span class="tabEnd"> </span></caption>
211 <th class="colFirst" scope="col">Modifier</th>
212 <th class="colLast" scope="col">Constructor and Description</th>
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> </td>
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228 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd"> </span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd"> </span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd"> </span></span></caption>
230 <th class="colFirst" scope="col">Modifier and Type</th>
231 <th class="colLast" scope="col">Method and Description</th>
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 sequence)</code>
236 <div class="block">Remove all non AA chars from the sequence</div>
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 sequence)</code>
242 <div class="block">Removes all whitespace chars in the sequence string</div>
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 log,
248 java.io.Closeable stream)</code>
249 <div class="block">Closes the Closable and logs the exception if any</div>
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[] annotValues)</code> </td>
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 sequence)</code>
259 <div class="block">Removes all special characters and digits as well as whitespace chars
260 from the sequence</div>
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 sequence)</code>
266 <div class="block">Check whether the sequence confirms to amboguous protein sequence</div>
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 sequence)</code>
272 <div class="block">Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
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> s)</code> </td>
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 sequence)</code> </td>
284 <tr id="i9" class="rowColor">
285 <td class="colFirst"><code>static java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>></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 inFilePath)</code>
287 <div class="block">Reads and parses Fasta or Clustal formatted file into a list of
288 FastaSequence objects</div>
291 <tr id="i10" class="altColor">
292 <td class="colFirst"><code>private static java.util.TreeSet<<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>></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 scan)</code>
294 <div class="block"># P53_HUMA
296 Number of globular domains: 2
298 globular domain 1.</div>
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 scan)</code> </td>
305 <tr id="i12" class="altColor">
306 <td class="colFirst"><code>private static java.util.TreeSet<<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>></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 resultType,
308 java.lang.String lines)</code>
309 <div class="block">Parsing:
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
316 # HOTLOOPS 190-204</div>
319 <tr id="i13" class="rowColor">
320 <td class="colFirst"><code>static java.util.HashSet<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></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 results)</code>
322 <div class="block">Read AACon result with no alignment files.</div>
325 <tr id="i14" class="altColor">
326 <td class="colFirst"><code>static java.util.HashMap<java.lang.String,java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>>></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 input)</code>
328 <div class="block">> Foobar_dundeefriends
330 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
336 # RESIDUE COILS REM465 HOTLOOPS
338 M 0.86010 0.88512 0.37094
340 T 0.79983 0.85864 0.44331
342 >Next Sequence name</div>
345 <tr id="i15" class="rowColor">
346 <td class="colFirst"><code>static java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>></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 inStream)</code>
348 <div class="block">Reads fasta sequences from inStream into the list of FastaSequence
352 <tr id="i16" class="altColor">
353 <td class="colFirst"><code>static java.util.HashMap<java.lang.String,java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>>></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 input)</code>
355 <div class="block">> Foobar_dundeefriends
357 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
363 # RESIDUE COILS REM465 HOTLOOPS
365 M 0.86010 0.88512 0.37094
367 T 0.79983 0.85864 0.44331
369 >Next Sequence name</div>
372 <tr id="i17" class="rowColor">
373 <td class="colFirst"><code>static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></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 result)</code>
375 <div class="block">Read IUPred output</div>
378 <tr id="i18" class="altColor">
379 <td class="colFirst"><code>private static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></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 input,
381 <a href="../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a> type)</code>
382 <div class="block">## Long Disorder
395 <tr id="i19" class="rowColor">
396 <td class="colFirst"><code>static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></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 result)</code> </td>
399 <tr id="i20" class="altColor">
400 <td class="colFirst"><code>static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></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 inStream)</code>
402 <div class="block">Reader for JRonn horizontal file format</div>
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 outStream,
408 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
409 char gapChar)</code> </td>
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 os,
414 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences)</code>
415 <div class="block">Writes FastaSequence in the file, each sequence will take one line only</div>
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 outstream,
421 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
422 int 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>
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 outstream,
430 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
431 int width)</code> </td>
434 <ul class="blockList">
435 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
438 <h3>Methods inherited from class java.lang.Object</h3>
439 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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">
454 <h3>Field Detail</h3>
455 <a name="WHITE_SPACE">
458 <ul class="blockList">
459 <li class="blockList">
461 <pre>public static final java.util.regex.Pattern WHITE_SPACE</pre>
462 <div class="block">A whitespace character: [\t\n\x0B\f\r]</div>
468 <ul class="blockList">
469 <li class="blockList">
471 <pre>public static final java.util.regex.Pattern DIGIT</pre>
472 <div class="block">A digit</div>
478 <ul class="blockList">
479 <li class="blockList">
481 <pre>public static final java.util.regex.Pattern NONWORD</pre>
482 <div class="block">Non word</div>
488 <ul class="blockList">
489 <li class="blockList">
491 <pre>public static final java.util.regex.Pattern AA</pre>
492 <div class="block">Valid Amino acids</div>
498 <ul class="blockList">
499 <li class="blockList">
501 <pre>public static final java.util.regex.Pattern NON_AA</pre>
502 <div class="block">inversion of AA pattern</div>
505 <a name="AMBIGUOUS_AA">
508 <ul class="blockList">
509 <li class="blockList">
510 <h4>AMBIGUOUS_AA</h4>
511 <pre>public static final java.util.regex.Pattern AMBIGUOUS_AA</pre>
512 <div class="block">Same as AA pattern but with two additional letters - XU</div>
515 <a name="NUCLEOTIDE">
518 <ul class="blockList">
519 <li class="blockList">
521 <pre>public static final java.util.regex.Pattern NUCLEOTIDE</pre>
522 <div class="block">Nucleotides a, t, g, c, u</div>
525 <a name="AMBIGUOUS_NUCLEOTIDE">
528 <ul class="blockList">
529 <li class="blockList">
530 <h4>AMBIGUOUS_NUCLEOTIDE</h4>
531 <pre>public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE</pre>
532 <div class="block">Ambiguous nucleotide</div>
535 <a name="NON_NUCLEOTIDE">
538 <ul class="blockList">
539 <li class="blockList">
540 <h4>NON_NUCLEOTIDE</h4>
541 <pre>public static final java.util.regex.Pattern NON_NUCLEOTIDE</pre>
542 <div class="block">Non nucleotide</div>
545 <a name="JRONN_WRONG_FORMAT_MESSAGE">
548 <ul class="blockListLast">
549 <li class="blockList">
550 <h4>JRONN_WRONG_FORMAT_MESSAGE</h4>
551 <pre>private static final java.lang.String JRONN_WRONG_FORMAT_MESSAGE</pre>
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>
560 <!-- ========= CONSTRUCTOR DETAIL ======== -->
561 <ul class="blockList">
562 <li class="blockList"><a name="constructor.detail">
565 <h3>Constructor Detail</h3>
566 <a name="SequenceUtil--">
569 <ul class="blockListLast">
570 <li class="blockList">
571 <h4>SequenceUtil</h4>
572 <pre>private SequenceUtil()</pre>
577 <!-- ============ METHOD DETAIL ========== -->
578 <ul class="blockList">
579 <li class="blockList"><a name="method.detail">
582 <h3>Method Detail</h3>
583 <a name="isNucleotideSequence-compbio.data.sequence.FastaSequence-">
586 <ul class="blockList">
587 <li class="blockList">
588 <h4>isNucleotideSequence</h4>
589 <pre>public static boolean isNucleotideSequence(<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a> s)</pre>
591 <dt><span class="returnLabel">Returns:</span></dt>
592 <dd>true is the sequence contains only letters a,c, t, g, u</dd>
596 <a name="isNonAmbNucleotideSequence-java.lang.String-">
599 <ul class="blockList">
600 <li class="blockList">
601 <h4>isNonAmbNucleotideSequence</h4>
602 <pre>public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)</pre>
603 <div class="block">Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
607 <a name="cleanSequence-java.lang.String-">
610 <ul class="blockList">
611 <li class="blockList">
612 <h4>cleanSequence</h4>
613 <pre>public static java.lang.String cleanSequence(java.lang.String sequence)</pre>
614 <div class="block">Removes all whitespace chars in the sequence string</div>
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>
623 <a name="deepCleanSequence-java.lang.String-">
626 <ul class="blockList">
627 <li class="blockList">
628 <h4>deepCleanSequence</h4>
629 <pre>public static java.lang.String deepCleanSequence(java.lang.String sequence)</pre>
630 <div class="block">Removes all special characters and digits as well as whitespace chars
631 from the sequence</div>
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>
640 <a name="cleanProteinSequence-java.lang.String-">
643 <ul class="blockList">
644 <li class="blockList">
645 <h4>cleanProteinSequence</h4>
646 <pre>public static java.lang.String cleanProteinSequence(java.lang.String sequence)</pre>
647 <div class="block">Remove all non AA chars from the sequence</div>
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>
656 <a name="isProteinSequence-java.lang.String-">
659 <ul class="blockList">
660 <li class="blockList">
661 <h4>isProteinSequence</h4>
662 <pre>public static boolean isProteinSequence(java.lang.String sequence)</pre>
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>
671 <a name="isAmbiguosProtein-java.lang.String-">
674 <ul class="blockList">
675 <li class="blockList">
676 <h4>isAmbiguosProtein</h4>
677 <pre>public static boolean isAmbiguosProtein(java.lang.String sequence)</pre>
678 <div class="block">Check whether the sequence confirms to amboguous protein sequence</div>
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
689 <a name="writeFasta-java.io.OutputStream-java.util.List-int-">
692 <ul class="blockList">
693 <li class="blockList">
695 <pre>public static void writeFasta(java.io.OutputStream outstream,
696 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
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>
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>
711 <a name="writeFastaKeepTheStream-java.io.OutputStream-java.util.List-int-">
714 <ul class="blockList">
715 <li class="blockList">
716 <h4>writeFastaKeepTheStream</h4>
717 <pre>public static void writeFastaKeepTheStream(java.io.OutputStream outstream,
718 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
720 throws java.io.IOException</pre>
722 <dt><span class="throwsLabel">Throws:</span></dt>
723 <dd><code>java.io.IOException</code></dd>
727 <a name="readFasta-java.io.InputStream-">
730 <ul class="blockList">
731 <li class="blockList">
733 <pre>public static java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> readFasta(java.io.InputStream inStream)
734 throws java.io.IOException</pre>
735 <div class="block">Reads fasta sequences from inStream into the list of FastaSequence
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>
747 <a name="writeFasta-java.io.OutputStream-java.util.List-">
750 <ul class="blockList">
751 <li class="blockList">
753 <pre>public static void writeFasta(java.io.OutputStream os,
754 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences)
755 throws java.io.IOException</pre>
756 <div class="block">Writes FastaSequence in the file, each sequence will take one line only</div>
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>
766 <a name="readIUPred-java.io.File-">
769 <ul class="blockList">
770 <li class="blockList">
772 <pre>public static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> readIUPred(java.io.File 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>
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>
787 <a name="readIUPred-java.io.InputStream-compbio.data.sequence.IUPredResult-">
790 <ul class="blockList">
791 <li class="blockList">
793 <pre>private static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> readIUPred(java.io.InputStream input,
794 <a href="../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a> 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
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>
815 <a name="parseIUPredDomains-java.util.Scanner-">
818 <ul class="blockList">
819 <li class="blockList">
820 <h4>parseIUPredDomains</h4>
821 <pre>private static java.util.TreeSet<<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>> parseIUPredDomains(java.util.Scanner scan)</pre>
822 <div class="block"># P53_HUMA
824 Number of globular domains: 2
826 globular domain 1. 98 - 269
828 globular domain 2. 431 - 482
832 meepqsdpsv epplsqetfs dlwkllpenn vlsplpsqam ddlmlspddi eqwftedpgp</div>
834 <dt><span class="paramLabel">Parameters:</span></dt>
835 <dd><code>scan</code> - </dd>
839 <a name="parseIUPredScores-java.util.Scanner-">
842 <ul class="blockList">
843 <li class="blockList">
844 <h4>parseIUPredScores</h4>
845 <pre>private static float[] parseIUPredScores(java.util.Scanner scan)
846 throws <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
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>
853 <a name="readJRonn-java.io.File-">
856 <ul class="blockList">
857 <li class="blockList">
859 <pre>public static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> readJRonn(java.io.File result)
860 throws java.io.IOException,
861 <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
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>
869 <a name="readJRonn-java.io.InputStream-">
872 <ul class="blockList">
873 <li class="blockList">
875 <pre>public static java.util.Map<java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> readJRonn(java.io.InputStream 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
881 >Foobar M G D T T A G 0.48 0.42
882 0.42 0.48 0.52 0.53 0.54
885 Where all values are tab delimited</div>
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>
898 <a name="convertToNumber-java.lang.String:A-">
901 <ul class="blockList">
902 <li class="blockList">
903 <h4>convertToNumber</h4>
904 <pre>private static float[] convertToNumber(java.lang.String[] annotValues)
905 throws <a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></pre>
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>
912 <a name="closeSilently-java.util.logging.Logger-java.io.Closeable-">
915 <ul class="blockList">
916 <li class="blockList">
917 <h4>closeSilently</h4>
918 <pre>public static final void closeSilently(java.util.logging.Logger log,
919 java.io.Closeable stream)</pre>
920 <div class="block">Closes the Closable and logs the exception if any</div>
922 <dt><span class="paramLabel">Parameters:</span></dt>
923 <dd><code>log</code> - </dd>
924 <dd><code>stream</code> - </dd>
928 <a name="readDisembl-java.io.InputStream-">
931 <ul class="blockList">
932 <li class="blockList">
934 <pre>public static java.util.HashMap<java.lang.String,java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>>> readDisembl(java.io.InputStream 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
939 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
945 # RESIDUE COILS REM465 HOTLOOPS
947 M 0.86010 0.88512 0.37094
949 T 0.79983 0.85864 0.44331
951 >Next Sequence name</div>
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>
963 <a name="parseRanges-java.lang.Enum-java.lang.String-">
966 <ul class="blockList">
967 <li class="blockList">
969 <pre>private static java.util.TreeSet<<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>> parseRanges(java.lang.Enum resultType,
970 java.lang.String lines)</pre>
971 <div class="block">Parsing:
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
978 # HOTLOOPS 190-204</div>
980 <dt><span class="paramLabel">Parameters:</span></dt>
981 <dd><code>lines</code> - </dd>
982 <dt><span class="returnLabel">Returns:</span></dt>
986 <a name="readGlobPlot-java.io.InputStream-">
989 <ul class="blockList">
990 <li class="blockList">
991 <h4>readGlobPlot</h4>
992 <pre>public static java.util.HashMap<java.lang.String,java.util.Set<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>>> readGlobPlot(java.io.InputStream 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
997 # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
1003 # RESIDUE COILS REM465 HOTLOOPS
1005 M 0.86010 0.88512 0.37094
1007 T 0.79983 0.85864 0.44331
1009 >Next Sequence name</div>
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>
1021 <a name="readAAConResults-java.io.InputStream-">
1024 <ul class="blockList">
1025 <li class="blockList">
1026 <h4>readAAConResults</h4>
1027 <pre>public static java.util.HashSet<<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> readAAConResults(java.io.InputStream results)</pre>
1028 <div class="block">Read AACon result with no alignment files. This method leaves incoming
1029 InputStream open!</div>
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>
1038 <a name="openInputStream-java.lang.String-">
1041 <ul class="blockList">
1042 <li class="blockList">
1043 <h4>openInputStream</h4>
1044 <pre>public static java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> openInputStream(java.lang.String 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>
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
1061 <a name="writeClustal-java.io.OutputStream-java.util.List-char-">
1064 <ul class="blockListLast">
1065 <li class="blockList">
1066 <h4>writeClustal</h4>
1067 <pre>public static void writeClustal(java.io.OutputStream outStream,
1068 java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
1070 throws java.io.IOException</pre>
1072 <dt><span class="throwsLabel">Throws:</span></dt>
1073 <dd><code>java.io.IOException</code></dd>
1083 <!-- ========= END OF CLASS DATA ========= -->
1084 <!-- ======= START OF BOTTOM NAVBAR ====== -->
1085 <div class="bottomNav"><a name="navbar.bottom">
1088 <div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
1089 <a name="navbar.bottom.firstrow">
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>
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1096 <li><a href="class-use/SequenceUtil.html">Use</a></li>
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1099 <li><a href="../../../index-files/index-1.html">Index</a></li>
1100 <li><a href="../../../help-doc.html">Help</a></li>
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 Class</span></a></li>
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1128 <ul class="subNavList">
1129 <li>Summary: </li>
1130 <li>Nested | </li>
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1132 <li><a href="#constructor.summary">Constr</a> | </li>
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