Refactored client class to accomodate new WS interface and reduce the complexity
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / SequenceUtil.html
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7 SequenceUtil\r
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79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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88 <!-- ======== START OF CLASS DATA ======== -->\r
89 <H2>\r
90 <FONT SIZE="-1">\r
91 compbio.data.sequence</FONT>\r
92 <BR>\r
93 Class SequenceUtil</H2>\r
94 <PRE>\r
95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SequenceUtil</B>\r
97 </PRE>\r
98 <HR>\r
99 <DL>\r
100 <DT><PRE>public final class <B>SequenceUtil</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
101 </PRE>\r
102 \r
103 <P>\r
104 Utility class for operations on sequences\r
105 <P>\r
106 \r
107 <P>\r
108 <DL>\r
109 <DT><B>Version:</B></DT>\r
110   <DD>1.0</DD>\r
111 <DT><B>Author:</B></DT>\r
112   <DD>Petr Troshin</DD>\r
113 </DL>\r
114 <HR>\r
115 \r
116 <P>\r
117 <!-- =========== FIELD SUMMARY =========== -->\r
118 \r
119 <A NAME="field_summary"><!-- --></A>\r
120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
123 <B>Field Summary</B></FONT></TH>\r
124 </TR>\r
125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
127 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
128 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>\r
129 \r
130 <BR>\r
131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Valid Amino acids</TD>\r
132 </TR>\r
133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
135 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
136 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>\r
137 \r
138 <BR>\r
139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Same as AA pattern but with two additional letters - XU</TD>\r
140 </TR>\r
141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
143 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
144 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>\r
145 \r
146 <BR>\r
147 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ambiguous nucleotide</TD>\r
148 </TR>\r
149 <TR BGCOLOR="white" CLASS="TableRowColor">\r
150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
151 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>\r
153 \r
154 <BR>\r
155 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A digit</TD>\r
156 </TR>\r
157 <TR BGCOLOR="white" CLASS="TableRowColor">\r
158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
159 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
160 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>\r
161 \r
162 <BR>\r
163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;inversion of AA pattern</TD>\r
164 </TR>\r
165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
167 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
168 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>\r
169 \r
170 <BR>\r
171 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Non nucleotide</TD>\r
172 </TR>\r
173 <TR BGCOLOR="white" CLASS="TableRowColor">\r
174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
175 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
176 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>\r
177 \r
178 <BR>\r
179 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Non word</TD>\r
180 </TR>\r
181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
183 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
184 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>\r
185 \r
186 <BR>\r
187 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Nucleotides a, t, g, c, u</TD>\r
188 </TR>\r
189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
191 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
192 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>\r
193 \r
194 <BR>\r
195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A whitespace character: [\t\n\x0B\f\r]</TD>\r
196 </TR>\r
197 </TABLE>\r
198 &nbsp;\r
199 <!-- ========== METHOD SUMMARY =========== -->\r
200 \r
201 <A NAME="method_summary"><!-- --></A>\r
202 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
203 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
204 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
205 <B>Method Summary</B></FONT></TH>\r
206 </TR>\r
207 <TR BGCOLOR="white" CLASS="TableRowColor">\r
208 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
209 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
210 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)">cleanSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</CODE>\r
211 \r
212 <BR>\r
213 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes all whitespace chars in the sequence string</TD>\r
214 </TR>\r
215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
216 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
217 <CODE>static&nbsp;void</CODE></FONT></TD>\r
218 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)">closeSilently</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/logging/Logger.html?is-external=true" title="class or interface in java.util.logging">Logger</A>&nbsp;log,\r
219               <A HREF="http://java.sun.com/javase/6/docs/api/java/io/Closeable.html?is-external=true" title="class or interface in java.io">Closeable</A>&nbsp;stream)</CODE>\r
220 \r
221 <BR>\r
222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Closes the Closable and logs the exception if any</TD>\r
223 </TR>\r
224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
226 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
227 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)">deepCleanSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</CODE>\r
228 \r
229 <BR>\r
230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes all special characters and digits as well as whitespace chars
231  from the sequence</TD>\r
232 </TR>\r
233 <TR BGCOLOR="white" CLASS="TableRowColor">\r
234 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
235 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
236 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)">isAmbiguosProtein</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</CODE>\r
237 \r
238 <BR>\r
239 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Check whether the sequence confirms to amboguous protein sequence</TD>\r
240 </TR>\r
241 <TR BGCOLOR="white" CLASS="TableRowColor">\r
242 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
243 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
244 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)">isNonAmbNucleotideSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</CODE>\r
245 \r
246 <BR>\r
247 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
248  (!) - B char</TD>\r
249 </TR>\r
250 <TR BGCOLOR="white" CLASS="TableRowColor">\r
251 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
252 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
253 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</CODE>\r
254 \r
255 <BR>\r
256 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
257 </TR>\r
258 <TR BGCOLOR="white" CLASS="TableRowColor">\r
259 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
260 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
261 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)">isProteinSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</CODE>\r
262 \r
263 <BR>\r
264 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
265 </TR>\r
266 <TR BGCOLOR="white" CLASS="TableRowColor">\r
267 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
268 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
269 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;inStream)</CODE>\r
270 \r
271 <BR>\r
272 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
273  objects</TD>\r
274 </TR>\r
275 <TR BGCOLOR="white" CLASS="TableRowColor">\r
276 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
277 <CODE>static&nbsp;void</CODE></FONT></TD>\r
278 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;os,\r
279            <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)</CODE>\r
280 \r
281 <BR>\r
282 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
283 </TR>\r
284 <TR BGCOLOR="white" CLASS="TableRowColor">\r
285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
286 <CODE>static&nbsp;void</CODE></FONT></TD>\r
287 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outstream,\r
288            <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
289            int&nbsp;width)</CODE>\r
290 \r
291 <BR>\r
292 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
293  so that it contains width chars on each line</TD>\r
294 </TR>\r
295 <TR BGCOLOR="white" CLASS="TableRowColor">\r
296 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
297 <CODE>static&nbsp;void</CODE></FONT></TD>\r
298 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outstream,\r
299                         <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
300                         int&nbsp;width)</CODE>\r
301 \r
302 <BR>\r
303 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
304 </TR>\r
305 </TABLE>\r
306 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
307 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
308 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
309 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
310 </TR>\r
311 <TR BGCOLOR="white" CLASS="TableRowColor">\r
312 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
313 </TR>\r
314 </TABLE>\r
315 &nbsp;\r
316 <P>\r
317 \r
318 <!-- ============ FIELD DETAIL =========== -->\r
319 \r
320 <A NAME="field_detail"><!-- --></A>\r
321 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
322 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
323 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
324 <B>Field Detail</B></FONT></TH>\r
325 </TR>\r
326 </TABLE>\r
327 \r
328 <A NAME="WHITE_SPACE"><!-- --></A><H3>\r
329 WHITE_SPACE</H3>\r
330 <PRE>\r
331 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>WHITE_SPACE</B></PRE>\r
332 <DL>\r
333 <DD>A whitespace character: [\t\n\x0B\f\r]\r
334 <P>\r
335 <DL>\r
336 </DL>\r
337 </DL>\r
338 <HR>\r
339 \r
340 <A NAME="DIGIT"><!-- --></A><H3>\r
341 DIGIT</H3>\r
342 <PRE>\r
343 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>DIGIT</B></PRE>\r
344 <DL>\r
345 <DD>A digit\r
346 <P>\r
347 <DL>\r
348 </DL>\r
349 </DL>\r
350 <HR>\r
351 \r
352 <A NAME="NONWORD"><!-- --></A><H3>\r
353 NONWORD</H3>\r
354 <PRE>\r
355 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NONWORD</B></PRE>\r
356 <DL>\r
357 <DD>Non word\r
358 <P>\r
359 <DL>\r
360 </DL>\r
361 </DL>\r
362 <HR>\r
363 \r
364 <A NAME="AA"><!-- --></A><H3>\r
365 AA</H3>\r
366 <PRE>\r
367 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AA</B></PRE>\r
368 <DL>\r
369 <DD>Valid Amino acids\r
370 <P>\r
371 <DL>\r
372 </DL>\r
373 </DL>\r
374 <HR>\r
375 \r
376 <A NAME="NON_AA"><!-- --></A><H3>\r
377 NON_AA</H3>\r
378 <PRE>\r
379 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NON_AA</B></PRE>\r
380 <DL>\r
381 <DD>inversion of AA pattern\r
382 <P>\r
383 <DL>\r
384 </DL>\r
385 </DL>\r
386 <HR>\r
387 \r
388 <A NAME="AMBIGUOUS_AA"><!-- --></A><H3>\r
389 AMBIGUOUS_AA</H3>\r
390 <PRE>\r
391 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AMBIGUOUS_AA</B></PRE>\r
392 <DL>\r
393 <DD>Same as AA pattern but with two additional letters - XU\r
394 <P>\r
395 <DL>\r
396 </DL>\r
397 </DL>\r
398 <HR>\r
399 \r
400 <A NAME="NUCLEOTIDE"><!-- --></A><H3>\r
401 NUCLEOTIDE</H3>\r
402 <PRE>\r
403 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NUCLEOTIDE</B></PRE>\r
404 <DL>\r
405 <DD>Nucleotides a, t, g, c, u\r
406 <P>\r
407 <DL>\r
408 </DL>\r
409 </DL>\r
410 <HR>\r
411 \r
412 <A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>\r
413 AMBIGUOUS_NUCLEOTIDE</H3>\r
414 <PRE>\r
415 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AMBIGUOUS_NUCLEOTIDE</B></PRE>\r
416 <DL>\r
417 <DD>Ambiguous nucleotide\r
418 <P>\r
419 <DL>\r
420 </DL>\r
421 </DL>\r
422 <HR>\r
423 \r
424 <A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>\r
425 NON_NUCLEOTIDE</H3>\r
426 <PRE>\r
427 public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NON_NUCLEOTIDE</B></PRE>\r
428 <DL>\r
429 <DD>Non nucleotide\r
430 <P>\r
431 <DL>\r
432 </DL>\r
433 </DL>\r
434 \r
435 <!-- ============ METHOD DETAIL ========== -->\r
436 \r
437 <A NAME="method_detail"><!-- --></A>\r
438 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
439 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
440 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
441 <B>Method Detail</B></FONT></TH>\r
442 </TR>\r
443 </TABLE>\r
444 \r
445 <A NAME="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>\r
446 isNucleotideSequence</H3>\r
447 <PRE>\r
448 public static boolean <B>isNucleotideSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&nbsp;s)</PRE>\r
449 <DL>\r
450 <DD><DL>\r
451 \r
452 <DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>\r
453 </DD>\r
454 </DL>\r
455 <HR>\r
456 \r
457 <A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>\r
458 isNonAmbNucleotideSequence</H3>\r
459 <PRE>\r
460 public static boolean <B>isNonAmbNucleotideSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</PRE>\r
461 <DL>\r
462 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
463  (!) - B char\r
464 <P>\r
465 <DD><DL>\r
466 </DL>\r
467 </DD>\r
468 </DL>\r
469 <HR>\r
470 \r
471 <A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>\r
472 cleanSequence</H3>\r
473 <PRE>\r
474 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>cleanSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</PRE>\r
475 <DL>\r
476 <DD>Removes all whitespace chars in the sequence string\r
477 <P>\r
478 <DD><DL>\r
479 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
480 <DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
481 </DD>\r
482 </DL>\r
483 <HR>\r
484 \r
485 <A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>\r
486 deepCleanSequence</H3>\r
487 <PRE>\r
488 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>deepCleanSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</PRE>\r
489 <DL>\r
490 <DD>Removes all special characters and digits as well as whitespace chars
491  from the sequence\r
492 <P>\r
493 <DD><DL>\r
494 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
495 <DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
496 </DD>\r
497 </DL>\r
498 <HR>\r
499 \r
500 <A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>\r
501 isProteinSequence</H3>\r
502 <PRE>\r
503 public static boolean <B>isProteinSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</PRE>\r
504 <DL>\r
505 <DD><DL>\r
506 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
507 <DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>\r
508 </DD>\r
509 </DL>\r
510 <HR>\r
511 \r
512 <A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>\r
513 isAmbiguosProtein</H3>\r
514 <PRE>\r
515 public static boolean <B>isAmbiguosProtein</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;sequence)</PRE>\r
516 <DL>\r
517 <DD>Check whether the sequence confirms to amboguous protein sequence\r
518 <P>\r
519 <DD><DL>\r
520 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
521 <DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
522          Return false otherwise. e.g. if the sequence is non-ambiguous
523          protein or DNA</DL>\r
524 </DD>\r
525 </DL>\r
526 <HR>\r
527 \r
528 <A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
529 writeFasta</H3>\r
530 <PRE>\r
531 public static void <B>writeFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outstream,\r
532                               <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
533                               int&nbsp;width)\r
534                        throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
535 <DL>\r
536 <DD>Writes list of FastaSequeces into the outstream formatting the sequence
537  so that it contains width chars on each line\r
538 <P>\r
539 <DD><DL>\r
540 <DT><B>Parameters:</B><DD><CODE>outstream</CODE> - <DD><CODE>sequences</CODE> - <DD><CODE>width</CODE> - - the maximum number of characters to write in one line\r
541 <DT><B>Throws:</B>\r
542 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
543 </DD>\r
544 </DL>\r
545 <HR>\r
546 \r
547 <A NAME="writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
548 writeFastaKeepTheStream</H3>\r
549 <PRE>\r
550 public static void <B>writeFastaKeepTheStream</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outstream,\r
551                                            <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
552                                            int&nbsp;width)\r
553                                     throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
554 <DL>\r
555 <DD><DL>\r
556 \r
557 <DT><B>Throws:</B>\r
558 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
559 </DD>\r
560 </DL>\r
561 <HR>\r
562 \r
563 <A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>\r
564 readFasta</H3>\r
565 <PRE>\r
566 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>readFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;inStream)\r
567                                      throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
568 <DL>\r
569 <DD>Reads fasta sequences from inStream into the list of FastaSequence
570  objects\r
571 <P>\r
572 <DD><DL>\r
573 <DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from\r
574 <DT><B>Returns:</B><DD>list of FastaSequence objects\r
575 <DT><B>Throws:</B>\r
576 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
577 </DD>\r
578 </DL>\r
579 <HR>\r
580 \r
581 <A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>\r
582 writeFasta</H3>\r
583 <PRE>\r
584 public static void <B>writeFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;os,\r
585                               <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences)\r
586                        throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
587 <DL>\r
588 <DD>Writes FastaSequence in the file, each sequence will take one line only\r
589 <P>\r
590 <DD><DL>\r
591 <DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> - \r
592 <DT><B>Throws:</B>\r
593 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
594 </DD>\r
595 </DL>\r
596 <HR>\r
597 \r
598 <A NAME="closeSilently(java.util.logging.Logger, java.io.Closeable)"><!-- --></A><H3>\r
599 closeSilently</H3>\r
600 <PRE>\r
601 public static final void <B>closeSilently</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/logging/Logger.html?is-external=true" title="class or interface in java.util.logging">Logger</A>&nbsp;log,\r
602                                        <A HREF="http://java.sun.com/javase/6/docs/api/java/io/Closeable.html?is-external=true" title="class or interface in java.io">Closeable</A>&nbsp;stream)</PRE>\r
603 <DL>\r
604 <DD>Closes the Closable and logs the exception if any\r
605 <P>\r
606 <DD><DL>\r
607 <DT><B>Parameters:</B><DD><CODE>log</CODE> - <DD><CODE>stream</CODE> - </DL>\r
608 </DD>\r
609 </DL>\r
610 <!-- ========= END OF CLASS DATA ========= -->\r
611 <HR>\r
612 \r
613 \r
614 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
615 <A NAME="navbar_bottom"><!-- --></A>\r
616 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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620 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
621 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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623   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
624   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
625   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
626   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SequenceUtil.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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631   </TR>\r
632 </TABLE>\r
633 </TD>\r
634 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
635 </EM>\r
636 </TD>\r
637 </TR>\r
638 \r
639 <TR>\r
640 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
641 &nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
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