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  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
 617 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 618 <TR>\r
 619 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 620 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 621 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 622   <TR ALIGN="center" VALIGN="top">\r
 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
 627   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 628   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 629   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 630   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 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
 642 &nbsp;<A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
 643 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 644   <A HREF="../../../index.html?compbio/data/sequence/SequenceUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 645 &nbsp;<A HREF="SequenceUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 646 &nbsp;<SCRIPT type="text/javascript">\r
 647   <!--\r
 648   if(window==top) {\r
 649     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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