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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>Since:</B></DT>\r
 110   <DD>1.0</DD>\r
 111 <DT><B>Version:</B></DT>\r
 112   <DD>2.0 June 2011</DD>\r
 113 <DT><B>Author:</B></DT>\r
 114   <DD>Peter Troshin</DD>\r
 115 </DL>\r
 116 <HR>\r
 117 \r
 118 <P>\r
 119 <!-- =========== FIELD SUMMARY =========== -->\r
 120 \r
 121 <A NAME="field_summary"><!-- --></A>\r
 122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 125 <B>Field Summary</B></FONT></TH>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <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
 130 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Valid Amino acids</TD>\r
 134 </TR>\r
 135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 137 <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
 138 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>\r
 139 \r
 140 <BR>\r
 141 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Same as AA pattern but with two additional letters - XU</TD>\r
 142 </TR>\r
 143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 145 <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
 146 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ambiguous nucleotide</TD>\r
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 153 <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
 154 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>\r
 155 \r
 156 <BR>\r
 157 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A digit</TD>\r
 158 </TR>\r
 159 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 161 <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
 162 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;inversion of AA pattern</TD>\r
 166 </TR>\r
 167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 169 <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
 170 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>\r
 171 \r
 172 <BR>\r
 173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Non nucleotide</TD>\r
 174 </TR>\r
 175 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 177 <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
 178 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>\r
 179 \r
 180 <BR>\r
 181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Non word</TD>\r
 182 </TR>\r
 183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 185 <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
 186 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>\r
 187 \r
 188 <BR>\r
 189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Nucleotides a, t, g, c, u</TD>\r
 190 </TR>\r
 191 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 192 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 193 <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
 194 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>\r
 195 \r
 196 <BR>\r
 197 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A whitespace character: [\t\n\x0B\f\r]</TD>\r
 198 </TR>\r
 199 </TABLE>\r
 200 &nbsp;\r
 201 <!-- ========== METHOD SUMMARY =========== -->\r
 202 \r
 203 <A NAME="method_summary"><!-- --></A>\r
 204 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 205 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 206 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 207 <B>Method Summary</B></FONT></TH>\r
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 211 <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
 212 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#cleanProteinSequence(java.lang.String)">cleanProteinSequence</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
 213 \r
 214 <BR>\r
 215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Remove all non AA chars from the sequence</TD>\r
 216 </TR>\r
 217 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 219 <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
 220 <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
 221 \r
 222 <BR>\r
 223 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes all whitespace chars in the sequence string</TD>\r
 224 </TR>\r
 225 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 226 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 227 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 228 <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
 229               <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
 230 \r
 231 <BR>\r
 232 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Closes the Closable and logs the exception if any</TD>\r
 233 </TR>\r
 234 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 236 <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
 237 <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
 238 \r
 239 <BR>\r
 240 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Removes all special characters and digits as well as whitespace chars
 241  from the sequence</TD>\r
 242 </TR>\r
 243 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 244 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 245 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 246 <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
 247 \r
 248 <BR>\r
 249 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Check whether the sequence confirms to amboguous protein sequence</TD>\r
 250 </TR>\r
 251 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 253 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 254 <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
 255 \r
 256 <BR>\r
 257 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 258  (!) - B char</TD>\r
 259 </TR>\r
 260 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 261 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 262 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 263 <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
 264 \r
 265 <BR>\r
 266 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 267 </TR>\r
 268 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 269 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 270 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 271 <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
 272 \r
 273 <BR>\r
 274 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 275 </TR>\r
 276 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 277 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 278 <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
 279 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)">openInputStream</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;inFilePath)</CODE>\r
 280 \r
 281 <BR>\r
 282 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads and parses Fasta or Clustal formatted file into a list of
 283  FastaSequence objects</TD>\r
 284 </TR>\r
 285 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 287 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 288 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)">readAAConResults</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;results)</CODE>\r
 289 \r
 290 <BR>\r
 291 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read AACon result with no alignment files.</TD>\r
 292 </TR>\r
 293 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 295 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
 296 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)">readDisembl</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;input)</CODE>\r
 297 \r
 298 <BR>\r
 299 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
 300
 301  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 302
 303  # REM465 355-368
 304
 305  # HOTLOOPS 190-204
 306
 307  # RESIDUE COILS REM465 HOTLOOPS
 308
 309  M 0.86010 0.88512 0.37094
 310
 311  T 0.79983 0.85864 0.44331
 312
 313  >Next Sequence name</TD>\r
 314 </TR>\r
 315 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 316 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 317 <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
 318 <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
 319 \r
 320 <BR>\r
 321 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads fasta sequences from inStream into the list of FastaSequence
 322  objects</TD>\r
 323 </TR>\r
 324 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 325 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 326 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
 327 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)">readGlobPlot</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;input)</CODE>\r
 328 \r
 329 <BR>\r
 330 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
 331
 332  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 333
 334  # REM465 355-368
 335
 336  # HOTLOOPS 190-204
 337
 338  # RESIDUE COILS REM465 HOTLOOPS
 339
 340  M 0.86010 0.88512 0.37094
 341
 342  T 0.79983 0.85864 0.44331
 343
 344  >Next Sequence name</TD>\r
 345 </TR>\r
 346 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 347 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 348 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 349 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)">readIUPred</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)</CODE>\r
 350 \r
 351 <BR>\r
 352 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read IUPred output</TD>\r
 353 </TR>\r
 354 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 355 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 356 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 357 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)</CODE>\r
 358 \r
 359 <BR>\r
 360 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 361 </TR>\r
 362 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 363 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 364 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 365 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</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
 366 \r
 367 <BR>\r
 368 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reader for JRonn horizontal file format</TD>\r
 369 </TR>\r
 370 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 371 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 372 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 373 <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
 374            <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
 375 \r
 376 <BR>\r
 377 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes FastaSequence in the file, each sequence will take one line only</TD>\r
 378 </TR>\r
 379 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 380 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 381 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 382 <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
 383            <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
 384            int&nbsp;width)</CODE>\r
 385 \r
 386 <BR>\r
 387 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes list of FastaSequeces into the outstream formatting the sequence
 388  so that it contains width chars on each line</TD>\r
 389 </TR>\r
 390 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 391 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 392 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 393 <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
 394                         <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
 395                         int&nbsp;width)</CODE>\r
 396 \r
 397 <BR>\r
 398 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 399 </TR>\r
 400 </TABLE>\r
 401 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 402 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 403 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 404 <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
 405 </TR>\r
 406 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 407 <TD><CODE><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#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
 408 </TR>\r
 409 </TABLE>\r
 410 &nbsp;\r
 411 <P>\r
 412 \r
 413 <!-- ============ FIELD DETAIL =========== -->\r
 414 \r
 415 <A NAME="field_detail"><!-- --></A>\r
 416 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 417 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 418 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 419 <B>Field Detail</B></FONT></TH>\r
 420 </TR>\r
 421 </TABLE>\r
 422 \r
 423 <A NAME="WHITE_SPACE"><!-- --></A><H3>\r
 424 WHITE_SPACE</H3>\r
 425 <PRE>\r
 426 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
 427 <DL>\r
 428 <DD>A whitespace character: [\t\n\x0B\f\r]\r
 429 <P>\r
 430 <DL>\r
 431 </DL>\r
 432 </DL>\r
 433 <HR>\r
 434 \r
 435 <A NAME="DIGIT"><!-- --></A><H3>\r
 436 DIGIT</H3>\r
 437 <PRE>\r
 438 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
 439 <DL>\r
 440 <DD>A digit\r
 441 <P>\r
 442 <DL>\r
 443 </DL>\r
 444 </DL>\r
 445 <HR>\r
 446 \r
 447 <A NAME="NONWORD"><!-- --></A><H3>\r
 448 NONWORD</H3>\r
 449 <PRE>\r
 450 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
 451 <DL>\r
 452 <DD>Non word\r
 453 <P>\r
 454 <DL>\r
 455 </DL>\r
 456 </DL>\r
 457 <HR>\r
 458 \r
 459 <A NAME="AA"><!-- --></A><H3>\r
 460 AA</H3>\r
 461 <PRE>\r
 462 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
 463 <DL>\r
 464 <DD>Valid Amino acids\r
 465 <P>\r
 466 <DL>\r
 467 </DL>\r
 468 </DL>\r
 469 <HR>\r
 470 \r
 471 <A NAME="NON_AA"><!-- --></A><H3>\r
 472 NON_AA</H3>\r
 473 <PRE>\r
 474 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
 475 <DL>\r
 476 <DD>inversion of AA pattern\r
 477 <P>\r
 478 <DL>\r
 479 </DL>\r
 480 </DL>\r
 481 <HR>\r
 482 \r
 483 <A NAME="AMBIGUOUS_AA"><!-- --></A><H3>\r
 484 AMBIGUOUS_AA</H3>\r
 485 <PRE>\r
 486 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
 487 <DL>\r
 488 <DD>Same as AA pattern but with two additional letters - XU\r
 489 <P>\r
 490 <DL>\r
 491 </DL>\r
 492 </DL>\r
 493 <HR>\r
 494 \r
 495 <A NAME="NUCLEOTIDE"><!-- --></A><H3>\r
 496 NUCLEOTIDE</H3>\r
 497 <PRE>\r
 498 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
 499 <DL>\r
 500 <DD>Nucleotides a, t, g, c, u\r
 501 <P>\r
 502 <DL>\r
 503 </DL>\r
 504 </DL>\r
 505 <HR>\r
 506 \r
 507 <A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>\r
 508 AMBIGUOUS_NUCLEOTIDE</H3>\r
 509 <PRE>\r
 510 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
 511 <DL>\r
 512 <DD>Ambiguous nucleotide\r
 513 <P>\r
 514 <DL>\r
 515 </DL>\r
 516 </DL>\r
 517 <HR>\r
 518 \r
 519 <A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>\r
 520 NON_NUCLEOTIDE</H3>\r
 521 <PRE>\r
 522 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
 523 <DL>\r
 524 <DD>Non nucleotide\r
 525 <P>\r
 526 <DL>\r
 527 </DL>\r
 528 </DL>\r
 529 \r
 530 <!-- ============ METHOD DETAIL ========== -->\r
 531 \r
 532 <A NAME="method_detail"><!-- --></A>\r
 533 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 534 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 535 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 536 <B>Method Detail</B></FONT></TH>\r
 537 </TR>\r
 538 </TABLE>\r
 539 \r
 540 <A NAME="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>\r
 541 isNucleotideSequence</H3>\r
 542 <PRE>\r
 543 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
 544 <DL>\r
 545 <DD><DL>\r
 546 \r
 547 <DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>\r
 548 </DD>\r
 549 </DL>\r
 550 <HR>\r
 551 \r
 552 <A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>\r
 553 isNonAmbNucleotideSequence</H3>\r
 554 <PRE>\r
 555 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
 556 <DL>\r
 557 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
 558  (!) - B char\r
 559 <P>\r
 560 <DD><DL>\r
 561 </DL>\r
 562 </DD>\r
 563 </DL>\r
 564 <HR>\r
 565 \r
 566 <A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>\r
 567 cleanSequence</H3>\r
 568 <PRE>\r
 569 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
 570 <DL>\r
 571 <DD>Removes all whitespace chars in the sequence string\r
 572 <P>\r
 573 <DD><DL>\r
 574 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
 575 <DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
 576 </DD>\r
 577 </DL>\r
 578 <HR>\r
 579 \r
 580 <A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>\r
 581 deepCleanSequence</H3>\r
 582 <PRE>\r
 583 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
 584 <DL>\r
 585 <DD>Removes all special characters and digits as well as whitespace chars
 586  from the sequence\r
 587 <P>\r
 588 <DD><DL>\r
 589 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
 590 <DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
 591 </DD>\r
 592 </DL>\r
 593 <HR>\r
 594 \r
 595 <A NAME="cleanProteinSequence(java.lang.String)"><!-- --></A><H3>\r
 596 cleanProteinSequence</H3>\r
 597 <PRE>\r
 598 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>cleanProteinSequence</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
 599 <DL>\r
 600 <DD>Remove all non AA chars from the sequence\r
 601 <P>\r
 602 <DD><DL>\r
 603 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence to clean\r
 604 <DT><B>Returns:</B><DD>cleaned sequence</DL>\r
 605 </DD>\r
 606 </DL>\r
 607 <HR>\r
 608 \r
 609 <A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>\r
 610 isProteinSequence</H3>\r
 611 <PRE>\r
 612 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
 613 <DL>\r
 614 <DD><DL>\r
 615 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
 616 <DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>\r
 617 </DD>\r
 618 </DL>\r
 619 <HR>\r
 620 \r
 621 <A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>\r
 622 isAmbiguosProtein</H3>\r
 623 <PRE>\r
 624 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
 625 <DL>\r
 626 <DD>Check whether the sequence confirms to amboguous protein sequence\r
 627 <P>\r
 628 <DD><DL>\r
 629 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
 630 <DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
 631          Return false otherwise. e.g. if the sequence is non-ambiguous
 632          protein or DNA</DL>\r
 633 </DD>\r
 634 </DL>\r
 635 <HR>\r
 636 \r
 637 <A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
 638 writeFasta</H3>\r
 639 <PRE>\r
 640 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
 641                               <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
 642                               int&nbsp;width)\r
 643                        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
 644 <DL>\r
 645 <DD>Writes list of FastaSequeces into the outstream formatting the sequence
 646  so that it contains width chars on each line\r
 647 <P>\r
 648 <DD><DL>\r
 649 <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
 650 <DT><B>Throws:</B>\r
 651 <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
 652 </DD>\r
 653 </DL>\r
 654 <HR>\r
 655 \r
 656 <A NAME="writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
 657 writeFastaKeepTheStream</H3>\r
 658 <PRE>\r
 659 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
 660                                            <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
 661                                            int&nbsp;width)\r
 662                                     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
 663 <DL>\r
 664 <DD><DL>\r
 665 \r
 666 <DT><B>Throws:</B>\r
 667 <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
 668 </DD>\r
 669 </DL>\r
 670 <HR>\r
 671 \r
 672 <A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>\r
 673 readFasta</H3>\r
 674 <PRE>\r
 675 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
 676                                      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
 677 <DL>\r
 678 <DD>Reads fasta sequences from inStream into the list of FastaSequence
 679  objects\r
 680 <P>\r
 681 <DD><DL>\r
 682 <DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from\r
 683 <DT><B>Returns:</B><DD>list of FastaSequence objects\r
 684 <DT><B>Throws:</B>\r
 685 <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
 686 </DD>\r
 687 </DL>\r
 688 <HR>\r
 689 \r
 690 <A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>\r
 691 writeFasta</H3>\r
 692 <PRE>\r
 693 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
 694                               <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
 695                        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
 696 <DL>\r
 697 <DD>Writes FastaSequence in the file, each sequence will take one line only\r
 698 <P>\r
 699 <DD><DL>\r
 700 <DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> - \r
 701 <DT><B>Throws:</B>\r
 702 <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
 703 </DD>\r
 704 </DL>\r
 705 <HR>\r
 706 \r
 707 <A NAME="readIUPred(java.io.File)"><!-- --></A><H3>\r
 708 readIUPred</H3>\r
 709 <PRE>\r
 710 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt; <B>readIUPred</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)\r
 711                                     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>,\r
 712                                            <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 713 <DL>\r
 714 <DD>Read IUPred output\r
 715 <P>\r
 716 <DD><DL>\r
 717 <DT><B>Parameters:</B><DD><CODE>result</CODE> - \r
 718 <DT><B>Returns:</B><DD>Map key->sequence name, value->Score\r
 719 <DT><B>Throws:</B>\r
 720 <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>\r
 721 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
 722 </DD>\r
 723 </DL>\r
 724 <HR>\r
 725 \r
 726 <A NAME="readJRonn(java.io.File)"><!-- --></A><H3>\r
 727 readJRonn</H3>\r
 728 <PRE>\r
 729 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt; <B>readJRonn</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;result)\r
 730                                    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>,\r
 731                                           <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 732 <DL>\r
 733 <DD><DL>\r
 734 \r
 735 <DT><B>Throws:</B>\r
 736 <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>\r
 737 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
 738 </DD>\r
 739 </DL>\r
 740 <HR>\r
 741 \r
 742 <A NAME="readJRonn(java.io.InputStream)"><!-- --></A><H3>\r
 743 readJRonn</H3>\r
 744 <PRE>\r
 745 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt; <B>readJRonn</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
 746                                    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>,\r
 747                                           <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 748 <DL>\r
 749 <DD>Reader for JRonn horizontal file format
 750
 751  <pre>
 752  &gtFoobar M G D T T A G 0.48 0.42
 753  0.42 0.48 0.52 0.53 0.54
 754
 755  <pre>
 756  Where all values are tab delimited\r
 757 <P>\r
 758 <DD><DL>\r
 759 <DT><B>Parameters:</B><DD><CODE>inStream</CODE> - the InputStream connected to the JRonn output file\r
 760 <DT><B>Returns:</B><DD>Map key=sequence name value=Score\r
 761 <DT><B>Throws:</B>\r
 762 <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> - is thrown if the inStream has problems accessing the data\r
 763 <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
 764  data, i.e. not a JRonn output</DL>\r
 765 </DD>\r
 766 </DL>\r
 767 <HR>\r
 768 \r
 769 <A NAME="closeSilently(java.util.logging.Logger, java.io.Closeable)"><!-- --></A><H3>\r
 770 closeSilently</H3>\r
 771 <PRE>\r
 772 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
 773                                        <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
 774 <DL>\r
 775 <DD>Closes the Closable and logs the exception if any\r
 776 <P>\r
 777 <DD><DL>\r
 778 <DT><B>Parameters:</B><DD><CODE>log</CODE> - <DD><CODE>stream</CODE> - </DL>\r
 779 </DD>\r
 780 </DL>\r
 781 <HR>\r
 782 \r
 783 <A NAME="readDisembl(java.io.InputStream)"><!-- --></A><H3>\r
 784 readDisembl</H3>\r
 785 <PRE>\r
 786 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt; <B>readDisembl</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;input)\r
 787                                               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>,\r
 788                                                      <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 789 <DL>\r
 790 <DD>> Foobar_dundeefriends
 791
 792  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 793
 794  # REM465 355-368
 795
 796  # HOTLOOPS 190-204
 797
 798  # RESIDUE COILS REM465 HOTLOOPS
 799
 800  M 0.86010 0.88512 0.37094
 801
 802  T 0.79983 0.85864 0.44331
 803
 804  >Next Sequence name\r
 805 <P>\r
 806 <DD><DL>\r
 807 <DT><B>Parameters:</B><DD><CODE>input</CODE> - the InputStream\r
 808 <DT><B>Returns:</B><DD>Map key=sequence name, value=set of score\r
 809 <DT><B>Throws:</B>\r
 810 <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>\r
 811 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
 812 </DD>\r
 813 </DL>\r
 814 <HR>\r
 815 \r
 816 <A NAME="readGlobPlot(java.io.InputStream)"><!-- --></A><H3>\r
 817 readGlobPlot</H3>\r
 818 <PRE>\r
 819 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt; <B>readGlobPlot</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;input)\r
 820                                                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>,\r
 821                                                       <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 822 <DL>\r
 823 <DD>> Foobar_dundeefriends
 824
 825  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 826
 827  # REM465 355-368
 828
 829  # HOTLOOPS 190-204
 830
 831  # RESIDUE COILS REM465 HOTLOOPS
 832
 833  M 0.86010 0.88512 0.37094
 834
 835  T 0.79983 0.85864 0.44331
 836
 837  >Next Sequence name\r
 838 <P>\r
 839 <DD><DL>\r
 840 <DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
 841 <DT><B>Returns:</B><DD>Map key=sequence name, value=set of score\r
 842 <DT><B>Throws:</B>\r
 843 <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>\r
 844 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
 845 </DD>\r
 846 </DL>\r
 847 <HR>\r
 848 \r
 849 <A NAME="readAAConResults(java.io.InputStream)"><!-- --></A><H3>\r
 850 readAAConResults</H3>\r
 851 <PRE>\r
 852 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashSet.html?is-external=true" title="class or interface in java.util">HashSet</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt; <B>readAAConResults</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;results)</PRE>\r
 853 <DL>\r
 854 <DD>Read AACon result with no alignment files. This method leaves incoming
 855  InputStream open!\r
 856 <P>\r
 857 <DD><DL>\r
 858 <DT><B>Parameters:</B><DD><CODE>results</CODE> - output file of AAConservation\r
 859 <DT><B>Returns:</B><DD>Map with keys <A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><CODE>ConservationMethod</CODE></A> -> float[]</DL>\r
 860 </DD>\r
 861 </DL>\r
 862 <HR>\r
 863 \r
 864 <A NAME="openInputStream(java.lang.String)"><!-- --></A><H3>\r
 865 openInputStream</H3>\r
 866 <PRE>\r
 867 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>openInputStream</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;inFilePath)\r
 868                                            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>,\r
 869                                                   <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 870 <DL>\r
 871 <DD>Reads and parses Fasta or Clustal formatted file into a list of
 872  FastaSequence objects\r
 873 <P>\r
 874 <DD><DL>\r
 875 <DT><B>Parameters:</B><DD><CODE>inFilePath</CODE> - the path to the input file\r
 876 <DT><B>Returns:</B><DD>the List of FastaSequence objects\r
 877 <DT><B>Throws:</B>\r
 878 <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> - if the file denoted by inFilePath cannot be read\r
 879 <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
 880              recognised</DL>\r
 881 </DD>\r
 882 </DL>\r
 883 <!-- ========= END OF CLASS DATA ========= -->\r
 884 <HR>\r
 885 \r
 886 \r
 887 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 888 <A NAME="navbar_bottom"><!-- --></A>\r
 889 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 890 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 891 <TR>\r
 892 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 893 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 894 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 895   <TR ALIGN="center" VALIGN="top">\r
 896   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 897   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 898   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 899   <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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