website/dm_javadoc/compbio/data/sequence/FastaSequence.html

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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class FastaSequence</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.FastaSequence</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE><FONT SIZE="-1">@Immutable\r
 101 </FONT>public class <B>FastaSequence</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
 102 </PRE>\r
 103 \r
 104 <P>\r
 105 A FASTA formatted sequence. Please note that this class does not make any
 106  assumptions as to what sequence it stores e.g. it could be nucleotide,
 107  protein or even gapped alignment sequence! The only guarantee it makes is
 108  that the sequence does not contain white space characters e.g. spaces, new
 109  lines etc\r
 110 <P>\r
 111 \r
 112 <P>\r
 113 <DL>\r
 114 <DT><B>Version:</B></DT>\r
 115   <DD>1.0 September 2009</DD>\r
 116 <DT><B>Author:</B></DT>\r
 117   <DD>pvtroshin</DD>\r
 118 </DL>\r
 119 <HR>\r
 120 \r
 121 <P>\r
 122 \r
 123 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 124 \r
 125 <A NAME="constructor_summary"><!-- --></A>\r
 126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 127 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 128 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 129 <B>Constructor Summary</B></FONT></TH>\r
 130 </TR>\r
 131 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 132 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</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;id,\r
 133               <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
 134 \r
 135 <BR>\r
 136 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Upon construction the any whitespace characters are removed from the
 137  sequence</TD>\r
 138 </TR>\r
 139 </TABLE>\r
 140 &nbsp;\r
 141 <!-- ========== METHOD SUMMARY =========== -->\r
 142 \r
 143 <A NAME="method_summary"><!-- --></A>\r
 144 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 145 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 146 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 147 <B>Method Summary</B></FONT></TH>\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;int</CODE></FONT></TD>\r
 152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</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;theString,\r
 153                        <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;theRegExp)</CODE>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(<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>&nbsp;obj)</CODE>\r
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 168 <CODE>&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
 169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int&nbsp;width)</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Format sequence per width letter in one string.</TD>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 176 <CODE>&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
 177 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>\r
 178 \r
 179 <BR>\r
 180 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 181 </TR>\r
 182 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 184 <CODE>&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
 185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>\r
 186 \r
 187 <BR>\r
 188 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the value of id</TD>\r
 189 </TR>\r
 190 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 192 <CODE>&nbsp;int</CODE></FONT></TD>\r
 193 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>\r
 194 \r
 195 <BR>\r
 196 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 197 </TR>\r
 198 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 199 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 200 <CODE>&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
 201 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>\r
 202 \r
 203 <BR>\r
 204 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 205 </TR>\r
 206 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 208 <CODE>&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
 209 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>\r
 210 \r
 211 <BR>\r
 212 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gets the value of sequence</TD>\r
 213 </TR>\r
 214 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 215 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 216 <CODE>&nbsp;int</CODE></FONT></TD>\r
 217 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></B>()</CODE>\r
 218 \r
 219 <BR>\r
 220 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 221 </TR>\r
 222 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 224 <CODE>&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
 225 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>\r
 226 \r
 227 <BR>\r
 228 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Same as oneLineFasta</TD>\r
 229 </TR>\r
 230 </TABLE>\r
 231 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 232 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 233 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 234 <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
 235 </TR>\r
 236 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 237 <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#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#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#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
 238 </TR>\r
 239 </TABLE>\r
 240 &nbsp;\r
 241 <P>\r
 242 \r
 243 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 244 \r
 245 <A NAME="constructor_detail"><!-- --></A>\r
 246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 248 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 249 <B>Constructor Detail</B></FONT></TH>\r
 250 </TR>\r
 251 </TABLE>\r
 252 \r
 253 <A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 254 FastaSequence</H3>\r
 255 <PRE>\r
 256 public <B>FastaSequence</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;id,\r
 257                      <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
 258 <DL>\r
 259 <DD>Upon construction the any whitespace characters are removed from the
 260  sequence\r
 261 <P>\r
 262 <DL>\r
 263 <DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </DL>\r
 264 </DL>\r
 265 \r
 266 <!-- ============ METHOD DETAIL ========== -->\r
 267 \r
 268 <A NAME="method_detail"><!-- --></A>\r
 269 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 270 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 271 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 272 <B>Method Detail</B></FONT></TH>\r
 273 </TR>\r
 274 </TABLE>\r
 275 \r
 276 <A NAME="getId()"><!-- --></A><H3>\r
 277 getId</H3>\r
 278 <PRE>\r
 279 public <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>getId</B>()</PRE>\r
 280 <DL>\r
 281 <DD>Gets the value of id\r
 282 <P>\r
 283 <DD><DL>\r
 284 \r
 285 <DT><B>Returns:</B><DD>the value of id</DL>\r
 286 </DD>\r
 287 </DL>\r
 288 <HR>\r
 289 \r
 290 <A NAME="getSequence()"><!-- --></A><H3>\r
 291 getSequence</H3>\r
 292 <PRE>\r
 293 public <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>getSequence</B>()</PRE>\r
 294 <DL>\r
 295 <DD>Gets the value of sequence\r
 296 <P>\r
 297 <DD><DL>\r
 298 \r
 299 <DT><B>Returns:</B><DD>the value of sequence</DL>\r
 300 </DD>\r
 301 </DL>\r
 302 <HR>\r
 303 \r
 304 <A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 305 countMatchesInSequence</H3>\r
 306 <PRE>\r
 307 public static int <B>countMatchesInSequence</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;theString,\r
 308                                          <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;theRegExp)</PRE>\r
 309 <DL>\r
 310 <DD><DL>\r
 311 </DL>\r
 312 </DD>\r
 313 </DL>\r
 314 <HR>\r
 315 \r
 316 <A NAME="getFormattedFasta()"><!-- --></A><H3>\r
 317 getFormattedFasta</H3>\r
 318 <PRE>\r
 319 public <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>getFormattedFasta</B>()</PRE>\r
 320 <DL>\r
 321 <DD><DL>\r
 322 </DL>\r
 323 </DD>\r
 324 </DL>\r
 325 <HR>\r
 326 \r
 327 <A NAME="getOnelineFasta()"><!-- --></A><H3>\r
 328 getOnelineFasta</H3>\r
 329 <PRE>\r
 330 public <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>getOnelineFasta</B>()</PRE>\r
 331 <DL>\r
 332 <DD><DL>\r
 333 \r
 334 <DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
 335          length is</DL>\r
 336 </DD>\r
 337 </DL>\r
 338 <HR>\r
 339 \r
 340 <A NAME="getFormatedSequence(int)"><!-- --></A><H3>\r
 341 getFormatedSequence</H3>\r
 342 <PRE>\r
 343 public <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>getFormatedSequence</B>(int&nbsp;width)</PRE>\r
 344 <DL>\r
 345 <DD>Format sequence per width letter in one string. Without spaces.\r
 346 <P>\r
 347 <DD><DL>\r
 348 \r
 349 <DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>\r
 350 </DD>\r
 351 </DL>\r
 352 <HR>\r
 353 \r
 354 <A NAME="getLength()"><!-- --></A><H3>\r
 355 getLength</H3>\r
 356 <PRE>\r
 357 public int <B>getLength</B>()</PRE>\r
 358 <DL>\r
 359 <DD><DL>\r
 360 \r
 361 <DT><B>Returns:</B><DD>sequence length</DL>\r
 362 </DD>\r
 363 </DL>\r
 364 <HR>\r
 365 \r
 366 <A NAME="toString()"><!-- --></A><H3>\r
 367 toString</H3>\r
 368 <PRE>\r
 369 public <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>toString</B>()</PRE>\r
 370 <DL>\r
 371 <DD>Same as oneLineFasta\r
 372 <P>\r
 373 <DD><DL>\r
 374 <DT><B>Overrides:</B><DD><CODE><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></CODE> in class <CODE><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></CODE></DL>\r
 375 </DD>\r
 376 <DD><DL>\r
 377 </DL>\r
 378 </DD>\r
 379 </DL>\r
 380 <HR>\r
 381 \r
 382 <A NAME="hashCode()"><!-- --></A><H3>\r
 383 hashCode</H3>\r
 384 <PRE>\r
 385 public int <B>hashCode</B>()</PRE>\r
 386 <DL>\r
 387 <DD><DL>\r
 388 <DT><B>Overrides:</B><DD><CODE><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></CODE> in class <CODE><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></CODE></DL>\r
 389 </DD>\r
 390 <DD><DL>\r
 391 </DL>\r
 392 </DD>\r
 393 </DL>\r
 394 <HR>\r
 395 \r
 396 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 397 equals</H3>\r
 398 <PRE>\r
 399 public boolean <B>equals</B>(<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>&nbsp;obj)</PRE>\r
 400 <DL>\r
 401 <DD><DL>\r
 402 <DT><B>Overrides:</B><DD><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></CODE> in class <CODE><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></CODE></DL>\r
 403 </DD>\r
 404 <DD><DL>\r
 405 </DL>\r
 406 </DD>\r
 407 </DL>\r
 408 <!-- ========= END OF CLASS DATA ========= -->\r
 409 <HR>\r
 410 \r
 411 \r
 412 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 413 <A NAME="navbar_bottom"><!-- --></A>\r
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 415 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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 418 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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 424   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/FastaSequence.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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 432 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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 436 \r
 437 <TR>\r
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 444 &nbsp;<SCRIPT type="text/javascript">\r
 445   <!--\r
 446   if(window==top) {\r
 447     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 448   }\r
 449   //-->\r
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 452   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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