website/full_javadoc/compbio/data/sequence/ScoreManager.html

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   7 ScoreManager\r
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  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="ScoreManager";\r
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  58 &nbsp;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
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  79   SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class ScoreManager</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.ScoreManager</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public class <B>ScoreManager</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 <HR>\r
 105 \r
 106 <P>\r
 107 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 108 \r
 109 <A NAME="nested_class_summary"><!-- --></A>\r
 110 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 111 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 112 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 113 <B>Nested Class Summary</B></FONT></TH>\r
 114 </TR>\r
 115 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 116 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 117 <CODE>static&nbsp;class</CODE></FONT></TD>\r
 118 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></B></CODE>\r
 119 \r
 120 <BR>\r
 121 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 122 </TR>\r
 123 </TABLE>\r
 124 &nbsp;<!-- =========== FIELD SUMMARY =========== -->\r
 125 \r
 126 <A NAME="field_summary"><!-- --></A>\r
 127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 130 <B>Field Summary</B></FONT></TH>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 134 <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
 135 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></B></CODE>\r
 136 \r
 137 <BR>\r
 138 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 139 </TR>\r
 140 </TABLE>\r
 141 &nbsp;\r
 142 <!-- ========== METHOD SUMMARY =========== -->\r
 143 \r
 144 <A NAME="method_summary"><!-- --></A>\r
 145 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 146 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 147 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 148 <B>Method Summary</B></FONT></TH>\r
 149 </TR>\r
 150 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 151 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 152 <CODE>&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="http://java.sun.com/javase/6/docs/api/java/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
 153 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#asMap()">asMap</A></B>()</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;<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;</CODE></FONT></TD>\r
 161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#asSet()">asSet</A></B>()</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;boolean</CODE></FONT></TD>\r
 169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.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
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></CODE></FONT></TD>\r
 177 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)">getAnnotationForSequence</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;seqId)</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;int</CODE></FONT></TD>\r
 185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#getNumberOfSeq()">getNumberOfSeq</A></B>()</CODE>\r
 186 \r
 187 <BR>\r
 188 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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/ScoreManager.html#hashCode()">hashCode</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>static&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 201 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)">newInstance</A></B>(<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="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;&nbsp;data)</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>static&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 209 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)">newInstanceSingleScore</A></B>(<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;&nbsp;seqScoresMap)</CODE>\r
 210 \r
 211 <BR>\r
 212 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>static&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 217 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)">newInstanceSingleSequence</A></B>(<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;&nbsp;data)</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;void</CODE></FONT></TD>\r
 225 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#writeOut(java.io.Writer)">writeOut</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A>&nbsp;outStream)</CODE>\r
 226 \r
 227 <BR>\r
 228 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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#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#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
 238 </TR>\r
 239 </TABLE>\r
 240 &nbsp;\r
 241 <P>\r
 242 \r
 243 <!-- ============ FIELD DETAIL =========== -->\r
 244 \r
 245 <A NAME="field_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>Field Detail</B></FONT></TH>\r
 250 </TR>\r
 251 </TABLE>\r
 252 \r
 253 <A NAME="SINGLE_ENTRY_KEY"><!-- --></A><H3>\r
 254 SINGLE_ENTRY_KEY</H3>\r
 255 <PRE>\r
 256 public static final <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>SINGLE_ENTRY_KEY</B></PRE>\r
 257 <DL>\r
 258 <DL>\r
 259 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY">Constant Field Values</A></DL>\r
 260 </DL>\r
 261 \r
 262 <!-- ============ METHOD DETAIL ========== -->\r
 263 \r
 264 <A NAME="method_detail"><!-- --></A>\r
 265 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 266 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 267 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 268 <B>Method Detail</B></FONT></TH>\r
 269 </TR>\r
 270 </TABLE>\r
 271 \r
 272 <A NAME="newInstance(java.util.Map)"><!-- --></A><H3>\r
 273 newInstance</H3>\r
 274 <PRE>\r
 275 public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstance</B>(<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="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;&nbsp;data)</PRE>\r
 276 <DL>\r
 277 <DD><DL>\r
 278 </DL>\r
 279 </DD>\r
 280 </DL>\r
 281 <HR>\r
 282 \r
 283 <A NAME="newInstanceSingleScore(java.util.Map)"><!-- --></A><H3>\r
 284 newInstanceSingleScore</H3>\r
 285 <PRE>\r
 286 public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstanceSingleScore</B>(<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;&nbsp;seqScoresMap)</PRE>\r
 287 <DL>\r
 288 <DD><DL>\r
 289 </DL>\r
 290 </DD>\r
 291 </DL>\r
 292 <HR>\r
 293 \r
 294 <A NAME="newInstanceSingleSequence(java.util.Set)"><!-- --></A><H3>\r
 295 newInstanceSingleSequence</H3>\r
 296 <PRE>\r
 297 public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstanceSingleSequence</B>(<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;&nbsp;data)</PRE>\r
 298 <DL>\r
 299 <DD><DL>\r
 300 </DL>\r
 301 </DD>\r
 302 </DL>\r
 303 <HR>\r
 304 \r
 305 <A NAME="asMap()"><!-- --></A><H3>\r
 306 asMap</H3>\r
 307 <PRE>\r
 308 public <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="http://java.sun.com/javase/6/docs/api/java/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt; <B>asMap</B>()</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="asSet()"><!-- --></A><H3>\r
 317 asSet</H3>\r
 318 <PRE>\r
 319 public <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; <B>asSet</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="getNumberOfSeq()"><!-- --></A><H3>\r
 328 getNumberOfSeq</H3>\r
 329 <PRE>\r
 330 public int <B>getNumberOfSeq</B>()</PRE>\r
 331 <DL>\r
 332 <DD><DL>\r
 333 </DL>\r
 334 </DD>\r
 335 </DL>\r
 336 <HR>\r
 337 \r
 338 <A NAME="getAnnotationForSequence(java.lang.String)"><!-- --></A><H3>\r
 339 getAnnotationForSequence</H3>\r
 340 <PRE>\r
 341 public <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A> <B>getAnnotationForSequence</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;seqId)</PRE>\r
 342 <DL>\r
 343 <DD><DL>\r
 344 </DL>\r
 345 </DD>\r
 346 </DL>\r
 347 <HR>\r
 348 \r
 349 <A NAME="writeOut(java.io.Writer)"><!-- --></A><H3>\r
 350 writeOut</H3>\r
 351 <PRE>\r
 352 public void <B>writeOut</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A>&nbsp;outStream)\r
 353               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
 354 <DL>\r
 355 <DD><DL>\r
 356 \r
 357 <DT><B>Throws:</B>\r
 358 <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
 359 </DD>\r
 360 </DL>\r
 361 <HR>\r
 362 \r
 363 <A NAME="hashCode()"><!-- --></A><H3>\r
 364 hashCode</H3>\r
 365 <PRE>\r
 366 public int <B>hashCode</B>()</PRE>\r
 367 <DL>\r
 368 <DD><DL>\r
 369 <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
 370 </DD>\r
 371 <DD><DL>\r
 372 </DL>\r
 373 </DD>\r
 374 </DL>\r
 375 <HR>\r
 376 \r
 377 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 378 equals</H3>\r
 379 <PRE>\r
 380 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
 381 <DL>\r
 382 <DD><DL>\r
 383 <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
 384 </DD>\r
 385 <DD><DL>\r
 386 </DL>\r
 387 </DD>\r
 388 </DL>\r
 389 <!-- ========= END OF CLASS DATA ========= -->\r
 390 <HR>\r
 391 \r
 392 \r
 393 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 394 <A NAME="navbar_bottom"><!-- --></A>\r
 395 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 396 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 397 <TR>\r
 398 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 399 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 400 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 401   <TR ALIGN="center" VALIGN="top">\r
 402   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 403   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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 405   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ScoreManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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 413 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 414 </EM>\r
 415 </TD>\r
 416 </TR>\r
 417 \r
 418 <TR>\r
 419 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 420 &nbsp;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
 421 &nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
 422 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 423   <A HREF="../../../index.html?compbio/data/sequence/ScoreManager.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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 425 &nbsp;<SCRIPT type="text/javascript">\r
 426   <!--\r
 427   if(window==top) {\r
 428     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 429   }\r
 430   //-->\r
 431 </SCRIPT>\r
 432 <NOSCRIPT>\r
 433   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 434 </NOSCRIPT>\r
 435 \r
 436 \r
 437 </FONT></TD>\r
 438 </TR>\r
 439 <TR>\r
 440 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 441   SUMMARY:&nbsp;<A HREF="#nested_class_summary">NESTED</A>&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 442 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 443 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;CONSTR&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 444 </TR>\r
 445 </TABLE>\r
 446 <A NAME="skip-navbar_bottom"></A>\r
 447 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 448 \r
 449 <HR>\r
 450 \r
 451 </BODY>\r
 452 </HTML>\r