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

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   7 Score\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">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 Score</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.Score</B>\r
  97 </PRE>\r
  98 <DL>\r
  99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</DD>\r
 100 </DL>\r
 101 <HR>\r
 102 <DL>\r
 103 <DT><PRE><FONT SIZE="-1">@Immutable\r
 104 </FONT>public class <B>Score</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><DT>implements <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 A value class for AACon annotation results storage. The objects of this type
 109  are immutable\r
 110 <P>\r
 111 \r
 112 <P>\r
 113 <DL>\r
 114 <DT><B>Author:</B></DT>\r
 115   <DD>pvtroshin</DD>\r
 116 </DL>\r
 117 <HR>\r
 118 \r
 119 <P>\r
 120 \r
 121 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 122 \r
 123 <A NAME="constructor_summary"><!-- --></A>\r
 124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 125 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 126 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 127 <B>Constructor Summary</B></FONT></TH>\r
 128 </TR>\r
 129 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 130 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 131       <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores)</CODE>\r
 132 \r
 133 <BR>\r
 134 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Instantiate the Score</TD>\r
 135 </TR>\r
 136 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 137 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 138       <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores,\r
 139       <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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</CODE>\r
 140 \r
 141 <BR>\r
 142 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 143 </TR>\r
 144 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 145 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, float[])">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 146       float[]&nbsp;scores)</CODE>\r
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 150 </TR>\r
 151 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 153       <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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</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 </TABLE>\r
 159 &nbsp;\r
 160 <!-- ========== METHOD SUMMARY =========== -->\r
 161 \r
 162 <A NAME="method_summary"><!-- --></A>\r
 163 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 164 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 165 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 166 <B>Method Summary</B></FONT></TH>\r
 167 </TR>\r
 168 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 170 <CODE>&nbsp;int</CODE></FONT></TD>\r
 171 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)">compareTo</A></B>(<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&nbsp;o)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 175 </TR>\r
 176 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 178 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 179 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.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
 180 \r
 181 <BR>\r
 182 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 186 <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
 187 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getMethod()">getMethod</A></B>()</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the ConservationMethod</TD>\r
 191 </TR>\r
 192 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 194 <CODE>&nbsp;<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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;</CODE></FONT></TD>\r
 195 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getRanges()">getRanges</A></B>()</CODE>\r
 196 \r
 197 <BR>\r
 198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return Ranges if any Collections.EMPTY_SET otherwise</TD>\r
 199 </TR>\r
 200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 202 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;</CODE></FONT></TD>\r
 203 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getScores()">getScores</A></B>()</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The column scores for the alignment</TD>\r
 207 </TR>\r
 208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 210 <CODE>&nbsp;int</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#hashCode()">hashCode</A></B>()</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 215 </TR>\r
 216 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 218 <CODE>&nbsp;void</CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)">setRanges</A></B>(<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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</CODE>\r
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 226 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 227 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#toString()">toString</A></B>()</CODE>\r
 228 \r
 229 <BR>\r
 230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 231 </TR>\r
 232 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 234 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 235 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)">write</A></B>(<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;&nbsp;scores,\r
 236       <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;writer)</CODE>\r
 237 \r
 238 <BR>\r
 239 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Outputs the List of Score objects into the Output stream.</TD>\r
 240 </TR>\r
 241 </TABLE>\r
 242 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 243 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 244 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 245 <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
 246 </TR>\r
 247 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 248 <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#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
 249 </TR>\r
 250 </TABLE>\r
 251 &nbsp;\r
 252 <P>\r
 253 \r
 254 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 255 \r
 256 <A NAME="constructor_detail"><!-- --></A>\r
 257 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 258 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 259 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 260 <B>Constructor Detail</B></FONT></TH>\r
 261 </TR>\r
 262 </TABLE>\r
 263 \r
 264 <A NAME="Score(java.lang.Enum, java.util.ArrayList)"><!-- --></A><H3>\r
 265 Score</H3>\r
 266 <PRE>\r
 267 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 268              <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores)</PRE>\r
 269 <DL>\r
 270 <DD>Instantiate the Score\r
 271 <P>\r
 272 <DL>\r
 273 <DT><B>Parameters:</B><DD><CODE>method</CODE> - the ConservationMethod with which <code>scores</code> were
 274             calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
 275             alignment</DL>\r
 276 </DL>\r
 277 <HR>\r
 278 \r
 279 <A NAME="Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><!-- --></A><H3>\r
 280 Score</H3>\r
 281 <PRE>\r
 282 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 283              <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores,\r
 284              <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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</PRE>\r
 285 <DL>\r
 286 <DL>\r
 287 <DT><B>Parameters:</B><DD><CODE>method</CODE> - the ConservationMethod with which <code>scores</code> were
 288             calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
 289             alignment<DD><CODE>ranges</CODE> - The set of ranges i.e. parts of the sequence with specific
 290             function, usually can be calculated based on scores</DL>\r
 291 </DL>\r
 292 <HR>\r
 293 \r
 294 <A NAME="Score(java.lang.Enum, java.util.TreeSet)"><!-- --></A><H3>\r
 295 Score</H3>\r
 296 <PRE>\r
 297 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 298              <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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</PRE>\r
 299 <DL>\r
 300 </DL>\r
 301 <HR>\r
 302 \r
 303 <A NAME="Score(java.lang.Enum, float[])"><!-- --></A><H3>\r
 304 Score</H3>\r
 305 <PRE>\r
 306 public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
 307              float[]&nbsp;scores)</PRE>\r
 308 <DL>\r
 309 </DL>\r
 310 \r
 311 <!-- ============ METHOD DETAIL ========== -->\r
 312 \r
 313 <A NAME="method_detail"><!-- --></A>\r
 314 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 315 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 316 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 317 <B>Method Detail</B></FONT></TH>\r
 318 </TR>\r
 319 </TABLE>\r
 320 \r
 321 <A NAME="getMethod()"><!-- --></A><H3>\r
 322 getMethod</H3>\r
 323 <PRE>\r
 324 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>getMethod</B>()</PRE>\r
 325 <DL>\r
 326 <DD>Returns the ConservationMethod\r
 327 <P>\r
 328 <DD><DL>\r
 329 </DL>\r
 330 </DD>\r
 331 <DD><DL>\r
 332 \r
 333 <DT><B>Returns:</B><DD>the ConservationMethod</DL>\r
 334 </DD>\r
 335 </DL>\r
 336 <HR>\r
 337 \r
 338 <A NAME="getScores()"><!-- --></A><H3>\r
 339 getScores</H3>\r
 340 <PRE>\r
 341 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt; <B>getScores</B>()</PRE>\r
 342 <DL>\r
 343 <DD>The column scores for the alignment\r
 344 <P>\r
 345 <DD><DL>\r
 346 </DL>\r
 347 </DD>\r
 348 <DD><DL>\r
 349 \r
 350 <DT><B>Returns:</B><DD>the column scores for the alignment</DL>\r
 351 </DD>\r
 352 </DL>\r
 353 <HR>\r
 354 \r
 355 <A NAME="getRanges()"><!-- --></A><H3>\r
 356 getRanges</H3>\r
 357 <PRE>\r
 358 public <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/Range.html" title="class in compbio.data.sequence">Range</A>&gt; <B>getRanges</B>()</PRE>\r
 359 <DL>\r
 360 <DD>Return Ranges if any Collections.EMPTY_SET otherwise\r
 361 <P>\r
 362 <DD><DL>\r
 363 </DL>\r
 364 </DD>\r
 365 <DD><DL>\r
 366 \r
 367 <DT><B>Returns:</B><DD>ordered set of Range</DL>\r
 368 </DD>\r
 369 </DL>\r
 370 <HR>\r
 371 \r
 372 <A NAME="setRanges(java.util.TreeSet)"><!-- --></A><H3>\r
 373 setRanges</H3>\r
 374 <PRE>\r
 375 public void <B>setRanges</B>(<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/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</PRE>\r
 376 <DL>\r
 377 <DD><DL>\r
 378 </DL>\r
 379 </DD>\r
 380 <DD><DL>\r
 381 </DL>\r
 382 </DD>\r
 383 </DL>\r
 384 <HR>\r
 385 \r
 386 <A NAME="toString()"><!-- --></A><H3>\r
 387 toString</H3>\r
 388 <PRE>\r
 389 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
 390 <DL>\r
 391 <DD><DL>\r
 392 <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
 393 </DD>\r
 394 <DD><DL>\r
 395 </DL>\r
 396 </DD>\r
 397 </DL>\r
 398 <HR>\r
 399 \r
 400 <A NAME="hashCode()"><!-- --></A><H3>\r
 401 hashCode</H3>\r
 402 <PRE>\r
 403 public int <B>hashCode</B>()</PRE>\r
 404 <DL>\r
 405 <DD><DL>\r
 406 <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
 407 </DD>\r
 408 <DD><DL>\r
 409 </DL>\r
 410 </DD>\r
 411 </DL>\r
 412 <HR>\r
 413 \r
 414 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 415 equals</H3>\r
 416 <PRE>\r
 417 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
 418 <DL>\r
 419 <DD><DL>\r
 420 <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
 421 </DD>\r
 422 <DD><DL>\r
 423 </DL>\r
 424 </DD>\r
 425 </DL>\r
 426 <HR>\r
 427 \r
 428 <A NAME="write(java.util.TreeSet, java.io.Writer)"><!-- --></A><H3>\r
 429 write</H3>\r
 430 <PRE>\r
 431 public static void <B>write</B>(<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;&nbsp;scores,\r
 432                          <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;writer)\r
 433                   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
 434 <DL>\r
 435 <DD>Outputs the List of Score objects into the Output stream. The output
 436  format is as follows:
 437
 438  <pre>
 439  <code>#MethodName &lt;space separated list of values&gt;
 440
 441  For example:
 442
 443  #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
 444  #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
 445  </code>
 446  </pre>
 447
 448  The maximum precision for values is 3 digits, but can be less.\r
 449 <P>\r
 450 <DD><DL>\r
 451 </DL>\r
 452 </DD>\r
 453 <DD><DL>\r
 454 <DT><B>Parameters:</B><DD><CODE>scores</CODE> - the list of scores to output<DD><CODE>writer</CODE> - \r
 455 <DT><B>Throws:</B>\r
 456 <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 OutputStream cannot be written into\r
 457 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the output stream is null</DL>\r
 458 </DD>\r
 459 </DL>\r
 460 <HR>\r
 461 \r
 462 <A NAME="compareTo(compbio.data.sequence.Score)"><!-- --></A><H3>\r
 463 compareTo</H3>\r
 464 <PRE>\r
 465 public int <B>compareTo</B>(<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&nbsp;o)</PRE>\r
 466 <DL>\r
 467 <DD><DL>\r
 468 <DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true#compareTo(T)" title="class or interface in java.lang">compareTo</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></DL>\r
 469 </DD>\r
 470 <DD><DL>\r
 471 </DL>\r
 472 </DD>\r
 473 </DL>\r
 474 <!-- ========= END OF CLASS DATA ========= -->\r
 475 <HR>\r
 476 \r
 477 \r
 478 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 479 <A NAME="navbar_bottom"><!-- --></A>\r
 480 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 481 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 482 <TR>\r
 483 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 484 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 485 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 486   <TR ALIGN="center" VALIGN="top">\r
 487   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 488   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 489   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 490   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Score.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 491   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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 495   </TR>\r
 496 </TABLE>\r
 497 </TD>\r
 498 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 499 </EM>\r
 500 </TD>\r
 501 </TR>\r
 502 \r
 503 <TR>\r
 504 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 505 &nbsp;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
 506 &nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
 507 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 508   <A HREF="../../../index.html?compbio/data/sequence/Score.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 509 &nbsp;<A HREF="Score.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 510 &nbsp;<SCRIPT type="text/javascript">\r
 511   <!--\r
 512   if(window==top) {\r
 513     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 514   }\r
 515   //-->\r
 516 </SCRIPT>\r
 517 <NOSCRIPT>\r
 518   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 519 </NOSCRIPT>\r
 520 \r
 521 \r
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 523 </TR>\r
 524 <TR>\r
 525 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 526   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 527 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 528 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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