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

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   7 Score\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 <HR>\r
  99 <DL>\r
 100 <DT><PRE><FONT SIZE="-1">@Immutable\r
 101 </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></DL>\r
 102 </PRE>\r
 103 \r
 104 <P>\r
 105 A value class for AACon annotation results storage\r
 106 <P>\r
 107 \r
 108 <P>\r
 109 <DL>\r
 110 <DT><B>Author:</B></DT>\r
 111   <DD>pvtroshin</DD>\r
 112 </DL>\r
 113 <HR>\r
 114 \r
 115 <P>\r
 116 \r
 117 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 118 \r
 119 <A NAME="constructor_summary"><!-- --></A>\r
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 123 <B>Constructor Summary</B></FONT></TH>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(compbio.data.sequence.ConservationMethod, java.util.List)">Score</A></B>(<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>&nbsp;method,\r
 127       <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="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
 128 \r
 129 <BR>\r
 130 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Instantiate the Score</TD>\r
 131 </TR>\r
 132 </TABLE>\r
 133 &nbsp;\r
 134 <!-- ========== METHOD SUMMARY =========== -->\r
 135 \r
 136 <A NAME="method_summary"><!-- --></A>\r
 137 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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 140 <B>Method Summary</B></FONT></TH>\r
 141 </TR>\r
 142 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 143 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 144 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 145 <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
 146 \r
 147 <BR>\r
 148 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A></CODE></FONT></TD>\r
 153 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getMethod()">getMethod</A></B>()</CODE>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the ConservationMethod</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/List.html?is-external=true" title="class or interface in java.util">List</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
 161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getScores()">getScores</A></B>()</CODE>\r
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The column scores for the alignment</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;int</CODE></FONT></TD>\r
 169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#hashCode()">hashCode</A></B>()</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="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/Score.html#toString()">toString</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>static&nbsp;void</CODE></FONT></TD>\r
 185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#write(java.util.Set, java.io.OutputStream)">write</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;scores,\r
 186       <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;output)</CODE>\r
 187 \r
 188 <BR>\r
 189 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Outputs the List of Score objects into the Output stream.</TD>\r
 190 </TR>\r
 191 </TABLE>\r
 192 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 194 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 195 <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
 196 </TR>\r
 197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 198 <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
 199 </TR>\r
 200 </TABLE>\r
 201 &nbsp;\r
 202 <P>\r
 203 \r
 204 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 205 \r
 206 <A NAME="constructor_detail"><!-- --></A>\r
 207 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 208 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 209 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 210 <B>Constructor Detail</B></FONT></TH>\r
 211 </TR>\r
 212 </TABLE>\r
 213 \r
 214 <A NAME="Score(compbio.data.sequence.ConservationMethod, java.util.List)"><!-- --></A><H3>\r
 215 Score</H3>\r
 216 <PRE>\r
 217 public <B>Score</B>(<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>&nbsp;method,\r
 218              <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="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
 219 <DL>\r
 220 <DD>Instantiate the Score\r
 221 <P>\r
 222 <DL>\r
 223 <DT><B>Parameters:</B><DD><CODE>method</CODE> - the ConservationMethod with which <code>scores</code> were
 224             calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
 225             alignment</DL>\r
 226 </DL>\r
 227 \r
 228 <!-- ============ METHOD DETAIL ========== -->\r
 229 \r
 230 <A NAME="method_detail"><!-- --></A>\r
 231 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 232 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 233 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 234 <B>Method Detail</B></FONT></TH>\r
 235 </TR>\r
 236 </TABLE>\r
 237 \r
 238 <A NAME="getMethod()"><!-- --></A><H3>\r
 239 getMethod</H3>\r
 240 <PRE>\r
 241 public <A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A> <B>getMethod</B>()</PRE>\r
 242 <DL>\r
 243 <DD>Returns the ConservationMethod\r
 244 <P>\r
 245 <DD><DL>\r
 246 \r
 247 <DT><B>Returns:</B><DD>the ConservationMethod</DL>\r
 248 </DD>\r
 249 </DL>\r
 250 <HR>\r
 251 \r
 252 <A NAME="getScores()"><!-- --></A><H3>\r
 253 getScores</H3>\r
 254 <PRE>\r
 255 public <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="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
 256 <DL>\r
 257 <DD>The column scores for the alignment\r
 258 <P>\r
 259 <DD><DL>\r
 260 \r
 261 <DT><B>Returns:</B><DD>the column scores for the alignment</DL>\r
 262 </DD>\r
 263 </DL>\r
 264 <HR>\r
 265 \r
 266 <A NAME="toString()"><!-- --></A><H3>\r
 267 toString</H3>\r
 268 <PRE>\r
 269 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
 270 <DL>\r
 271 <DD><DL>\r
 272 <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
 273 </DD>\r
 274 <DD><DL>\r
 275 </DL>\r
 276 </DD>\r
 277 </DL>\r
 278 <HR>\r
 279 \r
 280 <A NAME="hashCode()"><!-- --></A><H3>\r
 281 hashCode</H3>\r
 282 <PRE>\r
 283 public int <B>hashCode</B>()</PRE>\r
 284 <DL>\r
 285 <DD><DL>\r
 286 <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
 287 </DD>\r
 288 <DD><DL>\r
 289 </DL>\r
 290 </DD>\r
 291 </DL>\r
 292 <HR>\r
 293 \r
 294 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 295 equals</H3>\r
 296 <PRE>\r
 297 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
 298 <DL>\r
 299 <DD><DL>\r
 300 <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
 301 </DD>\r
 302 <DD><DL>\r
 303 </DL>\r
 304 </DD>\r
 305 </DL>\r
 306 <HR>\r
 307 \r
 308 <A NAME="write(java.util.Set, java.io.OutputStream)"><!-- --></A><H3>\r
 309 write</H3>\r
 310 <PRE>\r
 311 public static void <B>write</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;scores,\r
 312                          <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;output)\r
 313                   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
 314 <DL>\r
 315 <DD>Outputs the List of Score objects into the Output stream. The output
 316  format is as follows:
 317
 318  <pre>
 319  <code>#MethodName &lt;space separated list of values&gt;
 320
 321  For example:
 322
 323  #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
 324  #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
 325  </code>
 326  </pre>
 327
 328  The maximum precision for values is 3 digits, but can be less.\r
 329 <P>\r
 330 <DD><DL>\r
 331 <DT><B>Parameters:</B><DD><CODE>scores</CODE> - the list of scores to output<DD><CODE>output</CODE> - the stream to output the data to\r
 332 <DT><B>Throws:</B>\r
 333 <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
 334 <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
 335 </DD>\r
 336 </DL>\r
 337 <!-- ========= END OF CLASS DATA ========= -->\r
 338 <HR>\r
 339 \r
 340 \r
 341 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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