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

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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#enum_constant_summary">ENUM CONSTANTS</A>&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  81 DETAIL:&nbsp;<A HREF="#enum_constant_detail">ENUM CONSTANTS</A>&nbsp;|&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Enum SMERFSConstraints</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 "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A>&lt;<A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SMERFSConstraints</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <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/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public enum <B>SMERFSConstraints</B><DT>extends <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;<A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 Enumeration defining two constraints for SMERFS columns score calculation.
 109  MAX_SCORE gives the highest core of all the windows the column belongs to.
 110  MID_SCORE gives the window score to the column in the middle.\r
 111 <P>\r
 112 \r
 113 <P>\r
 114 <DL>\r
 115 <DT><B>Author:</B></DT>\r
 116   <DD>Agnieszka Golicz & Peter Troshin</DD>\r
 117 </DL>\r
 118 <HR>\r
 119 \r
 120 <P>\r
 121 <!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
 122 \r
 123 <A NAME="enum_constant_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>Enum Constant Summary</B></FONT></TH>\r
 128 </TR>\r
 129 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 130 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#MAX_SCORE">MAX_SCORE</A></B></CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 134 </TR>\r
 135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 136 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#MID_SCORE">MID_SCORE</A></B></CODE>\r
 137 \r
 138 <BR>\r
 139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 </TABLE>\r
 142 &nbsp;<!-- =========== FIELD SUMMARY =========== -->\r
 143 \r
 144 <A NAME="field_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>Field 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>static&nbsp;<A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></CODE></FONT></TD>\r
 153 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_COLUMN_SCORE">DEFAULT_COLUMN_SCORE</A></B></CODE>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Default column scoring schema</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>static&nbsp;double</CODE></FONT></TD>\r
 161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></B></CODE>\r
 162 \r
 163 <BR>\r
 164 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Default gap threshold value for SMERFS algorithm</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>static&nbsp;int</CODE></FONT></TD>\r
 169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></B></CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Default window size value for SMERFS algorithm</TD>\r
 173 </TR>\r
 174 </TABLE>\r
 175 &nbsp;\r
 176 <!-- ========== METHOD SUMMARY =========== -->\r
 177 \r
 178 <A NAME="method_summary"><!-- --></A>\r
 179 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 180 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 181 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 182 <B>Method Summary</B></FONT></TH>\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>static&nbsp;<A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></CODE></FONT></TD>\r
 187 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#getSMERFSColumnScore(java.lang.String)">getSMERFSColumnScore</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;score)</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>static&nbsp;<A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></CODE></FONT></TD>\r
 195 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#valueOf(java.lang.String)">valueOf</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;name)</CODE>\r
 196 \r
 197 <BR>\r
 198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the enum constant of this type with the specified name.</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>static&nbsp;<A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>[]</CODE></FONT></TD>\r
 203 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html#values()">values</A></B>()</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns an array containing the constants of this enum type, in
 207 the order they are declared.</TD>\r
 208 </TR>\r
 209 </TABLE>\r
 210 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
 211 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 212 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 213 <TH ALIGN="left"><B>Methods inherited from class java.lang.<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></B></TH>\r
 214 </TR>\r
 215 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 216 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.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/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.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/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.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/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
 217 </TR>\r
 218 </TABLE>\r
 219 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 220 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 221 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 222 <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
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <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
 226 </TR>\r
 227 </TABLE>\r
 228 &nbsp;\r
 229 <P>\r
 230 \r
 231 <!-- ============ ENUM CONSTANT DETAIL =========== -->\r
 232 \r
 233 <A NAME="enum_constant_detail"><!-- --></A>\r
 234 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 235 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 236 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 237 <B>Enum Constant Detail</B></FONT></TH>\r
 238 </TR>\r
 239 </TABLE>\r
 240 \r
 241 <A NAME="MAX_SCORE"><!-- --></A><H3>\r
 242 MAX_SCORE</H3>\r
 243 <PRE>\r
 244 public static final <A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A> <B>MAX_SCORE</B></PRE>\r
 245 <DL>\r
 246 <DL>\r
 247 </DL>\r
 248 </DL>\r
 249 <HR>\r
 250 \r
 251 <A NAME="MID_SCORE"><!-- --></A><H3>\r
 252 MID_SCORE</H3>\r
 253 <PRE>\r
 254 public static final <A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A> <B>MID_SCORE</B></PRE>\r
 255 <DL>\r
 256 <DL>\r
 257 </DL>\r
 258 </DL>\r
 259 \r
 260 <!-- ============ FIELD DETAIL =========== -->\r
 261 \r
 262 <A NAME="field_detail"><!-- --></A>\r
 263 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 264 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 265 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 266 <B>Field Detail</B></FONT></TH>\r
 267 </TR>\r
 268 </TABLE>\r
 269 \r
 270 <A NAME="DEFAULT_COLUMN_SCORE"><!-- --></A><H3>\r
 271 DEFAULT_COLUMN_SCORE</H3>\r
 272 <PRE>\r
 273 public static final <A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A> <B>DEFAULT_COLUMN_SCORE</B></PRE>\r
 274 <DL>\r
 275 <DD>Default column scoring schema\r
 276 <P>\r
 277 <DL>\r
 278 </DL>\r
 279 </DL>\r
 280 <HR>\r
 281 \r
 282 <A NAME="DEFAULT_WINDOW_SIZE"><!-- --></A><H3>\r
 283 DEFAULT_WINDOW_SIZE</H3>\r
 284 <PRE>\r
 285 public static final int <B>DEFAULT_WINDOW_SIZE</B></PRE>\r
 286 <DL>\r
 287 <DD>Default window size value for SMERFS algorithm\r
 288 <P>\r
 289 <DL>\r
 290 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE">Constant Field Values</A></DL>\r
 291 </DL>\r
 292 <HR>\r
 293 \r
 294 <A NAME="DEFAULT_GAP_THRESHOLD"><!-- --></A><H3>\r
 295 DEFAULT_GAP_THRESHOLD</H3>\r
 296 <PRE>\r
 297 public static final double <B>DEFAULT_GAP_THRESHOLD</B></PRE>\r
 298 <DL>\r
 299 <DD>Default gap threshold value for SMERFS algorithm\r
 300 <P>\r
 301 <DL>\r
 302 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD">Constant Field Values</A></DL>\r
 303 </DL>\r
 304 \r
 305 <!-- ============ METHOD DETAIL ========== -->\r
 306 \r
 307 <A NAME="method_detail"><!-- --></A>\r
 308 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 309 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 310 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 311 <B>Method Detail</B></FONT></TH>\r
 312 </TR>\r
 313 </TABLE>\r
 314 \r
 315 <A NAME="values()"><!-- --></A><H3>\r
 316 values</H3>\r
 317 <PRE>\r
 318 public static <A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>[] <B>values</B>()</PRE>\r
 319 <DL>\r
 320 <DD>Returns an array containing the constants of this enum type, in
 321 the order they are declared.  This method may be used to iterate
 322 over the constants as follows:
 323 <pre>
 324 for (SMERFSConstraints c : SMERFSConstraints.values())
 325 &nbsp;   System.out.println(c);
 326 </pre>\r
 327 <P>\r
 328 <DD><DL>\r
 329 \r
 330 <DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
 331 the order they are declared</DL>\r
 332 </DD>\r
 333 </DL>\r
 334 <HR>\r
 335 \r
 336 <A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
 337 valueOf</H3>\r
 338 <PRE>\r
 339 public static <A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A> <B>valueOf</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;name)</PRE>\r
 340 <DL>\r
 341 <DD>Returns the enum constant of this type with the specified name.
 342 The string must match <I>exactly</I> an identifier used to declare an
 343 enum constant in this type.  (Extraneous whitespace characters are
 344 not permitted.)\r
 345 <P>\r
 346 <DD><DL>\r
 347 <DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
 348 <DT><B>Returns:</B><DD>the enum constant with the specified name\r
 349 <DT><B>Throws:</B>\r
 350 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
 351 with the specified name\r
 352 <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 argument is null</DL>\r
 353 </DD>\r
 354 </DL>\r
 355 <HR>\r
 356 \r
 357 <A NAME="getSMERFSColumnScore(java.lang.String)"><!-- --></A><H3>\r
 358 getSMERFSColumnScore</H3>\r
 359 <PRE>\r
 360 public static <A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A> <B>getSMERFSColumnScore</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;score)</PRE>\r
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