website/full_javadoc/compbio/runner/conservation/AACon.html

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   7 AACon\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
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  18         parent.document.title="AACon";\r
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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner.conservation</FONT>\r
  92 <BR>\r
  93 Class AACon</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="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;\r
  97       <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.conservation.AACon</B>\r
  98 </PRE>\r
  99 <DL>\r
 100 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</DD>\r
 101 </DL>\r
 102 <HR>\r
 103 <DL>\r
 104 <DT><PRE>public class <B>AACon</B><DT>extends <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 Command line
 109
 110  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out\r
 111 <P>\r
 112 \r
 113 <P>\r
 114 <DL>\r
 115 <DT><B>Author:</B></DT>\r
 116   <DD>pvtroshin</DD>\r
 117 </DL>\r
 118 <HR>\r
 119 \r
 120 <P>\r
 121 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 122 \r
 123 <A NAME="nested_class_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>Nested Class Summary</B></FONT></TH>\r
 128 </TR>\r
 129 </TABLE>\r
 130 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 131 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 132 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 133 <TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 134 </TR>\r
 135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 136 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 137 </TR>\r
 138 </TABLE>\r
 139 &nbsp;\r
 140 <!-- =========== FIELD SUMMARY =========== -->\r
 141 \r
 142 <A NAME="field_summary"><!-- --></A>\r
 143 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 144 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 145 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 146 <B>Field Summary</B></FONT></TH>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 150 <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
 151 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</A></B></CODE>\r
 152 \r
 153 <BR>\r
 154 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 158 <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
 159 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#STAT_FILE">STAT_FILE</A></B></CODE>\r
 160 \r
 161 <BR>\r
 162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 163 </TR>\r
 164 </TABLE>\r
 165 &nbsp;<A NAME="fields_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 166 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 167 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 168 <TH ALIGN="left"><B>Fields inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
 169 </TR>\r
 170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 171 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</A></CODE></TD>\r
 172 </TR>\r
 173 </TABLE>\r
 174 &nbsp;\r
 175 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 176 \r
 177 <A NAME="constructor_summary"><!-- --></A>\r
 178 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 179 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 180 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 181 <B>Constructor Summary</B></FONT></TH>\r
 182 </TR>\r
 183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 184 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#AACon()">AACon</A></B>()</CODE>\r
 185 \r
 186 <BR>\r
 187 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 188 </TR>\r
 189 </TABLE>\r
 190 &nbsp;\r
 191 <!-- ========== METHOD SUMMARY =========== -->\r
 192 \r
 193 <A NAME="method_summary"><!-- --></A>\r
 194 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 195 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 196 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 197 <B>Method Summary</B></FONT></TH>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 201 <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/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
 202 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 203 \r
 204 <BR>\r
 205 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 206  created or not.</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;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</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;<A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#getResults(java.lang.String)">getResults</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;workDirectory)</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>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
 227 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#getStatFile()">getStatFile</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>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></FONT></TD>\r
 235 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#getType()">getType</A></B>()</CODE>\r
 236 \r
 237 <BR>\r
 238 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 239 </TR>\r
 240 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 241 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 242 <CODE>&nbsp;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></CODE></FONT></TD>\r
 243 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#setInput(java.lang.String)">setInput</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;inFile)</CODE>\r
 244 \r
 245 <BR>\r
 246 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 247 </TR>\r
 248 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 249 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 250 <CODE>&nbsp;void</CODE></FONT></TD>\r
 251 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#setNCore(int)">setNCore</A></B>(int&nbsp;ncoreNumber)</CODE>\r
 252 \r
 253 <BR>\r
 254 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 255 </TR>\r
 256 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 257 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 258 <CODE>&nbsp;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></CODE></FONT></TD>\r
 259 <TD><CODE><B><A HREF="../../../compbio/runner/conservation/AACon.html#setOutput(java.lang.String)">setOutput</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;outFile)</CODE>\r
 260 \r
 261 <BR>\r
 262 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 263 </TR>\r
 264 </TABLE>\r
 265 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.SkeletalExecutable"><!-- --></A>\r
 266 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 267 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 268 <TH ALIGN="left"><B>Methods inherited from class compbio.engine.client.<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></B></TH>\r
 269 </TR>\r
 270 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 271 <TD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A>, <A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></CODE></TD>\r
 272 </TR>\r
 273 </TABLE>\r
 274 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 275 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 276 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 277 <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
 278 </TR>\r
 279 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 280 <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
 281 </TR>\r
 282 </TABLE>\r
 283 &nbsp;\r
 284 <P>\r
 285 \r
 286 <!-- ============ FIELD DETAIL =========== -->\r
 287 \r
 288 <A NAME="field_detail"><!-- --></A>\r
 289 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 290 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 291 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 292 <B>Field Detail</B></FONT></TH>\r
 293 </TR>\r
 294 </TABLE>\r
 295 \r
 296 <A NAME="KEY_VALUE_SEPARATOR"><!-- --></A><H3>\r
 297 KEY_VALUE_SEPARATOR</H3>\r
 298 <PRE>\r
 299 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>KEY_VALUE_SEPARATOR</B></PRE>\r
 300 <DL>\r
 301 <DL>\r
 302 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.conservation.AACon.KEY_VALUE_SEPARATOR">Constant Field Values</A></DL>\r
 303 </DL>\r
 304 <HR>\r
 305 \r
 306 <A NAME="STAT_FILE"><!-- --></A><H3>\r
 307 STAT_FILE</H3>\r
 308 <PRE>\r
 309 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>STAT_FILE</B></PRE>\r
 310 <DL>\r
 311 <DL>\r
 312 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.runner.conservation.AACon.STAT_FILE">Constant Field Values</A></DL>\r
 313 </DL>\r
 314 \r
 315 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 316 \r
 317 <A NAME="constructor_detail"><!-- --></A>\r
 318 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 319 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 320 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 321 <B>Constructor Detail</B></FONT></TH>\r
 322 </TR>\r
 323 </TABLE>\r
 324 \r
 325 <A NAME="AACon()"><!-- --></A><H3>\r
 326 AACon</H3>\r
 327 <PRE>\r
 328 public <B>AACon</B>()</PRE>\r
 329 <DL>\r
 330 </DL>\r
 331 \r
 332 <!-- ============ METHOD DETAIL ========== -->\r
 333 \r
 334 <A NAME="method_detail"><!-- --></A>\r
 335 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 336 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 337 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 338 <B>Method Detail</B></FONT></TH>\r
 339 </TR>\r
 340 </TABLE>\r
 341 \r
 342 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 343 getResults</H3>\r
 344 <PRE>\r
 345 public <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getResults</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;workDirectory)\r
 346                         throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 347 <DL>\r
 348 <DD><DL>\r
 349 \r
 350 <DT><B>Throws:</B>\r
 351 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 352 </DD>\r
 353 </DL>\r
 354 <HR>\r
 355 \r
 356 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 357 getCreatedFiles</H3>\r
 358 <PRE>\r
 359 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/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt; <B>getCreatedFiles</B>()</PRE>\r
 360 <DL>\r
 361 <DD><B>Description copied from class: <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">SkeletalExecutable</A></CODE></B></DD>\r
 362 <DD>This method cannot really tell whether the files has actually been
 363  created or not. It must be overridden as required.\r
 364 <P>\r
 365 <DD><DL>\r
 366 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></DL>\r
 367 </DD>\r
 368 <DD><DL>\r
 369 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 370 </DD>\r
 371 </DL>\r
 372 <HR>\r
 373 \r
 374 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 375 setInput</H3>\r
 376 <PRE>\r
 377 public <A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A> <B>setInput</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;inFile)</PRE>\r
 378 <DL>\r
 379 <DD><DL>\r
 380 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></DL>\r
 381 </DD>\r
 382 <DD><DL>\r
 383 </DL>\r
 384 </DD>\r
 385 </DL>\r
 386 <HR>\r
 387 \r
 388 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 389 setOutput</H3>\r
 390 <PRE>\r
 391 public <A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A> <B>setOutput</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;outFile)</PRE>\r
 392 <DL>\r
 393 <DD><DL>\r
 394 <DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></DL>\r
 395 </DD>\r
 396 <DD><DL>\r
 397 </DL>\r
 398 </DD>\r
 399 </DL>\r
 400 <HR>\r
 401 \r
 402 <A NAME="getType()"><!-- --></A><H3>\r
 403 getType</H3>\r
 404 <PRE>\r
 405 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt; <B>getType</B>()</PRE>\r
 406 <DL>\r
 407 <DD><DL>\r
 408 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></DL>\r
 409 </DD>\r
 410 <DD><DL>\r
 411 \r
 412 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 413 </DD>\r
 414 </DL>\r
 415 <HR>\r
 416 \r
 417 <A NAME="getStatFile()"><!-- --></A><H3>\r
 418 getStatFile</H3>\r
 419 <PRE>\r
 420 public static <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>getStatFile</B>()</PRE>\r
 421 <DL>\r
 422 <DD><DL>\r
 423 </DL>\r
 424 </DD>\r
 425 </DL>\r
 426 <HR>\r
 427 \r
 428 <A NAME="setNCore(int)"><!-- --></A><H3>\r
 429 setNCore</H3>\r
 430 <PRE>\r
 431 public void <B>setNCore</B>(int&nbsp;ncoreNumber)</PRE>\r
 432 <DL>\r
 433 <DD><DL>\r
 434 </DL>\r
 435 </DD>\r
 436 </DL>\r
 437 <HR>\r
 438 \r
 439 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 440 getParameters</H3>\r
 441 <PRE>\r
 442 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
 443 <DL>\r
 444 <DD><DL>\r
 445 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in class <CODE><A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>&gt;</CODE></DL>\r
 446 </DD>\r
 447 <DD><DL>\r
 448 </DL>\r
 449 </DD>\r
 450 </DL>\r
 451 <!-- ========= END OF CLASS DATA ========= -->\r
 452 <HR>\r
 453 \r
 454 \r
 455 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 456 <A NAME="navbar_bottom"><!-- --></A>\r
 457 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 458 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 459 <TR>\r
 460 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 461 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 462 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 463   <TR ALIGN="center" VALIGN="top">\r
 464   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 465   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 466   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 467   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/AACon.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 468   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 469   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 470   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 471   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 472   </TR>\r
 473 </TABLE>\r
 474 </TD>\r
 475 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 476 </EM>\r
 477 </TD>\r
 478 </TR>\r
 479 \r
 480 <TR>\r
 481 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 482 &nbsp;PREV CLASS&nbsp;\r
 483 &nbsp;NEXT CLASS</FONT></TD>\r
 484 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 485   <A HREF="../../../index.html?compbio/runner/conservation/AACon.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 486 &nbsp;<A HREF="AACon.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 487 &nbsp;<SCRIPT type="text/javascript">\r
 488   <!--\r
 489   if(window==top) {\r
 490     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 491   }\r
 492   //-->\r
 493 </SCRIPT>\r
 494 <NOSCRIPT>\r
 495   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 496 </NOSCRIPT>\r
 497 \r
 498 \r
 499 </FONT></TD>\r
 500 </TR>\r
 501 <TR>\r
 502 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 503   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
 504 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 505 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 506 </TR>\r
 507 </TABLE>\r
 508 <A NAME="skip-navbar_bottom"></A>\r
 509 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 510 \r
 511 <HR>\r
 512 \r
 513 </BODY>\r
 514 </HTML>\r