website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html

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   7 _SkeletalCommandBuilder\r
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  58 &nbsp;<A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\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
  80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  81 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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  85 <!-- ========= END OF TOP NAVBAR ========= -->\r
  86 \r
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  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner</FONT>\r
  92 <BR>\r
  93 Class _SkeletalCommandBuilder</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.runner._SkeletalCommandBuilder</B>\r
  97 </PRE>\r
  98 <DL>\r
  99 <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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
 100 </DL>\r
 101 <DL>\r
 102 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></DD>\r
 103 </DL>\r
 104 <HR>\r
 105 <B>Deprecated.</B>\r
 106 <P>\r
 107 <DL>\r
 108 <DT><PRE><FONT SIZE="-1"><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Deprecated.html?is-external=true" title="class or interface in java.lang">@Deprecated</A>\r
 109 </FONT>public abstract class <B>_SkeletalCommandBuilder</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="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DL>\r
 110 </PRE>\r
 111 \r
 112 <P>\r
 113 <HR>\r
 114 \r
 115 <P>\r
 116 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 117 \r
 118 <A NAME="nested_class_summary"><!-- --></A>\r
 119 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 120 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 121 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 122 <B>Nested Class Summary</B></FONT></TH>\r
 123 </TR>\r
 124 </TABLE>\r
 125 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 127 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 128 <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
 129 </TR>\r
 130 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 131 <TD><CODE><A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 132 </TR>\r
 133 </TABLE>\r
 134 &nbsp;\r
 135 \r
 136 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 137 \r
 138 <A NAME="constructor_summary"><!-- --></A>\r
 139 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 140 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 141 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 142 <B>Constructor Summary</B></FONT></TH>\r
 143 </TR>\r
 144 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 145 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#_SkeletalCommandBuilder()">_SkeletalCommandBuilder</A></B>()</CODE>\r
 146 \r
 147 <BR>\r
 148 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 149 </TR>\r
 150 </TABLE>\r
 151 &nbsp;\r
 152 <!-- ========== METHOD SUMMARY =========== -->\r
 153 \r
 154 <A NAME="method_summary"><!-- --></A>\r
 155 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 156 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 157 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 158 <B>Method Summary</B></FONT></TH>\r
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 162 <CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 163 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</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;parameter)</CODE>\r
 164 \r
 165 <BR>\r
 166 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\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;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 171 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(<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;&nbsp;parameters)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;Adds parameter to the list of parameters for a native executable</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;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 179 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</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;parameters)</CODE>\r
 180 \r
 181 <BR>\r
 182 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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/runner/_SkeletalCommandBuilder.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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>&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
 195 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A></B>()</CODE>\r
 196 \r
 197 <BR>\r
 198 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</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/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 203 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A></B>()</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</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/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</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;presetName)</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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/runner/_SkeletalCommandBuilder.html#getName()">getName</A></B>()</CODE>\r
 228 \r
 229 <BR>\r
 230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
 235 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A></B>()</CODE>\r
 236 \r
 237 <BR>\r
 238 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
 243 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.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
 244 \r
 245 <BR>\r
 246 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&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>\r
 251 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 252 <TR ALIGN="right" VALIGN="">\r
 253 <TD NOWRAP><FONT SIZE="-1">\r
 254 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 255 </TR>\r
 256 </TABLE>\r
 257 </CODE></FONT></TD>\r
 258 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.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;directory)</CODE>\r
 259 \r
 260 <BR>\r
 261 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 262 </TR>\r
 263 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 264 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 265 <CODE>&nbsp;<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 266 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
 267 \r
 268 <BR>\r
 269 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 270 </TR>\r
 271 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 272 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 273 <CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 274 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</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;email)</CODE>\r
 275 \r
 276 <BR>\r
 277 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 278 </TR>\r
 279 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 280 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 281 <CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
 282 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</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
 283 \r
 284 <BR>\r
 285 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
 286 </TR>\r
 287 </TABLE>\r
 288 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 289 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 290 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 291 <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
 292 </TR>\r
 293 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 294 <TD><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>, <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#hashCode()" title="class or interface in java.lang">hashCode</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
 295 </TR>\r
 296 </TABLE>\r
 297 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 298 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 299 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 300 <TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
 301 </TR>\r
 302 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 303 <TD><CODE><A HREF="../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE></TD>\r
 304 </TR>\r
 305 </TABLE>\r
 306 &nbsp;\r
 307 <P>\r
 308 \r
 309 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 310 \r
 311 <A NAME="constructor_detail"><!-- --></A>\r
 312 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 313 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 314 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 315 <B>Constructor Detail</B></FONT></TH>\r
 316 </TR>\r
 317 </TABLE>\r
 318 \r
 319 <A NAME="_SkeletalCommandBuilder()"><!-- --></A><H3>\r
 320 _SkeletalCommandBuilder</H3>\r
 321 <PRE>\r
 322 public <B>_SkeletalCommandBuilder</B>()</PRE>\r
 323 <DL>\r
 324 <DD><B>Deprecated.</B>&nbsp;</DL>\r
 325 \r
 326 <!-- ============ METHOD DETAIL ========== -->\r
 327 \r
 328 <A NAME="method_detail"><!-- --></A>\r
 329 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 330 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 331 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 332 <B>Method Detail</B></FONT></TH>\r
 333 </TR>\r
 334 </TABLE>\r
 335 \r
 336 <A NAME="setEmail(java.lang.String)"><!-- --></A><H3>\r
 337 setEmail</H3>\r
 338 <PRE>\r
 339 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setEmail</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;email)</PRE>\r
 340 <DL>\r
 341 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 342 </DL>\r
 343 </DD>\r
 344 <DD><DL>\r
 345 </DL>\r
 346 </DD>\r
 347 </DL>\r
 348 <HR>\r
 349 \r
 350 <A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
 351 setName</H3>\r
 352 <PRE>\r
 353 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setName</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
 354 <DL>\r
 355 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 356 </DL>\r
 357 </DD>\r
 358 <DD><DL>\r
 359 </DL>\r
 360 </DD>\r
 361 </DL>\r
 362 <HR>\r
 363 \r
 364 <A NAME="getName()"><!-- --></A><H3>\r
 365 getName</H3>\r
 366 <PRE>\r
 367 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>getName</B>()</PRE>\r
 368 <DL>\r
 369 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 370 </DL>\r
 371 </DD>\r
 372 <DD><DL>\r
 373 </DL>\r
 374 </DD>\r
 375 </DL>\r
 376 <HR>\r
 377 \r
 378 <A NAME="getEmail()"><!-- --></A><H3>\r
 379 getEmail</H3>\r
 380 <PRE>\r
 381 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>getEmail</B>()</PRE>\r
 382 <DL>\r
 383 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 384 </DL>\r
 385 </DD>\r
 386 <DD><DL>\r
 387 </DL>\r
 388 </DD>\r
 389 </DL>\r
 390 <HR>\r
 391 \r
 392 <A NAME="addParameters(java.lang.String[])"><!-- --></A><H3>\r
 393 addParameters</H3>\r
 394 <PRE>\r
 395 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</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;parameters)</PRE>\r
 396 <DL>\r
 397 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 398 </DL>\r
 399 </DD>\r
 400 <DD><DL>\r
 401 </DL>\r
 402 </DD>\r
 403 </DL>\r
 404 <HR>\r
 405 \r
 406 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 407 addParameters</H3>\r
 408 <PRE>\r
 409 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(<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;&nbsp;parameters)</PRE>\r
 410 <DL>\r
 411 <DD><B>Deprecated.</B>&nbsp;<DD><B>Description copied from interface: <CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
 412 <DD>Adds parameter to the list of parameters for a native executable\r
 413 <P>\r
 414 <DD><DL>\r
 415 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 416 </DD>\r
 417 <DD><DL>\r
 418 \r
 419 <DT><B>Returns:</B><DD>this Executable</DL>\r
 420 </DD>\r
 421 </DL>\r
 422 <HR>\r
 423 \r
 424 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 425 getParameters</H3>\r
 426 <PRE>\r
 427 public <A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</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
 428 <DL>\r
 429 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 430 <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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 431 </DD>\r
 432 <DD><DL>\r
 433 </DL>\r
 434 </DD>\r
 435 </DL>\r
 436 <HR>\r
 437 \r
 438 <A NAME="addParameter(java.lang.String)"><!-- --></A><H3>\r
 439 addParameter</H3>\r
 440 <PRE>\r
 441 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameter</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;parameter)</PRE>\r
 442 <DL>\r
 443 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 444 </DL>\r
 445 </DD>\r
 446 <DD><DL>\r
 447 </DL>\r
 448 </DD>\r
 449 </DL>\r
 450 <HR>\r
 451 \r
 452 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 453 getResults</H3>\r
 454 <PRE>\r
 455 public &lt;V&gt; V <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;directory)</PRE>\r
 456 <DL>\r
 457 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 458 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 459 </DD>\r
 460 <DD><DL>\r
 461 </DL>\r
 462 </DD>\r
 463 </DL>\r
 464 <HR>\r
 465 \r
 466 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 467 loadRunConfiguration</H3>\r
 468 <PRE>\r
 469 public <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
 470 <DL>\r
 471 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 472 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 473 </DD>\r
 474 <DD><DL>\r
 475 </DL>\r
 476 </DD>\r
 477 </DL>\r
 478 <HR>\r
 479 \r
 480 <A NAME="getOutput()"><!-- --></A><H3>\r
 481 getOutput</H3>\r
 482 <PRE>\r
 483 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>getOutput</B>()</PRE>\r
 484 <DL>\r
 485 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 486 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getOutput()">getOutput</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 487 </DD>\r
 488 <DD><DL>\r
 489 </DL>\r
 490 </DD>\r
 491 </DL>\r
 492 <HR>\r
 493 \r
 494 <A NAME="getError()"><!-- --></A><H3>\r
 495 getError</H3>\r
 496 <PRE>\r
 497 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>getError</B>()</PRE>\r
 498 <DL>\r
 499 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 500 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getError()">getError</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 501 </DD>\r
 502 <DD><DL>\r
 503 </DL>\r
 504 </DD>\r
 505 </DL>\r
 506 <HR>\r
 507 \r
 508 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 509 getLimit</H3>\r
 510 <PRE>\r
 511 public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getLimit</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;presetName)</PRE>\r
 512 <DL>\r
 513 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 514 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 515 </DD>\r
 516 <DD><DL>\r
 517 </DL>\r
 518 </DD>\r
 519 </DL>\r
 520 <HR>\r
 521 \r
 522 <A NAME="getLimits()"><!-- --></A><H3>\r
 523 getLimits</H3>\r
 524 <PRE>\r
 525 public <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getLimits</B>()</PRE>\r
 526 <DL>\r
 527 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 528 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getLimits()">getLimits</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 529 </DD>\r
 530 <DD><DL>\r
 531 </DL>\r
 532 </DD>\r
 533 </DL>\r
 534 <HR>\r
 535 \r
 536 <A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
 537 getClusterJobSettings</H3>\r
 538 <PRE>\r
 539 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>getClusterJobSettings</B>()</PRE>\r
 540 <DL>\r
 541 <DD><B>Deprecated.</B>&nbsp;<DD><DL>\r
 542 <DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</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/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
 543 </DD>\r
 544 <DD><DL>\r
 545 </DL>\r
 546 </DD>\r
 547 </DL>\r
 548 <!-- ========= END OF CLASS DATA ========= -->\r
 549 <HR>\r
 550 \r
 551 \r
 552 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 553 <A NAME="navbar_bottom"><!-- --></A>\r
 554 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 555 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 556 <TR>\r
 557 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 558 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 559 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 560   <TR ALIGN="center" VALIGN="top">\r
 561   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 562   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 563   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 564   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_SkeletalCommandBuilder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 565   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 566   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 567   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 568   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 569   </TR>\r
 570 </TABLE>\r
 571 </TD>\r
 572 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 573 </EM>\r
 574 </TD>\r
 575 </TR>\r
 576 \r
 577 <TR>\r
 578 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 579 &nbsp;<A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
 580 &nbsp;<A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>NEXT CLASS</B></A></FONT></TD>\r
 581 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 582   <A HREF="../../index.html?compbio/runner/_SkeletalCommandBuilder.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 583 &nbsp;<A HREF="_SkeletalCommandBuilder.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 584 &nbsp;<SCRIPT type="text/javascript">\r
 585   <!--\r
 586   if(window==top) {\r
 587     document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 588   }\r
 589   //-->\r
 590 </SCRIPT>\r
 591 <NOSCRIPT>\r
 592   <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
 593 </NOSCRIPT>\r
 594 \r
 595 \r
 596 </FONT></TD>\r
 597 </TR>\r
 598 <TR>\r
 599 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 600   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
 601 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 602 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 603 </TR>\r
 604 </TABLE>\r
 605 <A NAME="skip-navbar_bottom"></A>\r
 606 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 607 \r
 608 <HR>\r
 609 \r
 610 </BODY>\r
 611 </HTML>\r