website/full_javadoc/compbio/runner/_impl/NetNglyc.html

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   7 NetNglyc\r
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   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\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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  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.runner._impl</FONT>\r
  92 <BR>\r
  93 Class NetNglyc</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._impl.NetNglyc</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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</DD>\r
 100 </DL>\r
 101 <HR>\r
 102 <DL>\r
 103 <DT><PRE>public class <B>NetNglyc</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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</DL>\r
 104 </PRE>\r
 105 \r
 106 <P>\r
 107 <HR>\r
 108 \r
 109 <P>\r
 110 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 111 \r
 112 <A NAME="nested_class_summary"><!-- --></A>\r
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 115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 116 <B>Nested Class Summary</B></FONT></TH>\r
 117 </TR>\r
 118 </TABLE>\r
 119 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 121 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 122 <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
 123 </TR>\r
 124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 125 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 126 </TR>\r
 127 </TABLE>\r
 128 &nbsp;\r
 129 \r
 130 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 131 \r
 132 <A NAME="constructor_summary"><!-- --></A>\r
 133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 134 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 135 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 136 <B>Constructor Summary</B></FONT></TH>\r
 137 </TR>\r
 138 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 139 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#NetNglyc()">NetNglyc</A></B>()</CODE>\r
 140 \r
 141 <BR>\r
 142 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 143 </TR>\r
 144 </TABLE>\r
 145 &nbsp;\r
 146 <!-- ========== METHOD SUMMARY =========== -->\r
 147 \r
 148 <A NAME="method_summary"><!-- --></A>\r
 149 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 150 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 151 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 152 <B>Method Summary</B></FONT></TH>\r
 153 </TR>\r
 154 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 155 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 156 <CODE>&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
 157 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.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
 158 \r
 159 <BR>\r
 160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 161 </TR>\r
 162 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 164 <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
 165 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
 166 \r
 167 <BR>\r
 168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 169 </TR>\r
 170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 172 <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
 173 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCommandName()">getCommandName</A></B>()</CODE>\r
 174 \r
 175 <BR>\r
 176 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 177 </TR>\r
 178 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 180 <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
 181 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 182 \r
 183 <BR>\r
 184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 185 </TR>\r
 186 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 187 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 188 <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
 189 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getError()">getError</A></B>()</CODE>\r
 190 \r
 191 <BR>\r
 192 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 193 </TR>\r
 194 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 196 <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
 197 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getInput()">getInput</A></B>()</CODE>\r
 198 \r
 199 <BR>\r
 200 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 201 </TR>\r
 202 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 204 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
 205 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.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
 206 \r
 207 <BR>\r
 208 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 209 </TR>\r
 210 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 211 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 212 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
 213 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimits()">getLimits</A></B>()</CODE>\r
 214 \r
 215 <BR>\r
 216 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 217 </TR>\r
 218 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 219 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 220 <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
 221 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getOutput()">getOutput</A></B>()</CODE>\r
 222 \r
 223 <BR>\r
 224 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 225 </TR>\r
 226 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 228 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
 229 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.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
 230 \r
 231 <BR>\r
 232 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 233 </TR>\r
 234 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 236 <CODE>\r
 237 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 238 <TR ALIGN="right" VALIGN="">\r
 239 <TD NOWRAP><FONT SIZE="-1">\r
 240 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
 241 </TR>\r
 242 </TABLE>\r
 243 </CODE></FONT></TD>\r
 244 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.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
 245 \r
 246 <BR>\r
 247 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 248 </TR>\r
 249 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 250 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 251 <CODE>static&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
 252 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestArgs()">getTestArgs</A></B>()</CODE>\r
 253 \r
 254 <BR>\r
 255 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 256 </TR>\r
 257 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 258 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 259 <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
 260 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
 261 \r
 262 <BR>\r
 263 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 264 </TR>\r
 265 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 266 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 267 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 268 <TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.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
 269 \r
 270 <BR>\r
 271 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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#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
 281 </TR>\r
 282 </TABLE>\r
 283 &nbsp;\r
 284 <P>\r
 285 \r
 286 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 287 \r
 288 <A NAME="constructor_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>Constructor Detail</B></FONT></TH>\r
 293 </TR>\r
 294 </TABLE>\r
 295 \r
 296 <A NAME="NetNglyc()"><!-- --></A><H3>\r
 297 NetNglyc</H3>\r
 298 <PRE>\r
 299 public <B>NetNglyc</B>()</PRE>\r
 300 <DL>\r
 301 </DL>\r
 302 \r
 303 <!-- ============ METHOD DETAIL ========== -->\r
 304 \r
 305 <A NAME="method_detail"><!-- --></A>\r
 306 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 307 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 308 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 309 <B>Method Detail</B></FONT></TH>\r
 310 </TR>\r
 311 </TABLE>\r
 312 \r
 313 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 314 getParameters</H3>\r
 315 <PRE>\r
 316 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</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
 317 <DL>\r
 318 <DD><DL>\r
 319 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 320 </DD>\r
 321 <DD><DL>\r
 322 </DL>\r
 323 </DD>\r
 324 </DL>\r
 325 <HR>\r
 326 \r
 327 <A NAME="getTestArgs()"><!-- --></A><H3>\r
 328 getTestArgs</H3>\r
 329 <PRE>\r
 330 public static <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>getTestArgs</B>()</PRE>\r
 331 <DL>\r
 332 <DD><DL>\r
 333 </DL>\r
 334 </DD>\r
 335 <DD><DL>\r
 336 </DL>\r
 337 </DD>\r
 338 </DL>\r
 339 <HR>\r
 340 \r
 341 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 342 addParameters</H3>\r
 343 <PRE>\r
 344 public <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</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
 345 <DL>\r
 346 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
 347 <DD>Adds parameter to the list of parameters for a native executable\r
 348 <P>\r
 349 <DD><DL>\r
 350 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 351 </DD>\r
 352 <DD><DL>\r
 353 \r
 354 <DT><B>Returns:</B><DD>this Executable</DL>\r
 355 </DD>\r
 356 </DL>\r
 357 <HR>\r
 358 \r
 359 <A NAME="getTestCommand()"><!-- --></A><H3>\r
 360 getTestCommand</H3>\r
 361 <PRE>\r
 362 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>getTestCommand</B>()</PRE>\r
 363 <DL>\r
 364 <DD><DL>\r
 365 </DL>\r
 366 </DD>\r
 367 <DD><DL>\r
 368 </DL>\r
 369 </DD>\r
 370 </DL>\r
 371 <HR>\r
 372 \r
 373 <A NAME="getCommandName()"><!-- --></A><H3>\r
 374 getCommandName</H3>\r
 375 <PRE>\r
 376 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>getCommandName</B>()</PRE>\r
 377 <DL>\r
 378 <DD><DL>\r
 379 </DL>\r
 380 </DD>\r
 381 <DD><DL>\r
 382 </DL>\r
 383 </DD>\r
 384 </DL>\r
 385 <HR>\r
 386 \r
 387 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 388 getCreatedFiles</H3>\r
 389 <PRE>\r
 390 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
 391 <DL>\r
 392 <DD><DL>\r
 393 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 394 </DD>\r
 395 <DD><DL>\r
 396 </DL>\r
 397 </DD>\r
 398 </DL>\r
 399 <HR>\r
 400 \r
 401 <A NAME="getInput()"><!-- --></A><H3>\r
 402 getInput</H3>\r
 403 <PRE>\r
 404 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>getInput</B>()</PRE>\r
 405 <DL>\r
 406 <DD><DL>\r
 407 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 408 </DD>\r
 409 <DD><DL>\r
 410 </DL>\r
 411 </DD>\r
 412 </DL>\r
 413 <HR>\r
 414 \r
 415 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
 416 getResults</H3>\r
 417 <PRE>\r
 418 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
 419 <DL>\r
 420 <DD><DL>\r
 421 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 422 </DD>\r
 423 <DD><DL>\r
 424 </DL>\r
 425 </DD>\r
 426 </DL>\r
 427 <HR>\r
 428 \r
 429 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 430 loadRunConfiguration</H3>\r
 431 <PRE>\r
 432 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
 433 <DL>\r
 434 <DD><DL>\r
 435 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 436 </DD>\r
 437 <DD><DL>\r
 438 </DL>\r
 439 </DD>\r
 440 </DL>\r
 441 <HR>\r
 442 \r
 443 <A NAME="getOutput()"><!-- --></A><H3>\r
 444 getOutput</H3>\r
 445 <PRE>\r
 446 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
 447 <DL>\r
 448 <DD><DL>\r
 449 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 450 </DD>\r
 451 <DD><DL>\r
 452 </DL>\r
 453 </DD>\r
 454 </DL>\r
 455 <HR>\r
 456 \r
 457 <A NAME="getError()"><!-- --></A><H3>\r
 458 getError</H3>\r
 459 <PRE>\r
 460 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
 461 <DL>\r
 462 <DD><DL>\r
 463 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 464 </DD>\r
 465 <DD><DL>\r
 466 </DL>\r
 467 </DD>\r
 468 </DL>\r
 469 <HR>\r
 470 \r
 471 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 472 getLimit</H3>\r
 473 <PRE>\r
 474 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</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
 475 <DL>\r
 476 <DD><DL>\r
 477 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 478 </DD>\r
 479 <DD><DL>\r
 480 </DL>\r
 481 </DD>\r
 482 </DL>\r
 483 <HR>\r
 484 \r
 485 <A NAME="getLimits()"><!-- --></A><H3>\r
 486 getLimits</H3>\r
 487 <PRE>\r
 488 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <B>getLimits</B>()</PRE>\r
 489 <DL>\r
 490 <DD><DL>\r
 491 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 492 </DD>\r
 493 <DD><DL>\r
 494 </DL>\r
 495 </DD>\r
 496 </DL>\r
 497 <HR>\r
 498 \r
 499 <A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
 500 getClusterJobSettings</H3>\r
 501 <PRE>\r
 502 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
 503 <DL>\r
 504 <DD><DL>\r
 505 <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/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
 506 </DD>\r
 507 <DD><DL>\r
 508 </DL>\r
 509 </DD>\r
 510 </DL>\r
 511 <!-- ========= END OF CLASS DATA ========= -->\r
 512 <HR>\r
 513 \r
 514 \r
 515 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 516 <A NAME="navbar_bottom"><!-- --></A>\r
 517 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 518 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 519 <TR>\r
 520 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 521 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 522 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 523   <TR ALIGN="center" VALIGN="top">\r
 524   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 525   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 526   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 527   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/NetNglyc.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 528   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 529   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 530   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 531   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 532   </TR>\r
 533 </TABLE>\r
 534 </TD>\r
 535 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 536 </EM>\r
 537 </TD>\r
 538 </TR>\r
 539 \r
 540 <TR>\r
 541 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 542 &nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
 543 &nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
 544 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 545   <A HREF="../../../index.html?compbio/runner/_impl/NetNglyc.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 546 &nbsp;<A HREF="NetNglyc.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 547 &nbsp;<SCRIPT type="text/javascript">\r
 548   <!--\r
 549   if(window==top) {\r
 550     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 551   }\r
 552   //-->\r
 553 </SCRIPT>\r
 554 <NOSCRIPT>\r
 555   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 556 </NOSCRIPT>\r
 557 \r
 558 \r
 559 </FONT></TD>\r
 560 </TR>\r
 561 <TR>\r
 562 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 563   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
 564 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 565 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 566 </TR>\r
 567 </TABLE>\r
 568 <A NAME="skip-navbar_bottom"></A>\r
 569 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 570 \r
 571 <HR>\r
 572 \r
 573 </BODY>\r
 574 </HTML>\r