website/full_javadoc/compbio/engine/client/SkeletalExecutable.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
   2 <!--NewPage-->\r
   3 <HTML>\r
   4 <HEAD>\r
   5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->\r
   6 <TITLE>\r
   7 SkeletalExecutable\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2011-08-12">\r
  11 \r
  12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
  13 \r
  14 <SCRIPT type="text/javascript">\r
  15 function windowTitle()\r
  16 {\r
  17     if (location.href.indexOf('is-external=true') == -1) {\r
  18         parent.document.title="SkeletalExecutable";\r
  19     }\r
  20 }\r
  21 </SCRIPT>\r
  22 <NOSCRIPT>\r
  23 </NOSCRIPT>\r
  24 \r
  25 </HEAD>\r
  26 \r
  27 <BODY BGCOLOR="white" onload="windowTitle();">\r
  28 <HR>\r
  29 \r
  30 \r
  31 <!-- ========= START OF TOP NAVBAR ======= -->\r
  32 <A NAME="navbar_top"><!-- --></A>\r
  33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
  34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
  35 <TR>\r
  36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
  37 <A NAME="navbar_top_firstrow"><!-- --></A>\r
  38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
  39   <TR ALIGN="center" VALIGN="top">\r
  40   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
  41   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
  42   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
  43   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SkeletalExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
  44   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
  45   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
  46   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
  47   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
  48   </TR>\r
  49 </TABLE>\r
  50 </TD>\r
  51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
  52 </EM>\r
  53 </TD>\r
  54 </TR>\r
  55 \r
  56 <TR>\r
  57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  58 &nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
  59 &nbsp;<A HREF="../../../compbio/engine/client/Util.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
  60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
  61   <A HREF="../../../index.html?compbio/engine/client/SkeletalExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
  62 &nbsp;<A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
  63 &nbsp;<SCRIPT type="text/javascript">\r
  64   <!--\r
  65   if(window==top) {\r
  66     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
  67   }\r
  68   //-->\r
  69 </SCRIPT>\r
  70 <NOSCRIPT>\r
  71   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
  72 </NOSCRIPT>\r
  73 \r
  74 \r
  75 </FONT></TD>\r
  76 </TR>\r
  77 <TR>\r
  78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
  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
  82 </TR>\r
  83 </TABLE>\r
  84 <A NAME="skip-navbar_top"></A>\r
  85 <!-- ========= END OF TOP NAVBAR ========= -->\r
  86 \r
  87 <HR>\r
  88 <!-- ======== START OF CLASS DATA ======== -->\r
  89 <H2>\r
  90 <FONT SIZE="-1">\r
  91 compbio.engine.client</FONT>\r
  92 <BR>\r
  93 Class SkeletalExecutable&lt;T&gt;</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.engine.client.SkeletalExecutable&lt;T&gt;</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;T&gt;</DD>\r
 100 </DL>\r
 101 <DL>\r
 102 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>, <A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>, <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>, <A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>, <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>, <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
 103 </DL>\r
 104 <HR>\r
 105 <DL>\r
 106 <DT><PRE>public abstract class <B>SkeletalExecutable&lt;T&gt;</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;T&gt;</DL>\r
 107 </PRE>\r
 108 \r
 109 <P>\r
 110 <HR>\r
 111 \r
 112 <P>\r
 113 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
 114 \r
 115 <A NAME="nested_class_summary"><!-- --></A>\r
 116 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 117 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 118 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 119 <B>Nested Class Summary</B></FONT></TH>\r
 120 </TR>\r
 121 </TABLE>\r
 122 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 123 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 124 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 125 <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
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
 129 </TR>\r
 130 </TABLE>\r
 131 &nbsp;\r
 132 <!-- =========== FIELD SUMMARY =========== -->\r
 133 \r
 134 <A NAME="field_summary"><!-- --></A>\r
 135 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 136 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 137 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 138 <B>Field Summary</B></FONT></TH>\r
 139 </TR>\r
 140 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 142 <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
 143 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</A></B></CODE>\r
 144 \r
 145 <BR>\r
 146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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/engine/client/SkeletalExecutable.html#INPUT">INPUT</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/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</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;\r
 166 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 167 \r
 168 <A NAME="constructor_summary"><!-- --></A>\r
 169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 172 <B>Constructor Summary</B></FONT></TH>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()">SkeletalExecutable</A></B>()</CODE>\r
 176 \r
 177 <BR>\r
 178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 179 </TR>\r
 180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 181 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)">SkeletalExecutable</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;parameterKeyValueDelimiter)</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 </TABLE>\r
 187 &nbsp;\r
 188 <!-- ========== METHOD SUMMARY =========== -->\r
 189 \r
 190 <A NAME="method_summary"><!-- --></A>\r
 191 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 192 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 193 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 194 <B>Method Summary</B></FONT></TH>\r
 195 </TR>\r
 196 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 198 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 199 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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
 200 \r
 201 <BR>\r
 202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 203 </TR>\r
 204 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 205 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 206 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 207 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</CODE>\r
 208 \r
 209 <BR>\r
 210 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 211 </TR>\r
 212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 214 <CODE>static&nbsp;int</CODE></FONT></TD>\r
 215 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</A></B>(<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;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;type)</CODE>\r
 216 \r
 217 <BR>\r
 218 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 219 </TR>\r
 220 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 221 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 222 <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
 223 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
 224 \r
 225 <BR>\r
 226 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 227 </TR>\r
 228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 230 <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
 231 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 232 \r
 233 <BR>\r
 234 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 235  created or not.</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 239 <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
 240 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A></B>()</CODE>\r
 241 \r
 242 <BR>\r
 243 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 244 </TR>\r
 245 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 246 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 247 <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
 248 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A></B>()</CODE>\r
 249 \r
 250 <BR>\r
 251 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 252 </TR>\r
 253 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 254 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 255 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 256 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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
 257 \r
 258 <BR>\r
 259 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 260 </TR>\r
 261 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 262 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 263 <CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 264 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A></B>()</CODE>\r
 265 \r
 266 <BR>\r
 267 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 268 </TR>\r
 269 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 270 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 271 <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
 272 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A></B>()</CODE>\r
 273 \r
 274 <BR>\r
 275 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 276 </TR>\r
 277 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 279 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 280 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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
 281 \r
 282 <BR>\r
 283 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 284 </TR>\r
 285 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 287 <CODE>abstract &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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 288 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>\r
 289 \r
 290 <BR>\r
 291 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 292 </TR>\r
 293 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 295 <CODE>&nbsp;int</CODE></FONT></TD>\r
 296 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A></B>()</CODE>\r
 297 \r
 298 <BR>\r
 299 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 300 </TR>\r
 301 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 302 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 303 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 304 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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
 305 \r
 306 <BR>\r
 307 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 308 </TR>\r
 309 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 310 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 311 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 312 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</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;errFile)</CODE>\r
 313 \r
 314 <BR>\r
 315 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 316 </TR>\r
 317 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 318 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 319 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 320 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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
 321 \r
 322 <BR>\r
 323 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 324 </TR>\r
 325 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 326 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 327 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 328 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.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
 329 \r
 330 <BR>\r
 331 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 332 </TR>\r
 333 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 334 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 335 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 336 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</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
 337 \r
 338 <BR>\r
 339 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 340 </TR>\r
 341 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 342 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 343 <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
 344 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></B>()</CODE>\r
 345 \r
 346 <BR>\r
 347 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 348 </TR>\r
 349 </TABLE>\r
 350 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 351 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 352 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 353 <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
 354 </TR>\r
 355 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 356 <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
 357 </TR>\r
 358 </TABLE>\r
 359 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 360 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 361 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 362 <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
 363 </TR>\r
 364 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 365 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE></TD>\r
 366 </TR>\r
 367 </TABLE>\r
 368 &nbsp;\r
 369 <P>\r
 370 \r
 371 <!-- ============ FIELD DETAIL =========== -->\r
 372 \r
 373 <A NAME="field_detail"><!-- --></A>\r
 374 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 375 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 376 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 377 <B>Field Detail</B></FONT></TH>\r
 378 </TR>\r
 379 </TABLE>\r
 380 \r
 381 <A NAME="INPUT"><!-- --></A><H3>\r
 382 INPUT</H3>\r
 383 <PRE>\r
 384 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>INPUT</B></PRE>\r
 385 <DL>\r
 386 <DL>\r
 387 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.INPUT">Constant Field Values</A></DL>\r
 388 </DL>\r
 389 <HR>\r
 390 \r
 391 <A NAME="OUTPUT"><!-- --></A><H3>\r
 392 OUTPUT</H3>\r
 393 <PRE>\r
 394 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>OUTPUT</B></PRE>\r
 395 <DL>\r
 396 <DL>\r
 397 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.OUTPUT">Constant Field Values</A></DL>\r
 398 </DL>\r
 399 <HR>\r
 400 \r
 401 <A NAME="ERROR"><!-- --></A><H3>\r
 402 ERROR</H3>\r
 403 <PRE>\r
 404 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>ERROR</B></PRE>\r
 405 <DL>\r
 406 <DL>\r
 407 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.ERROR">Constant Field Values</A></DL>\r
 408 </DL>\r
 409 \r
 410 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 411 \r
 412 <A NAME="constructor_detail"><!-- --></A>\r
 413 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 414 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 415 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 416 <B>Constructor Detail</B></FONT></TH>\r
 417 </TR>\r
 418 </TABLE>\r
 419 \r
 420 <A NAME="SkeletalExecutable()"><!-- --></A><H3>\r
 421 SkeletalExecutable</H3>\r
 422 <PRE>\r
 423 public <B>SkeletalExecutable</B>()</PRE>\r
 424 <DL>\r
 425 </DL>\r
 426 <HR>\r
 427 \r
 428 <A NAME="SkeletalExecutable(java.lang.String)"><!-- --></A><H3>\r
 429 SkeletalExecutable</H3>\r
 430 <PRE>\r
 431 public <B>SkeletalExecutable</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;parameterKeyValueDelimiter)</PRE>\r
 432 <DL>\r
 433 </DL>\r
 434 \r
 435 <!-- ============ METHOD DETAIL ========== -->\r
 436 \r
 437 <A NAME="method_detail"><!-- --></A>\r
 438 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 439 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 440 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 441 <B>Method Detail</B></FONT></TH>\r
 442 </TR>\r
 443 </TABLE>\r
 444 \r
 445 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 446 setInput</H3>\r
 447 <PRE>\r
 448 public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <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
 449 <DL>\r
 450 <DD><DL>\r
 451 </DL>\r
 452 </DD>\r
 453 <DD><DL>\r
 454 </DL>\r
 455 </DD>\r
 456 </DL>\r
 457 <HR>\r
 458 \r
 459 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 460 setOutput</H3>\r
 461 <PRE>\r
 462 public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <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
 463 <DL>\r
 464 <DD><DL>\r
 465 </DL>\r
 466 </DD>\r
 467 <DD><DL>\r
 468 </DL>\r
 469 </DD>\r
 470 </DL>\r
 471 <HR>\r
 472 \r
 473 <A NAME="setError(java.lang.String)"><!-- --></A><H3>\r
 474 setError</H3>\r
 475 <PRE>\r
 476 public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>setError</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;errFile)</PRE>\r
 477 <DL>\r
 478 <DD><DL>\r
 479 </DL>\r
 480 </DD>\r
 481 <DD><DL>\r
 482 </DL>\r
 483 </DD>\r
 484 </DL>\r
 485 <HR>\r
 486 \r
 487 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 488 getParameters</H3>\r
 489 <PRE>\r
 490 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</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
 491 <DL>\r
 492 <DD><DL>\r
 493 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 494 </DD>\r
 495 <DD><DL>\r
 496 </DL>\r
 497 </DD>\r
 498 </DL>\r
 499 <HR>\r
 500 \r
 501 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 502 addParameters</H3>\r
 503 <PRE>\r
 504 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <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
 505 <DL>\r
 506 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
 507 <DD>Adds parameter to the list of parameters for a native executable\r
 508 <P>\r
 509 <DD><DL>\r
 510 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 511 </DD>\r
 512 <DD><DL>\r
 513 \r
 514 <DT><B>Returns:</B><DD>this Executable</DL>\r
 515 </DD>\r
 516 </DL>\r
 517 <HR>\r
 518 \r
 519 <A NAME="setParameter(java.lang.String)"><!-- --></A><H3>\r
 520 setParameter</H3>\r
 521 <PRE>\r
 522 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>setParameter</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
 523 <DL>\r
 524 <DD><DL>\r
 525 </DL>\r
 526 </DD>\r
 527 <DD><DL>\r
 528 </DL>\r
 529 </DD>\r
 530 </DL>\r
 531 <HR>\r
 532 \r
 533 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 534 getCreatedFiles</H3>\r
 535 <PRE>\r
 536 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
 537 <DL>\r
 538 <DD>This method cannot really tell whether the files has actually been
 539  created or not. It must be overridden as required.\r
 540 <P>\r
 541 <DD><DL>\r
 542 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 543 </DD>\r
 544 <DD><DL>\r
 545 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 546 </DD>\r
 547 </DL>\r
 548 <HR>\r
 549 \r
 550 <A NAME="getInput()"><!-- --></A><H3>\r
 551 getInput</H3>\r
 552 <PRE>\r
 553 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
 554 <DL>\r
 555 <DD><DL>\r
 556 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 557 </DD>\r
 558 <DD><DL>\r
 559 </DL>\r
 560 </DD>\r
 561 </DL>\r
 562 <HR>\r
 563 \r
 564 <A NAME="getOutput()"><!-- --></A><H3>\r
 565 getOutput</H3>\r
 566 <PRE>\r
 567 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
 568 <DL>\r
 569 <DD><DL>\r
 570 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 571 </DD>\r
 572 <DD><DL>\r
 573 </DL>\r
 574 </DD>\r
 575 </DL>\r
 576 <HR>\r
 577 \r
 578 <A NAME="getError()"><!-- --></A><H3>\r
 579 getError</H3>\r
 580 <PRE>\r
 581 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
 582 <DL>\r
 583 <DD><DL>\r
 584 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 585 </DD>\r
 586 <DD><DL>\r
 587 </DL>\r
 588 </DD>\r
 589 </DL>\r
 590 <HR>\r
 591 \r
 592 <A NAME="toString()"><!-- --></A><H3>\r
 593 toString</H3>\r
 594 <PRE>\r
 595 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
 596 <DL>\r
 597 <DD><DL>\r
 598 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 599 </DD>\r
 600 <DD><DL>\r
 601 </DL>\r
 602 </DD>\r
 603 </DL>\r
 604 <HR>\r
 605 \r
 606 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 607 loadRunConfiguration</H3>\r
 608 <PRE>\r
 609 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
 610 <DL>\r
 611 <DD><DL>\r
 612 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 613 </DD>\r
 614 <DD><DL>\r
 615 </DL>\r
 616 </DD>\r
 617 </DL>\r
 618 <HR>\r
 619 \r
 620 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 621 equals</H3>\r
 622 <PRE>\r
 623 public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A>&nbsp;obj)</PRE>\r
 624 <DL>\r
 625 <DD><DL>\r
 626 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 627 </DD>\r
 628 <DD><DL>\r
 629 </DL>\r
 630 </DD>\r
 631 </DL>\r
 632 <HR>\r
 633 \r
 634 <A NAME="hashCode()"><!-- --></A><H3>\r
 635 hashCode</H3>\r
 636 <PRE>\r
 637 public int <B>hashCode</B>()</PRE>\r
 638 <DL>\r
 639 <DD><DL>\r
 640 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
 641 </DD>\r
 642 <DD><DL>\r
 643 </DL>\r
 644 </DD>\r
 645 </DL>\r
 646 <HR>\r
 647 \r
 648 <A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
 649 getClusterJobSettings</H3>\r
 650 <PRE>\r
 651 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
 652 <DL>\r
 653 <DD><DL>\r
 654 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 655 </DD>\r
 656 <DD><DL>\r
 657 </DL>\r
 658 </DD>\r
 659 </DL>\r
 660 <HR>\r
 661 \r
 662 <A NAME="getClusterCpuNum(java.lang.Class)"><!-- --></A><H3>\r
 663 getClusterCpuNum</H3>\r
 664 <PRE>\r
 665 public static int <B>getClusterCpuNum</B>(<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;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;type)</PRE>\r
 666 <DL>\r
 667 <DD><DL>\r
 668 </DL>\r
 669 </DD>\r
 670 <DD><DL>\r
 671 \r
 672 <DT><B>Returns:</B><DD>number of cpus to use on the cluster or 0 if the value is
 673          undefined</DL>\r
 674 </DD>\r
 675 </DL>\r
 676 <HR>\r
 677 \r
 678 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
 679 getLimit</H3>\r
 680 <PRE>\r
 681 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</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
 682 <DL>\r
 683 <DD><DL>\r
 684 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 685 </DD>\r
 686 <DD><DL>\r
 687 </DL>\r
 688 </DD>\r
 689 </DL>\r
 690 <HR>\r
 691 \r
 692 <A NAME="getLimits()"><!-- --></A><H3>\r
 693 getLimits</H3>\r
 694 <PRE>\r
 695 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>getLimits</B>()</PRE>\r
 696 <DL>\r
 697 <DD><DL>\r
 698 <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></DL>\r
 699 </DD>\r
 700 <DD><DL>\r
 701 </DL>\r
 702 </DD>\r
 703 </DL>\r
 704 <HR>\r
 705 \r
 706 <A NAME="getType()"><!-- --></A><H3>\r
 707 getType</H3>\r
 708 <PRE>\r
 709 public abstract <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/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt; <B>getType</B>()</PRE>\r
 710 <DL>\r
 711 <DD><DL>\r
 712 </DL>\r
 713 </DD>\r
 714 <DD><DL>\r
 715 \r
 716 <DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
 717 </DD>\r
 718 </DL>\r
 719 <!-- ========= END OF CLASS DATA ========= -->\r
 720 <HR>\r
 721 \r
 722 \r
 723 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 724 <A NAME="navbar_bottom"><!-- --></A>\r
 725 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 726 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 727 <TR>\r
 728 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 729 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 730 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 731   <TR ALIGN="center" VALIGN="top">\r
 732   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 733   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 734   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 735   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SkeletalExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 736   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 737   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 738   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 739   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 740   </TR>\r
 741 </TABLE>\r
 742 </TD>\r
 743 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 744 </EM>\r
 745 </TD>\r
 746 </TR>\r
 747 \r
 748 <TR>\r
 749 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 750 &nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 751 &nbsp;<A HREF="../../../compbio/engine/client/Util.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
 752 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 753   <A HREF="../../../index.html?compbio/engine/client/SkeletalExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 754 &nbsp;<A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 755 &nbsp;<SCRIPT type="text/javascript">\r
 756   <!--\r
 757   if(window==top) {\r
 758     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 759   }\r
 760   //-->\r
 761 </SCRIPT>\r
 762 <NOSCRIPT>\r
 763   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 764 </NOSCRIPT>\r
 765 \r
 766 \r
 767 </FONT></TD>\r
 768 </TR>\r
 769 <TR>\r
 770 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 771   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
 772 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 773 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
 774 </TR>\r
 775 </TABLE>\r
 776 <A NAME="skip-navbar_bottom"></A>\r
 777 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 778 \r
 779 <HR>\r
 780 \r
 781 </BODY>\r
 782 </HTML>\r