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_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
   6 <TITLE>\r
   7 SkeletalExecutable\r
   8 </TITLE>\r
   9 \r
  10 <META NAME="date" CONTENT="2010-02-17">\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;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
  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 java.lang.Object\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/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</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/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</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 java.lang.Object<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 \r
 133 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 134 \r
 135 <A NAME="constructor_summary"><!-- --></A>\r
 136 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 137 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 139 <B>Constructor Summary</B></FONT></TH>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable()">SkeletalExecutable</A></B>()</CODE>\r
 143 \r
 144 <BR>\r
 145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 146 </TR>\r
 147 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 148 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)">SkeletalExecutable</A></B>(java.lang.String&nbsp;parameterKeyValueDelimiter)</CODE>\r
 149 \r
 150 <BR>\r
 151 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 152 </TR>\r
 153 </TABLE>\r
 154 &nbsp;\r
 155 <!-- ========== METHOD SUMMARY =========== -->\r
 156 \r
 157 <A NAME="method_summary"><!-- --></A>\r
 158 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 159 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 160 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 161 <B>Method Summary</B></FONT></TH>\r
 162 </TR>\r
 163 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 164 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 165 <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
 166 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
 167 \r
 168 <BR>\r
 169 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
 170 </TR>\r
 171 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 172 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 173 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 174 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>\r
 175 \r
 176 <BR>\r
 177 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 178 </TR>\r
 179 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 180 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 181 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 182 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A></B>()</CODE>\r
 183 \r
 184 <BR>\r
 185 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 186 </TR>\r
 187 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 189 <CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
 190 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
 191 \r
 192 <BR>\r
 193 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method cannot really tell whether the files has actually been
 194  created or not.</TD>\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;java.lang.String</CODE></FONT></TD>\r
 199 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A></B>()</CODE>\r
 200 \r
 201 <BR>\r
 202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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;java.lang.String</CODE></FONT></TD>\r
 207 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A></B>()</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>&nbsp;java.lang.String</CODE></FONT></TD>\r
 215 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getOutput()">getOutput</A></B>()</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="../../../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
 223 <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
 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>abstract &nbsp;java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 231 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>\r
 232 \r
 233 <BR>\r
 234 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 235 </TR>\r
 236 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 237 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 238 <CODE>&nbsp;int</CODE></FONT></TD>\r
 239 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#hashCode()">hashCode</A></B>()</CODE>\r
 240 \r
 241 <BR>\r
 242 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 243 </TR>\r
 244 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 245 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 246 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
 247 <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
 248 \r
 249 <BR>\r
 250 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 251 </TR>\r
 252 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 253 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 254 <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
 255 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A></B>(java.lang.String&nbsp;errFile)</CODE>\r
 256 \r
 257 <BR>\r
 258 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 259 </TR>\r
 260 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 261 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 262 <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
 263 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String&nbsp;inFile)</CODE>\r
 264 \r
 265 <BR>\r
 266 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 267 </TR>\r
 268 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 269 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 270 <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
 271 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String&nbsp;outFile)</CODE>\r
 272 \r
 273 <BR>\r
 274 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 275 </TR>\r
 276 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 277 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 278 <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
 279 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
 280 \r
 281 <BR>\r
 282 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 283 </TR>\r
 284 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 286 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
 287 <TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></B>()</CODE>\r
 288 \r
 289 <BR>\r
 290 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 291 </TR>\r
 292 </TABLE>\r
 293 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 294 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 295 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 296 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 297 </TR>\r
 298 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 299 <TD><CODE>getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
 300 </TR>\r
 301 </TABLE>\r
 302 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
 303 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 304 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 305 <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
 306 </TR>\r
 307 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 308 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE></TD>\r
 309 </TR>\r
 310 </TABLE>\r
 311 &nbsp;\r
 312 <P>\r
 313 \r
 314 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 315 \r
 316 <A NAME="constructor_detail"><!-- --></A>\r
 317 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 318 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 319 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 320 <B>Constructor Detail</B></FONT></TH>\r
 321 </TR>\r
 322 </TABLE>\r
 323 \r
 324 <A NAME="SkeletalExecutable()"><!-- --></A><H3>\r
 325 SkeletalExecutable</H3>\r
 326 <PRE>\r
 327 public <B>SkeletalExecutable</B>()</PRE>\r
 328 <DL>\r
 329 </DL>\r
 330 <HR>\r
 331 \r
 332 <A NAME="SkeletalExecutable(java.lang.String)"><!-- --></A><H3>\r
 333 SkeletalExecutable</H3>\r
 334 <PRE>\r
 335 public <B>SkeletalExecutable</B>(java.lang.String&nbsp;parameterKeyValueDelimiter)</PRE>\r
 336 <DL>\r
 337 </DL>\r
 338 \r
 339 <!-- ============ METHOD DETAIL ========== -->\r
 340 \r
 341 <A NAME="method_detail"><!-- --></A>\r
 342 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 343 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 344 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 345 <B>Method Detail</B></FONT></TH>\r
 346 </TR>\r
 347 </TABLE>\r
 348 \r
 349 <A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
 350 setInput</H3>\r
 351 <PRE>\r
 352 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>(java.lang.String&nbsp;inFile)</PRE>\r
 353 <DL>\r
 354 <DD><DL>\r
 355 </DL>\r
 356 </DD>\r
 357 <DD><DL>\r
 358 </DL>\r
 359 </DD>\r
 360 </DL>\r
 361 <HR>\r
 362 \r
 363 <A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
 364 setOutput</H3>\r
 365 <PRE>\r
 366 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>(java.lang.String&nbsp;outFile)</PRE>\r
 367 <DL>\r
 368 <DD><DL>\r
 369 </DL>\r
 370 </DD>\r
 371 <DD><DL>\r
 372 </DL>\r
 373 </DD>\r
 374 </DL>\r
 375 <HR>\r
 376 \r
 377 <A NAME="setError(java.lang.String)"><!-- --></A><H3>\r
 378 setError</H3>\r
 379 <PRE>\r
 380 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>(java.lang.String&nbsp;errFile)</PRE>\r
 381 <DL>\r
 382 <DD><DL>\r
 383 </DL>\r
 384 </DD>\r
 385 <DD><DL>\r
 386 </DL>\r
 387 </DD>\r
 388 </DL>\r
 389 <HR>\r
 390 \r
 391 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
 392 getParameters</H3>\r
 393 <PRE>\r
 394 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
 395 <DL>\r
 396 <DD><DL>\r
 397 <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
 398 </DD>\r
 399 <DD><DL>\r
 400 </DL>\r
 401 </DD>\r
 402 </DL>\r
 403 <HR>\r
 404 \r
 405 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
 406 addParameters</H3>\r
 407 <PRE>\r
 408 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>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
 409 <DL>\r
 410 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
 411 <DD>Adds parameter to the list of parameters for a native executable\r
 412 <P>\r
 413 <DD><DL>\r
 414 <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
 415 </DD>\r
 416 <DD><DL>\r
 417 \r
 418 <DT><B>Returns:</B><DD>this Executable</DL>\r
 419 </DD>\r
 420 </DL>\r
 421 <HR>\r
 422 \r
 423 <A NAME="setParameter(java.lang.String)"><!-- --></A><H3>\r
 424 setParameter</H3>\r
 425 <PRE>\r
 426 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>(java.lang.String&nbsp;parameter)</PRE>\r
 427 <DL>\r
 428 <DD><DL>\r
 429 </DL>\r
 430 </DD>\r
 431 <DD><DL>\r
 432 </DL>\r
 433 </DD>\r
 434 </DL>\r
 435 <HR>\r
 436 \r
 437 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
 438 getCreatedFiles</H3>\r
 439 <PRE>\r
 440 public java.util.List&lt;java.lang.String&gt; <B>getCreatedFiles</B>()</PRE>\r
 441 <DL>\r
 442 <DD>This method cannot really tell whether the files has actually been
 443  created or not. It must be overridden as required.\r
 444 <P>\r
 445 <DD><DL>\r
 446 <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
 447 </DD>\r
 448 <DD><DL>\r
 449 <DT><B>See Also:</B><DD><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()"><CODE>Executable.getCreatedFiles()</CODE></A></DL>\r
 450 </DD>\r
 451 </DL>\r
 452 <HR>\r
 453 \r
 454 <A NAME="getInput()"><!-- --></A><H3>\r
 455 getInput</H3>\r
 456 <PRE>\r
 457 public java.lang.String <B>getInput</B>()</PRE>\r
 458 <DL>\r
 459 <DD><DL>\r
 460 <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
 461 </DD>\r
 462 <DD><DL>\r
 463 </DL>\r
 464 </DD>\r
 465 </DL>\r
 466 <HR>\r
 467 \r
 468 <A NAME="getOutput()"><!-- --></A><H3>\r
 469 getOutput</H3>\r
 470 <PRE>\r
 471 public java.lang.String <B>getOutput</B>()</PRE>\r
 472 <DL>\r
 473 <DD><DL>\r
 474 <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
 475 </DD>\r
 476 <DD><DL>\r
 477 </DL>\r
 478 </DD>\r
 479 </DL>\r
 480 <HR>\r
 481 \r
 482 <A NAME="getError()"><!-- --></A><H3>\r
 483 getError</H3>\r
 484 <PRE>\r
 485 public java.lang.String <B>getError</B>()</PRE>\r
 486 <DL>\r
 487 <DD><DL>\r
 488 <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
 489 </DD>\r
 490 <DD><DL>\r
 491 </DL>\r
 492 </DD>\r
 493 </DL>\r
 494 <HR>\r
 495 \r
 496 <A NAME="toString()"><!-- --></A><H3>\r
 497 toString</H3>\r
 498 <PRE>\r
 499 public java.lang.String <B>toString</B>()</PRE>\r
 500 <DL>\r
 501 <DD><DL>\r
 502 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 503 </DD>\r
 504 <DD><DL>\r
 505 </DL>\r
 506 </DD>\r
 507 </DL>\r
 508 <HR>\r
 509 \r
 510 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
 511 loadRunConfiguration</H3>\r
 512 <PRE>\r
 513 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
 514 <DL>\r
 515 <DD><DL>\r
 516 <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
 517 </DD>\r
 518 <DD><DL>\r
 519 </DL>\r
 520 </DD>\r
 521 </DL>\r
 522 <HR>\r
 523 \r
 524 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
 525 equals</H3>\r
 526 <PRE>\r
 527 public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>\r
 528 <DL>\r
 529 <DD><DL>\r
 530 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 531 </DD>\r
 532 <DD><DL>\r
 533 </DL>\r
 534 </DD>\r
 535 </DL>\r
 536 <HR>\r
 537 \r
 538 <A NAME="hashCode()"><!-- --></A><H3>\r
 539 hashCode</H3>\r
 540 <PRE>\r
 541 public int <B>hashCode</B>()</PRE>\r
 542 <DL>\r
 543 <DD><DL>\r
 544 <DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
 545 </DD>\r
 546 <DD><DL>\r
 547 </DL>\r
 548 </DD>\r
 549 </DL>\r
 550 <HR>\r
 551 \r
 552 <A NAME="getClusterSettings()"><!-- --></A><H3>\r
 553 getClusterSettings</H3>\r
 554 <PRE>\r
 555 public java.lang.String <B>getClusterSettings</B>()</PRE>\r
 556 <DL>\r
 557 <DD><DL>\r
 558 </DL>\r
 559 </DD>\r
 560 <DD><DL>\r
 561 </DL>\r
 562 </DD>\r
 563 </DL>\r
 564 <HR>\r
 565 \r
 566 <A NAME="getType()"><!-- --></A><H3>\r
 567 getType</H3>\r
 568 <PRE>\r
 569 public abstract java.lang.Class&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt; <B>getType</B>()</PRE>\r
 570 <DL>\r
 571 <DD><DL>\r
 572 </DL>\r
 573 </DD>\r
 574 <DD><DL>\r
 575 </DL>\r
 576 </DD>\r
 577 </DL>\r
 578 <!-- ========= END OF CLASS DATA ========= -->\r
 579 <HR>\r
 580 \r
 581 \r
 582 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 583 <A NAME="navbar_bottom"><!-- --></A>\r
 584 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 585 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 586 <TR>\r
 587 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 588 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 589 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 590   <TR ALIGN="center" VALIGN="top">\r
 591   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 592   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 593   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 594   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/SkeletalExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 595   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 596   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 597   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 598   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 599   </TR>\r
 600 </TABLE>\r
 601 </TD>\r
 602 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 603 </EM>\r
 604 </TD>\r
 605 </TR>\r
 606 \r
 607 <TR>\r
 608 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 609 &nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 610 &nbsp;<A HREF="../../../compbio/engine/client/Util.html" title="class in compbio.engine.client"><B>NEXT CLASS</B></A></FONT></TD>\r
 611 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 612   <A HREF="../../../index.html?compbio/engine/client/SkeletalExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 613 &nbsp;<A HREF="SkeletalExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 614 &nbsp;<SCRIPT type="text/javascript">\r
 615   <!--\r
 616   if(window==top) {\r
 617     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 618   }\r
 619   //-->\r
 620 </SCRIPT>\r
 621 <NOSCRIPT>\r
 622   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 623 </NOSCRIPT>\r
 624 \r
 625 \r
 626 </FONT></TD>\r
 627 </TR>\r
 628 <TR>\r
 629 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 630   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
 631 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 632 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 633 </TR>\r
 634 </TABLE>\r
 635 <A NAME="skip-navbar_bottom"></A>\r
 636 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 637 \r
 638 <HR>\r
 639 \r
 640 </BODY>\r
 641 </HTML>\r