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

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   7 Util\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
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  91 compbio.engine.client</FONT>\r
  92 <BR>\r
  93 Class Util</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.Util</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>Util</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></DL>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 <HR>\r
 105 \r
 106 <P>\r
 107 \r
 108 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 109 \r
 110 <A NAME="constructor_summary"><!-- --></A>\r
 111 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 112 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 113 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 114 <B>Constructor Summary</B></FONT></TH>\r
 115 </TR>\r
 116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 117 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#Util()">Util</A></B>()</CODE>\r
 118 \r
 119 <BR>\r
 120 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 121 </TR>\r
 122 </TABLE>\r
 123 &nbsp;\r
 124 <!-- ========== METHOD SUMMARY =========== -->\r
 125 \r
 126 <A NAME="method_summary"><!-- --></A>\r
 127 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 128 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 129 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 130 <B>Method Summary</B></FONT></TH>\r
 131 </TR>\r
 132 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 134 <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
 135 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)">convertToAbsolute</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;relativePath)</CODE>\r
 136 \r
 137 <BR>\r
 138 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\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/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider,\r
 144            <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;?&gt;&nbsp;clazz)</CODE>\r
 145 \r
 146 <BR>\r
 147 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 148 </TR>\r
 149 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 151 <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
 152 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)">getExecProperty</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;propertySpec,\r
 153                 <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;?&gt;&nbsp;clazz)</CODE>\r
 154 \r
 155 <BR>\r
 156 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 157 </TR>\r
 158 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 160 <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
 161 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</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;propertySpec,\r
 162                 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 166 </TR>\r
 167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 169 <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
 170 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)">getFullPath</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 171             <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;fileName)</CODE>\r
 172 \r
 173 <BR>\r
 174 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 175 </TR>\r
 176 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 178 <CODE>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
 179 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getJava()">getJava</A></B>()</CODE>\r
 180 \r
 181 <BR>\r
 182 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the absolute path to the Java executable from JAVA_HOME</TD>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 186 <CODE>static\r
 187 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 188 <TR ALIGN="right" VALIGN="">\r
 189 <TD NOWRAP><FONT SIZE="-1">\r
 190 <CODE>&lt;T&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</CODE></FONT></TD>\r
 191 </TR>\r
 192 </TABLE>\r
 193 </CODE></FONT></TD>\r
 194 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getLimits(java.lang.Class)">getLimits</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;T&gt;&nbsp;clazz)</CODE>\r
 195 \r
 196 <BR>\r
 197 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;For now just assume that all parameters which came in needs setting it
 198  will be a client responsibility to prepare RunnerConfig object then</TD>\r
 199 </TR>\r
 200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 202 <CODE>static&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
 203 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)">getSupportedRuntimes</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;?&gt;&nbsp;clazz)</CODE>\r
 204 \r
 205 <BR>\r
 206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 207 </TR>\r
 208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 210 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isJavaLibrary(java.lang.Class)">isJavaLibrary</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;?&gt;&nbsp;clazz)</CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns true of executableName.jar.file property has some value in the
 215  Executable.properties file, false otherwise.</TD>\r
 216 </TR>\r
 217 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 219 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 220 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)">isMarked</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 221          <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;marker)</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>static&nbsp;boolean</CODE></FONT></TD>\r
 229 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isValidJobId(java.lang.String)">isValidJobId</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;key)</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>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 237 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</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;taskId)</CODE>\r
 238 \r
 239 <BR>\r
 240 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 241 </TR>\r
 242 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 243 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 244 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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
 245 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)">mergeEnvVariables</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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;sysEnvTobeModified,\r
 246                   <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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;variables)</CODE>\r
 247 \r
 248 <BR>\r
 249 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 250 </TR>\r
 251 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 253 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 254 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)">writeFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 255           <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;fileAndEventName,\r
 256           <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;content,\r
 257           boolean&nbsp;override)</CODE>\r
 258 \r
 259 <BR>\r
 260 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 261 </TR>\r
 262 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 263 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 264 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 265 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)">writeMarker</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 266             <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;fileType)</CODE>\r
 267 \r
 268 <BR>\r
 269 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 270 </TR>\r
 271 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 272 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 273 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 274 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeStatFile(java.lang.String, java.lang.String)">writeStatFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 275               <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;fileAndEventName)</CODE>\r
 276 \r
 277 <BR>\r
 278 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 279 </TR>\r
 280 </TABLE>\r
 281 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 282 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 283 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 284 <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
 285 </TR>\r
 286 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 287 <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
 288 </TR>\r
 289 </TABLE>\r
 290 &nbsp;\r
 291 <P>\r
 292 \r
 293 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 294 \r
 295 <A NAME="constructor_detail"><!-- --></A>\r
 296 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 297 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 298 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 299 <B>Constructor Detail</B></FONT></TH>\r
 300 </TR>\r
 301 </TABLE>\r
 302 \r
 303 <A NAME="Util()"><!-- --></A><H3>\r
 304 Util</H3>\r
 305 <PRE>\r
 306 public <B>Util</B>()</PRE>\r
 307 <DL>\r
 308 </DL>\r
 309 \r
 310 <!-- ============ METHOD DETAIL ========== -->\r
 311 \r
 312 <A NAME="method_detail"><!-- --></A>\r
 313 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 314 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 315 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 316 <B>Method Detail</B></FONT></TH>\r
 317 </TR>\r
 318 </TABLE>\r
 319 \r
 320 <A NAME="isValidJobId(java.lang.String)"><!-- --></A><H3>\r
 321 isValidJobId</H3>\r
 322 <PRE>\r
 323 public static boolean <B>isValidJobId</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;key)</PRE>\r
 324 <DL>\r
 325 <DD><DL>\r
 326 </DL>\r
 327 </DD>\r
 328 </DL>\r
 329 <HR>\r
 330 \r
 331 <A NAME="writeStatFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 332 writeStatFile</H3>\r
 333 <PRE>\r
 334 public static void <B>writeStatFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 335                                  <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;fileAndEventName)</PRE>\r
 336 <DL>\r
 337 <DD><DL>\r
 338 </DL>\r
 339 </DD>\r
 340 </DL>\r
 341 <HR>\r
 342 \r
 343 <A NAME="writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>\r
 344 writeFile</H3>\r
 345 <PRE>\r
 346 public static void <B>writeFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 347                              <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;fileAndEventName,\r
 348                              <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;content,\r
 349                              boolean&nbsp;override)</PRE>\r
 350 <DL>\r
 351 <DD><DL>\r
 352 </DL>\r
 353 </DD>\r
 354 </DL>\r
 355 <HR>\r
 356 \r
 357 <A NAME="writeMarker(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>\r
 358 writeMarker</H3>\r
 359 <PRE>\r
 360 public static final boolean <B>writeMarker</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 361                                         <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;fileType)</PRE>\r
 362 <DL>\r
 363 <DD><DL>\r
 364 </DL>\r
 365 </DD>\r
 366 </DL>\r
 367 <HR>\r
 368 \r
 369 <A NAME="isMarked(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>\r
 370 isMarked</H3>\r
 371 <PRE>\r
 372 public static boolean <B>isMarked</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 373                                <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;marker)</PRE>\r
 374 <DL>\r
 375 <DD><DL>\r
 376 </DL>\r
 377 </DD>\r
 378 </DL>\r
 379 <HR>\r
 380 \r
 381 <A NAME="mergeEnvVariables(java.util.Map, java.util.Map)"><!-- --></A><H3>\r
 382 mergeEnvVariables</H3>\r
 383 <PRE>\r
 384 public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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>mergeEnvVariables</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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;sysEnvTobeModified,\r
 385                                                    <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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;variables)</PRE>\r
 386 <DL>\r
 387 <DD><DL>\r
 388 </DL>\r
 389 </DD>\r
 390 </DL>\r
 391 <HR>\r
 392 \r
 393 <A NAME="convertToAbsolute(java.lang.String)"><!-- --></A><H3>\r
 394 convertToAbsolute</H3>\r
 395 <PRE>\r
 396 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>convertToAbsolute</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;relativePath)</PRE>\r
 397 <DL>\r
 398 <DD><DL>\r
 399 </DL>\r
 400 </DD>\r
 401 </DL>\r
 402 <HR>\r
 403 \r
 404 <A NAME="getExecProperty(java.lang.String, compbio.engine.client.Executable)"><!-- --></A><H3>\r
 405 getExecProperty</H3>\r
 406 <PRE>\r
 407 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>getExecProperty</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;propertySpec,\r
 408                                      <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</PRE>\r
 409 <DL>\r
 410 <DD><DL>\r
 411 </DL>\r
 412 </DD>\r
 413 </DL>\r
 414 <HR>\r
 415 \r
 416 <A NAME="getExecProperty(java.lang.String, java.lang.Class)"><!-- --></A><H3>\r
 417 getExecProperty</H3>\r
 418 <PRE>\r
 419 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>getExecProperty</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;propertySpec,\r
 420                                      <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;?&gt;&nbsp;clazz)</PRE>\r
 421 <DL>\r
 422 <DD><DL>\r
 423 </DL>\r
 424 </DD>\r
 425 </DL>\r
 426 <HR>\r
 427 \r
 428 <A NAME="getFullPath(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
 429 getFullPath</H3>\r
 430 <PRE>\r
 431 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>getFullPath</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
 432                                  <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;fileName)</PRE>\r
 433 <DL>\r
 434 <DD><DL>\r
 435 </DL>\r
 436 </DD>\r
 437 </DL>\r
 438 <HR>\r
 439 \r
 440 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><!-- --></A><H3>\r
 441 getCommand</H3>\r
 442 <PRE>\r
 443 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>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider,\r
 444                                 <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;?&gt;&nbsp;clazz)</PRE>\r
 445 <DL>\r
 446 <DD><DL>\r
 447 </DL>\r
 448 </DD>\r
 449 </DL>\r
 450 <HR>\r
 451 \r
 452 <A NAME="isJavaLibrary(java.lang.Class)"><!-- --></A><H3>\r
 453 isJavaLibrary</H3>\r
 454 <PRE>\r
 455 public static boolean <B>isJavaLibrary</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;?&gt;&nbsp;clazz)</PRE>\r
 456 <DL>\r
 457 <DD>Returns true of executableName.jar.file property has some value in the
 458  Executable.properties file, false otherwise.\r
 459 <P>\r
 460 <DD><DL>\r
 461 <DT><B>Parameters:</B><DD><CODE>clazz</CODE> - \r
 462 <DT><B>Returns:</B><DD></DL>\r
 463 </DD>\r
 464 </DL>\r
 465 <HR>\r
 466 \r
 467 <A NAME="getJava()"><!-- --></A><H3>\r
 468 getJava</H3>\r
 469 <PRE>\r
 470 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>getJava</B>()</PRE>\r
 471 <DL>\r
 472 <DD>Returns the absolute path to the Java executable from JAVA_HOME\r
 473 <P>\r
 474 <DD><DL>\r
 475 \r
 476 <DT><B>Returns:</B><DD>returns the absolute path to the Java executable from JAVA_HOME</DL>\r
 477 </DD>\r
 478 </DL>\r
 479 <HR>\r
 480 \r
 481 <A NAME="getSupportedRuntimes(java.lang.Class)"><!-- --></A><H3>\r
 482 getSupportedRuntimes</H3>\r
 483 <PRE>\r
 484 public static <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</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;?&gt;&nbsp;clazz)</PRE>\r
 485 <DL>\r
 486 <DD><DL>\r
 487 </DL>\r
 488 </DD>\r
 489 </DL>\r
 490 <HR>\r
 491 \r
 492 <A NAME="loadExecutable(java.lang.String)"><!-- --></A><H3>\r
 493 loadExecutable</H3>\r
 494 <PRE>\r
 495 public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadExecutable</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;taskId)\r
 496                                               throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 497 <DL>\r
 498 <DD><DL>\r
 499 \r
 500 <DT><B>Throws:</B>\r
 501 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
 502 </DD>\r
 503 </DL>\r
 504 <HR>\r
 505 \r
 506 <A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>\r
 507 getLimits</H3>\r
 508 <PRE>\r
 509 public static &lt;T&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt; <B>getLimits</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;T&gt;&nbsp;clazz)</PRE>\r
 510 <DL>\r
 511 <DD>For now just assume that all parameters which came in needs setting it
 512  will be a client responsibility to prepare RunnerConfig object then\r
 513 <P>\r
 514 <DD><DL>\r
 515 <DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
 516 <DT><B>Returns:</B><DD>public static List<String> toOptionString(RunnerConfig<?>
 517          rconfig) { String option = ""; List<String> options = new
 518          ArrayList<String>(); for (Parameter<?> par :
 519          rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
 520          { option = par.getOptionName(); } else { option =
 521          par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
 522          separate options options.add(option); } return options; }</DL>\r
 523 </DD>\r
 524 </DL>\r
 525 <!-- ========= END OF CLASS DATA ========= -->\r
 526 <HR>\r
 527 \r
 528 \r
 529 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 530 <A NAME="navbar_bottom"><!-- --></A>\r
 531 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 532 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
 533 <TR>\r
 534 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 535 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 536 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 537   <TR ALIGN="center" VALIGN="top">\r
 538   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 539   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
 540   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
 541   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 542   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 543   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
 544   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
 545   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
 546   </TR>\r
 547 </TABLE>\r
 548 </TD>\r
 549 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
 550 </EM>\r
 551 </TD>\r
 552 </TR>\r
 553 \r
 554 <TR>\r
 555 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 556 &nbsp;<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
 557 &nbsp;NEXT CLASS</FONT></TD>\r
 558 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 559   <A HREF="../../../index.html?compbio/engine/client/Util.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 560 &nbsp;<A HREF="Util.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
 561 &nbsp;<SCRIPT type="text/javascript">\r
 562   <!--\r
 563   if(window==top) {\r
 564     document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 565   }\r
 566   //-->\r
 567 </SCRIPT>\r
 568 <NOSCRIPT>\r
 569   <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 570 </NOSCRIPT>\r
 571 \r
 572 \r
 573 </FONT></TD>\r
 574 </TR>\r
 575 <TR>\r
 576 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 577   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
 578 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
 579 DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
 580 </TR>\r
 581 </TABLE>\r
 582 <A NAME="skip-navbar_bottom"></A>\r
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 584 \r
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