website/full_javadoc/compbio/engine/local/ExecutableWrapper.html

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  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
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  89 <H2>\r
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  91 compbio.engine.local</FONT>\r
  92 <BR>\r
  93 Class ExecutableWrapper</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.local.ExecutableWrapper</B>\r
  97 </PRE>\r
  98 <DL>\r
  99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Callable.html?is-external=true" title="class or interface in java.util.concurrent">Callable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</DD>\r
 100 </DL>\r
 101 <HR>\r
 102 <DL>\r
 103 <DT><PRE><FONT SIZE="-1">@Immutable\r
 104 </FONT>public final class <B>ExecutableWrapper</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="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Callable.html?is-external=true" title="class or interface in java.util.concurrent">Callable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</DL>\r
 105 </PRE>\r
 106 \r
 107 <P>\r
 108 <HR>\r
 109 \r
 110 <P>\r
 111 <!-- =========== FIELD SUMMARY =========== -->\r
 112 \r
 113 <A NAME="field_summary"><!-- --></A>\r
 114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 115 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 116 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 117 <B>Field Summary</B></FONT></TH>\r
 118 </TR>\r
 119 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 120 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 121 <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
 122 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</A></B></CODE>\r
 123 \r
 124 <BR>\r
 125 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <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
 130 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</A></B></CODE>\r
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 134 </TR>\r
 135 </TABLE>\r
 136 &nbsp;\r
 137 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 138 \r
 139 <A NAME="constructor_summary"><!-- --></A>\r
 140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 141 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 143 <B>Constructor Summary</B></FONT></TH>\r
 144 </TR>\r
 145 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 146 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
 147                   <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)</CODE>\r
 148 \r
 149 <BR>\r
 150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 151 </TR>\r
 152 </TABLE>\r
 153 &nbsp;\r
 154 <!-- ========== METHOD SUMMARY =========== -->\r
 155 \r
 156 <A NAME="method_summary"><!-- --></A>\r
 157 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 158 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 159 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 160 <B>Method Summary</B></FONT></TH>\r
 161 </TR>\r
 162 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 164 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
 165 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#call()">call</A></B>()</CODE>\r
 166 \r
 167 <BR>\r
 168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;It is vital that output and error streams are captured immediately for
 169  this call() to succeed.</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>static&nbsp;void</CODE></FONT></TD>\r
 174 <TD><CODE><B><A HREF="../../../compbio/engine/local/ExecutableWrapper.html#shutdownService()">shutdownService</A></B>()</CODE>\r
 175 \r
 176 <BR>\r
 177 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stops internal executor service which captures streams of native
 178  executables.</TD>\r
 179 </TR>\r
 180 </TABLE>\r
 181 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 182 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 183 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 184 <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
 185 </TR>\r
 186 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 187 <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
 188 </TR>\r
 189 </TABLE>\r
 190 &nbsp;\r
 191 <P>\r
 192 \r
 193 <!-- ============ FIELD DETAIL =========== -->\r
 194 \r
 195 <A NAME="field_detail"><!-- --></A>\r
 196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 197 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 198 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 199 <B>Field Detail</B></FONT></TH>\r
 200 </TR>\r
 201 </TABLE>\r
 202 \r
 203 <A NAME="PROC_OUT_FILE"><!-- --></A><H3>\r
 204 PROC_OUT_FILE</H3>\r
 205 <PRE>\r
 206 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>PROC_OUT_FILE</B></PRE>\r
 207 <DL>\r
 208 <DL>\r
 209 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE">Constant Field Values</A></DL>\r
 210 </DL>\r
 211 <HR>\r
 212 \r
 213 <A NAME="PROC_ERR_FILE"><!-- --></A><H3>\r
 214 PROC_ERR_FILE</H3>\r
 215 <PRE>\r
 216 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>PROC_ERR_FILE</B></PRE>\r
 217 <DL>\r
 218 <DL>\r
 219 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE">Constant Field Values</A></DL>\r
 220 </DL>\r
 221 \r
 222 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 223 \r
 224 <A NAME="constructor_detail"><!-- --></A>\r
 225 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 226 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 227 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 228 <B>Constructor Detail</B></FONT></TH>\r
 229 </TR>\r
 230 </TABLE>\r
 231 \r
 232 <A NAME="ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)"><!-- --></A><H3>\r
 233 ExecutableWrapper</H3>\r
 234 <PRE>\r
 235 public <B>ExecutableWrapper</B>(<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
 236                          <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
 237                   throws <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
 238 <DL>\r
 239 <DL>\r
 240 \r
 241 <DT><B>Throws:</B>\r
 242 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
 243 </DL>\r
 244 \r
 245 <!-- ============ METHOD DETAIL ========== -->\r
 246 \r
 247 <A NAME="method_detail"><!-- --></A>\r
 248 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 249 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 250 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 251 <B>Method Detail</B></FONT></TH>\r
 252 </TR>\r
 253 </TABLE>\r
 254 \r
 255 <A NAME="shutdownService()"><!-- --></A><H3>\r
 256 shutdownService</H3>\r
 257 <PRE>\r
 258 public static final void <B>shutdownService</B>()</PRE>\r
 259 <DL>\r
 260 <DD>Stops internal executor service which captures streams of native
 261  executables. This method is intended for stopping service if deployed in
 262  the web application content. There is NO NEED of using this method
 263  otherwise as the executor service is taken care of internally.\r
 264 <P>\r
 265 <DD><DL>\r
 266 </DL>\r
 267 </DD>\r
 268 <DD><DL>\r
 269 </DL>\r
 270 </DD>\r
 271 </DL>\r
 272 <HR>\r
 273 \r
 274 <A NAME="call()"><!-- --></A><H3>\r
 275 call</H3>\r
 276 <PRE>\r
 277 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>call</B>()\r
 278                              throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
 279 <DL>\r
 280 <DD>It is vital that output and error streams are captured immediately for
 281  this call() to succeed. Thus each instance if ExecutableWrapper has 2 its
 282  own thread ready to capture the output. If executor could not execute
 283  capture immediately this could lead to the call method to stale, as
 284  execution could not proceed without output being captured. Every call to
 285  call() method will use 2 threads\r
 286 <P>\r
 287 <DD><DL>\r
 288 <DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Callable.html?is-external=true#call()" title="class or interface in java.util.concurrent">call</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Callable.html?is-external=true" title="class or interface in java.util.concurrent">Callable</A>&lt;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</CODE></DL>\r
 289 </DD>\r
 290 <DD><DL>\r
 291 \r
 292 <DT><B>Throws:</B>\r
 293 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
 294 </DD>\r
 295 </DL>\r
 296 <!-- ========= END OF CLASS DATA ========= -->\r
 297 <HR>\r
 298 \r
 299 \r
 300 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
 301 <A NAME="navbar_bottom"><!-- --></A>\r
 302 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
 303 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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 305 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
 306 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
 307 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
 308   <TR ALIGN="center" VALIGN="top">\r
 309   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
 310   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
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 312   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/ExecutableWrapper.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
 313   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
 314   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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 317   </TR>\r
 318 </TABLE>\r
 319 </TD>\r
 320 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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