1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
\r
5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->
\r
10 <META NAME="date" CONTENT="2011-12-07">
\r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
\r
14 <SCRIPT type="text/javascript">
\r
15 function windowTitle()
\r
17 if (location.href.indexOf('is-external=true') == -1) {
\r
18 parent.document.title="Util";
\r
27 <BODY BGCOLOR="white" onload="windowTitle();">
\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
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> </TD>
\r
41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
44 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
45 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
46 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
47 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
58 <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>
\r
59 NEXT CLASS</FONT></TD>
\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
61 <A HREF="../../../index.html?compbio/engine/client/Util.html" target="_top"><B>FRAMES</B></A>
\r
62 <A HREF="Util.html" target="_top"><B>NO FRAMES</B></A>
\r
63 <SCRIPT type="text/javascript">
\r
66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
79 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
81 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
84 <A NAME="skip-navbar_top"></A>
\r
85 <!-- ========= END OF TOP NAVBAR ========= -->
\r
88 <!-- ======== START OF CLASS DATA ======== -->
\r
91 compbio.engine.client</FONT>
\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
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
108 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
\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
116 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
117 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#Util()">Util</A></B>()</CODE>
\r
120 </TD>
\r
124 <!-- ========== METHOD SUMMARY =========== -->
\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
132 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
134 <CODE>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></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> relativePath)</CODE>
\r
138 </TD>
\r
140 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
142 <CODE>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></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> 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><?> clazz)</CODE>
\r
147 </TD>
\r
149 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
151 <CODE>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></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> 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><?> clazz)</CODE>
\r
156 </TD>
\r
158 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
160 <CODE>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></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> propertySpec,
\r
162 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> exec)</CODE>
\r
165 </TD>
\r
167 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
169 <CODE>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></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> 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> fileName)</CODE>
\r
174 </TD>
\r
176 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
178 <CODE>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></CODE></FONT></TD>
\r
179 <TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getJava()">getJava</A></B>()</CODE>
\r
182 Returns the absolute path to the Java executable from JAVA_HOME</TD>
\r
184 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\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><T> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T></CODE></FONT></TD>
\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><T> clazz)</CODE>
\r
197 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
200 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
202 <CODE>static <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><?> clazz)</CODE>
\r
206 </TD>
\r
208 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
210 <CODE>static 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><?> clazz)</CODE>
\r
214 Returns true of executableName.jar.file property has some value in the
215 Executable.properties file, false otherwise.</TD>
\r
217 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
219 <CODE>static 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> workDirectory,
\r
221 <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> marker)</CODE>
\r
224 </TD>
\r
226 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
227 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
228 <CODE>static 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> key)</CODE>
\r
232 </TD>
\r
234 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
236 <CODE>static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></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> taskId)</CODE>
\r
240 </TD>
\r
242 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
243 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
244 <CODE>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><<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>></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><<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>> 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><<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>> variables)</CODE>
\r
249 </TD>
\r
251 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
253 <CODE>static 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> 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> 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> content,
\r
257 boolean override)</CODE>
\r
260 </TD>
\r
262 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
263 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
264 <CODE>static 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> workDirectory,
\r
266 <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> fileType)</CODE>
\r
269 </TD>
\r
271 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
272 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
273 <CODE>static 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> 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> fileAndEventName)</CODE>
\r
278 </TD>
\r
281 <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
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
293 <!-- ========= CONSTRUCTOR DETAIL ======== -->
\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
303 <A NAME="Util()"><!-- --></A><H3>
\r
306 public <B>Util</B>()</PRE>
\r
310 <!-- ============ METHOD DETAIL ========== -->
\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
320 <A NAME="isValidJobId(java.lang.String)"><!-- --></A><H3>
\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> key)</PRE>
\r
331 <A NAME="writeStatFile(java.lang.String, java.lang.String)"><!-- --></A><H3>
\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> 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> fileAndEventName)</PRE>
\r
343 <A NAME="writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>
\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> 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> 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> content,
\r
349 boolean override)</PRE>
\r
357 <A NAME="writeMarker(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>
\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> workDirectory,
\r
361 <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> fileType)</PRE>
\r
369 <A NAME="isMarked(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>
\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> workDirectory,
\r
373 <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> marker)</PRE>
\r
381 <A NAME="mergeEnvVariables(java.util.Map, java.util.Map)"><!-- --></A><H3>
\r
382 mergeEnvVariables</H3>
\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><<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>> <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><<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>> 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><<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>> variables)</PRE>
\r
393 <A NAME="convertToAbsolute(java.lang.String)"><!-- --></A><H3>
\r
394 convertToAbsolute</H3>
\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> relativePath)</PRE>
\r
404 <A NAME="getExecProperty(java.lang.String, compbio.engine.client.Executable)"><!-- --></A><H3>
\r
405 getExecProperty</H3>
\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> propertySpec,
\r
408 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> exec)</PRE>
\r
416 <A NAME="getExecProperty(java.lang.String, java.lang.Class)"><!-- --></A><H3>
\r
417 getExecProperty</H3>
\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> 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><?> clazz)</PRE>
\r
428 <A NAME="getFullPath(java.lang.String, java.lang.String)"><!-- --></A><H3>
\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> 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> fileName)</PRE>
\r
440 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><!-- --></A><H3>
\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> 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><?> clazz)</PRE>
\r
452 <A NAME="isJavaLibrary(java.lang.Class)"><!-- --></A><H3>
\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><?> clazz)</PRE>
\r
457 <DD>Returns true of executableName.jar.file property has some value in the
458 Executable.properties file, false otherwise.
\r
461 <DT><B>Parameters:</B><DD><CODE>clazz</CODE> -
\r
462 <DT><B>Returns:</B><DD></DL>
\r
467 <A NAME="getJava()"><!-- --></A><H3>
\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
472 <DD>Returns the absolute path to the Java executable from JAVA_HOME
\r
476 <DT><B>Returns:</B><DD>returns the absolute path to the Java executable from JAVA_HOME</DL>
\r
481 <A NAME="getSupportedRuntimes(java.lang.Class)"><!-- --></A><H3>
\r
482 getSupportedRuntimes</H3>
\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><?> clazz)</PRE>
\r
492 <A NAME="loadExecutable(java.lang.String)"><!-- --></A><H3>
\r
493 loadExecutable</H3>
\r
495 public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <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> taskId)
\r
496 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
501 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>
\r
506 <A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>
\r
509 public static <T> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T> <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><T> clazz)</PRE>
\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
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
525 <!-- ========= END OF CLASS DATA ========= -->
\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
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> </TD>
\r
539 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
540 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
541 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
542 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
543 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
544 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
545 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
549 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
555 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
556 <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>
\r
557 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>
\r
560 <A HREF="Util.html" target="_top"><B>NO FRAMES</B></A>
\r
561 <SCRIPT type="text/javascript">
\r
564 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
569 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
576 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
577 SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
578 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
579 DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
582 <A NAME="skip-navbar_bottom"></A>
\r
583 <!-- ======== END OF BOTTOM NAVBAR ======= -->
\r