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5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->\r
6 <TITLE>\r
7 ConfExecutable\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2011-08-12">\r
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15 function windowTitle()\r
16 {\r
17     if (location.href.indexOf('is-external=true') == -1) {\r
18         parent.document.title="ConfExecutable";\r
19     }\r
20 }\r
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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/ConfExecutable.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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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/CommandBuilder.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A>&nbsp;\r
59 &nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface 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/ConfExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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73 \r
74 \r
75 </FONT></TD>\r
76 </TR>\r
77 <TR>\r
78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
81 DETAIL:&nbsp;<A HREF="#field_detail">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
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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 ConfExecutable&lt;T&gt;</H2>\r
94 <PRE>\r
95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.ConfExecutable&lt;T&gt;</B>\r
97 </PRE>\r
98 <DL>\r
99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;, <A HREF="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A>&lt;T&gt;</DD>\r
100 </DL>\r
101 <HR>\r
102 <DL>\r
103 <DT><PRE>public class <B>ConfExecutable&lt;T&gt;</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><DT>implements <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</DL>\r
104 </PRE>\r
105 \r
106 <P>\r
107 <HR>\r
108 \r
109 <P>\r
110 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
111 \r
112 <A NAME="nested_class_summary"><!-- --></A>\r
113 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
114 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
115 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
116 <B>Nested Class Summary</B></FONT></TH>\r
117 </TR>\r
118 </TABLE>\r
119 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
121 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
122 <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
123 </TR>\r
124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
125 <TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
126 </TR>\r
127 </TABLE>\r
128 &nbsp;\r
129 <!-- =========== FIELD SUMMARY =========== -->\r
130 \r
131 <A NAME="field_summary"><!-- --></A>\r
132 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
133 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
134 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
135 <B>Field Summary</B></FONT></TH>\r
136 </TR>\r
137 <TR BGCOLOR="white" CLASS="TableRowColor">\r
138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
139 <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
140 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</A></B></CODE>\r
141 \r
142 <BR>\r
143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
144 </TR>\r
145 </TABLE>\r
146 &nbsp;\r
147 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
148 \r
149 <A NAME="constructor_summary"><!-- --></A>\r
150 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
151 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
152 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
153 <B>Constructor Summary</B></FONT></TH>\r
154 </TR>\r
155 <TR BGCOLOR="white" CLASS="TableRowColor">\r
156 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#ConfExecutable(compbio.engine.client.Executable, java.lang.String)">ConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
157                <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;taskDirectory)</CODE>\r
158 \r
159 <BR>\r
160 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
161 </TR>\r
162 </TABLE>\r
163 &nbsp;\r
164 <!-- ========== METHOD SUMMARY =========== -->\r
165 \r
166 <A NAME="method_summary"><!-- --></A>\r
167 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
168 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
169 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
170 <B>Method Summary</B></FONT></TH>\r
171 </TR>\r
172 <TR BGCOLOR="white" CLASS="TableRowColor">\r
173 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
174 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
175 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#addParameters(java.util.List)">addParameters</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;parameters)</CODE>\r
176 \r
177 <BR>\r
178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
179 </TR>\r
180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
182 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
183 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
184 \r
185 <BR>\r
186 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
187 </TR>\r
188 <TR BGCOLOR="white" CLASS="TableRowColor">\r
189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
190 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
191 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
192 \r
193 <BR>\r
194 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
199 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getCreatedFiles()">getCreatedFiles</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;<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
207 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getEnvironment()">getEnvironment</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;<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
215 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getError()">getError</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/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
223 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecProvider()">getExecProvider</A></B>()</CODE>\r
224 \r
225 <BR>\r
226 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
227 </TR>\r
228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
230 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
231 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</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;<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
239 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getInput()">getInput</A></B>()</CODE>\r
240 \r
241 <BR>\r
242 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not all input paths are relative! Input path could be absolute!</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/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
247 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimit(java.lang.String)">getLimit</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;presetName)</CODE>\r
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/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
255 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getLimits()">getLimits</A></B>()</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="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
263 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getOutput()">getOutput</A></B>()</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/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
271 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getParameters()">getParameters</A></B>()</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/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></FONT></TD>\r
279 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.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
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>\r
287 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
288 <TR ALIGN="right" VALIGN="">\r
289 <TD NOWRAP><FONT SIZE="-1">\r
290 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
291 </TR>\r
292 </TABLE>\r
293 </CODE></FONT></TD>\r
294 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults()">getResults</A></B>()</CODE>\r
295 \r
296 <BR>\r
297 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
298 </TR>\r
299 <TR BGCOLOR="white" CLASS="TableRowColor">\r
300 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
301 <CODE>\r
302 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
303 <TR ALIGN="right" VALIGN="">\r
304 <TD NOWRAP><FONT SIZE="-1">\r
305 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
306 </TR>\r
307 </TABLE>\r
308 </CODE></FONT></TD>\r
309 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getResults(java.lang.String)">getResults</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;directory)</CODE>\r
310 \r
311 <BR>\r
312 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
313 </TR>\r
314 <TR BGCOLOR="white" CLASS="TableRowColor">\r
315 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
316 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A></CODE></FONT></TD>\r
317 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunConfiguration()">getRunConfiguration</A></B>()</CODE>\r
318 \r
319 <BR>\r
320 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
321 </TR>\r
322 <TR BGCOLOR="white" CLASS="TableRowColor">\r
323 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
324 <CODE>static\r
325 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
326 <TR ALIGN="right" VALIGN="">\r
327 <TD NOWRAP><FONT SIZE="-1">\r
328 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt;</CODE></FONT></TD>\r
329 </TR>\r
330 </TABLE>\r
331 </CODE></FONT></TD>\r
332 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerLimits(java.lang.Class)">getRunnerLimits</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;V&gt;&nbsp;clazz)</CODE>\r
333 \r
334 <BR>\r
335 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This method should be executed once and result of its execution reused.</TD>\r
336 </TR>\r
337 <TR BGCOLOR="white" CLASS="TableRowColor">\r
338 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
339 <CODE>static\r
340 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
341 <TR ALIGN="right" VALIGN="">\r
342 <TD NOWRAP><FONT SIZE="-1">\r
343 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
344 </TR>\r
345 </TABLE>\r
346 </CODE></FONT></TD>\r
347 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerOptions(java.lang.Class)">getRunnerOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
348 \r
349 <BR>\r
350 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
351 </TR>\r
352 <TR BGCOLOR="white" CLASS="TableRowColor">\r
353 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
354 <CODE>static\r
355 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
356 <TR ALIGN="right" VALIGN="">\r
357 <TD NOWRAP><FONT SIZE="-1">\r
358 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
359 </TR>\r
360 </TABLE>\r
361 </CODE></FONT></TD>\r
362 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getRunnerPresets(java.lang.Class)">getRunnerPresets</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)</CODE>\r
363 \r
364 <BR>\r
365 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
366 </TR>\r
367 <TR BGCOLOR="white" CLASS="TableRowColor">\r
368 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
369 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
370 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></B>()</CODE>\r
371 \r
372 <BR>\r
373 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
374 </TR>\r
375 <TR BGCOLOR="white" CLASS="TableRowColor">\r
376 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
377 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
378 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getTaskId()">getTaskId</A></B>()</CODE>\r
379 \r
380 <BR>\r
381 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
382 </TR>\r
383 <TR BGCOLOR="white" CLASS="TableRowColor">\r
384 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
385 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
386 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
387 \r
388 <BR>\r
389 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
390 </TR>\r
391 <TR BGCOLOR="white" CLASS="TableRowColor">\r
392 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
393 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
394 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)</CODE>\r
395 \r
396 <BR>\r
397 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
398 </TR>\r
399 <TR BGCOLOR="white" CLASS="TableRowColor">\r
400 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
401 <CODE>&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
402 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.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;rconf)</CODE>\r
403 \r
404 <BR>\r
405 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
406 </TR>\r
407 <TR BGCOLOR="white" CLASS="TableRowColor">\r
408 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
409 <CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
410 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
411 \r
412 <BR>\r
413 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
414 </TR>\r
415 <TR BGCOLOR="white" CLASS="TableRowColor">\r
416 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
417 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
418 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></B>()</CODE>\r
419 \r
420 <BR>\r
421 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
422 </TR>\r
423 <TR BGCOLOR="white" CLASS="TableRowColor">\r
424 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
425 <CODE>&nbsp;void</CODE></FONT></TD>\r
426 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setExecProvider(compbio.engine.client.Executable.ExecProvider)">setExecProvider</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
427 \r
428 <BR>\r
429 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
430 </TR>\r
431 <TR BGCOLOR="white" CLASS="TableRowColor">\r
432 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
433 <CODE>&nbsp;void</CODE></FONT></TD>\r
434 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</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)</CODE>\r
435 \r
436 <BR>\r
437 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
438 </TR>\r
439 <TR BGCOLOR="white" CLASS="TableRowColor">\r
440 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
441 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
442 <TD><CODE><B><A HREF="../../../compbio/engine/client/ConfExecutable.html#toString()">toString</A></B>()</CODE>\r
443 \r
444 <BR>\r
445 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
446 </TR>\r
447 </TABLE>\r
448 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
449 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
450 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
451 <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
452 </TR>\r
453 <TR BGCOLOR="white" CLASS="TableRowColor">\r
454 <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#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
455 </TR>\r
456 </TABLE>\r
457 &nbsp;\r
458 <P>\r
459 \r
460 <!-- ============ FIELD DETAIL =========== -->\r
461 \r
462 <A NAME="field_detail"><!-- --></A>\r
463 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
464 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
465 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
466 <B>Field Detail</B></FONT></TH>\r
467 </TR>\r
468 </TABLE>\r
469 \r
470 <A NAME="CLUSTER_TASK_ID_PREFIX"><!-- --></A><H3>\r
471 CLUSTER_TASK_ID_PREFIX</H3>\r
472 <PRE>\r
473 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>CLUSTER_TASK_ID_PREFIX</B></PRE>\r
474 <DL>\r
475 <DL>\r
476 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX">Constant Field Values</A></DL>\r
477 </DL>\r
478 \r
479 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
480 \r
481 <A NAME="constructor_detail"><!-- --></A>\r
482 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
483 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
484 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
485 <B>Constructor Detail</B></FONT></TH>\r
486 </TR>\r
487 </TABLE>\r
488 \r
489 <A NAME="ConfExecutable(compbio.engine.client.Executable, java.lang.String)"><!-- --></A><H3>\r
490 ConfExecutable</H3>\r
491 <PRE>\r
492 public <B>ConfExecutable</B>(<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;&nbsp;executable,\r
493                       <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;taskDirectory)</PRE>\r
494 <DL>\r
495 </DL>\r
496 \r
497 <!-- ============ METHOD DETAIL ========== -->\r
498 \r
499 <A NAME="method_detail"><!-- --></A>\r
500 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
501 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
502 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
503 <B>Method Detail</B></FONT></TH>\r
504 </TR>\r
505 </TABLE>\r
506 \r
507 <A NAME="getExecProvider()"><!-- --></A><H3>\r
508 getExecProvider</H3>\r
509 <PRE>\r
510 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getExecProvider</B>()</PRE>\r
511 <DL>\r
512 <DD><DL>\r
513 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecProvider()">getExecProvider</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
514 </DD>\r
515 <DD><DL>\r
516 </DL>\r
517 </DD>\r
518 </DL>\r
519 <HR>\r
520 \r
521 <A NAME="setExecProvider(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
522 setExecProvider</H3>\r
523 <PRE>\r
524 public void <B>setExecProvider</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
525 <DL>\r
526 <DD><DL>\r
527 </DL>\r
528 </DD>\r
529 <DD><DL>\r
530 </DL>\r
531 </DD>\r
532 </DL>\r
533 <HR>\r
534 \r
535 <A NAME="getCommand(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
536 getCommand</H3>\r
537 <PRE>\r
538 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)\r
539                   throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></PRE>\r
540 <DL>\r
541 <DD><DL>\r
542 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getCommand(compbio.engine.client.Executable.ExecProvider)">getCommand</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
543 </DD>\r
544 <DD><DL>\r
545 \r
546 <DT><B>Throws:</B>\r
547 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE></DL>\r
548 </DD>\r
549 </DL>\r
550 <HR>\r
551 \r
552 <A NAME="getSupportedRuntimes()"><!-- --></A><H3>\r
553 getSupportedRuntimes</H3>\r
554 <PRE>\r
555 public <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>()</PRE>\r
556 <DL>\r
557 <DD><DL>\r
558 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getSupportedRuntimes()">getSupportedRuntimes</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></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="getLimit(java.lang.String)"><!-- --></A><H3>\r
567 getLimit</H3>\r
568 <PRE>\r
569 public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getLimit</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;presetName)</PRE>\r
570 <DL>\r
571 <DD><DL>\r
572 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
573 </DD>\r
574 <DD><DL>\r
575 </DL>\r
576 </DD>\r
577 </DL>\r
578 <HR>\r
579 \r
580 <A NAME="getLimits()"><!-- --></A><H3>\r
581 getLimits</H3>\r
582 <PRE>\r
583 public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getLimits</B>()</PRE>\r
584 <DL>\r
585 <DD><DL>\r
586 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
587 </DD>\r
588 <DD><DL>\r
589 </DL>\r
590 </DD>\r
591 </DL>\r
592 <HR>\r
593 \r
594 <A NAME="getTaskId()"><!-- --></A><H3>\r
595 getTaskId</H3>\r
596 <PRE>\r
597 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getTaskId</B>()</PRE>\r
598 <DL>\r
599 <DD><DL>\r
600 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getTaskId()">getTaskId</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
601 </DD>\r
602 <DD><DL>\r
603 </DL>\r
604 </DD>\r
605 </DL>\r
606 <HR>\r
607 \r
608 <A NAME="setWorkDirectory(java.lang.String)"><!-- --></A><H3>\r
609 setWorkDirectory</H3>\r
610 <PRE>\r
611 public void <B>setWorkDirectory</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)</PRE>\r
612 <DL>\r
613 <DD><DL>\r
614 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#setWorkDirectory(java.lang.String)">setWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
615 </DD>\r
616 <DD><DL>\r
617 </DL>\r
618 </DD>\r
619 </DL>\r
620 <HR>\r
621 \r
622 <A NAME="getWorkDirectory()"><!-- --></A><H3>\r
623 getWorkDirectory</H3>\r
624 <PRE>\r
625 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getWorkDirectory</B>()</PRE>\r
626 <DL>\r
627 <DD><DL>\r
628 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
629 </DD>\r
630 <DD><DL>\r
631 </DL>\r
632 </DD>\r
633 </DL>\r
634 <HR>\r
635 \r
636 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
637 addParameters</H3>\r
638 <PRE>\r
639 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>addParameters</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;parameters)</PRE>\r
640 <DL>\r
641 <DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
642 <DD>Adds parameter to the list of parameters for a native executable\r
643 <P>\r
644 <DD><DL>\r
645 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
646 </DD>\r
647 <DD><DL>\r
648 \r
649 <DT><B>Returns:</B><DD>this Executable</DL>\r
650 </DD>\r
651 </DL>\r
652 <HR>\r
653 \r
654 <A NAME="getOutput()"><!-- --></A><H3>\r
655 getOutput</H3>\r
656 <PRE>\r
657 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getOutput</B>()</PRE>\r
658 <DL>\r
659 <DD><DL>\r
660 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
661 </DD>\r
662 <DD><DL>\r
663 </DL>\r
664 </DD>\r
665 </DL>\r
666 <HR>\r
667 \r
668 <A NAME="getError()"><!-- --></A><H3>\r
669 getError</H3>\r
670 <PRE>\r
671 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getError</B>()</PRE>\r
672 <DL>\r
673 <DD><DL>\r
674 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
675 </DD>\r
676 <DD><DL>\r
677 </DL>\r
678 </DD>\r
679 </DL>\r
680 <HR>\r
681 \r
682 <A NAME="getCreatedFiles()"><!-- --></A><H3>\r
683 getCreatedFiles</H3>\r
684 <PRE>\r
685 public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt; <B>getCreatedFiles</B>()</PRE>\r
686 <DL>\r
687 <DD><DL>\r
688 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
689 </DD>\r
690 <DD><DL>\r
691 </DL>\r
692 </DD>\r
693 </DL>\r
694 <HR>\r
695 \r
696 <A NAME="getInput()"><!-- --></A><H3>\r
697 getInput</H3>\r
698 <PRE>\r
699 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getInput</B>()</PRE>\r
700 <DL>\r
701 <DD>Not all input paths are relative! Input path could be absolute!\r
702 <P>\r
703 <DD><DL>\r
704 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
705 </DD>\r
706 <DD><DL>\r
707 <DT><B>See Also:</B><DD><CODE>compbio.engine.client.Executable#getInputFiles()</CODE></DL>\r
708 </DD>\r
709 </DL>\r
710 <HR>\r
711 \r
712 <A NAME="getParameters()"><!-- --></A><H3>\r
713 getParameters</H3>\r
714 <PRE>\r
715 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getParameters</B>()</PRE>\r
716 <DL>\r
717 <DD><DL>\r
718 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getParameters()">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
719 </DD>\r
720 <DD><DL>\r
721 </DL>\r
722 </DD>\r
723 </DL>\r
724 <HR>\r
725 \r
726 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
727 getParameters</H3>\r
728 <PRE>\r
729 public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">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
730 <DL>\r
731 <DD><DL>\r
732 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
733 </DD>\r
734 <DD><DL>\r
735 </DL>\r
736 </DD>\r
737 </DL>\r
738 <HR>\r
739 \r
740 <A NAME="getExecutable()"><!-- --></A><H3>\r
741 getExecutable</H3>\r
742 <PRE>\r
743 public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt; <B>getExecutable</B>()</PRE>\r
744 <DL>\r
745 <DD><DL>\r
746 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
747 </DD>\r
748 <DD><DL>\r
749 </DL>\r
750 </DD>\r
751 </DL>\r
752 <HR>\r
753 \r
754 <A NAME="getResults()"><!-- --></A><H3>\r
755 getResults</H3>\r
756 <PRE>\r
757 public &lt;V&gt; V <B>getResults</B>()\r
758              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
759 <DL>\r
760 <DD><DL>\r
761 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getResults()">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
762 </DD>\r
763 <DD><DL>\r
764 \r
765 <DT><B>Throws:</B>\r
766 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
767 </DD>\r
768 </DL>\r
769 <HR>\r
770 \r
771 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
772 getResults</H3>\r
773 <PRE>\r
774 public &lt;V&gt; V <B>getResults</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;directory)\r
775              throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
776 <DL>\r
777 <DD><DL>\r
778 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
779 </DD>\r
780 <DD><DL>\r
781 \r
782 <DT><B>Throws:</B>\r
783 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
784 </DD>\r
785 </DL>\r
786 <HR>\r
787 \r
788 <A NAME="getRunnerOptions(java.lang.Class)"><!-- --></A><H3>\r
789 getRunnerOptions</H3>\r
790 <PRE>\r
791 public static &lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt; <B>getRunnerOptions</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
792                                         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
793 <DL>\r
794 <DD><DL>\r
795 </DL>\r
796 </DD>\r
797 <DD><DL>\r
798 \r
799 <DT><B>Throws:</B>\r
800 <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
801 </DD>\r
802 </DL>\r
803 <HR>\r
804 \r
805 <A NAME="getRunnerPresets(java.lang.Class)"><!-- --></A><H3>\r
806 getRunnerPresets</H3>\r
807 <PRE>\r
808 public static &lt;V&gt; <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt; <B>getRunnerPresets</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&gt;&nbsp;clazz)\r
809                                          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
810 <DL>\r
811 <DD><DL>\r
812 </DL>\r
813 </DD>\r
814 <DD><DL>\r
815 \r
816 <DT><B>Throws:</B>\r
817 <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
818 </DD>\r
819 </DL>\r
820 <HR>\r
821 \r
822 <A NAME="getRunnerLimits(java.lang.Class)"><!-- --></A><H3>\r
823 getRunnerLimits</H3>\r
824 <PRE>\r
825 public static &lt;V&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;V&gt; <B>getRunnerLimits</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;V&gt;&nbsp;clazz)\r
826                                         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
827 <DL>\r
828 <DD>This method should be executed once and result of its execution reused.
829  If not used carefully it could slow down the system!\r
830 <P>\r
831 <DD><DL>\r
832 </DL>\r
833 </DD>\r
834 <DD><DL>\r
835 <DT><B>Type Parameters:</B><DD><CODE>V</CODE> - <DT><B>Parameters:</B><DD><CODE>clazz</CODE> - \r
836 <DT><B>Returns:</B><DD>LimitsManager instance\r
837 <DT><B>Throws:</B>\r
838 <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
839 </DD>\r
840 </DL>\r
841 <HR>\r
842 \r
843 <A NAME="getEnvironment()"><!-- --></A><H3>\r
844 getEnvironment</H3>\r
845 <PRE>\r
846 public <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>getEnvironment</B>()</PRE>\r
847 <DL>\r
848 <DD><DL>\r
849 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#getEnvironment()">getEnvironment</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
850 </DD>\r
851 <DD><DL>\r
852 </DL>\r
853 </DD>\r
854 </DL>\r
855 <HR>\r
856 \r
857 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
858 loadRunConfiguration</H3>\r
859 <PRE>\r
860 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</PRE>\r
861 <DL>\r
862 <DD><DL>\r
863 <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/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
864 </DD>\r
865 <DD><DL>\r
866 </DL>\r
867 </DD>\r
868 </DL>\r
869 <HR>\r
870 \r
871 <A NAME="newConfExecutable(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
872 newConfExecutable</H3>\r
873 <PRE>\r
874 public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>newConfExecutable</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</PRE>\r
875 <DL>\r
876 <DD><DL>\r
877 </DL>\r
878 </DD>\r
879 <DD><DL>\r
880 </DL>\r
881 </DD>\r
882 </DL>\r
883 <HR>\r
884 \r
885 <A NAME="saveRunConfiguration()"><!-- --></A><H3>\r
886 saveRunConfiguration</H3>\r
887 <PRE>\r
888 public boolean <B>saveRunConfiguration</B>()\r
889                              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
890 <DL>\r
891 <DD><DL>\r
892 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#saveRunConfiguration()">saveRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
893 </DD>\r
894 <DD><DL>\r
895 \r
896 <DT><B>Throws:</B>\r
897 <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
898 </DD>\r
899 </DL>\r
900 <HR>\r
901 \r
902 <A NAME="getRunConfiguration()"><!-- --></A><H3>\r
903 getRunConfiguration</H3>\r
904 <PRE>\r
905 public <A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A> <B>getRunConfiguration</B>()</PRE>\r
906 <DL>\r
907 <DD><DL>\r
908 </DL>\r
909 </DD>\r
910 <DD><DL>\r
911 </DL>\r
912 </DD>\r
913 </DL>\r
914 <HR>\r
915 \r
916 <A NAME="loadRunConfiguration(java.io.InputStream)"><!-- --></A><H3>\r
917 loadRunConfiguration</H3>\r
918 <PRE>\r
919 public <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)\r
920                                              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
921 <DL>\r
922 <DD><DL>\r
923 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
924 </DD>\r
925 <DD><DL>\r
926 \r
927 <DT><B>Throws:</B>\r
928 <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
929 </DD>\r
930 </DL>\r
931 <HR>\r
932 \r
933 <A NAME="toString()"><!-- --></A><H3>\r
934 toString</H3>\r
935 <PRE>\r
936 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>\r
937 <DL>\r
938 <DD><DL>\r
939 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
940 </DD>\r
941 <DD><DL>\r
942 </DL>\r
943 </DD>\r
944 </DL>\r
945 <HR>\r
946 \r
947 <A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
948 getClusterJobSettings</H3>\r
949 <PRE>\r
950 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getClusterJobSettings</B>()</PRE>\r
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953 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</A>&gt;</CODE></DL>\r
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