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7 Uses of Interface compbio.engine.client.Executable\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
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42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
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61   <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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79 <!-- ========= END OF TOP NAVBAR ========= -->\r
80 \r
81 <HR>\r
82 <CENTER>\r
83 <H2>\r
84 <B>Uses of Interface<br>compbio.engine.client.Executable</B></H2>\r
85 </CENTER>\r
86 \r
87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
90 Packages that use <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
94 <TD>&nbsp;&nbsp;</TD>\r
95 </TR>\r
96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
97 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
98 <TD>&nbsp;&nbsp;</TD>\r
99 </TR>\r
100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
101 <TD><A HREF="#compbio.engine.conf"><B>compbio.engine.conf</B></A></TD>\r
102 <TD>&nbsp;&nbsp;</TD>\r
103 </TR>\r
104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
105 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
106 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
107 </TR>\r
108 <TR BGCOLOR="white" CLASS="TableRowColor">\r
109 <TD><A HREF="#compbio.runner._impl"><B>compbio.runner._impl</B></A></TD>\r
110 <TD>&nbsp;&nbsp;</TD>\r
111 </TR>\r
112 <TR BGCOLOR="white" CLASS="TableRowColor">\r
113 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
114 <TD>&nbsp;&nbsp;</TD>\r
115 </TR>\r
116 <TR BGCOLOR="white" CLASS="TableRowColor">\r
117 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
118 <TD>&nbsp;&nbsp;</TD>\r
119 </TR>\r
120 <TR BGCOLOR="white" CLASS="TableRowColor">\r
121 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
122 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
123 </TR>\r
124 <TR BGCOLOR="white" CLASS="TableRowColor">\r
125 <TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
126 <TD>A command line client and web services testing client for    
127  JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
128 </TR>\r
129 </TABLE>\r
130 &nbsp;\r
131 <P>\r
132 <A NAME="compbio.engine"><!-- --></A>\r
133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
134 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
135 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
136 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
137 </TR>\r
138 </TABLE>\r
139 &nbsp;\r
140 <P>\r
141 \r
142 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
143 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
144 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
145 </TR>\r
146 <TR BGCOLOR="white" CLASS="TableRowColor">\r
147 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
148 <CODE>static\r
149 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
150 <TR ALIGN="right" VALIGN="">\r
151 <TD NOWRAP><FONT SIZE="-1">\r
152 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
153 </TR>\r
154 </TABLE>\r
155 </CODE></FONT></TD>\r
156 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
157 \r
158 <BR>\r
159 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
160 </TR>\r
161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
163 <CODE>static\r
164 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
165 <TR ALIGN="right" VALIGN="">\r
166 <TD NOWRAP><FONT SIZE="-1">\r
167 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
168 </TR>\r
169 </TABLE>\r
170 </CODE></FONT></TD>\r
171 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
172                     <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
173 \r
174 <BR>\r
175 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
176 </TR>\r
177 <TR BGCOLOR="white" CLASS="TableRowColor">\r
178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
179 <CODE>static\r
180 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
181 <TR ALIGN="right" VALIGN="">\r
182 <TD NOWRAP><FONT SIZE="-1">\r
183 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
184 </TR>\r
185 </TABLE>\r
186 </CODE></FONT></TD>\r
187 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
188                     <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="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
189 \r
190 <BR>\r
191 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
192 </TR>\r
193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
195 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
196 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
197 \r
198 <BR>\r
199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
200 </TR>\r
201 <TR BGCOLOR="white" CLASS="TableRowColor">\r
202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
203 <CODE>static\r
204 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
205 <TR ALIGN="right" VALIGN="">\r
206 <TD NOWRAP><FONT SIZE="-1">\r
207 <CODE>&lt;T,V&gt; <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
208 </TR>\r
209 </TABLE>\r
210 </CODE></FONT></TD>\r
211 <TD><CODE><B>LoadBalancer.</B><B><A HREF="../../../../compbio/engine/LoadBalancer.html#getEngine(compbio.engine.client.Executable, java.util.List)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;V&gt;&nbsp;executable,\r
212           <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="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
213 \r
214 <BR>\r
215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
216 </TR>\r
217 </TABLE>\r
218 &nbsp;\r
219 <P>\r
220 <A NAME="compbio.engine.client"><!-- --></A>\r
221 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
222 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
223 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
224 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
225 </TR>\r
226 </TABLE>\r
227 &nbsp;\r
228 <P>\r
229 \r
230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
231 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
232 <TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
233 </TR>\r
234 <TR BGCOLOR="white" CLASS="TableRowColor">\r
235 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
236 <CODE>&nbsp;interface</CODE></FONT></TD>\r
237 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable&lt;T&gt;</A></B></CODE>\r
238 \r
239 <BR>\r
240 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
241 </TR>\r
242 <TR BGCOLOR="white" CLASS="TableRowColor">\r
243 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
244 <CODE>&nbsp;interface</CODE></FONT></TD>\r
245 <TD><CODE><B><A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable&lt;T&gt;</A></B></CODE>\r
246 \r
247 <BR>\r
248 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This is a marker interface to indicate that the output of the process must be
249  captured.</TD>\r
250 </TR>\r
251 </TABLE>\r
252 &nbsp;\r
253 <P>\r
254 \r
255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
256 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
257 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
258 </TR>\r
259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
261 <CODE>&nbsp;class</CODE></FONT></TD>\r
262 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
263 \r
264 <BR>\r
265 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
266 </TR>\r
267 <TR BGCOLOR="white" CLASS="TableRowColor">\r
268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
269 <CODE>&nbsp;class</CODE></FONT></TD>\r
270 <TD><CODE><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable&lt;T&gt;</A></B></CODE>\r
271 \r
272 <BR>\r
273 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
274 </TR>\r
275 </TABLE>\r
276 &nbsp;\r
277 <P>\r
278 \r
279 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
280 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
281 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
282 </TR>\r
283 <TR BGCOLOR="white" CLASS="TableRowColor">\r
284 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
285 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/Executable.html" title="type parameter in Executable">T</A>&gt;</CODE></FONT></TD>\r
286 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.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
287 \r
288 <BR>\r
289 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
290 </TR>\r
291 <TR BGCOLOR="white" CLASS="TableRowColor">\r
292 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
293 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
294 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.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
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>&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
302 <TD><CODE><B>ConfExecutable.</B><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
303 \r
304 <BR>\r
305 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
306 </TR>\r
307 <TR BGCOLOR="white" CLASS="TableRowColor">\r
308 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
309 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="type parameter in ConfiguredExecutable">T</A>&gt;</CODE></FONT></TD>\r
310 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
311 \r
312 <BR>\r
313 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
314 </TR>\r
315 <TR BGCOLOR="white" CLASS="TableRowColor">\r
316 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
317 <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
318 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#getExecutable()">getExecutable</A></B>()</CODE>\r
319 \r
320 <BR>\r
321 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
322 </TR>\r
323 <TR BGCOLOR="white" CLASS="TableRowColor">\r
324 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
325 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
326 <TD><CODE><B>Executable.</B><B><A HREF="../../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
327 \r
328 <BR>\r
329 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
330 </TR>\r
331 <TR BGCOLOR="white" CLASS="TableRowColor">\r
332 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
333 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
334 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
335 \r
336 <BR>\r
337 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
338 </TR>\r
339 <TR BGCOLOR="white" CLASS="TableRowColor">\r
340 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
341 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
342 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</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;parameter)</CODE>\r
343 \r
344 <BR>\r
345 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
346 </TR>\r
347 </TABLE>\r
348 &nbsp;\r
349 <P>\r
350 \r
351 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
352 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
353 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
354 </TR>\r
355 <TR BGCOLOR="white" CLASS="TableRowColor">\r
356 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
357 <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
358 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;propertySpec,\r
359                 <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
360 \r
361 <BR>\r
362 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
363 </TR>\r
364 </TABLE>\r
365 &nbsp;\r
366 <P>\r
367 \r
368 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
369 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
370 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
371 </TR>\r
372 <TR BGCOLOR="white" CLASS="TableRowColor">\r
373 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
374 <CODE>static&nbsp;int</CODE></FONT></TD>\r
375 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</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;?&gt;&gt;&nbsp;type)</CODE>\r
376 \r
377 <BR>\r
378 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
379 </TR>\r
380 <TR BGCOLOR="white" CLASS="TableRowColor">\r
381 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
382 <CODE>static\r
383 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
384 <TR ALIGN="right" VALIGN="">\r
385 <TD NOWRAP><FONT SIZE="-1">\r
386 <CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
387 </TR>\r
388 </TABLE>\r
389 </CODE></FONT></TD>\r
390 <TD><CODE><B>ConfExecutable.</B><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
391 \r
392 <BR>\r
393 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
394 </TR>\r
395 <TR BGCOLOR="white" CLASS="TableRowColor">\r
396 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
397 <CODE>static\r
398 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
399 <TR ALIGN="right" VALIGN="">\r
400 <TD NOWRAP><FONT SIZE="-1">\r
401 <CODE>&lt;V&gt; <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;V&gt;</CODE></FONT></TD>\r
402 </TR>\r
403 </TABLE>\r
404 </CODE></FONT></TD>\r
405 <TD><CODE><B>ConfExecutable.</B><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
406 \r
407 <BR>\r
408 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
409 </TR>\r
410 </TABLE>\r
411 &nbsp;\r
412 <P>\r
413 \r
414 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
415 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
416 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> with parameters of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
417 </TR>\r
418 <TR BGCOLOR="white" CLASS="TableRowColor">\r
419 <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
420                <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
421 \r
422 <BR>\r
423 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
424 </TR>\r
425 </TABLE>\r
426 &nbsp;\r
427 <P>\r
428 <A NAME="compbio.engine.conf"><!-- --></A>\r
429 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
430 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
431 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
432 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A></FONT></TH>\r
433 </TR>\r
434 </TABLE>\r
435 &nbsp;\r
436 <P>\r
437 \r
438 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
439 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
440 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/conf/package-summary.html">compbio.engine.conf</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
441 </TR>\r
442 <TR BGCOLOR="white" CLASS="TableRowColor">\r
443 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
444 <CODE>static&nbsp;<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;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
445 <TD><CODE><B>DirectoryManager.</B><B><A HREF="../../../../compbio/engine/conf/DirectoryManager.html#getClass(java.lang.String)">getClass</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
446 \r
447 <BR>\r
448 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
449 </TR>\r
450 </TABLE>\r
451 &nbsp;\r
452 <P>\r
453 <A NAME="compbio.runner"><!-- --></A>\r
454 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
455 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
456 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
457 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
458 </TR>\r
459 </TABLE>\r
460 &nbsp;\r
461 <P>\r
462 \r
463 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
464 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
465 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
466 </TR>\r
467 <TR BGCOLOR="white" CLASS="TableRowColor">\r
468 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
469 <CODE>&nbsp;class</CODE></FONT></TD>\r
470 <TD><CODE><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></B></CODE>\r
471 \r
472 <BR>\r
473 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;</TD>\r
474 </TR>\r
475 </TABLE>\r
476 &nbsp;\r
477 <P>\r
478 \r
479 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
480 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
481 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
482 </TR>\r
483 <TR BGCOLOR="white" CLASS="TableRowColor">\r
484 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
485 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
486 <TD><CODE><B>_SkeletalCommandBuilder.</B><B><A HREF="../../../../compbio/runner/_SkeletalCommandBuilder.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
487 \r
488 <BR>\r
489 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;&nbsp;</TD>\r
490 </TR>\r
491 </TABLE>\r
492 &nbsp;\r
493 <P>\r
494 \r
495 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
496 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
497 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
498 </TR>\r
499 <TR BGCOLOR="white" CLASS="TableRowColor">\r
500 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
501 <CODE>static&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
502 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</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;? extends <A HREF="../../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
503                          <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
504 \r
505 <BR>\r
506 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
507 </TR>\r
508 <TR BGCOLOR="white" CLASS="TableRowColor">\r
509 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
510 <CODE>static\r
511 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
512 <TR ALIGN="right" VALIGN="">\r
513 <TD NOWRAP><FONT SIZE="-1">\r
514 <CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;T&gt;</CODE></FONT></TD>\r
515 </TR>\r
516 </TABLE>\r
517 </CODE></FONT></TD>\r
518 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</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;T&gt;&gt;&nbsp;clazz)</CODE>\r
519 \r
520 <BR>\r
521 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
522 </TR>\r
523 <TR BGCOLOR="white" CLASS="TableRowColor">\r
524 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
525 <CODE>static\r
526 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
527 <TR ALIGN="right" VALIGN="">\r
528 <TD NOWRAP><FONT SIZE="-1">\r
529 <CODE>&lt;T&gt; <A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
530 </TR>\r
531 </TABLE>\r
532 </CODE></FONT></TD>\r
533 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</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;T&gt;&gt;&nbsp;clazz)</CODE>\r
534 \r
535 <BR>\r
536 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
537 </TR>\r
538 </TABLE>\r
539 &nbsp;\r
540 <P>\r
541 \r
542 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
543 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
544 <TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
545 </TR>\r
546 <TR BGCOLOR="white" CLASS="TableRowColor">\r
547 <TD><CODE><B><A HREF="../../../../compbio/runner/OptionCombinator.html#OptionCombinator(compbio.metadata.RunnerConfig)">OptionCombinator</A></B>(<A HREF="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
548 \r
549 <BR>\r
550 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
551 </TR>\r
552 </TABLE>\r
553 &nbsp;\r
554 <P>\r
555 <A NAME="compbio.runner._impl"><!-- --></A>\r
556 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
557 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
558 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
559 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A></FONT></TH>\r
560 </TR>\r
561 </TABLE>\r
562 &nbsp;\r
563 <P>\r
564 \r
565 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
566 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
567 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
568 </TR>\r
569 <TR BGCOLOR="white" CLASS="TableRowColor">\r
570 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
571 <CODE>&nbsp;class</CODE></FONT></TD>\r
572 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A></B></CODE>\r
573 \r
574 <BR>\r
575 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
576 </TR>\r
577 <TR BGCOLOR="white" CLASS="TableRowColor">\r
578 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
579 <CODE>&nbsp;class</CODE></FONT></TD>\r
580 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A></B></CODE>\r
581 \r
582 <BR>\r
583 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
584 </TR>\r
585 <TR BGCOLOR="white" CLASS="TableRowColor">\r
586 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
587 <CODE>&nbsp;class</CODE></FONT></TD>\r
588 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></B></CODE>\r
589 \r
590 <BR>\r
591 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
592 </TR>\r
593 <TR BGCOLOR="white" CLASS="TableRowColor">\r
594 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
595 <CODE>&nbsp;class</CODE></FONT></TD>\r
596 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A></B></CODE>\r
597 \r
598 <BR>\r
599 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;TODO this needs fixing! Executable does not work</TD>\r
600 </TR>\r
601 <TR BGCOLOR="white" CLASS="TableRowColor">\r
602 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
603 <CODE>&nbsp;class</CODE></FONT></TD>\r
604 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A></B></CODE>\r
605 \r
606 <BR>\r
607 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
608 </TR>\r
609 <TR BGCOLOR="white" CLASS="TableRowColor">\r
610 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
611 <CODE>&nbsp;class</CODE></FONT></TD>\r
612 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A></B></CODE>\r
613 \r
614 <BR>\r
615 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
616 </TR>\r
617 <TR BGCOLOR="white" CLASS="TableRowColor">\r
618 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
619 <CODE>&nbsp;class</CODE></FONT></TD>\r
620 <TD><CODE><B><A HREF="../../../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></B></CODE>\r
621 \r
622 <BR>\r
623 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
624 </TR>\r
625 </TABLE>\r
626 &nbsp;\r
627 <P>\r
628 \r
629 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
630 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
631 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A> that return <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
632 </TR>\r
633 <TR BGCOLOR="white" CLASS="TableRowColor">\r
634 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
635 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
636 <TD><CODE><B>NetNglyc.</B><B><A HREF="../../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
637 \r
638 <BR>\r
639 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
640 </TR>\r
641 </TABLE>\r
642 &nbsp;\r
643 <P>\r
644 <A NAME="compbio.runner.conservation"><!-- --></A>\r
645 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
646 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
647 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
648 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
649 </TR>\r
650 </TABLE>\r
651 &nbsp;\r
652 <P>\r
653 \r
654 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
655 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
656 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
657 </TR>\r
658 <TR BGCOLOR="white" CLASS="TableRowColor">\r
659 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
660 <CODE>&nbsp;class</CODE></FONT></TD>\r
661 <TD><CODE><B><A HREF="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></B></CODE>\r
662 \r
663 <BR>\r
664 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line
665  
666  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>\r
667 </TR>\r
668 </TABLE>\r
669 &nbsp;\r
670 <P>\r
671 <A NAME="compbio.runner.disorder"><!-- --></A>\r
672 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
673 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
674 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
675 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
676 </TR>\r
677 </TABLE>\r
678 &nbsp;\r
679 <P>\r
680 \r
681 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
682 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
683 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
684 </TR>\r
685 <TR BGCOLOR="white" CLASS="TableRowColor">\r
686 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
687 <CODE>&nbsp;class</CODE></FONT></TD>\r
688 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></B></CODE>\r
689 \r
690 <BR>\r
691 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
692  fold_rem465 sequence_file print
693  
694  'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
695  
696  This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
697  capable of outputting raw values
698  
699  The values of the parameters are hard coded in DisEMBL.py script.</TD>\r
700 </TR>\r
701 <TR BGCOLOR="white" CLASS="TableRowColor">\r
702 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
703 <CODE>&nbsp;class</CODE></FONT></TD>\r
704 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></B></CODE>\r
705 \r
706 <BR>\r
707 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
708  
709  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
710  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
711  
712  Hard-coded values are 10 15 74 4 5.</TD>\r
713 </TR>\r
714 <TR BGCOLOR="white" CLASS="TableRowColor">\r
715 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
716 <CODE>&nbsp;class</CODE></FONT></TD>\r
717 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></B></CODE>\r
718 \r
719 <BR>\r
720 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;iupred sequenceFile <short long glob >
721  
722  Maximum sequence length is 40000 chars.</TD>\r
723 </TR>\r
724 <TR BGCOLOR="white" CLASS="TableRowColor">\r
725 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
726 <CODE>&nbsp;class</CODE></FONT></TD>\r
727 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></B></CODE>\r
728 \r
729 <BR>\r
730 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line
731  
732  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>\r
733 </TR>\r
734 </TABLE>\r
735 &nbsp;\r
736 <P>\r
737 <A NAME="compbio.runner.msa"><!-- --></A>\r
738 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
739 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
740 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
741 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
742 </TR>\r
743 </TABLE>\r
744 &nbsp;\r
745 <P>\r
746 \r
747 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
748 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
749 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
750 </TR>\r
751 <TR BGCOLOR="white" CLASS="TableRowColor">\r
752 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
753 <CODE>&nbsp;class</CODE></FONT></TD>\r
754 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></B></CODE>\r
755 \r
756 <BR>\r
757 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
758 </TR>\r
759 <TR BGCOLOR="white" CLASS="TableRowColor">\r
760 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
761 <CODE>&nbsp;class</CODE></FONT></TD>\r
762 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>\r
763 \r
764 <BR>\r
765 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
766 </TR>\r
767 <TR BGCOLOR="white" CLASS="TableRowColor">\r
768 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
769 <CODE>&nbsp;class</CODE></FONT></TD>\r
770 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
771 \r
772 <BR>\r
773 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
774 </TR>\r
775 <TR BGCOLOR="white" CLASS="TableRowColor">\r
776 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
777 <CODE>&nbsp;class</CODE></FONT></TD>\r
778 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>\r
779 \r
780 <BR>\r
781 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
782 </TR>\r
783 <TR BGCOLOR="white" CLASS="TableRowColor">\r
784 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
785 <CODE>&nbsp;class</CODE></FONT></TD>\r
786 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
787 \r
788 <BR>\r
789 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
790 </TR>\r
791 <TR BGCOLOR="white" CLASS="TableRowColor">\r
792 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
793 <CODE>&nbsp;class</CODE></FONT></TD>\r
794 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
795 \r
796 <BR>\r
797 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
798 </TR>\r
799 </TABLE>\r
800 &nbsp;\r
801 <P>\r
802 <A NAME="compbio.ws.client"><!-- --></A>\r
803 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
804 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
805 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
806 Uses of <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
807 </TR>\r
808 </TABLE>\r
809 &nbsp;\r
810 <P>\r
811 \r
812 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
813 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
814 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
815 </TR>\r
816 <TR BGCOLOR="white" CLASS="TableRowColor">\r
817 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
818 <CODE>static&nbsp;<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;?&gt;&gt;</CODE></FONT></TD>\r
819 <TD><CODE><B>ServicesUtil.</B><B><A HREF="../../../../compbio/ws/client/ServicesUtil.html#getRunnerByJobDirectory(java.io.File)">getRunnerByJobDirectory</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;jobdir)</CODE>\r
820 \r
821 <BR>\r
822 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
823 </TR>\r
824 <TR BGCOLOR="white" CLASS="TableRowColor">\r
825 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
826 <CODE>static&nbsp;<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;?&gt;&gt;</CODE></FONT></TD>\r
827 <TD><CODE><B>ServicesUtil.</B><B><A HREF="../../../../compbio/ws/client/ServicesUtil.html#getServiceImpl(compbio.ws.client.Services)">getServiceImpl</A></B>(<A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>&nbsp;service)</CODE>\r
828 \r
829 <BR>\r
830 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
831 </TR>\r
832 </TABLE>\r
833 &nbsp;\r
834 <P>\r
835 \r
836 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
837 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
838 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> with type arguments of type <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></FONT></TH>\r
839 </TR>\r
840 <TR BGCOLOR="white" CLASS="TableRowColor">\r
841 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
842 <CODE>static&nbsp;<A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
843 <TD><CODE><B>ServicesUtil.</B><B><A HREF="../../../../compbio/ws/client/ServicesUtil.html#getServiceByRunner(java.lang.Class)">getServiceByRunner</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;<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;runnerClassName)</CODE>\r
844 \r
845 <BR>\r
846 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
847 </TR>\r
848 </TABLE>\r
849 &nbsp;\r
850 <P>\r
851 <HR>\r
852 \r
853 \r
854 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
855 <A NAME="navbar_bottom"><!-- --></A>\r
856 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
857 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
858 <TR>\r
859 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
860 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
861 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
862   <TR ALIGN="center" VALIGN="top">\r
863   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
864   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
865   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
866   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
867   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
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870   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</TD>\r
871   </TR>\r
872 </TABLE>\r
873 </TD>\r
874 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
875 </EM>\r
876 </TD>\r
877 </TR>\r
878 \r
879 <TR>\r
880 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
881 &nbsp;PREV&nbsp;\r
882 &nbsp;NEXT</FONT></TD>\r
883 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
884   <A HREF="../../../../index.html?compbio/engine/client/\class-useExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
885 &nbsp;<A HREF="Executable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
886 &nbsp;<SCRIPT type="text/javascript">\r
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889     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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895 </NOSCRIPT>\r
896 \r
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898 </FONT></TD>\r
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903 \r
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