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5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
6 <TITLE>\r
7 Uses of Class compbio.metadata.RunnerConfig\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2011-08-12">\r
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18         parent.document.title="Uses of Class compbio.metadata.RunnerConfig";\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="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
43   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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61   <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.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 Class<br>compbio.metadata.RunnerConfig</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/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
94 <TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
95 </TR>\r
96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
97 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</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.client"><B>compbio.engine.client</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.metadata"><B>compbio.metadata</B></A></TD>\r
106 <TD>A meta-data model for multiple sequence alignment web services 
107  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>\r
108 </TR>\r
109 <TR BGCOLOR="white" CLASS="TableRowColor">\r
110 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
111 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
112 </TR>\r
113 <TR BGCOLOR="white" CLASS="TableRowColor">\r
114 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
115 <TD>&nbsp;&nbsp;</TD>\r
116 </TR>\r
117 </TABLE>\r
118 &nbsp;\r
119 <P>\r
120 <A NAME="compbio.data.msa"><!-- --></A>\r
121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
122 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
123 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
124 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
125 </TR>\r
126 </TABLE>\r
127 &nbsp;\r
128 <P>\r
129 \r
130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
131 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
132 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
133 </TR>\r
134 <TR BGCOLOR="white" CLASS="TableRowColor">\r
135 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
136 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>&gt;</CODE></FONT></TD>\r
137 <TD><CODE><B>Metadata.</B><B><A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
138 \r
139 <BR>\r
140 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Get options supported by a web service</TD>\r
141 </TR>\r
142 </TABLE>\r
143 &nbsp;\r
144 <P>\r
145 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
146 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
147 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
148 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
149 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
150 </TR>\r
151 </TABLE>\r
152 &nbsp;\r
153 <P>\r
154 \r
155 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
156 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
157 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
158 </TR>\r
159 <TR BGCOLOR="white" CLASS="TableRowColor">\r
160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
161 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></CODE></FONT></TD>\r
162 <TD><CODE><B>GetRunnerOptionsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#getReturn()">getReturn</A></B>()</CODE>\r
163 \r
164 <BR>\r
165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
166 </TR>\r
167 </TABLE>\r
168 &nbsp;\r
169 <P>\r
170 \r
171 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
172 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
173 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
174 </TR>\r
175 <TR BGCOLOR="white" CLASS="TableRowColor">\r
176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
177 <CODE>&nbsp;void</CODE></FONT></TD>\r
178 <TD><CODE><B>GetRunnerOptionsResponse.</B><B><A HREF="../../../compbio/data/msa/jaxws/GetRunnerOptionsResponse.html#setReturn(compbio.metadata.RunnerConfig)">setReturn</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&nbsp;_return)</CODE>\r
179 \r
180 <BR>\r
181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
182 </TR>\r
183 </TABLE>\r
184 &nbsp;\r
185 <P>\r
186 <A NAME="compbio.engine.client"><!-- --></A>\r
187 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
188 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
189 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
190 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
191 </TR>\r
192 </TABLE>\r
193 &nbsp;\r
194 <P>\r
195 \r
196 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
197 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
198 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
199 </TR>\r
200 <TR BGCOLOR="white" CLASS="TableRowColor">\r
201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
202 <CODE>static\r
203 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
204 <TR ALIGN="right" VALIGN="">\r
205 <TD NOWRAP><FONT SIZE="-1">\r
206 <CODE>&lt;V&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;V&gt;</CODE></FONT></TD>\r
207 </TR>\r
208 </TABLE>\r
209 </CODE></FONT></TD>\r
210 <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
211 \r
212 <BR>\r
213 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
214 </TR>\r
215 </TABLE>\r
216 &nbsp;\r
217 <P>\r
218 <A NAME="compbio.metadata"><!-- --></A>\r
219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
220 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
221 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
222 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
223 </TR>\r
224 </TABLE>\r
225 &nbsp;\r
226 <P>\r
227 \r
228 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
229 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
230 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
231 </TR>\r
232 <TR BGCOLOR="white" CLASS="TableRowColor">\r
233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
234 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
235 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;?&gt;&nbsp;runnerConf)</CODE>\r
236 \r
237 <BR>\r
238 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
239 </TR>\r
240 </TABLE>\r
241 &nbsp;\r
242 <P>\r
243 \r
244 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
245 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
246 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
247 </TR>\r
248 <TR BGCOLOR="white" CLASS="TableRowColor">\r
249 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
250 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
251 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;?&gt;&nbsp;runnerConf)</CODE>\r
252 \r
253 <BR>\r
254 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
255 </TR>\r
256 <TR BGCOLOR="white" CLASS="TableRowColor">\r
257 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
258 <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="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
259 <TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
260 \r
261 <BR>\r
262 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
263 </TR>\r
264 <TR BGCOLOR="white" CLASS="TableRowColor">\r
265 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
266 <CODE>&nbsp;void</CODE></FONT></TD>\r
267 <TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;&nbsp;options)</CODE>\r
268 \r
269 <BR>\r
270 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Checks whether preset option and parameter are defined in RunnerConfig
271  object.</TD>\r
272 </TR>\r
273 </TABLE>\r
274 &nbsp;\r
275 <P>\r
276 <A NAME="compbio.runner"><!-- --></A>\r
277 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
278 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
279 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
280 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
281 </TR>\r
282 </TABLE>\r
283 &nbsp;\r
284 <P>\r
285 \r
286 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
287 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
288 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
289 </TR>\r
290 <TR BGCOLOR="white" CLASS="TableRowColor">\r
291 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
292 <CODE>static\r
293 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
294 <TR ALIGN="right" VALIGN="">\r
295 <TD NOWRAP><FONT SIZE="-1">\r
296 <CODE>&lt;T&gt; <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;T&gt;</CODE></FONT></TD>\r
297 </TR>\r
298 </TABLE>\r
299 </CODE></FONT></TD>\r
300 <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
301 \r
302 <BR>\r
303 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
304 </TR>\r
305 </TABLE>\r
306 &nbsp;\r
307 <P>\r
308 \r
309 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
310 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
311 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
312 </TR>\r
313 <TR BGCOLOR="white" CLASS="TableRowColor">\r
314 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
315 <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
316 <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
317                          <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
318 \r
319 <BR>\r
320 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
321 </TR>\r
322 </TABLE>\r
323 &nbsp;\r
324 <P>\r
325 \r
326 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
327 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
328 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
329 </TR>\r
330 <TR BGCOLOR="white" CLASS="TableRowColor">\r
331 <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
332 \r
333 <BR>\r
334 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
335 </TR>\r
336 </TABLE>\r
337 &nbsp;\r
338 <P>\r
339 <A NAME="compbio.ws.server"><!-- --></A>\r
340 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
341 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
342 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
343 Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
344 </TR>\r
345 </TABLE>\r
346 &nbsp;\r
347 <P>\r
348 \r
349 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
350 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
351 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></TH>\r
352 </TR>\r
353 <TR BGCOLOR="white" CLASS="TableRowColor">\r
354 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
355 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/ws/server/GenericMetadataService.html" title="type parameter in GenericMetadataService">T</A>&gt;</CODE></FONT></TD>\r
356 <TD><CODE><B>GenericMetadataService.</B><B><A HREF="../../../compbio/ws/server/GenericMetadataService.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
357 \r
358 <BR>\r
359 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
360 </TR>\r
361 <TR BGCOLOR="white" CLASS="TableRowColor">\r
362 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
363 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;</CODE></FONT></TD>\r
364 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
365 \r
366 <BR>\r
367 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
368 </TR>\r
369 <TR BGCOLOR="white" CLASS="TableRowColor">\r
370 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
371 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;</CODE></FONT></TD>\r
372 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
373 \r
374 <BR>\r
375 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
376 </TR>\r
377 <TR BGCOLOR="white" CLASS="TableRowColor">\r
378 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
379 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;</CODE></FONT></TD>\r
380 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
381 \r
382 <BR>\r
383 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
384 </TR>\r
385 <TR BGCOLOR="white" CLASS="TableRowColor">\r
386 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
387 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;</CODE></FONT></TD>\r
388 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
389 \r
390 <BR>\r
391 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
392 </TR>\r
393 <TR BGCOLOR="white" CLASS="TableRowColor">\r
394 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
395 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;</CODE></FONT></TD>\r
396 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
397 \r
398 <BR>\r
399 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
400 </TR>\r
401 <TR BGCOLOR="white" CLASS="TableRowColor">\r
402 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
403 <CODE>&nbsp;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;</CODE></FONT></TD>\r
404 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
405 \r
406 <BR>\r
407 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
408 </TR>\r
409 </TABLE>\r
410 &nbsp;\r
411 <P>\r
412 <HR>\r
413 \r
414 \r
415 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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424   <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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