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5 <!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
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7 _SkeletalCommandBuilder\r
8 </TITLE>\r
9 \r
10 <META NAME="date" CONTENT="2010-02-17">\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="_SkeletalCommandBuilder";\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/_SkeletalCommandBuilder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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54 </TR>\r
55 \r
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57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
58 &nbsp;<A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</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;FIELD&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;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_detail">METHOD</A></FONT></TD>\r
82 </TR>\r
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84 <A NAME="skip-navbar_top"></A>\r
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.runner</FONT>\r
92 <BR>\r
93 Class _SkeletalCommandBuilder</H2>\r
94 <PRE>\r
95 java.lang.Object\r
96   <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner._SkeletalCommandBuilder</B>\r
97 </PRE>\r
98 <DL>\r
99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DD>\r
100 </DL>\r
101 <DL>\r
102 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/runner/_impl/BlastAll.html" title="class in compbio.runner._impl">BlastAll</A>, <A HREF="../../compbio/runner/_impl/Disembl.html" title="class in compbio.runner._impl">Disembl</A>, <A HREF="../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl">Mcl</A>, <A HREF="../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>, <A HREF="../../compbio/runner/_impl/PSIBlast.html" title="class in compbio.runner._impl">PSIBlast</A>, <A HREF="../../compbio/runner/_impl/Ronn.html" title="class in compbio.runner._impl">Ronn</A>, <A HREF="../../compbio/runner/_impl/RPSBlast.html" title="class in compbio.runner._impl">RPSBlast</A></DD>\r
103 </DL>\r
104 <HR>\r
105 <DL>\r
106 <DT><PRE>public abstract class <B>_SkeletalCommandBuilder</B><DT>extends java.lang.Object<DT>implements <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</DL>\r
107 </PRE>\r
108 \r
109 <P>\r
110 <HR>\r
111 \r
112 <P>\r
113 <!-- ======== NESTED CLASS SUMMARY ======== -->\r
114 \r
115 <A NAME="nested_class_summary"><!-- --></A>\r
116 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
117 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
118 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
119 <B>Nested Class Summary</B></FONT></TH>\r
120 </TR>\r
121 </TABLE>\r
122 &nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
123 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
124 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
125 <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
126 </TR>\r
127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
128 <TD><CODE><A HREF="../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
129 </TR>\r
130 </TABLE>\r
131 &nbsp;\r
132 \r
133 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
134 \r
135 <A NAME="constructor_summary"><!-- --></A>\r
136 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
137 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
138 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
139 <B>Constructor Summary</B></FONT></TH>\r
140 </TR>\r
141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
142 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#_SkeletalCommandBuilder()">_SkeletalCommandBuilder</A></B>()</CODE>\r
143 \r
144 <BR>\r
145 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
146 </TR>\r
147 </TABLE>\r
148 &nbsp;\r
149 <!-- ========== METHOD SUMMARY =========== -->\r
150 \r
151 <A NAME="method_summary"><!-- --></A>\r
152 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
153 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
154 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
155 <B>Method Summary</B></FONT></TH>\r
156 </TR>\r
157 <TR BGCOLOR="white" CLASS="TableRowColor">\r
158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
159 <CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
160 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameter(java.lang.String)">addParameter</A></B>(java.lang.String&nbsp;parameter)</CODE>\r
161 \r
162 <BR>\r
163 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
164 </TR>\r
165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
167 <CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
168 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</CODE>\r
169 \r
170 <BR>\r
171 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
172 </TR>\r
173 <TR BGCOLOR="white" CLASS="TableRowColor">\r
174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
175 <CODE>&nbsp;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
176 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#addParameters(java.lang.String[])">addParameters</A></B>(java.lang.String[]&nbsp;parameters)</CODE>\r
177 \r
178 <BR>\r
179 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
180 </TR>\r
181 <TR BGCOLOR="white" CLASS="TableRowColor">\r
182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
183 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
184 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getEmail()">getEmail</A></B>()</CODE>\r
185 \r
186 <BR>\r
187 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
188 </TR>\r
189 <TR BGCOLOR="white" CLASS="TableRowColor">\r
190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
191 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
192 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getError()">getError</A></B>()</CODE>\r
193 \r
194 <BR>\r
195 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
196 </TR>\r
197 <TR BGCOLOR="white" CLASS="TableRowColor">\r
198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
199 <CODE>&nbsp;<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
200 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String&nbsp;presetName)</CODE>\r
201 \r
202 <BR>\r
203 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
204 </TR>\r
205 <TR BGCOLOR="white" CLASS="TableRowColor">\r
206 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
207 <CODE>&nbsp;<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
208 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getLimits()">getLimits</A></B>()</CODE>\r
209 \r
210 <BR>\r
211 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
212 </TR>\r
213 <TR BGCOLOR="white" CLASS="TableRowColor">\r
214 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
215 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
216 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getName()">getName</A></B>()</CODE>\r
217 \r
218 <BR>\r
219 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
220 </TR>\r
221 <TR BGCOLOR="white" CLASS="TableRowColor">\r
222 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
223 <CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
224 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getOutput()">getOutput</A></B>()</CODE>\r
225 \r
226 <BR>\r
227 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
228 </TR>\r
229 <TR BGCOLOR="white" CLASS="TableRowColor">\r
230 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
231 <CODE>&nbsp;<A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></FONT></TD>\r
232 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.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
233 \r
234 <BR>\r
235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
236 </TR>\r
237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
239 <CODE>\r
240 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
241 <TR ALIGN="right" VALIGN="">\r
242 <TD NOWRAP><FONT SIZE="-1">\r
243 <CODE>&lt;V&gt; V</CODE></FONT></TD>\r
244 </TR>\r
245 </TABLE>\r
246 </CODE></FONT></TD>\r
247 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#getResults(java.lang.String)">getResults</A></B>(java.lang.String&nbsp;directory)</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/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
255 <TD><CODE><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
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="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
263 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setEmail(java.lang.String)">setEmail</A></B>(java.lang.String&nbsp;email)</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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A></CODE></FONT></TD>\r
271 <TD><CODE><B><A HREF="../../compbio/runner/_SkeletalCommandBuilder.html#setName(java.lang.String)">setName</A></B>(java.lang.String&nbsp;name)</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 </TABLE>\r
277 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
278 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
279 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
280 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
281 </TR>\r
282 <TR BGCOLOR="white" CLASS="TableRowColor">\r
283 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
284 </TR>\r
285 </TABLE>\r
286 &nbsp;<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
287 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
288 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
289 <TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
290 </TR>\r
291 <TR BGCOLOR="white" CLASS="TableRowColor">\r
292 <TD><CODE><A HREF="../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A>, <A HREF="../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE></TD>\r
293 </TR>\r
294 </TABLE>\r
295 &nbsp;\r
296 <P>\r
297 \r
298 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
299 \r
300 <A NAME="constructor_detail"><!-- --></A>\r
301 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
302 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
303 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
304 <B>Constructor Detail</B></FONT></TH>\r
305 </TR>\r
306 </TABLE>\r
307 \r
308 <A NAME="_SkeletalCommandBuilder()"><!-- --></A><H3>\r
309 _SkeletalCommandBuilder</H3>\r
310 <PRE>\r
311 public <B>_SkeletalCommandBuilder</B>()</PRE>\r
312 <DL>\r
313 </DL>\r
314 \r
315 <!-- ============ METHOD DETAIL ========== -->\r
316 \r
317 <A NAME="method_detail"><!-- --></A>\r
318 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
319 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
320 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
321 <B>Method Detail</B></FONT></TH>\r
322 </TR>\r
323 </TABLE>\r
324 \r
325 <A NAME="setEmail(java.lang.String)"><!-- --></A><H3>\r
326 setEmail</H3>\r
327 <PRE>\r
328 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setEmail</B>(java.lang.String&nbsp;email)</PRE>\r
329 <DL>\r
330 <DD><DL>\r
331 </DL>\r
332 </DD>\r
333 <DD><DL>\r
334 </DL>\r
335 </DD>\r
336 </DL>\r
337 <HR>\r
338 \r
339 <A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
340 setName</H3>\r
341 <PRE>\r
342 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>setName</B>(java.lang.String&nbsp;name)</PRE>\r
343 <DL>\r
344 <DD><DL>\r
345 </DL>\r
346 </DD>\r
347 <DD><DL>\r
348 </DL>\r
349 </DD>\r
350 </DL>\r
351 <HR>\r
352 \r
353 <A NAME="getName()"><!-- --></A><H3>\r
354 getName</H3>\r
355 <PRE>\r
356 public java.lang.String <B>getName</B>()</PRE>\r
357 <DL>\r
358 <DD><DL>\r
359 </DL>\r
360 </DD>\r
361 <DD><DL>\r
362 </DL>\r
363 </DD>\r
364 </DL>\r
365 <HR>\r
366 \r
367 <A NAME="getEmail()"><!-- --></A><H3>\r
368 getEmail</H3>\r
369 <PRE>\r
370 public java.lang.String <B>getEmail</B>()</PRE>\r
371 <DL>\r
372 <DD><DL>\r
373 </DL>\r
374 </DD>\r
375 <DD><DL>\r
376 </DL>\r
377 </DD>\r
378 </DL>\r
379 <HR>\r
380 \r
381 <A NAME="addParameters(java.lang.String[])"><!-- --></A><H3>\r
382 addParameters</H3>\r
383 <PRE>\r
384 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.lang.String[]&nbsp;parameters)</PRE>\r
385 <DL>\r
386 <DD><DL>\r
387 </DL>\r
388 </DD>\r
389 <DD><DL>\r
390 </DL>\r
391 </DD>\r
392 </DL>\r
393 <HR>\r
394 \r
395 <A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
396 addParameters</H3>\r
397 <PRE>\r
398 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameters</B>(java.util.List&lt;java.lang.String&gt;&nbsp;parameters)</PRE>\r
399 <DL>\r
400 <DD><B>Description copied from interface: <CODE><A HREF="../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
401 <DD>Adds parameter to the list of parameters for a native executable\r
402 <P>\r
403 <DD><DL>\r
404 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
405 </DD>\r
406 <DD><DL>\r
407 \r
408 <DT><B>Returns:</B><DD>this Executable</DL>\r
409 </DD>\r
410 </DL>\r
411 <HR>\r
412 \r
413 <A NAME="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
414 getParameters</H3>\r
415 <PRE>\r
416 public <A HREF="../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</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
417 <DL>\r
418 <DD><DL>\r
419 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
420 </DD>\r
421 <DD><DL>\r
422 </DL>\r
423 </DD>\r
424 </DL>\r
425 <HR>\r
426 \r
427 <A NAME="addParameter(java.lang.String)"><!-- --></A><H3>\r
428 addParameter</H3>\r
429 <PRE>\r
430 public <A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A> <B>addParameter</B>(java.lang.String&nbsp;parameter)</PRE>\r
431 <DL>\r
432 <DD><DL>\r
433 </DL>\r
434 </DD>\r
435 <DD><DL>\r
436 </DL>\r
437 </DD>\r
438 </DL>\r
439 <HR>\r
440 \r
441 <A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
442 getResults</H3>\r
443 <PRE>\r
444 public &lt;V&gt; V <B>getResults</B>(java.lang.String&nbsp;directory)</PRE>\r
445 <DL>\r
446 <DD><DL>\r
447 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
448 </DD>\r
449 <DD><DL>\r
450 </DL>\r
451 </DD>\r
452 </DL>\r
453 <HR>\r
454 \r
455 <A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
456 loadRunConfiguration</H3>\r
457 <PRE>\r
458 public <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
459 <DL>\r
460 <DD><DL>\r
461 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
462 </DD>\r
463 <DD><DL>\r
464 </DL>\r
465 </DD>\r
466 </DL>\r
467 <HR>\r
468 \r
469 <A NAME="getOutput()"><!-- --></A><H3>\r
470 getOutput</H3>\r
471 <PRE>\r
472 public java.lang.String <B>getOutput</B>()</PRE>\r
473 <DL>\r
474 <DD><DL>\r
475 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
476 </DD>\r
477 <DD><DL>\r
478 </DL>\r
479 </DD>\r
480 </DL>\r
481 <HR>\r
482 \r
483 <A NAME="getError()"><!-- --></A><H3>\r
484 getError</H3>\r
485 <PRE>\r
486 public java.lang.String <B>getError</B>()</PRE>\r
487 <DL>\r
488 <DD><DL>\r
489 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
490 </DD>\r
491 <DD><DL>\r
492 </DL>\r
493 </DD>\r
494 </DL>\r
495 <HR>\r
496 \r
497 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
498 getLimit</H3>\r
499 <PRE>\r
500 public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getLimit</B>(java.lang.String&nbsp;presetName)</PRE>\r
501 <DL>\r
502 <DD><DL>\r
503 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
504 </DD>\r
505 <DD><DL>\r
506 </DL>\r
507 </DD>\r
508 </DL>\r
509 <HR>\r
510 \r
511 <A NAME="getLimits()"><!-- --></A><H3>\r
512 getLimits</H3>\r
513 <PRE>\r
514 public <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../compbio/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt; <B>getLimits</B>()</PRE>\r
515 <DL>\r
516 <DD><DL>\r
517 <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/runner/_SkeletalCommandBuilder.html" title="class in compbio.runner">_SkeletalCommandBuilder</A>&gt;</CODE></DL>\r
518 </DD>\r
519 <DD><DL>\r
520 </DL>\r
521 </DD>\r
522 </DL>\r
523 <!-- ========= END OF CLASS DATA ========= -->\r
524 <HR>\r
525 \r
526 \r
527 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
528 <A NAME="navbar_bottom"><!-- --></A>\r
529 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
530 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
531 <TR>\r
532 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
533 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
534 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
535   <TR ALIGN="center" VALIGN="top">\r
536   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
537   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
538   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
539   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/_SkeletalCommandBuilder.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
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550 </TR>\r
551 \r
552 <TR>\r
553 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
554 &nbsp;<A HREF="../../compbio/runner/_NativeSpecHelper.html" title="class in compbio.runner"><B>PREV CLASS</B></A>&nbsp;\r
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561   if(window==top) {\r
562     document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
563   }\r
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565 </SCRIPT>\r
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567   <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
568 </NOSCRIPT>\r
569 \r
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573 <TR>\r
574 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
575   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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