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5 <!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
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7 Uses of Class compbio.metadata.Option\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.Option";\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/Option.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-useOption.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.Option</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/Option.html" title="class in compbio.metadata">Option</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/Option.html" title="class in compbio.metadata">Option</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">Method parameters in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</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="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
137 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
138             <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/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
139 \r
140 <BR>\r
141 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
142 </TR>\r
143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
145 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
146 <TD><CODE><B>SequenceAnnotation.</B><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
147               <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/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>&gt;&gt;&nbsp;options)</CODE>\r
148 \r
149 <BR>\r
150 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
151  list.</TD>\r
152 </TR>\r
153 </TABLE>\r
154 &nbsp;\r
155 <P>\r
156 <A NAME="compbio.data.msa.jaxws"><!-- --></A>\r
157 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
158 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
159 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
160 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
161 </TR>\r
162 </TABLE>\r
163 &nbsp;\r
164 <P>\r
165 \r
166 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
167 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
168 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
169 </TR>\r
170 <TR BGCOLOR="white" CLASS="TableRowColor">\r
171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
172 <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>&gt;</CODE></FONT></TD>\r
173 <TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAnalize.html#getOptions()">getOptions</A></B>()</CODE>\r
174 \r
175 <BR>\r
176 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
177 </TR>\r
178 <TR BGCOLOR="white" CLASS="TableRowColor">\r
179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
180 <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>&gt;</CODE></FONT></TD>\r
181 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#getOptions()">getOptions</A></B>()</CODE>\r
182 \r
183 <BR>\r
184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
185 </TR>\r
186 </TABLE>\r
187 &nbsp;\r
188 <P>\r
189 \r
190 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
191 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
192 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
193 </TR>\r
194 <TR BGCOLOR="white" CLASS="TableRowColor">\r
195 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
196 <CODE>&nbsp;void</CODE></FONT></TD>\r
197 <TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAnalize.html#setOptions(java.util.List)">setOptions</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="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
198 \r
199 <BR>\r
200 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
201 </TR>\r
202 <TR BGCOLOR="white" CLASS="TableRowColor">\r
203 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
204 <CODE>&nbsp;void</CODE></FONT></TD>\r
205 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)">setOptions</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="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
206 \r
207 <BR>\r
208 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
209 </TR>\r
210 </TABLE>\r
211 &nbsp;\r
212 <P>\r
213 <A NAME="compbio.engine.client"><!-- --></A>\r
214 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
215 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
216 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
217 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
218 </TR>\r
219 </TABLE>\r
220 &nbsp;\r
221 <P>\r
222 \r
223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
224 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
225 <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/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
226 </TR>\r
227 <TR BGCOLOR="white" CLASS="TableRowColor">\r
228 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
229 <CODE>static\r
230 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
231 <TR ALIGN="right" VALIGN="">\r
232 <TD NOWRAP><FONT SIZE="-1">\r
233 <CODE>&lt;T&gt; <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;T&gt;</CODE></FONT></TD>\r
234 </TR>\r
235 </TABLE>\r
236 </CODE></FONT></TD>\r
237 <TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</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;T&gt;&gt;&nbsp;arguments,\r
238                   <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;nameValueSeparator)</CODE>\r
239 \r
240 <BR>\r
241 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
242 </TR>\r
243 </TABLE>\r
244 &nbsp;\r
245 <P>\r
246 <A NAME="compbio.metadata"><!-- --></A>\r
247 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
248 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
249 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
250 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
251 </TR>\r
252 </TABLE>\r
253 &nbsp;\r
254 <P>\r
255 \r
256 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
257 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
258 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\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;class</CODE></FONT></TD>\r
263 <TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter&lt;T&gt;</A></B></CODE>\r
264 \r
265 <BR>\r
266 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing an option supported by the web service e.g.</TD>\r
267 </TR>\r
268 </TABLE>\r
269 &nbsp;\r
270 <P>\r
271 \r
272 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
273 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
274 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
275 </TR>\r
276 <TR BGCOLOR="white" CLASS="TableRowColor">\r
277 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
278 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
279 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</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;name)</CODE>\r
280 \r
281 <BR>\r
282 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by its name if found, NULL otherwise.</TD>\r
283 </TR>\r
284 <TR BGCOLOR="white" CLASS="TableRowColor">\r
285 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
286 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
287 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</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;optionName)</CODE>\r
288 \r
289 <BR>\r
290 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by option name, NULL if the argument is not found</TD>\r
291 </TR>\r
292 </TABLE>\r
293 &nbsp;\r
294 <P>\r
295 \r
296 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
297 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
298 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
299 </TR>\r
300 <TR BGCOLOR="white" CLASS="TableRowColor">\r
301 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
302 <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/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
303 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
304 \r
305 <BR>\r
306 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns list of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
307  runner</TD>\r
308 </TR>\r
309 <TR BGCOLOR="white" CLASS="TableRowColor">\r
310 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
311 <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
312 <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
313 \r
314 <BR>\r
315 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Converts list of options as String to type Option</TD>\r
316 </TR>\r
317 <TR BGCOLOR="white" CLASS="TableRowColor">\r
318 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
319 <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/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
320 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
321 \r
322 <BR>\r
323 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the list of the Options supported by the executable of type T</TD>\r
324 </TR>\r
325 </TABLE>\r
326 &nbsp;\r
327 <P>\r
328 \r
329 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
330 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
331 <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/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
332 </TR>\r
333 <TR BGCOLOR="white" CLASS="TableRowColor">\r
334 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
335 <CODE>&nbsp;void</CODE></FONT></TD>\r
336 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;option)</CODE>\r
337 \r
338 <BR>\r
339 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds Option to the internal list of options</TD>\r
340 </TR>\r
341 </TABLE>\r
342 &nbsp;\r
343 <P>\r
344 \r
345 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
346 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
347 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
348 </TR>\r
349 <TR BGCOLOR="white" CLASS="TableRowColor">\r
350 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
351 <CODE>&nbsp;void</CODE></FONT></TD>\r
352 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</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="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
353 \r
354 <BR>\r
355 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds the list of options or parameters to the internal list of options</TD>\r
356 </TR>\r
357 </TABLE>\r
358 &nbsp;\r
359 <P>\r
360 \r
361 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
362 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
363 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
364 </TR>\r
365 <TR BGCOLOR="white" CLASS="TableRowColor">\r
366 <TD><CODE><B><A HREF="../../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&nbsp;option)</CODE>\r
367 \r
368 <BR>\r
369 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
370 </TR>\r
371 </TABLE>\r
372 &nbsp;\r
373 <P>\r
374 <A NAME="compbio.runner"><!-- --></A>\r
375 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
376 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
377 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
378 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
379 </TR>\r
380 </TABLE>\r
381 &nbsp;\r
382 <P>\r
383 \r
384 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
385 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
386 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/runner/package-summary.html">compbio.runner</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
387 </TR>\r
388 <TR BGCOLOR="white" CLASS="TableRowColor">\r
389 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
390 <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;?&gt;&gt;</CODE></FONT></TD>\r
391 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</A></B>()</CODE>\r
392 \r
393 <BR>\r
394 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
395 </TR>\r
396 </TABLE>\r
397 &nbsp;\r
398 <P>\r
399 \r
400 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
401 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
402 <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/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
403 </TR>\r
404 <TR BGCOLOR="white" CLASS="TableRowColor">\r
405 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
406 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
407 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">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)</CODE>\r
408 \r
409 <BR>\r
410 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
411 </TR>\r
412 <TR BGCOLOR="white" CLASS="TableRowColor">\r
413 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
414 <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
415 <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
416                          <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
417 \r
418 <BR>\r
419 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
420 </TR>\r
421 <TR BGCOLOR="white" CLASS="TableRowColor">\r
422 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
423 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
424 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</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="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;options)</CODE>\r
425 \r
426 <BR>\r
427 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
428 </TR>\r
429 </TABLE>\r
430 &nbsp;\r
431 <P>\r
432 <A NAME="compbio.ws.server"><!-- --></A>\r
433 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
434 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
435 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
436 Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
437 </TR>\r
438 </TABLE>\r
439 &nbsp;\r
440 <P>\r
441 \r
442 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
443 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
444 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
445 </TR>\r
446 <TR BGCOLOR="white" CLASS="TableRowColor">\r
447 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
448 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
449 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
450             <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/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;&gt;&nbsp;options)</CODE>\r
451 \r
452 <BR>\r
453 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
454 </TR>\r
455 <TR BGCOLOR="white" CLASS="TableRowColor">\r
456 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
457 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
458 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
459             <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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
460 \r
461 <BR>\r
462 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
463 </TR>\r
464 <TR BGCOLOR="white" CLASS="TableRowColor">\r
465 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
466 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
467 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
468             <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/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
469 \r
470 <BR>\r
471 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
472 </TR>\r
473 <TR BGCOLOR="white" CLASS="TableRowColor">\r
474 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
475 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
476 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
477             <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/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
478 \r
479 <BR>\r
480 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
481 </TR>\r
482 <TR BGCOLOR="white" CLASS="TableRowColor">\r
483 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
484 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
485 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
486             <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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
487 \r
488 <BR>\r
489 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
490 </TR>\r
491 <TR BGCOLOR="white" CLASS="TableRowColor">\r
492 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
493 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
494 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
495             <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/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&gt;&nbsp;options)</CODE>\r
496 \r
497 <BR>\r
498 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
499 </TR>\r
500 <TR BGCOLOR="white" CLASS="TableRowColor">\r
501 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
502 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
503 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
504             <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/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
505 \r
506 <BR>\r
507 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
508 </TR>\r
509 <TR BGCOLOR="white" CLASS="TableRowColor">\r
510 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
511 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
512 <TD><CODE><B>DisemblWS.</B><B><A HREF="../../../compbio/ws/server/DisemblWS.html#customAnalize(java.util.List, java.util.List)">customAnalize</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
513               <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/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&gt;&nbsp;options)</CODE>\r
514 \r
515 <BR>\r
516 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
517 </TR>\r
518 <TR BGCOLOR="white" CLASS="TableRowColor">\r
519 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
520 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
521 <TD><CODE><B>GlobPlotWS.</B><B><A HREF="../../../compbio/ws/server/GlobPlotWS.html#customAnalize(java.util.List, java.util.List)">customAnalize</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
522               <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/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;&gt;&nbsp;options)</CODE>\r
523 \r
524 <BR>\r
525 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
526 </TR>\r
527 <TR BGCOLOR="white" CLASS="TableRowColor">\r
528 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
529 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
530 <TD><CODE><B>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)">customAnalize</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
531               <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/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&gt;&nbsp;options)</CODE>\r
532 \r
533 <BR>\r
534 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
535 </TR>\r
536 <TR BGCOLOR="white" CLASS="TableRowColor">\r
537 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
538 <CODE>static\r
539 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
540 <TR ALIGN="right" VALIGN="">\r
541 <TD NOWRAP><FONT SIZE="-1">\r
542 <CODE>&lt;T&gt; <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
543 </TR>\r
544 </TABLE>\r
545 </CODE></FONT></TD>\r
546 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</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="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
547             <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;keyValueSeparator)</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 <HR>\r
556 \r
557 \r
558 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
559 <A NAME="navbar_bottom"><!-- --></A>\r
560 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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562 <TR>\r
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564 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
565 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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567   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
568   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
569   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
570   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
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575   </TR>\r
576 </TABLE>\r
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578 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
579 </EM>\r
580 </TD>\r
581 </TR>\r
582 \r
583 <TR>\r
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585 &nbsp;PREV&nbsp;\r
586 &nbsp;NEXT</FONT></TD>\r
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588   <A HREF="../../../index.html?compbio/metadata/\class-useOption.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
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590 &nbsp;<SCRIPT type="text/javascript">\r
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