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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.data.sequence.Alignment\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.data.sequence.Alignment";\r
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42   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\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.data.sequence.Alignment</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
102 <TD>A data model for multiple sequence alignment web services and utility methods
103  that work on the objects of this model.&nbsp;</TD>\r
104 </TR>\r
105 <TR BGCOLOR="white" CLASS="TableRowColor">\r
106 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
107 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
108 </TR>\r
109 <TR BGCOLOR="white" CLASS="TableRowColor">\r
110 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
111 <TD>Wrappers for native executables for multiple sequence alignment (msa)&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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
137 <TD><CODE><B>MsaWS.</B><B><A HREF="../../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
138 \r
139 <BR>\r
140 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return the result of the job.</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
162 <TD><CODE><B>GetResultResponse.</B><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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>GetResultResponse.</B><B><A HREF="../../../../compbio/data/msa/jaxws/GetResultResponse.html#setReturn(compbio.data.sequence.Alignment)">setReturn</A></B>(<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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.data.sequence"><!-- --></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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</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/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
203 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;file)</CODE>\r
204 \r
205 <BR>\r
206 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
207 </TR>\r
208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
210 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
211 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;instream)</CODE>\r
212 \r
213 <BR>\r
214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
215 </TR>\r
216 </TABLE>\r
217 &nbsp;\r
218 <P>\r
219 \r
220 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
221 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
222 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
223 </TR>\r
224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
226 <CODE>static&nbsp;void</CODE></FONT></TD>\r
227 <TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A>&nbsp;out,\r
228                       <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
229 \r
230 <BR>\r
231 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Write Clustal formatted alignment Limitations: does not record the
232  consensus.</TD>\r
233 </TR>\r
234 </TABLE>\r
235 &nbsp;\r
236 <P>\r
237 <A NAME="compbio.runner"><!-- --></A>\r
238 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
239 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
240 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
241 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
242 </TR>\r
243 </TABLE>\r
244 &nbsp;\r
245 <P>\r
246 \r
247 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
248 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
249 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
250 </TR>\r
251 <TR BGCOLOR="white" CLASS="TableRowColor">\r
252 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
253 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
254 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory,\r
255                 <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;clustFile)</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 </TABLE>\r
261 &nbsp;\r
262 <P>\r
263 <A NAME="compbio.runner.msa"><!-- --></A>\r
264 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
265 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
266 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
267 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
268 </TR>\r
269 </TABLE>\r
270 &nbsp;\r
271 <P>\r
272 \r
273 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
274 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
275 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
276 </TR>\r
277 <TR BGCOLOR="white" CLASS="TableRowColor">\r
278 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
279 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
280 <TD><CODE><B>Mafft.</B><B><A HREF="../../../../compbio/runner/msa/Mafft.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
281 \r
282 <BR>\r
283 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
284 </TR>\r
285 <TR BGCOLOR="white" CLASS="TableRowColor">\r
286 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
287 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
288 <TD><CODE><B>ClustalW.</B><B><A HREF="../../../../compbio/runner/msa/ClustalW.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
289 \r
290 <BR>\r
291 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
292 </TR>\r
293 <TR BGCOLOR="white" CLASS="TableRowColor">\r
294 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
295 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
296 <TD><CODE><B>Tcoffee.</B><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
297 \r
298 <BR>\r
299 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
300 </TR>\r
301 <TR BGCOLOR="white" CLASS="TableRowColor">\r
302 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
303 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
304 <TD><CODE><B>Muscle.</B><B><A HREF="../../../../compbio/runner/msa/Muscle.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
305 \r
306 <BR>\r
307 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
312 <TD><CODE><B>ClustalO.</B><B><A HREF="../../../../compbio/runner/msa/ClustalO.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
313 \r
314 <BR>\r
315 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
320 <TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
321 \r
322 <BR>\r
323 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
324 </TR>\r
325 </TABLE>\r
326 &nbsp;\r
327 <P>\r
328 <A NAME="compbio.ws.server"><!-- --></A>\r
329 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
330 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
331 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
332 Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
333 </TR>\r
334 </TABLE>\r
335 &nbsp;\r
336 <P>\r
337 \r
338 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
339 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
340 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
341 </TR>\r
342 <TR BGCOLOR="white" CLASS="TableRowColor">\r
343 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
344 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
345 <TD><CODE><B>ClustalWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
346 \r
347 <BR>\r
348 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
349 </TR>\r
350 <TR BGCOLOR="white" CLASS="TableRowColor">\r
351 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
352 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
353 <TD><CODE><B>_MsaService.</B><B><A HREF="../../../../compbio/ws/server/_MsaService.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
354 \r
355 <BR>\r
356 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
357 </TR>\r
358 <TR BGCOLOR="white" CLASS="TableRowColor">\r
359 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
360 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
361 <TD><CODE><B>MuscleWS.</B><B><A HREF="../../../../compbio/ws/server/MuscleWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
362 \r
363 <BR>\r
364 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
365 </TR>\r
366 <TR BGCOLOR="white" CLASS="TableRowColor">\r
367 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
368 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
369 <TD><CODE><B>MafftWS.</B><B><A HREF="../../../../compbio/ws/server/MafftWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
370 \r
371 <BR>\r
372 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
373 </TR>\r
374 <TR BGCOLOR="white" CLASS="TableRowColor">\r
375 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
376 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
377 <TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../../compbio/ws/server/TcoffeeWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
378 \r
379 <BR>\r
380 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
381 </TR>\r
382 <TR BGCOLOR="white" CLASS="TableRowColor">\r
383 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
384 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
385 <TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
386 \r
387 <BR>\r
388 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
389 </TR>\r
390 <TR BGCOLOR="white" CLASS="TableRowColor">\r
391 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
392 <CODE>&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
393 <TD><CODE><B>ClustalOWS.</B><B><A HREF="../../../../compbio/ws/server/ClustalOWS.html#getResult(java.lang.String)">getResult</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;jobId)</CODE>\r
394 \r
395 <BR>\r
396 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
397 </TR>\r
398 </TABLE>\r
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