1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
\r
5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:08:24 GMT 2011 -->
\r
10 <META NAME="date" CONTENT="2011-12-07">
\r
12 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
\r
14 <SCRIPT type="text/javascript">
\r
15 function windowTitle()
\r
17 if (location.href.indexOf('is-external=true') == -1) {
\r
18 parent.document.title="MsaWS";
\r
27 <BODY BGCOLOR="white" onload="windowTitle();">
\r
31 <!-- ========= START OF TOP NAVBAR ======= -->
\r
32 <A NAME="navbar_top"><!-- --></A>
\r
33 <A HREF="#skip-navbar_top" title="Skip navigation links"></A>
\r
34 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
36 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
37 <A NAME="navbar_top_firstrow"><!-- --></A>
\r
38 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
39 <TR ALIGN="center" VALIGN="top">
\r
40 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
41 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
42 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
43 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
44 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
45 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
46 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
47 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
51 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
57 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
58 <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A>
\r
59 <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>
\r
60 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
61 <A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A>
\r
62 <A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A>
\r
63 <SCRIPT type="text/javascript">
\r
66 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
71 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
78 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
79 SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
80 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
81 DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
84 <A NAME="skip-navbar_top"></A>
\r
85 <!-- ========= END OF TOP NAVBAR ========= -->
\r
88 <!-- ======== START OF CLASS DATA ======== -->
\r
91 compbio.data.msa</FONT>
\r
93 Interface MsaWS<T></H2>
\r
95 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type / web service type</DL>
\r
97 <DT><B>All Superinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DD>
\r
101 <DT><PRE>public interface <B>MsaWS<T></B><DT>extends <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DL>
\r
105 Multiple Sequence Alignment (MSA) Web Services Interface
\r
110 <DT><B>Author:</B></DT>
\r
113 Date November 2010</DD>
\r
118 <!-- =========== FIELD SUMMARY =========== -->
\r
120 <A NAME="field_summary"><!-- --></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 <B>Field Summary</B></FONT></TH>
\r
127 <A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>
\r
128 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
129 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
130 <TH ALIGN="left"><B>Fields inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></B></TH>
\r
132 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
133 <TD><CODE><A HREF="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A>, <A HREF="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>
\r
137 <!-- ========== METHOD SUMMARY =========== -->
\r
139 <A NAME="method_summary"><!-- --></A>
\r
140 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
141 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
142 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
\r
143 <B>Method Summary</B></FONT></TH>
\r
145 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
146 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
147 <CODE> java.lang.String</CODE></FONT></TD>
\r
148 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
\r
151 Align a list of sequences with default settings.</TD>
\r
153 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
154 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
155 <CODE> java.lang.String</CODE></FONT></TD>
\r
156 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
157 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)</CODE>
\r
160 Align a list of sequences with options.</TD>
\r
162 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
164 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
\r
165 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
\r
168 Return the result of the job.</TD>
\r
170 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
171 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
\r
172 <CODE> java.lang.String</CODE></FONT></TD>
\r
173 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
174 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)</CODE>
\r
177 Align a list of sequences with preset.</TD>
\r
180 <A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>
\r
181 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
182 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
183 <TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TH>
\r
185 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
186 <TD><CODE><A HREF="../../../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)">cancelJob</A>, <A HREF="../../../compbio/data/msa/JManagement.html#getJobStatus(java.lang.String)">getJobStatus</A>, <A HREF="../../../compbio/data/msa/JManagement.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE></TD>
\r
189 <A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>
\r
190 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
191 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
\r
192 <TH ALIGN="left"><B>Methods inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></B></TH>
\r
194 <TR BGCOLOR="white" CLASS="TableRowColor">
\r
195 <TD><CODE><A HREF="../../../compbio/data/msa/Metadata.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getPresets()">getPresets</A>, <A HREF="../../../compbio/data/msa/Metadata.html#getRunnerOptions()">getRunnerOptions</A></CODE></TD>
\r
201 <!-- ============ METHOD DETAIL ========== -->
\r
203 <A NAME="method_detail"><!-- --></A>
\r
204 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
\r
205 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
\r
206 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
\r
207 <B>Method Detail</B></FONT></TH>
\r
211 <A NAME="align(java.util.List)"><!-- --></A><H3>
\r
214 java.lang.String <B>align</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)
\r
215 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
\r
216 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
\r
217 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
\r
219 <DD>Align a list of sequences with default settings.
221 Any dataset containing a greater number of sequences or when the average
222 length of the sequences are greater then defined in the default Limit,
223 will not be accepted for an alignment operation and
224 JobSubmissionException will be thrown.
\r
230 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
231 any sequence validity checks. Nor does it checks whether the
232 sequences names are unique. It is responsibility of the caller
233 to make sure of this
\r
234 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
\r
236 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
237 following reasons: 1) The number of sequences in the
238 submission or their average length is greater then defined by
239 the default Limit. 2) Any problems on the server side e.g. it
240 is misconfigured or malfunction, is reported via this
241 exception. In the first case the information on the limit
242 could be obtained from an exception.
\r
243 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of FASTA sequences is null or empty
\r
244 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
245 given web service, e.g. JABAWS is deployed on Windows and
246 Mafft service is called
\r
247 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or their average
248 length exceeds what is defined by the limit</DL>
\r
253 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
\r
256 java.lang.String <B>customAlign</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
257 java.util.List<<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>>> options)
\r
258 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
\r
259 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
\r
260 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
\r
261 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
\r
263 <DD>Align a list of sequences with options.
\r
269 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
270 any sequence validity checks. Nor does it checks whether the
271 sequences names are unique. It is responsibility of the caller
272 to validate this information<DD><CODE>options</CODE> - A list of Options
\r
273 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
\r
275 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
276 following reasons: 1) The number of sequences in the
277 submission or their average length is greater then defined by
278 the default Limit. 2) Any problems on the server side e.g. it
279 is misconfigured or malfunction, is reported via this
280 exception. In the first case the information on the limit
281 could be obtained from an exception.
\r
282 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
283 supported, 2) The value of the option is defined outside the
284 boundaries. In both cases exception object contain the
285 information on the violating Option.
\r
286 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of FASTA sequence is null or empty
\r
287 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
288 given web service, e.g. JABAWS is deployed on Windows and
289 Mafft service is called
\r
290 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or their average
291 length exceeds what is defined by the limit<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Default Limit is used to decide whether the calculation will be
292 permitted or denied</CODE></A></DL>
\r
297 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
\r
300 java.lang.String <B>presetAlign</B>(java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
\r
301 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> preset)
\r
302 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
\r
303 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
\r
304 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
\r
305 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
\r
307 <DD>Align a list of sequences with preset.
309 Limit for a presetName is used whether the calculation will be permitted
310 or denied. If no Limit was defined for a presetName, than default limit
317 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
318 any sequence validity checks. Nor does it checks whether the
319 sequences names are unique. It is responsibility of the caller
320 to validate this information<DD><CODE>preset</CODE> - A list of Options
\r
321 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
\r
323 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - is thrown when the job could not be submitted due to the
324 following reasons: 1) The number of sequences in the
325 submission or their average length is greater then defined by
326 the default Limit. 2) Any problems on the server side e.g. it
327 is misconfigured or malfunction, is reported via this
328 exception. In the first case the information on the limit
329 could be obtained from an exception.
\r
330 <DD><CODE><A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is throws when 1) One of the Options provided is not
331 supported, 2) The value of the option is defined outside the
332 boundaries. In both cases exception object contain the
333 information on the violating Option.
\r
334 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of FASTA sequence is null or empty
\r
335 <DD><CODE><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></CODE> - thrown if server OS does not support native executables for a
336 given web service, e.g. JABAWS is deployed on Windows and
337 Mafft service is called
\r
338 <DD><CODE><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE> - is throw if the input sequences number or average length
339 exceeds what is defined by the limit<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></DL>
\r
344 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
\r
347 <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String jobId)
\r
348 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
\r
350 <DD>Return the result of the job. This method waits for the job
351 <code>jobId</code> to complete before return.
\r
357 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
\r
358 <DT><B>Returns:</B><DD>Alignment
\r
360 <DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE> - this exception is throw if the job execution was not
361 successful or the result of the execution could not be found.
362 (e.g. removed). Exception could also be thrown due to the
363 lower level problems on the server i.e. IOException,
364 FileNotFoundException problems as well as
365 UnknownFileFormatException.
\r
366 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or is not recognised e.g. in invalid
370 <!-- ========= END OF CLASS DATA ========= -->
\r
374 <!-- ======= START OF BOTTOM NAVBAR ====== -->
\r
375 <A NAME="navbar_bottom"><!-- --></A>
\r
376 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>
\r
377 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">
\r
379 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
\r
380 <A NAME="navbar_bottom_firstrow"><!-- --></A>
\r
381 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">
\r
382 <TR ALIGN="center" VALIGN="top">
\r
383 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
\r
384 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
\r
385 <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
\r
386 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>
\r
387 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
\r
388 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
\r
389 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
\r
390 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
\r
394 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
\r
400 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
401 <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A>
\r
402 <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>
\r
403 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
\r
404 <A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A>
\r
405 <A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A>
\r
406 <SCRIPT type="text/javascript">
\r
409 document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');
\r
414 <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>
\r
421 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
422 SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
\r
423 <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
\r
424 DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
\r
427 <A NAME="skip-navbar_bottom"></A>
\r
428 <!-- ======== END OF BOTTOM NAVBAR ======= -->
\r