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18 parent.document.title="MsaWS";
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79 SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
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91 compbio.data.msa</FONT>
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93 Interface MsaWS<T></H2>
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95 <DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type / web service type</DL>
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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>
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100 <DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../compbio/ws/server/ClustalOWS.html" title="class in compbio.ws.server">ClustalOWS</A>, <A HREF="../../../compbio/ws/server/ClustalWS.html" title="class in compbio.ws.server">ClustalWS</A>, <A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server">MafftWS</A>, <A HREF="../../../compbio/ws/server/MuscleWS.html" title="class in compbio.ws.server">MuscleWS</A>, <A HREF="../../../compbio/ws/server/ProbconsWS.html" title="class in compbio.ws.server">ProbconsWS</A>, <A HREF="../../../compbio/ws/server/TcoffeeWS.html" title="class in compbio.ws.server">TcoffeeWS</A></DD>
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104 <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>
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108 Multiple Sequence Alignment (MSA) Web Services Interface
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113 <DT><B>Author:</B></DT>
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116 Date November 2010</DD>
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121 <!-- =========== FIELD SUMMARY =========== -->
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123 <A NAME="field_summary"><!-- --></A>
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124 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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127 <B>Field Summary</B></FONT></TH>
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130 <A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>
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131 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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132 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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133 <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>
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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <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>
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140 <!-- ========== METHOD SUMMARY =========== -->
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142 <A NAME="method_summary"><!-- --></A>
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143 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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144 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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145 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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146 <B>Method Summary</B></FONT></TH>
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148 <TR BGCOLOR="white" CLASS="TableRowColor">
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149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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150 <CODE> <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>
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151 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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154 Align a list of sequences with default settings.</TD>
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156 <TR BGCOLOR="white" CLASS="TableRowColor">
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157 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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158 <CODE> <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>
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159 <TD><CODE><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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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160 <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><<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>
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163 Align a list of sequences with options.</TD>
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165 <TR BGCOLOR="white" CLASS="TableRowColor">
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166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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167 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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168 <TD><CODE><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> jobId)</CODE>
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171 Return the result of the job.</TD>
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173 <TR BGCOLOR="white" CLASS="TableRowColor">
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174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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175 <CODE> <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>
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176 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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177 <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>
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180 Align a list of sequences with preset.</TD>
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183 <A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>
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184 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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185 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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186 <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>
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188 <TR BGCOLOR="white" CLASS="TableRowColor">
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189 <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>
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192 <A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>
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193 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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194 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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195 <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>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <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>
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204 <!-- ============ METHOD DETAIL ========== -->
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206 <A NAME="method_detail"><!-- --></A>
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207 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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209 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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210 <B>Method Detail</B></FONT></TH>
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214 <A NAME="align(java.util.List)"><!-- --></A><H3>
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217 <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> <B>align</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)
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218 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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219 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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220 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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222 <DD>Align a list of sequences with default settings.
224 Any dataset containing a greater number of sequences or when the average
225 length of the sequences are greater then defined in the default Limit,
226 will not be accepted for an alignment operation and
227 JobSubmissionException will be thrown.
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233 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
234 any sequence validity checks. Nor does it checks whether the
235 sequences names are unique. It is responsibility of the caller
236 to make sure of this
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237 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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239 <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
240 following reasons: 1) The number of sequences in the
241 submission or their average length is greater then defined by
242 the default Limit. 2) Any problems on the server side e.g. it
243 is misconfigured or malfunction, is reported via this
244 exception. In the first case the information on the limit
245 could be obtained from an exception.
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246 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of FASTA sequences is null or empty
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247 <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
248 given web service, e.g. JABAWS is deployed on Windows and
249 Mafft service is called
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250 <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
251 length exceeds what is defined by the limit</DL>
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256 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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259 <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> <B>customAlign</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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260 <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><<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)
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261 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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262 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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263 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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264 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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266 <DD>Align a list of sequences with options.
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272 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
273 any sequence validity checks. Nor does it checks whether the
274 sequences names are unique. It is responsibility of the caller
275 to validate this information<DD><CODE>options</CODE> - A list of Options
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276 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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278 <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
279 following reasons: 1) The number of sequences in the
280 submission or their average length is greater then defined by
281 the default Limit. 2) Any problems on the server side e.g. it
282 is misconfigured or malfunction, is reported via this
283 exception. In the first case the information on the limit
284 could be obtained from an exception.
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285 <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
286 supported, 2) The value of the option is defined outside the
287 boundaries. In both cases exception object contain the
288 information on the violating Option.
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289 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of FASTA sequence is null or empty
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290 <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
291 given web service, e.g. JABAWS is deployed on Windows and
292 Mafft service is called
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293 <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
294 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
295 permitted or denied</CODE></A></DL>
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300 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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303 <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> <B>presetAlign</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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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304 <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)
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305 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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306 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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307 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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308 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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310 <DD>Align a list of sequences with preset.
312 Limit for a presetName is used whether the calculation will be permitted
313 or denied. If no Limit was defined for a presetName, than default limit
320 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
321 any sequence validity checks. Nor does it checks whether the
322 sequences names are unique. It is responsibility of the caller
323 to validate this information<DD><CODE>preset</CODE> - A list of Options
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324 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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326 <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
327 following reasons: 1) The number of sequences in the
328 submission or their average length is greater then defined by
329 the default Limit. 2) Any problems on the server side e.g. it
330 is misconfigured or malfunction, is reported via this
331 exception. In the first case the information on the limit
332 could be obtained from an exception.
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333 <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
334 supported, 2) The value of the option is defined outside the
335 boundaries. In both cases exception object contain the
336 information on the violating Option.
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337 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if input list of FASTA sequence is null or empty
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338 <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
339 given web service, e.g. JABAWS is deployed on Windows and
340 Mafft service is called
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341 <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
342 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>
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347 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
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350 <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</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> jobId)
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351 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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353 <DD>Return the result of the job. This method waits for the job
354 <code>jobId</code> to complete before return.
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360 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
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361 <DT><B>Returns:</B><DD>Alignment
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363 <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
364 successful or the result of the execution could not be found.
365 (e.g. removed). Exception could also be thrown due to the
366 lower level problems on the server i.e. IOException,
367 FileNotFoundException problems as well as
368 UnknownFileFormatException.
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369 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/security/InvalidParameterException.html?is-external=true" title="class or interface in java.security">InvalidParameterException</A></CODE> - thrown if jobId is empty or is not recognised e.g. in invalid
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