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91 compbio.data.msa</FONT>
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93 Interface SequenceAnnotation<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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101 <DT><PRE>public interface <B>SequenceAnnotation<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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105 Interface for tools that results to one or more annotation to sequence(s)
107 Single, multiple sequences their groups or alignments can be annotated
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112 <DT><B>Version:</B></DT>
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113 <DD>1.0 November 2010</DD>
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114 <DT><B>Author:</B></DT>
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115 <DD>Peter Troshin</DD>
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120 <!-- =========== FIELD SUMMARY =========== -->
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122 <A NAME="field_summary"><!-- --></A>
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123 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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126 <B>Field Summary</B></FONT></TH>
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129 <A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>
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130 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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131 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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132 <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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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <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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139 <!-- ========== METHOD SUMMARY =========== -->
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142 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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144 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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145 <B>Method Summary</B></FONT></TH>
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147 <TR BGCOLOR="white" CLASS="TableRowColor">
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148 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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149 <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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150 <TD><CODE><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)">analize</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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153 Analyse the sequences.</TD>
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155 <TR BGCOLOR="white" CLASS="TableRowColor">
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156 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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157 <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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158 <TD><CODE><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><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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159 <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/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>>> options)</CODE>
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162 Analyse the sequences according to custom settings defined in options
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/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>
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168 <TD><CODE><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#getAnnotation(java.lang.String)">getAnnotation</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/SequenceAnnotation.html#presetAnalize(java.util.List, compbio.metadata.Preset)">presetAnalize</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/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> preset)</CODE>
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180 Analyse the sequences according to the preset settings.</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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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="analize(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>analize</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>Analyse the sequences. The actual analysis algorithm is defined by the
225 Any dataset containing a greater number of sequences or the average
226 length of the sequences are greater then defined in the default Limit
227 will not be accepted for an alignment operation and
228 JobSubmissionException will be thrown.
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234 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
235 any sequence validity checks. Nor does it checks whether the
236 sequences names are unique. It is responsibility of the caller
237 to validate this information
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238 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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240 <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
241 following reasons: 1) The number of sequences in the
242 submission or their average length is greater then defined by
243 the default Limit. 2) Any problems on the server side e.g. it
244 is misconfigured or malfunction, is reported via this
245 exception. In the first case the information on the limit
246 could be obtained from an exception.
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247 <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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248 <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
249 given web service, e.g. JABAWS is deployed on Windows and
250 Mafft service is called
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251 <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
252 exceeds what is defined by the limit</DL>
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257 <A NAME="customAnalize(java.util.List, java.util.List)"><!-- --></A><H3>
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260 <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>customAnalize</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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261 <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/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>>> options)
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262 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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263 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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264 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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265 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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267 <DD>Analyse the sequences according to custom settings defined in options
268 list. The actual analysis algorithm is defined by the type T. Default
269 Limit is used to decide whether the calculation will be permitted or
276 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
277 any sequence validity checks. Nor does it checks whether the
278 sequences names are unique. It is responsibility of the caller
279 to validate this information<DD><CODE>options</CODE> - A list of Options
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280 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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282 <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
283 following reasons: 1) The number of sequences in the
284 submission or their average length is greater then defined by
285 the default Limit. 2) Any problems on the server side e.g. it
286 is misconfigured or malfunction, is reported via this
287 exception. In the first case the information on the limit
288 could be obtained from an exception.
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289 <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
290 supported, 2) The value of the option is defined outside the
291 boundaries. In both cases exception object contain the
292 information on the violating Option.
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293 <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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294 <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
295 given web service, e.g. JABAWS is deployed on Windows and
296 Mafft service is called
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297 <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
298 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>Option</CODE></A></DL>
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303 <A NAME="presetAnalize(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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306 <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>presetAnalize</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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307 <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>> preset)
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308 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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309 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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310 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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311 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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313 <DD>Analyse the sequences according to the preset settings. The actual
314 analysis algorithm is defined by the type T.
316 Limit for a presetName is used whether the calculation will be permitted
317 or denied. If no Limit was defined for a presetName, than default limit
324 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
325 any sequence validity checks. Nor does it checks whether the
326 sequences names are unique. It is responsibility of the caller
327 to validate this information<DD><CODE>preset</CODE> - A list of Options
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328 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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330 <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
331 following reasons: 1) The number of sequences in the
332 submission or their average length is greater then defined by
333 the default Limit. 2) Any problems on the server side e.g. it
334 is misconfigured or malfunction, is reported via this
335 exception. In the first case the information on the limit
336 could be obtained from an exception.
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337 <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
338 supported, 2) The value of the option is defined outside the
339 boundaries. In both cases exception object contain the
340 information on the violating Option.
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341 <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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342 <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
343 given web service, e.g. JABAWS is deployed on Windows and
344 Mafft service is called
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345 <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
346 exceeds what is defined by the limit</DL>
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351 <A NAME="getAnnotation(java.lang.String)"><!-- --></A><H3>
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354 <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>getAnnotation</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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355 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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357 <DD>Return the result of the job.
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363 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
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364 <DT><B>Returns:</B><DD>the Map with the sequence names, sequence group names or the word
365 'Alignment' in case of alignments and values the represented by a
366 Set of Score objects. The alignment can be represented in as
367 little as one key->value pair in this map, the list of sequences
368 will be represented by multiple key->value mappings. If multiple
369 annotations were calculated, then they are represented as a Set
372 <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
373 successful or the result of the execution could not be found.
374 (e.g. removed). Exception could also be thrown is dues to the
375 lower level problems on the server i.e. IOException,
376 FileNotFoundException problems as well as
377 UnknownFileFormatException.
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378 <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 cannot be recognised e.g. in
379 invalid format</DL>
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