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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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98 <DT><PRE>public interface <B>MsaWS<T></B></DL>
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102 Multiple Sequence Alignment (MSA) Web Services Interface
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107 <DT><B>Version:</B></DT>
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108 <DD>1.0 September 2009</DD>
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109 <DT><B>Author:</B></DT>
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116 <!-- ========== METHOD SUMMARY =========== -->
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118 <A NAME="method_summary"><!-- --></A>
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119 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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120 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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121 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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122 <B>Method Summary</B></FONT></TH>
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124 <TR BGCOLOR="white" CLASS="TableRowColor">
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125 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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126 <CODE> java.lang.String</CODE></FONT></TD>
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127 <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>
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130 Align a list of sequences with default settings.</TD>
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132 <TR BGCOLOR="white" CLASS="TableRowColor">
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133 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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134 <CODE> boolean</CODE></FONT></TD>
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135 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String jobId)</CODE>
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138 Stop running the job <code>jobId</code> but leave its output untouched</TD>
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140 <TR BGCOLOR="white" CLASS="TableRowColor">
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141 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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142 <CODE> java.lang.String</CODE></FONT></TD>
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143 <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,
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144 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>
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147 Align a list of sequences with options.</TD>
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149 <TR BGCOLOR="white" CLASS="TableRowColor">
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150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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151 <CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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152 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String jobId)</CODE>
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155 Return the status of the job.</TD>
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157 <TR BGCOLOR="white" CLASS="TableRowColor">
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158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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159 <CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>></CODE></FONT></TD>
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160 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>
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163 Get a Limit for a preset.</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/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>></CODE></FONT></TD>
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168 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></B>()</CODE>
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171 List Limits supported by a web service.</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="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>></CODE></FONT></TD>
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176 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></B>()</CODE>
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179 Get presets supported by a web service</TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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183 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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184 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>
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187 Return the result of the job.</TD>
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189 <TR BGCOLOR="white" CLASS="TableRowColor">
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190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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191 <CODE> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>></CODE></FONT></TD>
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192 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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195 Get options supported by a web service</TD>
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197 <TR BGCOLOR="white" CLASS="TableRowColor">
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198 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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199 <CODE> java.lang.String</CODE></FONT></TD>
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200 <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,
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201 <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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204 Align a list of sequences with preset.</TD>
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206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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208 <CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>
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209 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String jobId,
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210 long position)</CODE>
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213 Reads 1kb chunk from the statistics file which is specific to a given web
214 service from the <code>position</code>.</TD>
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220 <!-- ============ METHOD DETAIL ========== -->
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222 <A NAME="method_detail"><!-- --></A>
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223 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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224 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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225 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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226 <B>Method Detail</B></FONT></TH>
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230 <A NAME="align(java.util.List)"><!-- --></A><H3>
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233 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)
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234 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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235 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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236 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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238 <DD>Align a list of sequences with default settings.
240 Any dataset containing a greater number of sequences or when the average
241 length of the sequences are greater then defined in the default Limit,
242 will not be accepted for an alignment operation and
243 JobSubmissionException will be thrown.
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246 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
247 any sequence validity checks. Nor does it checks whether the
248 sequences names are unique. It is responsibility of the caller
249 to make sure of this
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250 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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252 <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
253 following reasons: 1) The number of sequences in the
254 submission or their average length is greater then defined by
255 the default Limit. 2) Any problems on the server side e.g. it
256 is misconfigured or malfunction, is reported via this
257 exception. In the first case the information on the limit
258 could be obtained from an exception.
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259 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of FASTA sequences is null or empty
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260 <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
261 given web service, e.g. JABAWS is deployed on Windows and
262 Mafft service is called
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263 <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
264 length exceeds what is defined by the limit</DL>
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269 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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272 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,
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273 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)
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274 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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275 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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276 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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277 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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279 <DD>Align a list of sequences with options.
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282 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
283 any sequence validity checks. Nor does it checks whether the
284 sequences names are unique. It is responsibility of the caller
285 to validate this information<DD><CODE>options</CODE> - A list of Options
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286 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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288 <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
289 following reasons: 1) The number of sequences in the
290 submission or their average length is greater then defined by
291 the default Limit. 2) Any problems on the server side e.g. it
292 is misconfigured or malfunction, is reported via this
293 exception. In the first case the information on the limit
294 could be obtained from an exception.
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295 <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
296 supported, 2) The value of the option is defined outside the
297 boundaries. In both cases exception object contain the
298 information on the violating Option.
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299 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of FASTA sequence is null or empty
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300 <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
301 given web service, e.g. JABAWS is deployed on Windows and
302 Mafft service is called
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303 <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
304 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
305 permitted or denied</CODE></A></DL>
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310 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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313 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,
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314 <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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315 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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316 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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317 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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318 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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320 <DD>Align a list of sequences with preset.
322 Limit for a presetName is used whether the calculation will be permitted
323 or denied. If no Limit was defined for a presetName, than default limit
327 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
328 any sequence validity checks. Nor does it checks whether the
329 sequences names are unique. It is responsibility of the caller
330 to validate this information<DD><CODE>preset</CODE> - A list of Options
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331 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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333 <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
334 following reasons: 1) The number of sequences in the
335 submission or their average length is greater then defined by
336 the default Limit. 2) Any problems on the server side e.g. it
337 is misconfigured or malfunction, is reported via this
338 exception. In the first case the information on the limit
339 could be obtained from an exception.
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340 <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
341 supported, 2) The value of the option is defined outside the
342 boundaries. In both cases exception object contain the
343 information on the violating Option.
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344 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of FASTA sequence is null or empty
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345 <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
346 given web service, e.g. JABAWS is deployed on Windows and
347 Mafft service is called
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348 <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
349 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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354 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
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357 <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String jobId)
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358 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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360 <DD>Return the result of the job. This method waits for the job
361 <code>jobId</code> to complete before return.
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364 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
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365 <DT><B>Returns:</B><DD>Alignment
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367 <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
368 successful or the result of the execution could not be found.
369 (e.g. removed). Exception could also be thrown due to the
370 lower level problems on the server i.e. IOException,
371 FileNotFoundException problems as well as
372 UnknownFileFormatException.
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373 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or is not recognised e.g. in invalid
379 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
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382 boolean <B>cancelJob</B>(java.lang.String jobId)</PRE>
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384 <DD>Stop running the job <code>jobId</code> but leave its output untouched
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388 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise
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390 <DD><CODE>java.security.InvalidParameterException</CODE> - is thrown if jobId is empty or cannot be recognised e.g. in
391 invalid format</DL>
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396 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
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399 <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String jobId)</PRE>
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401 <DD>Return the status of the job.
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404 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier
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405 <DT><B>Returns:</B><DD>JobStatus - status of the job
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407 <DD><CODE>java.security.InvalidParameterException</CODE> - is thrown if jobId is empty or cannot be recognised e.g. in
408 invalid format<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></DL>
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413 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>
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414 pullExecStatistics</H3>
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416 <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String jobId,
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417 long position)</PRE>
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419 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
420 service from the <code>position</code>. If in time of a request less then
421 1kb data is available from the position to the end of the file, then it
422 returns all the data available from the position to the end of the file.
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425 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read
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426 <DT><B>Returns:</B><DD>ChunkHolder - which contains a chunk of data and a next position
427 within the file from which no data has been read
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429 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
430 invalid format and also if the position value is negative<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><CODE>ChunkHolder</CODE></A></DL>
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435 <A NAME="getRunnerOptions()"><!-- --></A><H3>
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436 getRunnerOptions</H3>
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438 <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> <B>getRunnerOptions</B>()</PRE>
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440 <DD>Get options supported by a web service
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444 <DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
450 <A NAME="getPresets()"><!-- --></A><H3>
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453 <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> <B>getPresets</B>()</PRE>
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455 <DD>Get presets supported by a web service
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459 <DT><B>Returns:</B><DD>PresetManager the object contains information about presets
460 supported by a web service</DL>
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465 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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468 <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>
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470 <DD>Get a Limit for a preset.
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473 <DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
474 default preset is returned. If no limit for a particular
475 preset is defined then the default preset is returned
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476 <DT><B>Returns:</B><DD>Limit</DL>
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481 <A NAME="getLimits()"><!-- --></A><H3>
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484 <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> <B>getLimits</B>()</PRE>
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486 <DD>List Limits supported by a web service.
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490 <DT><B>Returns:</B><DD>LimitManager</DL>
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