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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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85 <!-- ========= END OF TOP NAVBAR ========= -->
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88 <!-- ======== START OF CLASS DATA ======== -->
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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 Known Implementing Classes:</B> <DD><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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101 <DT><PRE>public interface <B>MsaWS<T></B></DL>
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105 Multiple Sequence Alignment (MSA) Web Services Interface
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110 <DT><B>Author:</B></DT>
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113 Date September 2009</DD>
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119 <!-- ========== METHOD SUMMARY =========== -->
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121 <A NAME="method_summary"><!-- --></A>
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122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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125 <B>Method Summary</B></FONT></TH>
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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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129 <CODE> java.lang.String</CODE></FONT></TD>
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130 <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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133 Align a list of sequences with default settings.</TD>
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135 <TR BGCOLOR="white" CLASS="TableRowColor">
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136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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137 <CODE> boolean</CODE></FONT></TD>
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138 <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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141 Stop running job but leave its output untouched</TD>
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143 <TR BGCOLOR="white" CLASS="TableRowColor">
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144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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145 <CODE> java.lang.String</CODE></FONT></TD>
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146 <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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147 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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150 Align a list of sequences with options.</TD>
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152 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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154 <CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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155 <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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158 Return the status of the job.</TD>
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160 <TR BGCOLOR="white" CLASS="TableRowColor">
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161 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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162 <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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163 <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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166 Get a Limit for a preset.</TD>
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168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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170 <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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171 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></B>()</CODE>
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174 List Limits supported by a web service.</TD>
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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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178 <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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179 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></B>()</CODE>
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182 Get presets supported by a web service</TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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187 <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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190 Return the result of the job.</TD>
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192 <TR BGCOLOR="white" CLASS="TableRowColor">
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193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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194 <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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195 <TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>
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198 Get options supported by a web service</TD>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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202 <CODE> java.lang.String</CODE></FONT></TD>
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203 <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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204 <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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207 Align a list of sequences with preset.</TD>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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211 <CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>
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212 <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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213 long position)</CODE>
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216 Reads 1kb chunk from the statistics file which is specific to a given web
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217 service from the position.</TD>
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223 <!-- ============ METHOD DETAIL ========== -->
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225 <A NAME="method_detail"><!-- --></A>
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226 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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227 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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228 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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229 <B>Method Detail</B></FONT></TH>
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233 <A NAME="align(java.util.List)"><!-- --></A><H3>
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236 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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237 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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238 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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239 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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241 <DD>Align a list of sequences with default settings.
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243 Any dataset containing a greater number of sequences or the average
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244 length of the sequences are greater then defined in the default Limit
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245 will not be accepted for an alignment operation and
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246 JobSubmissionException will be thrown.
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249 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
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250 any sequence validity checks. Nor does it checks whether the
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251 sequences names are unique. It is responsibility of the caller
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252 to validate this information
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253 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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255 <DD><CODE>JobSubmissionException.</CODE> - This
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256 exception is thrown when the job could not be submitted due
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257 to the following reasons: 1) The number of sequences in the
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258 submission or their average length is greater then defined by
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259 the default Limit. 2) Any problems on the server side e.g. it
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260 is misconfigured or malfunction, is reported via this
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261 exception. In the first case the information on the limit
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262 could be obtained from an exception.
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263 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty
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264 <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
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265 given web service, e.g. JABAWS is deployed on Windows and Mafft
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267 <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
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268 exceeds what is defined by the limit
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269 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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274 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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277 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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278 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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279 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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280 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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281 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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282 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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284 <DD>Align a list of sequences with options.
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287 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
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288 any sequence validity checks. Nor does it checks whether the
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289 sequences names are unique. It is responsibility of the caller
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290 to validate this information<DD><CODE>options</CODE> - A list of Options
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291 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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293 <DD><CODE>JobSubmissionException.</CODE> - This
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294 exception is thrown when the job could not be submitted due
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295 to the following reasons: 1) The number of sequences in the
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296 submission or their average length is greater then defined by
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297 the default Limit. 2) Any problems on the server side e.g. it
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298 is misconfigured or malfunction, is reported via this
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299 exception. In the first case the information on the limit
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300 could be obtained from an exception.
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301 <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
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302 supported, 2) The value of the option is defined outside the
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303 boundaries. In both cases exception object contain the
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304 information on the violating Option.
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305 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty
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306 <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
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307 given web service, e.g. JABAWS is deployed on Windows and Mafft
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309 <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
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310 exceeds what is defined by the limit
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311 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE><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
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312 permitted or denied</CODE></A></DL>
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317 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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320 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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321 <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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322 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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323 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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324 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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325 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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327 <DD>Align a list of sequences with preset. @see Preset
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329 Limit for a presetName is used whether the calculation will be permitted
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330 or denied. If no Limit was defined for a presetName, than default limit
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334 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
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335 any sequence validity checks. Nor does it checks whether the
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336 sequences names are unique. It is responsibility of the caller
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337 to validate this information<DD><CODE>preset</CODE> - A list of Options
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338 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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340 <DD><CODE>JobSubmissionException.</CODE> - This
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341 exception is thrown when the job could not be submitted due
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342 to the following reasons: 1) The number of sequences in the
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343 submission or their average length is greater then defined by
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344 the default Limit. 2) Any problems on the server side e.g. it
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345 is misconfigured or malfunction, is reported via this
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346 exception. In the first case the information on the limit
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347 could be obtained from an exception.
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348 <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
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349 supported, 2) The value of the option is defined outside the
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350 boundaries. In both cases exception object contain the
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351 information on the violating Option.
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352 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty
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353 <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
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354 given web service, e.g. JABAWS is deployed on Windows and Mafft
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356 <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
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357 exceeds what is defined by the limit
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358 <DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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363 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
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366 <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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367 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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369 <DD>Return the result of the job.
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372 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
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373 <DT><B>Returns:</B><DD>Alignment
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375 <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
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376 successful or the result of the execution could not be found.
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377 (e.g. removed). Exception could also be thrown is dues to the
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378 lower level problems on the server i.e. IOException,
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379 FileNotFoundException problems as well as
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380 UnknownFileFormatException.
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381 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
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382 invalid format</DL>
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387 <A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>
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390 boolean <B>cancelJob</B>(java.lang.String jobId)</PRE>
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392 <DD>Stop running job but leave its output untouched
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396 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise
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398 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
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399 invalid format</DL>
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404 <A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>
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407 <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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409 <DD>Return the status of the job. @see JobStatus
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412 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier
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413 <DT><B>Returns:</B><DD>JobStatus - status of the job
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415 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
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416 invalid format</DL>
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421 <A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>
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422 pullExecStatistics</H3>
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424 <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String jobId,
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425 long position)</PRE>
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427 <DD>Reads 1kb chunk from the statistics file which is specific to a given web
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428 service from the position. If in time of a request less then 1kb data is
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429 available from the position to the end of the file, then it returns all
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430 the data available from the position to the end of the file.
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433 <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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434 <DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data
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435 and a next position within the file from which no data has been
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438 <DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
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439 invalid format and also if the position value is negative</DL>
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444 <A NAME="getRunnerOptions()"><!-- --></A><H3>
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445 getRunnerOptions</H3>
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447 <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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449 <DD>Get options supported by a web service
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453 <DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
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459 <A NAME="getPresets()"><!-- --></A><H3>
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462 <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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464 <DD>Get presets supported by a web service
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468 <DT><B>Returns:</B><DD>PresetManager the object contains information about presets
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469 supported by a web service</DL>
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474 <A NAME="getLimit(java.lang.String)"><!-- --></A><H3>
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477 <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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479 <DD>Get a Limit for a preset.
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482 <DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
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483 default preset is returned. If no limit for a particular
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484 preset is defined then the default preset is returned
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485 <DT><B>Returns:</B><DD>Limit</DL>
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490 <A NAME="getLimits()"><!-- --></A><H3>
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493 <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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495 <DD>List Limits supported by a web service.
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498 <DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
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499 default preset is returned. If no limit for a particular
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500 preset is defined then the default preset is returned
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501 <DT><B>Returns:</B><DD>LimitManager</DL>
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