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18 parent.document.title="MsaWS";
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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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101 <DT><PRE>public interface <B>MsaWS<T></B><DT>extends <A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A>, <A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>, <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A><T></DL>
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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 November 2010</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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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> <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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130 <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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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> <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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138 <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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139 <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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142 Align a list of sequences with options.</TD>
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144 <TR BGCOLOR="white" CLASS="TableRowColor">
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145 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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146 <CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>
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147 <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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150 Return the result of the job.</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="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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155 <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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156 <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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159 Align a list of sequences with preset.</TD>
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162 <A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></A>
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163 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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164 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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165 <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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167 <TR BGCOLOR="white" CLASS="TableRowColor">
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168 <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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171 <A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></A>
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172 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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173 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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174 <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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176 <TR BGCOLOR="white" CLASS="TableRowColor">
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177 <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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183 <!-- ============ METHOD DETAIL ========== -->
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188 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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189 <B>Method Detail</B></FONT></TH>
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193 <A NAME="align(java.util.List)"><!-- --></A><H3>
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196 <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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197 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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198 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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199 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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201 <DD>Align a list of sequences with default settings.
203 Any dataset containing a greater number of sequences or when the average
204 length of the sequences are greater then defined in the default Limit,
205 will not be accepted for an alignment operation and
206 JobSubmissionException will be thrown.
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212 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
213 any sequence validity checks. Nor does it checks whether the
214 sequences names are unique. It is responsibility of the caller
215 to make sure of this
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216 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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218 <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
219 following reasons: 1) The number of sequences in the
220 submission or their average length is greater then defined by
221 the default Limit. 2) Any problems on the server side e.g. it
222 is misconfigured or malfunction, is reported via this
223 exception. In the first case the information on the limit
224 could be obtained from an exception.
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225 <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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226 <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
227 given web service, e.g. JABAWS is deployed on Windows and
228 Mafft service is called
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229 <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
230 length exceeds what is defined by the limit</DL>
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235 <A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>
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238 <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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239 <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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240 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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241 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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242 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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243 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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245 <DD>Align a list of sequences with options.
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251 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
252 any sequence validity checks. Nor does it checks whether the
253 sequences names are unique. It is responsibility of the caller
254 to validate this information<DD><CODE>options</CODE> - A list of Options
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255 <DT><B>Returns:</B><DD>jobId - unique identifier for the job
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257 <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
258 following reasons: 1) The number of sequences in the
259 submission or their average length is greater then defined by
260 the default Limit. 2) Any problems on the server side e.g. it
261 is misconfigured or malfunction, is reported via this
262 exception. In the first case the information on the limit
263 could be obtained from an exception.
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264 <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
265 supported, 2) The value of the option is defined outside the
266 boundaries. In both cases exception object contain the
267 information on the violating Option.
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268 <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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269 <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
270 given web service, e.g. JABAWS is deployed on Windows and
271 Mafft service is called
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272 <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
273 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
274 permitted or denied</CODE></A></DL>
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279 <A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>
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282 <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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283 <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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284 throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,
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285 <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,
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286 <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,
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287 <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>
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289 <DD>Align a list of sequences with preset.
291 Limit for a presetName is used whether the calculation will be permitted
292 or denied. If no Limit was defined for a presetName, than default limit
299 <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
300 any sequence validity checks. Nor does it checks whether the
301 sequences names are unique. It is responsibility of the caller
302 to validate this information<DD><CODE>preset</CODE> - A list of Options
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303 <DT><B>Returns:</B><DD>String - jobId - unique identifier for the job
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305 <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
306 following reasons: 1) The number of sequences in the
307 submission or their average length is greater then defined by
308 the default Limit. 2) Any problems on the server side e.g. it
309 is misconfigured or malfunction, is reported via this
310 exception. In the first case the information on the limit
311 could be obtained from an exception.
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312 <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
313 supported, 2) The value of the option is defined outside the
314 boundaries. In both cases exception object contain the
315 information on the violating Option.
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316 <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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317 <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
318 given web service, e.g. JABAWS is deployed on Windows and
319 Mafft service is called
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320 <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
321 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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326 <A NAME="getResult(java.lang.String)"><!-- --></A><H3>
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329 <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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330 throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>
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332 <DD>Return the result of the job. This method waits for the job
333 <code>jobId</code> to complete before return.
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339 <DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier
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340 <DT><B>Returns:</B><DD>Alignment
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342 <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
343 successful or the result of the execution could not be found.
344 (e.g. removed). Exception could also be thrown due to the
345 lower level problems on the server i.e. IOException,
346 FileNotFoundException problems as well as
347 UnknownFileFormatException.
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348 <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
352 <!-- ========= END OF CLASS DATA ========= -->
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