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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<TITLE>\r
+MsaWS\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-02-17">\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+</TR>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.data.msa</FONT>\r
+<BR>\r
+Interface MsaWS<T></H2>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type / web service type</DL>\r
+<DL>\r
+<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>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>MsaWS<T></B></DL>\r
+</PRE>\r
+\r
+<P>\r
+Multiple Sequence Alignment (MSA) Web Services Interface\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin\r
+ \r
+ Date September 2009</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> java.lang.String</CODE></FONT></TD>\r
+<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>\r
+\r
+<BR>\r
+ Align a list of sequences with default settings.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></B>(java.lang.String jobId)</CODE>\r
+\r
+<BR>\r
+ Stop running job but leave its output untouched</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> java.lang.String</CODE></FONT></TD>\r
+<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,\r
+ 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>\r
+\r
+<BR>\r
+ Align a list of sequences with options.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></B>(java.lang.String jobId)</CODE>\r
+\r
+<BR>\r
+ Return the status of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<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>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></B>(java.lang.String presetName)</CODE>\r
+\r
+<BR>\r
+ Get a Limit for a preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<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>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+ List Limits supported by a web service.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<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>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></B>()</CODE>\r
+\r
+<BR>\r
+ Get presets supported by a web service</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></B>(java.lang.String jobId)</CODE>\r
+\r
+<BR>\r
+ Return the result of the job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<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>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+ Get options supported by a web service</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> java.lang.String</CODE></FONT></TD>\r
+<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,\r
+ <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>\r
+\r
+<BR>\r
+ Align a list of sequences with preset.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></B>(java.lang.String jobId,\r
+ long position)</CODE>\r
+\r
+<BR>\r
+ Reads 1kb chunk from the statistics file which is specific to a given web\r
+ service from the position.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="align(java.util.List)"><!-- --></A><H3>\r
+align</H3>\r
+<PRE>\r
+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)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD>Align a list of sequences with default settings.\r
+ \r
+ Any dataset containing a greater number of sequences or the average\r
+ length of the sequences are greater then defined in the default Limit\r
+ will not be accepted for an alignment operation and\r
+ JobSubmissionException will be thrown.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform\r
+ any sequence validity checks. Nor does it checks whether the\r
+ sequences names are unique. It is responsibility of the caller\r
+ to validate this information\r
+<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE>JobSubmissionException.</CODE> - This\r
+ exception is thrown when the job could not be submitted due\r
+ to the following reasons: 1) The number of sequences in the\r
+ submission or their average length is greater then defined by\r
+ the default Limit. 2) Any problems on the server side e.g. it\r
+ is misconfigured or malfunction, is reported via this\r
+ exception. In the first case the information on the limit\r
+ could be obtained from an exception.\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
+<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\r
+ given web service, e.g. JABAWS is deployed on Windows and Mafft\r
+ service is called\r
+<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\r
+ exceeds what is defined by the limit\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
+customAlign</H3>\r
+<PRE>\r
+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,\r
+ 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)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
+ <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Align a list of sequences with options.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform\r
+ any sequence validity checks. Nor does it checks whether the\r
+ sequences names are unique. It is responsibility of the caller\r
+ to validate this information<DD><CODE>options</CODE> - A list of Options\r
+<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE>JobSubmissionException.</CODE> - This\r
+ exception is thrown when the job could not be submitted due\r
+ to the following reasons: 1) The number of sequences in the\r
+ submission or their average length is greater then defined by\r
+ the default Limit. 2) Any problems on the server side e.g. it\r
+ is misconfigured or malfunction, is reported via this\r
+ exception. In the first case the information on the limit\r
+ could be obtained from an exception.\r
+<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\r
+ supported, 2) The value of the option is defined outside the\r
+ boundaries. In both cases exception object contain the\r
+ information on the violating Option.\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
+<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\r
+ given web service, e.g. JABAWS is deployed on Windows and Mafft\r
+ service is called\r
+<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\r
+ exceeds what is defined by the limit\r
+<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\r
+ permitted or denied</CODE></A></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
+presetAlign</H3>\r
+<PRE>\r
+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,\r
+ <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)\r
+ throws <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>,\r
+ <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>,\r
+ <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>,\r
+ <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Align a list of sequences with preset. @see Preset\r
+ \r
+ Limit for a presetName is used whether the calculation will be permitted\r
+ or denied. If no Limit was defined for a presetName, than default limit\r
+ is used.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform\r
+ any sequence validity checks. Nor does it checks whether the\r
+ sequences names are unique. It is responsibility of the caller\r
+ to validate this information<DD><CODE>preset</CODE> - A list of Options\r
+<DT><B>Returns:</B><DD>String - jobId - unique identifier for the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE>JobSubmissionException.</CODE> - This\r
+ exception is thrown when the job could not be submitted due\r
+ to the following reasons: 1) The number of sequences in the\r
+ submission or their average length is greater then defined by\r
+ the default Limit. 2) Any problems on the server side e.g. it\r
+ is misconfigured or malfunction, is reported via this\r
+ exception. In the first case the information on the limit\r
+ could be obtained from an exception.\r
+<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\r
+ supported, 2) The value of the option is defined outside the\r
+ boundaries. In both cases exception object contain the\r
+ information on the violating Option.\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
+<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\r
+ given web service, e.g. JABAWS is deployed on Windows and Mafft\r
+ service is called\r
+<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\r
+ exceeds what is defined by the limit\r
+<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
+getResult</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>getResult</B>(java.lang.String jobId)\r
+ throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
+<DL>\r
+<DD>Return the result of the job.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - a unique job identifier\r
+<DT><B>Returns:</B><DD>Alignment\r
+<DT><B>Throws:</B>\r
+<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\r
+ successful or the result of the execution could not be found.\r
+ (e.g. removed). Exception could also be thrown is dues to the\r
+ lower level problems on the server i.e. IOException,\r
+ FileNotFoundException problems as well as\r
+ UnknownFileFormatException.\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
+ invalid format</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
+cancelJob</H3>\r
+<PRE>\r
+boolean <B>cancelJob</B>(java.lang.String jobId)</PRE>\r
+<DL>\r
+<DD>Stop running job but leave its output untouched\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise\r
+<DT><B>Throws:</B>\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
+ invalid format</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
+getJobStatus</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>(java.lang.String jobId)</PRE>\r
+<DL>\r
+<DD>Return the status of the job. @see JobStatus\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier\r
+<DT><B>Returns:</B><DD>JobStatus - status of the job\r
+<DT><B>Throws:</B>\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
+ invalid format</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
+pullExecStatistics</H3>\r
+<PRE>\r
+<A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> <B>pullExecStatistics</B>(java.lang.String jobId,\r
+ long position)</PRE>\r
+<DL>\r
+<DD>Reads 1kb chunk from the statistics file which is specific to a given web\r
+ service from the position. If in time of a request less then 1kb data is\r
+ available from the position to the end of the file, then it returns all\r
+ the data available from the position to the end of the file.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>position</CODE> - - next position within the file to read\r
+<DT><B>Returns:</B><DD>ChunkHolder - @see ChunkHolder which contains a chuink of data\r
+ and a next position within the file from which no data has been\r
+ read\r
+<DT><B>Throws:</B>\r
+<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in\r
+ invalid format and also if the position value is negative</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
+getRunnerOptions</H3>\r
+<PRE>\r
+<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>\r
+<DL>\r
+<DD>Get options supported by a web service\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a\r
+ web service.</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPresets()"><!-- --></A><H3>\r
+getPresets</H3>\r
+<PRE>\r
+<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>\r
+<DL>\r
+<DD>Get presets supported by a web service\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>PresetManager the object contains information about presets\r
+ supported by a web service</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
+getLimit</H3>\r
+<PRE>\r
+<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>\r
+<DL>\r
+<DD>Get a Limit for a preset.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the\r
+ default preset is returned. If no limit for a particular\r
+ preset is defined then the default preset is returned\r
+<DT><B>Returns:</B><DD>Limit</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimits()"><!-- --></A><H3>\r
+getLimits</H3>\r
+<PRE>\r
+<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>\r
+<DL>\r
+<DD>List Limits supported by a web service.\r
+<P>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the\r
+ default preset is returned. If no limit for a particular\r
+ preset is defined then the default preset is returned\r
+<DT><B>Returns:</B><DD>LimitManager</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/MsaWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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