+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
-<TITLE>\r
-ClustalWS\r
-</TITLE>\r
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-<META NAME="date" CONTENT="2010-02-17">\r
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-function windowTitle()\r
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- parent.document.title="ClustalWS";\r
- }\r
-}\r
-</SCRIPT>\r
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-</HEAD>\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/ClustalWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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- PREV CLASS \r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.server</FONT>\r
-<BR>\r
-Class ClustalWS</H2>\r
-<PRE>\r
-java.lang.Object\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.server.ClustalWS</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ClustalWS</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_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>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.html#ClustalWS()">ClustalWS</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\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/ws/server/ClustalWS.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/ws/server/ClustalWS.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/ws/server/ClustalWS.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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</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/ws/server/ClustalWS.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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.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/ws/server/ClustalWS.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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/server/ClustalWS.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/ws/server/ClustalWS.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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</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/ws/server/ClustalWS.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
- service from the position.</TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_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>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="ClustalWS()"><!-- --></A><H3>\r
-ClustalWS</H3>\r
-<PRE>\r
-public <B>ClustalWS</B>()</PRE>\r
-<DL>\r
-</DL>\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
-public 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/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with default settings.
-
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
- will not be accepted for an alignment operation and
- JobSubmissionException will be thrown.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#align(java.util.List)">align</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
- any sequence validity checks. Nor does it checks whether the
- sequences names are unique. It is responsibility of the caller
- to validate this information\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\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
- given web service, e.g. JWS2 is deployed on Windows and Mafft
- 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
- 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="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<PRE>\r
-public 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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> preset)\r
- throws <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><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with preset. @see Preset
-
- Limit for a presetName is used whether the calculation will be permitted
- or denied. If no Limit was defined for a presetName, than default limit
- is used.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
- any sequence validity checks. Nor does it checks whether the
- sequences names are unique. It is responsibility of the caller
- 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><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
- given web service, e.g. JWS2 is deployed on Windows and Mafft
- 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
- exceeds what is defined by the limit\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
- supported, 2) The value of the option is defined outside the
- boundaries. In both cases exception object contain the
- information on the violating Option.\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
-public 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/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>>> options)\r
- throws <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><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">MsaWS</A></CODE></B></DD>\r
-<DD>Align a list of sequences with options.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - List of FastaSequence objects. The programme does not perform
- any sequence validity checks. Nor does it checks whether the
- sequences names are unique. It is responsibility of the caller
- 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><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
- given web service, e.g. JWS2 is deployed on Windows and Mafft
- 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
- exceeds what is defined by the limit\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
- supported, 2) The value of the option is defined outside the
- boundaries. In both cases exception object contain the
- information on the violating Option.\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
- permitted or denied</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerOptions()"><!-- --></A><H3>\r
-getRunnerOptions</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getRunnerOptions</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">MsaWS</A></CODE></B></DD>\r
-<DD>Get options supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getRunnerOptions()">getRunnerOptions</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>RunnerConfig the list of options and parameters supported by a
- web service.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getResult(java.lang.String)"><!-- --></A><H3>\r
-getResult</H3>\r
-<PRE>\r
-public <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><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the result of the job.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getResult(java.lang.String)">getResult</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\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
- successful or the result of the execution could not be found.
- (e.g. removed). Exception could also be thrown is dues to the
- lower level problems on the server i.e. IOException,
- FileNotFoundException problems as well as
- UnknownFileFormatException.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
-getLimit</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getLimit</B>(java.lang.String presetName)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Get a Limit for a preset.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - the name of the preset. if no name is provided, then the
- default preset is returned. If no limit for a particular
- 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
-public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">MsaWS</A></CODE></B></DD>\r
-<DD>List Limits supported by a web service.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>LimitManager</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-public boolean <B>cancelJob</B>(java.lang.String jobId)</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Stop running job but leave its output untouched\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)">cancelJob</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJobStatus(java.lang.String)"><!-- --></A><H3>\r
-getJobStatus</H3>\r
-<PRE>\r
-public <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><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">MsaWS</A></CODE></B></DD>\r
-<DD>Return the status of the job. @see JobStatus\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\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</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>> <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">MsaWS</A></CODE></B></DD>\r
-<DD>Get presets supported by a web service\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#getPresets()">getPresets</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>PresetManager the object contains information about presets
- supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="pullExecStatistics(java.lang.String, long)"><!-- --></A><H3>\r
-pullExecStatistics</H3>\r
-<PRE>\r
-public <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><B>Description copied from interface: <CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">MsaWS</A></CODE></B></DD>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the position. If in time of a request less then 1kb data is
- available from the position to the end of the file, then it returns all
- the data available from the position to the end of the file.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</A></CODE> in interface <CODE><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>></CODE></DL>\r
-</DD>\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
- and a next position within the file from which no data has been
- read</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
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <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/ClustalWS.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- <A HREF="../../../compbio/ws/server/MafftWS.html" title="class in compbio.ws.server"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/server/ClustalWS.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="ClustalWS.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
- //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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