<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 03 14:32:20 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:03 BST 2011 -->\r
<TITLE>\r
MsaWS\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-02-03">\r
+<META NAME="date" CONTENT="2011-08-12">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
\r
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<TR>\r
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- NEXT CLASS</FONT></TD>\r
+ <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
<A HREF="../../../index.html?compbio/data/msa/MsaWS.html" target="_top"><B>FRAMES</B></A> \r
<A HREF="MsaWS.html" target="_top"><B>NO FRAMES</B></A> \r
<BR>\r
Interface MsaWS<T></H2>\r
<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</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
+<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>\r
</DL>\r
<HR>\r
<DL>\r
-<DT><PRE>public interface <B>MsaWS<T></B></DL>\r
+<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>\r
</PRE>\r
\r
<P>\r
<DT><B>Author:</B></DT>\r
<DD>pvtroshin
- Date September 2009</DD>\r
+ Date November 2010</DD>\r
</DL>\r
<HR>\r
\r
<P>\r
+<!-- =========== FIELD SUMMARY =========== -->\r
\r
+<A NAME="field_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>Field Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="fields_inherited_from_class_compbio.data.msa.JABAService"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Fields inherited from interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A>, <A HREF="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
<!-- ========== METHOD SUMMARY =========== -->\r
\r
<A NAME="method_summary"><!-- --></A>\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
+<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>\r
+<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>\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
+<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>\r
+<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,\r
+ <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>\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#getLimits(java.lang.String)">getLimits</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/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
+<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>\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
+<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>\r
+<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,\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
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.msa.JManagement"><!-- --></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 interface compbio.data.msa.<A HREF="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A></B></TH>\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
- service from the position.</TD>\r
+<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>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_compbio.data.msa.Metadata"><!-- --></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 interface compbio.data.msa.<A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<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>\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/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<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)\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.
- Any dataset containing a greater number of sequences or the average
- length of the sequences are greater then defined in the default Limit
+ Any dataset containing a greater number of sequences or when 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
+</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
+ to make sure of this\r
<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
<DT><B>Throws:</B>\r
-<DD><CODE>JobSubmissionException.</CODE> - This
- exception is thrown when the job could not be submitted due
- to the following reasons: 1) The number of sequences in the
+<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
+ following reasons: 1) The number of sequences in the
submission or their average length is greater then defined by
the default Limit. 2) Any problems on the server side e.g. it
is misconfigured or malfunction, is reported via this
exception. In the first case the information on the limit
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/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+<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\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. JABAWS 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 their average
+ length exceeds what is defined by the limit</DL>\r
</DD>\r
</DL>\r
<HR>\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/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
+<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,\r
+ <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)\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
+</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>JobSubmissionException.</CODE> - This
- exception is thrown when the job could not be submitted due
- to the following reasons: 1) The number of sequences in the
+<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
+ following reasons: 1) The number of sequences in the
submission or their average length is greater then defined by
the default Limit. 2) Any problems on the server side e.g. it
is misconfigured or malfunction, is reported via this
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>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\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
+<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\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. JABAWS 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 their average
+ 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
permitted or denied</CODE></A></DL>\r
</DD>\r
</DL>\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/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
+<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,\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
+<DD>Align a list of sequences with 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
+</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
+ 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
- exception is thrown when the job could not be submitted due
- to the following reasons: 1) The number of sequences in the
+<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
+ following reasons: 1) The number of sequences in the
submission or their average length is greater then defined by
the default Limit. 2) Any problems on the server side e.g. it
is misconfigured or malfunction, is reported via this
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>java.security.InvalidParameterException</CODE> - thrown if input list of fasta sequence is null or empty\r
-<DD><CODE><A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+<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\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. JABAWS 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<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></DL>\r
</DD>\r
</DL>\r
<HR>\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
+<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)\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
+<DD>Return the result of the job. This method waits for the job
+ <code>jobId</code> to complete before return.\r
<P>\r
<DD><DL>\r
+</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
+ (e.g. removed). Exception could also be thrown due to the
lower level problems on the server i.e. IOException,
FileNotFoundException problems as well as
UnknownFileFormatException.\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
- 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
- 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
- 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
- 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>Parameters:</B><DD><CODE>jobId</CODE> - - unique job identifier<DD><CODE>long</CODE> - position - 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\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.security.InvalidParameterException</CODE> - thrown if jobId is empty or cannot be recognised e.g. in
- 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
- 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
- supported by a web service</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits(java.lang.String)"><!-- --></A><H3>\r
-getLimits</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>getLimits</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
- 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><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
+ format</DL>\r
</DD>\r
</DL>\r
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+ <A HREF="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
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