<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:43 GMT 2011 -->\r
<TITLE>\r
Uses of Package compbio.metadata\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD> </TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines. </TD>\r
+<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
-<TD>An cluster engine classes responsible for execution of Executables on the clusters. </TD>\r
+<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.engine.local"><B>compbio.engine.local</B></A></TD>\r
-<TD>An local engine classes responsible for execution of Executables on the local computer
- (the same machine as JVM running these classes). </TD>\r
+<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>\r
+<TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
+<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
+<TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
+<TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
<TD> </TD>\r
</TR>\r
<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa"><B>ChunkHolder</B></A></B>\r
\r
<BR>\r
- Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
+ Represents a chunk of a string data together with the position in a file for
+ the next read operation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa"><B>JobStatus</B></A></B>\r
<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>\r
\r
<BR>\r
- Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
+ This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.data.msa"><B>LimitsManager</B></A></B>\r
<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.data.msa.jaxws"><B>ChunkHolder</B></A></B>\r
\r
<BR>\r
- Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
+ Represents a chunk of a string data together with the position in a file for
+ the next read operation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.data.msa.jaxws"><B>JobStatus</B></A></B>\r
<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.engine"><B>ChunkHolder</B></A></B>\r
\r
<BR>\r
- Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
+ Represents a chunk of a string data together with the position in a file for
+ the next read operation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/JobExecutionException.html#compbio.engine"><B>JobExecutionException</B></A></B>\r
<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>\r
\r
<BR>\r
- Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
+ This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/Option.html#compbio.metadata"><B>Option</B></A></B>\r
<TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.metadata"><B>Parameter</B></A></B>\r
\r
<BR>\r
- A single value containing option supported by the web service e.g.</TD>\r
+ A single value containing an option supported by the web service e.g.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.metadata"><B>Preset</B></A></B>\r
Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.runner"><B>JobSubmissionException</B></A></B>\r
+\r
+<BR>\r
+ Exception for generic problems with JobSubmission it is often thrown as a
+ wrapper for the lower level exceptions like IOException or DrmaaException.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner"><B>Limit</B></A></B>\r
\r
<BR>\r
<TD><B><A HREF="../../compbio/metadata/class-use/Parameter.html#compbio.runner"><B>Parameter</B></A></B>\r
\r
<BR>\r
- A single value containing option supported by the web service e.g.</TD>\r
+ A single value containing an option supported by the web service e.g.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.runner"><B>PresetManager</B></A></B>\r
</TABLE>\r
\r
<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
+<A NAME="compbio.runner.conservation"><!-- --></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
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
+Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner.msa"><B>Limit</B></A></B>\r
-\r
-<BR>\r
- A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner.msa"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
- A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.msa"><B>ResultNotAvailableException</B></A></B>\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.conservation"><B>ResultNotAvailableException</B></A></B>\r
\r
<BR>\r
ResultNotAvailableException is thrown wherever the results of the calculation
</TABLE>\r
\r
<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
+<A NAME="compbio.runner.disorder"><!-- --></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
-Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
+Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.runner.psiblast"><B>Limit</B></A></B>\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.disorder"><B>ResultNotAvailableException</B></A></B>\r
\r
<BR>\r
- A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.</TD>\r
+ ResultNotAvailableException is thrown wherever the results of the calculation
+ cannot be obtained.</TD>\r
</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.runner.psiblast"><B>LimitsManager</B></A></B>\r
-\r
-<BR>\r
- A collection of Limits</TD>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.runner.msa"><!-- --></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
+Classes in <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A> used by <A HREF="../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.psiblast"><B>ResultNotAvailableException</B></A></B>\r
+<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.runner.msa"><B>ResultNotAvailableException</B></A></B>\r
\r
<BR>\r
ResultNotAvailableException is thrown wherever the results of the calculation
<TD><B><A HREF="../../compbio/metadata/class-use/ChunkHolder.html#compbio.ws.server"><B>ChunkHolder</B></A></B>\r
\r
<BR>\r
- Represents a chunk of string data together with the position in a file from
- where corresponding to of the data.</TD>\r
+ Represents a chunk of a string data together with the position in a file for
+ the next read operation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.ws.server"><B>JobStatus</B></A></B>\r
<TD><B><A HREF="../../compbio/metadata/class-use/LimitExceededException.html#compbio.ws.server"><B>LimitExceededException</B></A></B>\r
\r
<BR>\r
- Thrown if the task larger in size that the limit that applies to the
- calculation.</TD>\r
+ This exception is thrown if the task larger in size that the limit that
+ applies to the calculation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/LimitsManager.html#compbio.ws.server"><B>LimitsManager</B></A></B>\r
The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../compbio/metadata/class-use/UnsupportedRuntimeException.html#compbio.ws.server"><B>UnsupportedRuntimeException</B></A></B>\r
+\r
+<BR>\r
+ Indicates that the server could not execute native executables.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.ws.server"><B>WrongParameterException</B></A></B>\r
\r
<BR>\r
git://source.jalview.org / jabaws.git / blobdiff