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-<B>Uses of Package<br>compbio.metadata</B></H2>\r
-</CENTER>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></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
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
-<TD>A meta-data model for multiple sequence alignment web services
- Classes in this package have no dependencies to other sources in the project. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.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/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\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 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
-\r
-<BR>\r
- The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.data.msa"><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.data.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/LimitExceededException.html#compbio.data.msa"><B>LimitExceededException</B></A></B>\r
-\r
-<BR>\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
-\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/Option.html#compbio.data.msa"><B>Option</B></A></B>\r
-\r
-<BR>\r
- Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa"><B>Preset</B></A></B>\r
-\r
-<BR>\r
- Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
- Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ResultNotAvailableException.html#compbio.data.msa"><B>ResultNotAvailableException</B></A></B>\r
-\r
-<BR>\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/RunnerConfig.html#compbio.data.msa"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\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.data.msa"><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.data.msa"><B>WrongParameterException</B></A></B>\r
-\r
-<BR>\r
- WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.msa.jaxws"><!-- --></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/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\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 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
-\r
-<BR>\r
- The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Limit.html#compbio.data.msa.jaxws"><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.data.msa.jaxws"><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/Option.html#compbio.data.msa.jaxws"><B>Option</B></A></B>\r
-\r
-<BR>\r
- Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Preset.html#compbio.data.msa.jaxws"><B>Preset</B></A></B>\r
-\r
-<BR>\r
- Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.data.msa.jaxws"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
- Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.data.msa.jaxws"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\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
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.metadata"><!-- --></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/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/Argument.html#compbio.metadata"><B>Argument</B></A></B>\r
-\r
-<BR>\r
- An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobStatus.html#compbio.metadata"><B>JobStatus</B></A></B>\r
-\r
-<BR>\r
- The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/JobSubmissionException.html#compbio.metadata"><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.metadata"><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/LimitExceededException.html#compbio.metadata"><B>LimitExceededException</B></A></B>\r
-\r
-<BR>\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
-\r
-<BR>\r
- Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\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 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
-\r
-<BR>\r
- Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/PresetManager.html#compbio.metadata"><B>PresetManager</B></A></B>\r
-\r
-<BR>\r
- Collection of presets and methods to manipulate them @see <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/RunnerConfig.html#compbio.metadata"><B>RunnerConfig</B></A></B>\r
-\r
-<BR>\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/ValueConstrain.html#compbio.metadata"><B>ValueConstrain</B></A></B>\r
-\r
-<BR>\r
- The type and the lower and upper boundaries for numerical value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/ValueConstrain.Type.html#compbio.metadata"><B>ValueConstrain.Type</B></A></B>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../compbio/metadata/class-use/WrongParameterException.html#compbio.metadata"><B>WrongParameterException</B></A></B>\r
-\r
-<BR>\r
- WrongParameterException is thrown wherever the <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><CODE>RunnerConfig</CODE></A> object
- does not match the actual runnable or then attempting to set the value of
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> to invalid value.</TD>\r
-</TR>\r
-</TABLE>\r
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