+++ /dev/null
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-<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa" target="classFrame"><I>MsaWS</I></A>\r
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-\r
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+++ /dev/null
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-\r
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-\r
-\r
-</HEAD>\r
-\r
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-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
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-<A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<BR>\r
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-<BR>\r
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-<BR>\r
-<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
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-<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
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-<A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
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-<A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
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-<BR>\r
-<A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
-<BR>\r
-<A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
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-<A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
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-<BR>\r
-<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<BR>\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-MsaWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="MsaWS";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/MsaWS.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
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-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="MsaWS.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- 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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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= 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
-<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>Version:</B></DT>\r
- <DD>1.0 September 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</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> <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>(<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
- Stop running the job <code>jobId</code> 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> <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>(<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 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>(<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> 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>(<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> <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
-<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>(<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
- long position)</CODE>\r
-\r
-<BR>\r
- Reads 1kb chunk from the statistics file which is specific to a given web
- service from the <code>position</code>.</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
-<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 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
-<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 make sure of this\r
-<DT><B>Returns:</B><DD>jobId - unique identifier for the job\r
-<DT><B>Throws:</B>\r
-<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><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
-\r
-<A NAME="customAlign(java.util.List, java.util.List)"><!-- --></A><H3>\r
-customAlign</H3>\r
-<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
-<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/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><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="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
-<HR>\r
-\r
-<A NAME="presetAlign(java.util.List, compbio.metadata.Preset)"><!-- --></A><H3>\r
-presetAlign</H3>\r
-<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.
-
- 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>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/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><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="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
-\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>(<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. This method waits for the job
- <code>jobId</code> to complete before return.\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
- successful or the result of the execution could not be found.
- (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><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
-<HR>\r
-\r
-<A NAME="cancelJob(java.lang.String)"><!-- --></A><H3>\r
-cancelJob</H3>\r
-<PRE>\r
-boolean <B>cancelJob</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)</PRE>\r
-<DL>\r
-<DD>Stop running the job <code>jobId</code> 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><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> - is 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>(<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)</PRE>\r
-<DL>\r
-<DD>Return the status of the job.\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><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> - is thrown if jobId is empty or cannot be recognised e.g. in
- invalid format<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><CODE>JobStatus</CODE></A></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>(<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
- long position)</PRE>\r
-<DL>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the <code>position</code>. 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>position</CODE> - - next position within the file to read\r
-<DT><B>Returns:</B><DD>ChunkHolder - which contains a chunk of data and a next position
- within the file from which no data has been read\r
-<DT><B>Throws:</B>\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 cannot be recognised e.g. in
- invalid format and also if the position value is negative<DT><B>See Also:</B><DD><A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><CODE>ChunkHolder</CODE></A></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="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>(<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> 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>\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
-\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
-<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/MsaWS.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- NEXT CLASS</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
- <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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- 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
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.data.msa.MsaWS\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Interface compbio.data.msa.MsaWS";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </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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- </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 \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../../index.html?compbio/data/msa/\class-useMsaWS.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="MsaWS.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Interface<br>compbio.data.msa.MsaWS</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></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
-Uses of <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Jws2Client.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</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> host,\r
- <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
-\r
-<BR>\r
- Connects to a web service by the host and the service name</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../../index.html?compbio/data/msa/\class-useMsaWS.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="MsaWS.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-compbio.data.msa\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../../compbio/data/msa/package-summary.html" target="classFrame">compbio.data.msa</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Interfaces</FONT> \r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="MsaWS.html" title="interface in compbio.data.msa" target="classFrame"><I>MsaWS</I></A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-compbio.data.msa\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="compbio.data.msa";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV PACKAGE \r
- <A HREF="../../../compbio/data/sequence/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
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- <A HREF="../../../index.html?compbio/data/msa/package-summary.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="package-summary.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
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.data.msa\r
-</H2>\r
-Web Service interfaces for JAva Bioinformatics Analysis Web Services.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
- <A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\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>Interface Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS<T></A></B></TD>\r
-<TD>Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.data.msa Description\r
-</H2>\r
-\r
-<P>\r
-Web Service interfaces for JAva Bioinformatics Analysis Web Services.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 April 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>Peter Troshin</DD>\r
-</DL>\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="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV PACKAGE \r
- <A HREF="../../../compbio/data/sequence/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/msa/package-summary.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="package-summary.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-compbio.data.msa Class Hierarchy\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="compbio.data.msa Class Hierarchy";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- <A HREF="../../../compbio/data/sequence/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/msa/package-tree.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="package-tree.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-Hierarchy For Package compbio.data.msa\r
-</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../../overview-tree.html">All Packages</A></DL>\r
-<HR>\r
-<H2>\r
-Interface Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">compbio.data.msa.<A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T></UL>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </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
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- <A HREF="../../../compbio/data/sequence/package-tree.html"><B>NEXT</B></A></FONT></TD>\r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-</NOSCRIPT>\r
-\r
-\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-Packages that use <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></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/data/msa/package-summary.html">compbio.data.msa</A> used by <A HREF="../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/msa/class-use/MsaWS.html#compbio.ws.client"><B>MsaWS</B></A></B>\r
-\r
-<BR>\r
- Multiple Sequence Alignment (MSA) Web Services Interface</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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- PREV \r
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- <A HREF="package-use.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
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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
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-<TITLE>\r
-Alignment\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
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-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Alignment";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/Alignment.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <SCRIPT type="text/javascript">\r
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-</NOSCRIPT>\r
-\r
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-<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
-</TR>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class Alignment</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Alignment</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public final class <B>Alignment</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Multiple sequence alignment.
-
- Does not give any guarantees on the content of individual FastaSequece
- records. It does not guarantee neither the uniqueness of the names of
- sequences nor it guarantees the uniqueness of the sequences.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 September 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><CODE>FastaSequence</CODE></A>, \r
-<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><CODE>AlignmentMetadata</CODE></A></DL>\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/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</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/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</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/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- Please note that this implementation does not take the order of sequences
- into account!</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/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSize()">getSize</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/Alignment.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
-Alignment</H3>\r
-<PRE>\r
-public <B>Alignment</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/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>program</CODE> - <DD><CODE>gapchar</CODE> - </DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>\r
-Alignment</H3>\r
-<PRE>\r
-public <B>Alignment</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/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequences</CODE> - <DD><CODE>metadata</CODE> - </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="getSequences()"><!-- --></A><H3>\r
-getSequences</H3>\r
-<PRE>\r
-public <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>> <B>getSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of FastaSequence records</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSize()"><!-- --></A><H3>\r
-getSize</H3>\r
-<PRE>\r
-public int <B>getSize</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>a number of sequence in the alignment</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMetadata()"><!-- --></A><H3>\r
-getMetadata</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> <B>getMetadata</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>AlignmentMetadata object</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD>Please note that this implementation does not take the order of sequences
- into account!\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</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/Alignment.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/sequence/Alignment.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Alignment.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-AlignmentMetadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="AlignmentMetadata";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/AlignmentMetadata.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/sequence/AlignmentMetadata.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="AlignmentMetadata.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class AlignmentMetadata</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.AlignmentMetadata</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public class <B>AlignmentMetadata</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Alignment metadata e.g. method/program being used to generate the alignment
- and its parameters\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 September 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\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/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> char</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#getGapchar()">getGapchar</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="AlignmentMetadata(compbio.data.sequence.Program, char)"><!-- --></A><H3>\r
-AlignmentMetadata</H3>\r
-<PRE>\r
-public <B>AlignmentMetadata</B>(<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</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="getProgram()"><!-- --></A><H3>\r
-getProgram</H3>\r
-<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>getProgram</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getGapchar()"><!-- --></A><H3>\r
-getGapchar</H3>\r
-<PRE>\r
-public char <B>getGapchar</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</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/AlignmentMetadata.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/sequence/AlignmentMetadata.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="AlignmentMetadata.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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-compbio.data.sequence</FONT>\r
-<BR>\r
-Class ClustalAlignmentUtil</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.ClustalAlignmentUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>ClustalAlignmentUtil</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Tools to read and write clustal formated files\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 September 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>Petr Troshin based on jimp class</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
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static char</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></B></CODE>\r
-\r
-<BR>\r
- Dash char to be used as gap char in the alignments</TD>\r
-</TR>\r
-</TABLE>\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/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()">ClustalAlignmentUtil</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
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-<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>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)">isValidClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</CODE>\r
-\r
-<BR>\r
- Please note this method closes the input stream provided as a parameter</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)</CODE>\r
-\r
-<BR>\r
- Read Clustal formatted alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outStream,\r
- <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)</CODE>\r
-\r
-<BR>\r
- Write Clustal formatted alignment Limitations: does not record the
- consensus.</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_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>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="gapchar"><!-- --></A><H3>\r
-gapchar</H3>\r
-<PRE>\r
-public static final char <B>gapchar</B></PRE>\r
-<DL>\r
-<DD>Dash char to be used as gap char in the alignments\r
-<P>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.gapchar">Constant Field Values</A></DL>\r
-</DL>\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="ClustalAlignmentUtil()"><!-- --></A><H3>\r
-ClustalAlignmentUtil</H3>\r
-<PRE>\r
-public <B>ClustalAlignmentUtil</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="readClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
-readClustalFile</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
- <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
-<DL>\r
-<DD>Read Clustal formatted alignment. Limitations: Does not read consensus
-
- Sequence names as well as the sequences are not guaranteed to be unique!\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE>{@link</CODE> - IOException}\r
-<DD><CODE>{@link</CODE> - UnknownFileFormatException}\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
-<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isValidClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
-isValidClustalFile</H3>\r
-<PRE>\r
-public static boolean <B>isValidClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> input)</PRE>\r
-<DL>\r
-<DD>Please note this method closes the input stream provided as a parameter\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
-<DT><B>Returns:</B><DD>true if the file is recognised as Clustal formatted alignment,
- false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
-writeClustalAlignment</H3>\r
-<PRE>\r
-public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outStream,\r
- <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD>Write Clustal formatted alignment Limitations: does not record the
- consensus. Potential bug - records 60 chars length alignment where
- Clustal would have recorded 50 chars.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readClustalFile(java.io.File)"><!-- --></A><H3>\r
-readClustalFile</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)\r
- throws <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-FastaSequence\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
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-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="FastaSequence";\r
- }\r
-}\r
-</SCRIPT>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\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.data.sequence</FONT>\r
-<BR>\r
-Class FastaSequence</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaSequence</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public class <B>FastaSequence</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-A FASTA formatted sequence. Please note that this class does not make any
- assumptions as to what sequence it stores e.g. it could be nucleotide,
- protein or even gapped alignment sequence! The only guarantee it makes is
- that the sequence does not contain white space characters e.g. spaces, new
- lines etc\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 September 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\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/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</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> id,\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> sequence)</CODE>\r
-\r
-<BR>\r
- Upon construction the any whitespace characters are removed from the
- sequence</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>static int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</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> theString,\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> theRegExp)</CODE>\r
-\r
-<BR>\r
- </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/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int width)</CODE>\r
-\r
-<BR>\r
- Format sequence per width letter in one string.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>\r
-\r
-<BR>\r
- Gets the value of id</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>\r
-\r
-<BR>\r
- Gets the value of sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- Same as oneLineFasta</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-FastaSequence</H3>\r
-<PRE>\r
-public <B>FastaSequence</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> id,\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> sequence)</PRE>\r
-<DL>\r
-<DD>Upon construction the any whitespace characters are removed from the
- sequence\r
-<P>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </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="getId()"><!-- --></A><H3>\r
-getId</H3>\r
-<PRE>\r
-public <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>getId</B>()</PRE>\r
-<DL>\r
-<DD>Gets the value of id\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the value of id</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequence()"><!-- --></A><H3>\r
-getSequence</H3>\r
-<PRE>\r
-public <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>getSequence</B>()</PRE>\r
-<DL>\r
-<DD>Gets the value of sequence\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the value of sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-countMatchesInSequence</H3>\r
-<PRE>\r
-public static int <B>countMatchesInSequence</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> theString,\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> theRegExp)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFormattedFasta()"><!-- --></A><H3>\r
-getFormattedFasta</H3>\r
-<PRE>\r
-public <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>getFormattedFasta</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOnelineFasta()"><!-- --></A><H3>\r
-getOnelineFasta</H3>\r
-<PRE>\r
-public <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>getOnelineFasta</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
- length is</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFormatedSequence(int)"><!-- --></A><H3>\r
-getFormatedSequence</H3>\r
-<PRE>\r
-public <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>getFormatedSequence</B>(int width)</PRE>\r
-<DL>\r
-<DD>Format sequence per width letter in one string. Without spaces.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLength()"><!-- --></A><H3>\r
-getLength</H3>\r
-<PRE>\r
-public int <B>getLength</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>sequence length</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD>Same as oneLineFasta\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</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/FastaSequence.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
-\r
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- }\r
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-compbio.data.sequence</FONT>\r
-<BR>\r
-Enum Program</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Program</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>Program</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>></DL>\r
-</PRE>\r
-\r
-<P>\r
-The list of programmes that can produce alignments\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_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>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#CLUSTAL">CLUSTAL</A></B></CODE>\r
-\r
-<BR>\r
- ClustalW</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MAFFT">MAFFT</A></B></CODE>\r
-\r
-<BR>\r
- Mafft</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#MUSCLE">MUSCLE</A></B></CODE>\r
-\r
-<BR>\r
- Muscle</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Probcons">Probcons</A></B></CODE>\r
-\r
-<BR>\r
- Probcons</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#Tcoffee">Tcoffee</A></B></CODE>\r
-\r
-<BR>\r
- Tcoffee</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>static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_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>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="CLUSTAL"><!-- --></A><H3>\r
-CLUSTAL</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>CLUSTAL</B></PRE>\r
-<DL>\r
-<DD>ClustalW\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="MAFFT"><!-- --></A><H3>\r
-MAFFT</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MAFFT</B></PRE>\r
-<DL>\r
-<DD>Mafft\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="MUSCLE"><!-- --></A><H3>\r
-MUSCLE</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>MUSCLE</B></PRE>\r
-<DL>\r
-<DD>Muscle\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Tcoffee"><!-- --></A><H3>\r
-Tcoffee</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Tcoffee</B></PRE>\r
-<DL>\r
-<DD>Tcoffee\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Probcons"><!-- --></A><H3>\r
-Probcons</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>Probcons</B></PRE>\r
-<DL>\r
-<DD>Probcons\r
-<P>\r
-<DL>\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="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared. This method may be used to iterate
-over the constants as follows:
-<pre>
-for (Program c : Program.values())
- System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> <B>valueOf</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> name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type. (Extraneous whitespace characters are
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</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
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-SequenceUtil\r
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-compbio.data.sequence</FONT>\r
-<BR>\r
-Class SequenceUtil</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SequenceUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>SequenceUtil</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Utility class for operations on sequences\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>Petr Troshin</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
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>\r
-\r
-<BR>\r
- Valid Amino acids</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>\r
-\r
-<BR>\r
- Same as AA pattern but with two additional letters - XU</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
- Ambiguous nucleotide</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>\r
-\r
-<BR>\r
- A digit</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>\r
-\r
-<BR>\r
- inversion of AA pattern</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
- Non nucleotide</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>\r
-\r
-<BR>\r
- Non word</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
- Nucleotides a, t, g, c, u</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>\r
-\r
-<BR>\r
- A whitespace character: [\t\n\x0B\f\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>static <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/sequence/SequenceUtil.html#cleanSequence(java.lang.String)">cleanSequence</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> sequence)</CODE>\r
-\r
-<BR>\r
- Removes all whitespace chars in the sequence string</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)">closeSilently</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/logging/Logger.html?is-external=true" title="class or interface in java.util.logging">Logger</A> log,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/io/Closeable.html?is-external=true" title="class or interface in java.io">Closeable</A> stream)</CODE>\r
-\r
-<BR>\r
- Closes the Closable and logs the exception if any</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)">deepCleanSequence</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> sequence)</CODE>\r
-\r
-<BR>\r
- Removes all special characters and digits as well as whitespace chars
- from the sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)">isAmbiguosProtein</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> sequence)</CODE>\r
-\r
-<BR>\r
- Check whether the sequence confirms to amboguous protein sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)">isNonAmbNucleotideSequence</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> sequence)</CODE>\r
-\r
-<BR>\r
- Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)">isProteinSequence</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> sequence)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
-\r
-<BR>\r
- Reads fasta sequences from inStream into the list of FastaSequence
- objects</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> os,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
-\r
-<BR>\r
- Writes FastaSequence in the file, each sequence will take one line only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)</CODE>\r
-\r
-<BR>\r
- Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_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>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="WHITE_SPACE"><!-- --></A><H3>\r
-WHITE_SPACE</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>WHITE_SPACE</B></PRE>\r
-<DL>\r
-<DD>A whitespace character: [\t\n\x0B\f\r]\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="DIGIT"><!-- --></A><H3>\r
-DIGIT</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>DIGIT</B></PRE>\r
-<DL>\r
-<DD>A digit\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NONWORD"><!-- --></A><H3>\r
-NONWORD</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NONWORD</B></PRE>\r
-<DL>\r
-<DD>Non word\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AA"><!-- --></A><H3>\r
-AA</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AA</B></PRE>\r
-<DL>\r
-<DD>Valid Amino acids\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NON_AA"><!-- --></A><H3>\r
-NON_AA</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NON_AA</B></PRE>\r
-<DL>\r
-<DD>inversion of AA pattern\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AMBIGUOUS_AA"><!-- --></A><H3>\r
-AMBIGUOUS_AA</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AMBIGUOUS_AA</B></PRE>\r
-<DL>\r
-<DD>Same as AA pattern but with two additional letters - XU\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NUCLEOTIDE"><!-- --></A><H3>\r
-NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Nucleotides a, t, g, c, u\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>\r
-AMBIGUOUS_NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>AMBIGUOUS_NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Ambiguous nucleotide\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>\r
-NON_NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final <A HREF="http://java.sun.com/javase/6/docs/api/java/util/regex/Pattern.html?is-external=true" title="class or interface in java.util.regex">Pattern</A> <B>NON_NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Non nucleotide\r
-<P>\r
-<DL>\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="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>\r
-isNucleotideSequence</H3>\r
-<PRE>\r
-public static boolean <B>isNucleotideSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>\r
-isNonAmbNucleotideSequence</H3>\r
-<PRE>\r
-public static boolean <B>isNonAmbNucleotideSequence</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> sequence)</PRE>\r
-<DL>\r
-<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>\r
-cleanSequence</H3>\r
-<PRE>\r
-public static <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>cleanSequence</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> sequence)</PRE>\r
-<DL>\r
-<DD>Removes all whitespace chars in the sequence string\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>\r
-deepCleanSequence</H3>\r
-<PRE>\r
-public static <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>deepCleanSequence</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> sequence)</PRE>\r
-<DL>\r
-<DD>Removes all special characters and digits as well as whitespace chars
- from the sequence\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>\r
-isProteinSequence</H3>\r
-<PRE>\r
-public static boolean <B>isProteinSequence</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> sequence)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>\r
-isAmbiguosProtein</H3>\r
-<PRE>\r
-public static boolean <B>isAmbiguosProtein</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> sequence)</PRE>\r
-<DL>\r
-<DD>Check whether the sequence confirms to amboguous protein sequence\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
- Return false otherwise. e.g. if the sequence is non-ambiguous
- protein or DNA</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
-writeFasta</H3>\r
-<PRE>\r
-public static void <B>writeFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD>Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>outstream</CODE> - <DD><CODE>sequences</CODE> - <DD><CODE>width</CODE> - - the maximum number of characters to write in one line\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
-writeFastaKeepTheStream</H3>\r
-<PRE>\r
-public static void <B>writeFastaKeepTheStream</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>\r
-readFasta</H3>\r
-<PRE>\r
-public static <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>> <B>readFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD>Reads fasta sequences from inStream into the list of FastaSequence
- objects\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from\r
-<DT><B>Returns:</B><DD>list of FastaSequence objects\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>\r
-writeFasta</H3>\r
-<PRE>\r
-public static void <B>writeFasta</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> os,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD>Writes FastaSequence in the file, each sequence will take one line only\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="closeSilently(java.util.logging.Logger, java.io.Closeable)"><!-- --></A><H3>\r
-closeSilently</H3>\r
-<PRE>\r
-public static final void <B>closeSilently</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/logging/Logger.html?is-external=true" title="class or interface in java.util.logging">Logger</A> log,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/io/Closeable.html?is-external=true" title="class or interface in java.io">Closeable</A> stream)</PRE>\r
-<DL>\r
-<DD>Closes the Closable and logs the exception if any\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>log</CODE> - <DD><CODE>stream</CODE> - </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/SequenceUtil.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/sequence/SequenceUtil.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="SequenceUtil.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-UnknownFileFormatException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="UnknownFileFormatException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/UnknownFileFormatException.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/data/sequence/UnknownFileFormatException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="UnknownFileFormatException.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
-\r
-</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="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class UnknownFileFormatException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.UnknownFileFormatException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>UnknownFileFormatException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../../serialized-form.html#compbio.data.sequence.UnknownFileFormatException">Serialized Form</A></DL>\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/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException()">UnknownFileFormatException</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.io.File, java.lang.Throwable)">UnknownFileFormatException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
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-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</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> message)</PRE>\r
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-UnknownFileFormatException</H3>\r
-<PRE>\r
-public <B>UnknownFileFormatException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</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.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model. </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
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><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
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></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
-Uses of <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)</CODE>\r
-\r
-<BR>\r
- Read Clustal formatted alignment.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outStream,\r
- <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> alignment)</CODE>\r
-\r
-<BR>\r
- Write Clustal formatted alignment Limitations: does not record the
- consensus.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Packages that use <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-Uses of <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></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/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></CODE></FONT></TD>\r
-<TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getMetadata()">getMetadata</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</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/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
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-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.FastaSequence</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</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.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model. </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
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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> <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>MsaWS.</B><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="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>MsaWS.</B><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
- \r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></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
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return types with arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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>></CODE></FONT></TD>\r
-<TD><CODE><B>Alignment.</B><B><A HREF="../../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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>></CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inStream)</CODE>\r
-\r
-<BR>\r
- Reads fasta sequences from inStream into the list of FastaSequence
- objects</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> os,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
-\r
-<BR>\r
- Writes FastaSequence in the file, each sequence will take one line only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)</CODE>\r
-\r
-<BR>\r
- Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)">writeFastaKeepTheStream</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A> outstream,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructor parameters in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</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/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A> metadata)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</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/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</CODE>\r
-\r
-<BR>\r
- </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
-Uses of <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static int</CODE></FONT></TD>\r
-<TD><CODE><B>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</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>> data)</CODE>\r
-\r
-<BR>\r
- Calculates an average sequence length of the dataset</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>Limit.</B><B><A HREF="../../../../compbio/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</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>> data)</CODE>\r
-\r
-<BR>\r
- Checks if the number of sequences or their average length in the dataset
- exceeds this limit.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
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-</TITLE>\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.Program</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></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
-Uses of <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that return <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></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/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B>AlignmentMetadata.</B><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#getProgram()">getProgram</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></CODE></FONT></TD>\r
-<TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>Program.</B><B><A HREF="../../../../compbio/data/sequence/Program.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> with parameters of type <A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</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/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)">AlignmentMetadata</A></B>(<A HREF="../../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A> program,\r
- char gapchar)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
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-Uses of Class compbio.data.sequence.SequenceUtil\r
-</TITLE>\r
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- parent.document.title="Uses of Class compbio.data.sequence.SequenceUtil";\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<B>Uses of Class<br>compbio.data.sequence.SequenceUtil</B></H2>\r
-</CENTER>\r
-No usage of compbio.data.sequence.SequenceUtil\r
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- <SCRIPT type="text/javascript">\r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.data.sequence.UnknownFileFormatException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
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-\r
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-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.data.sequence.UnknownFileFormatException";\r
- }\r
-}\r
-</SCRIPT>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-\r
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-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.data.sequence.UnknownFileFormatException</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></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
-Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> file)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>ClustalAlignmentUtil.</B><B><A HREF="../../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> instream)</CODE>\r
-\r
-<BR>\r
- Read Clustal formatted alignment.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-Package compbio.data.sequence\r
-</H2>\r
-A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
- <A HREF="#package_description"><B>Description</B></A>\r
-<P>\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
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></B></TD>\r
-<TD>Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></B></TD>\r
-<TD>Alignment metadata e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></B></TD>\r
-<TD>Tools to read and write clustal formated files</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TD>\r
-<TD>A FASTA formatted sequence.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A></B></TD>\r
-<TD>Utility class for operations on sequences</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-\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>Enum Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></B></TD>\r
-<TD>The list of programmes that can produce alignments</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-\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>Exception Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.data.sequence Description\r
-</H2>\r
-\r
-<P>\r
-A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model.
- Classes in this package have no dependencies to other sources in the project.
- They form a base layer of JAva Bioinformatics Analysis Web Services.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 January 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>Petr Troshin</DD>\r
-</DL>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-Class Hierarchy\r
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-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
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-</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.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model. </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
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-Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</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/data/sequence/class-use/Alignment.html#compbio.data.msa"><B>Alignment</B></A></B>\r
-\r
-<BR>\r
- Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
- A FASTA formatted sequence.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.data.sequence"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence"><B>Alignment</B></A></B>\r
-\r
-<BR>\r
- Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence"><B>AlignmentMetadata</B></A></B>\r
-\r
-<BR>\r
- Alignment metadata e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
- A FASTA formatted sequence.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
-\r
-<BR>\r
- The list of programmes that can produce alignments</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
-\r
-<BR>\r
- </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
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-Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</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/data/sequence/class-use/FastaSequence.html#compbio.metadata"><B>FastaSequence</B></A></B>\r
-\r
-<BR>\r
- A FASTA formatted sequence.</TD>\r
-</TR>\r
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-<HR>\r
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-Argument\r
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-\r
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-</TABLE>\r
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-DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-compbio.metadata</FONT>\r
-<BR>\r
-Interface Argument<T></H2>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
-<DL>\r
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>, <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public interface <B>Argument<T></B></DL>\r
-</PRE>\r
-\r
-<P>\r
-An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin
-
- Date December 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>, \r
-<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></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> <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/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Argument.html#getDescription()">getDescription</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Argument.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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="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/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</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> defaultValue)</CODE>\r
-\r
-<BR>\r
- Set default values for the parameter or an option</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="getFurtherDetails()"><!-- --></A><H3>\r
-getFurtherDetails</H3>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> <B>getFurtherDetails</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDefaultValue()"><!-- --></A><H3>\r
-getDefaultValue</H3>\r
-<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>getDefaultValue</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDescription()"><!-- --></A><H3>\r
-getDescription</H3>\r
-<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>getDescription</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<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>getName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</H3>\r
-<PRE>\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="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>getPossibleValues</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
-setValue</H3>\r
-<PRE>\r
-void <B>setValue</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> defaultValue)\r
- throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Set default values for the parameter or an option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>defaultValue</CODE> - the value to be set\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
- numeric parameter is the value defined outside it , for
- string type parameter, wrong value is the one which is not
- listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></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/Argument.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Argument.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Argument.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- 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
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-ChunkHolder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="ChunkHolder";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/ChunkHolder.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/ChunkHolder.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="ChunkHolder.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class ChunkHolder</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ChunkHolder</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ChunkHolder</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Represents a chunk of a string data together with the position in a file for
- the next read operation.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 December 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\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/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)">ChunkHolder</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> chunk,\r
- long position)</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/ChunkHolder.html#getChunk()">getChunk</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> long</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#getNextPosition()">getNextPosition</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ChunkHolder.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/ChunkHolder.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="ChunkHolder(java.lang.String, long)"><!-- --></A><H3>\r
-ChunkHolder</H3>\r
-<PRE>\r
-public <B>ChunkHolder</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> chunk,\r
- long position)</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="getChunk()"><!-- --></A><H3>\r
-getChunk</H3>\r
-<PRE>\r
-public <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>getChunk</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNextPosition()"><!-- --></A><H3>\r
-getNextPosition</H3>\r
-<PRE>\r
-public long <B>getNextPosition</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</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/ChunkHolder.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- }\r
-}\r
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-compbio.metadata</FONT>\r
-<BR>\r
-Class JobExecutionException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobExecutionException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>JobExecutionException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained. For cluster execution it hides DrmaaException\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 October 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.JobExecutionException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)">JobExecutionException</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> message)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String, java.lang.Throwable)">JobExecutionException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.Throwable)">JobExecutionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
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-<A NAME="method_summary"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
-</TR>\r
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-</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="JobExecutionException(java.lang.String)"><!-- --></A><H3>\r
-JobExecutionException</H3>\r
-<PRE>\r
-public <B>JobExecutionException</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> message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobExecutionException(java.lang.Throwable)"><!-- --></A><H3>\r
-JobExecutionException</H3>\r
-<PRE>\r
-public <B>JobExecutionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobExecutionException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-JobExecutionException</H3>\r
-<PRE>\r
-public <B>JobExecutionException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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- <!--\r
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- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<NOSCRIPT>\r
- <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
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-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
-</TR>\r
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-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-JobStatus\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="JobStatus";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
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-</TABLE>\r
-</TD>\r
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-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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- <A HREF="../../index.html?compbio/metadata/JobStatus.html" target="_top"><B>FRAMES</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Enum JobStatus</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobStatus</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>JobStatus</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>></DL>\r
-</PRE>\r
-\r
-<P>\r
-The status of the job.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 October 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_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>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#CANCELLED">CANCELLED</A></B></CODE>\r
-\r
-<BR>\r
- Jobs that has been cancelled</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#COLLECTED">COLLECTED</A></B></CODE>\r
-\r
-<BR>\r
- Results has been collected</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#FAILED">FAILED</A></B></CODE>\r
-\r
-<BR>\r
- Failed jobs</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#FINISHED">FINISHED</A></B></CODE>\r
-\r
-<BR>\r
- Finished jobs</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#PENDING">PENDING</A></B></CODE>\r
-\r
-<BR>\r
- Jobs which are in the queue and awaiting execution reported for cluster
- jobs only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#RUNNING">RUNNING</A></B></CODE>\r
-\r
-<BR>\r
- Jobs that are running</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#STARTED">STARTED</A></B></CODE>\r
-\r
-<BR>\r
- Job calculation has been started.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#SUBMITTED">SUBMITTED</A></B></CODE>\r
-\r
-<BR>\r
- Job has been submitted.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#UNDEFINED">UNDEFINED</A></B></CODE>\r
-\r
-<BR>\r
- Represents jobs with unknown status</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>static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobStatus.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_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>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="PENDING"><!-- --></A><H3>\r
-PENDING</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>PENDING</B></PRE>\r
-<DL>\r
-<DD>Jobs which are in the queue and awaiting execution reported for cluster
- jobs only\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="RUNNING"><!-- --></A><H3>\r
-RUNNING</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>RUNNING</B></PRE>\r
-<DL>\r
-<DD>Jobs that are running\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="CANCELLED"><!-- --></A><H3>\r
-CANCELLED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>CANCELLED</B></PRE>\r
-<DL>\r
-<DD>Jobs that has been cancelled\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="FINISHED"><!-- --></A><H3>\r
-FINISHED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>FINISHED</B></PRE>\r
-<DL>\r
-<DD>Finished jobs\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="FAILED"><!-- --></A><H3>\r
-FAILED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>FAILED</B></PRE>\r
-<DL>\r
-<DD>Failed jobs\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="UNDEFINED"><!-- --></A><H3>\r
-UNDEFINED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>UNDEFINED</B></PRE>\r
-<DL>\r
-<DD>Represents jobs with unknown status\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="STARTED"><!-- --></A><H3>\r
-STARTED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>STARTED</B></PRE>\r
-<DL>\r
-<DD>Job calculation has been started. First status reported by the local
- engine\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="SUBMITTED"><!-- --></A><H3>\r
-SUBMITTED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>SUBMITTED</B></PRE>\r
-<DL>\r
-<DD>Job has been submitted. This status is only set for cluster jobs\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="COLLECTED"><!-- --></A><H3>\r
-COLLECTED</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>COLLECTED</B></PRE>\r
-<DL>\r
-<DD>Results has been collected\r
-<P>\r
-<DL>\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="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared. This method may be used to iterate
-over the constants as follows:
-<pre>
-for (JobStatus c : JobStatus.values())
- System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>valueOf</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> name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type. (Extraneous whitespace characters are
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
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-<HR>\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-\r
-<HR>\r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-JobSubmissionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-function windowTitle()\r
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- parent.document.title="JobSubmissionException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-compbio.metadata</FONT>\r
-<BR>\r
-Class JobSubmissionException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.JobSubmissionException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>, <A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>JobSubmissionException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException. If
- this exception is thrown the task has not been calculated\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin
-
- Date December 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.JobSubmissionException">Serialized Form</A></DL>\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/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)">JobSubmissionException</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> message)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)">JobSubmissionException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.Throwable)">JobSubmissionException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
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-<B>Method Summary</B></FONT></TH>\r
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-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="JobSubmissionException(java.lang.String)"><!-- --></A><H3>\r
-JobSubmissionException</H3>\r
-<PRE>\r
-public <B>JobSubmissionException</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> message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobSubmissionException(java.lang.Throwable)"><!-- --></A><H3>\r
-JobSubmissionException</H3>\r
-<PRE>\r
-public <B>JobSubmissionException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="JobSubmissionException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-JobSubmissionException</H3>\r
-<PRE>\r
-public <B>JobSubmissionException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <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
-\r
-</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="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Limit\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Limit";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Limit.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Limit.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Limit<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Limit<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - the type of an executable for which this limit is defined.</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Limit<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset. Also contains static method for determining the
- number of sequence and their average length in the List<FastaSequence>\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 January 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><CODE>LimitsManager</CODE></A></DL>\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/metadata/Limit.html#Limit(int, int, java.lang.String)">Limit</A></B>(int seqNumber,\r
- int seqLength,\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> preset)</CODE>\r
-\r
-<BR>\r
- Instantiate the limit</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)">Limit</A></B>(int seqNumber,\r
- int seqLength,\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> preset,\r
- boolean isDefault)</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getAvgSeqLength()">getAvgSeqLength</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)">getAvgSequenceLength</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>> data)</CODE>\r
-\r
-<BR>\r
- Calculates an average sequence length of the dataset</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Limit.html#getPreset()">getPreset</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#getSeqNumber()">getSeqNumber</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Limit.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/metadata/Limit.html#isDefault()">isDefault</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/metadata/Limit.html#isExceeded(java.util.List)">isExceeded</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>> data)</CODE>\r
-\r
-<BR>\r
- Checks if the number of sequences or their average length in the dataset
- exceeds this limit.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Limit.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="Limit(int, int, java.lang.String)"><!-- --></A><H3>\r
-Limit</H3>\r
-<PRE>\r
-public <B>Limit</B>(int seqNumber,\r
- int seqLength,\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> preset)</PRE>\r
-<DL>\r
-<DD>Instantiate the limit\r
-<P>\r
-<DL>\r
-<DT><B>Parameters:</B><DD><CODE>seqNumber</CODE> - the maximum number of sequences allowed for calculation.
- Required<DD><CODE>seqLength</CODE> - the average length of the sequence, optional<DD><CODE>preset</CODE> - the name of preset if any, optional\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if the seqNumber is not supplied or the seqLength is negative</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Limit(int, int, java.lang.String, boolean)"><!-- --></A><H3>\r
-Limit</H3>\r
-<PRE>\r
-public <B>Limit</B>(int seqNumber,\r
- int seqLength,\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> preset,\r
- boolean isDefault)</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="getPreset()"><!-- --></A><H3>\r
-getPreset</H3>\r
-<PRE>\r
-public <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>getPreset</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAvgSeqLength()"><!-- --></A><H3>\r
-getAvgSeqLength</H3>\r
-<PRE>\r
-public int <B>getAvgSeqLength</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the allowed average sequence length</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSeqNumber()"><!-- --></A><H3>\r
-getSeqNumber</H3>\r
-<PRE>\r
-public int <B>getSeqNumber</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the maximum number of sequences allowed</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isDefault()"><!-- --></A><H3>\r
-isDefault</H3>\r
-<PRE>\r
-public boolean <B>isDefault</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is this is a default limit to be used, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isExceeded(java.util.List)"><!-- --></A><H3>\r
-isExceeded</H3>\r
-<PRE>\r
-public boolean <B>isExceeded</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>> data)</PRE>\r
-<DL>\r
-<DD>Checks if the number of sequences or their average length in the dataset
- exceeds this limit.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>data</CODE> - the dataset to measure\r
-<DT><B>Returns:</B><DD>true if a limit is exceeded (what is the dataset is larger then
- the limit), false otherwise. First check the number of sequences
- in the dataset and if it exceeds the limit return true
- irrespective of the average length. If the number of sequences in
- the dataset is less than the limit and average length is defined,
- then check whether the total number of letters (number of
- sequence multiplied by the average sequence length) is greater
- then the total number of letters in the dataset. Returns true if
- the total number of letters in the dataset is greater than the
- limit, false otherwise.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getAvgSequenceLength(java.util.List)"><!-- --></A><H3>\r
-getAvgSequenceLength</H3>\r
-<PRE>\r
-public static int <B>getAvgSequenceLength</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>> data)</PRE>\r
-<DL>\r
-<DD>Calculates an average sequence length of the dataset\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>data</CODE> - \r
-<DT><B>Returns:</B><DD>an average sequence length in the input dataset</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/Limit.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Limit.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Limit.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-LimitExceededException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="LimitExceededException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/LimitExceededException.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/LimitExceededException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="LimitExceededException.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class LimitExceededException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.LimitExceededException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>LimitExceededException</B><DT>extends <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-This exception is thrown if the task larger in size that the limit that
- applies to the calculation.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 February 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A>, \r
-<A HREF="../../serialized-form.html#compbio.metadata.LimitExceededException">Serialized Form</A></DL>\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/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)">LimitExceededException</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> message)</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> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()">getActualNumberofSequences</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()">getNumberOfSequencesAllowed</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()">getSequenceLenghtActual</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()">getSequenceLenghtAllowed</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="LimitExceededException(java.lang.String)"><!-- --></A><H3>\r
-LimitExceededException</H3>\r
-<PRE>\r
-public <B>LimitExceededException</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> message)</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="newLimitExceeded(compbio.metadata.Limit, java.util.List)"><!-- --></A><H3>\r
-newLimitExceeded</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> <B>newLimitExceeded</B>(<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getNumberOfSequencesAllowed()"><!-- --></A><H3>\r
-getNumberOfSequencesAllowed</H3>\r
-<PRE>\r
-public int <B>getNumberOfSequencesAllowed</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getActualNumberofSequences()"><!-- --></A><H3>\r
-getActualNumberofSequences</H3>\r
-<PRE>\r
-public int <B>getActualNumberofSequences</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequenceLenghtAllowed()"><!-- --></A><H3>\r
-getSequenceLenghtAllowed</H3>\r
-<PRE>\r
-public int <B>getSequenceLenghtAllowed</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSequenceLenghtActual()"><!-- --></A><H3>\r
-getSequenceLenghtActual</H3>\r
-<PRE>\r
-public int <B>getSequenceLenghtActual</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/LimitExceededException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A> \r
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- <!--\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
-\r
-</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
-</TR>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-LimitsManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="LimitsManager";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <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/LimitsManager.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
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-</TABLE>\r
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-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/LimitsManager.html" target="_top"><B>FRAMES</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class LimitsManager<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.LimitsManager<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>LimitsManager<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-A collection of Limits\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 January 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A></DL>\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/metadata/LimitsManager.html#LimitsManager()">LimitsManager</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> <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getDefaultLimit()">getDefaultLimit</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)">getLimitByName</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> presetName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/LimitsManager.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)">validate</A></B>(<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> presets)</CODE>\r
-\r
-<BR>\r
- Validate Limits</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="LimitsManager()"><!-- --></A><H3>\r
-LimitsManager</H3>\r
-<PRE>\r
-public <B>LimitsManager</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="getLimits()"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public <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/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>>> <B>getLimits</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>all limits defined for an executable T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimitByName(java.lang.String)"><!-- --></A><H3>\r
-getLimitByName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> <B>getLimitByName</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> presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - \r
-<DT><B>Returns:</B><DD>Limit defined for the executable T and presetName. If no limit is
- defined for the presetName then default Limit is returned. If
- presetName is empty or null than the default Limit will be
- returned. If not limit defined for the type T than NULL will be
- returned</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDefaultLimit()"><!-- --></A><H3>\r
-getDefaultLimit</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> <B>getDefaultLimit</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>the default Limit for an executable type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate(compbio.metadata.PresetManager)"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>(<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> presets)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
-<DL>\r
-<DD>Validate Limits\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presets</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if any of the Limit defined is found to be invalid. That is
- when
-
- 1) No default limit is defined
-
- 2) More than 1 default limit is defined
-
- 3) Limit's preset name does not match any presets for type T<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><CODE>Limit</CODE></A>, \r
-<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A></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/LimitsManager.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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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/LimitsManager.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="LimitsManager.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
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- <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Option\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Option";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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
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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/Option.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Option.html" target="_top"><B>FRAMES</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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- <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</TR>\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <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: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Option<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Option<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable</DL>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Option<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A><DT>implements <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DL>\r
-</PRE>\r
-\r
-<P>\r
-Command line option/flag or multiple exclusive options with no value. Example
- -protein, -dna, -auto\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 October 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</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
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>protected <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/metadata/Option.html#defaultValue">defaultValue</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>protected <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/metadata/Option.html#description">description</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>protected <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#furtherDetails">furtherDetails</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>protected boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#isRequired">isRequired</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>protected <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/metadata/Option.html#name">name</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\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/metadata/Option.html#Option(java.lang.String, java.lang.String)">Option</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> name,\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> description)</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> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</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>... value)</CODE>\r
-\r
-<BR>\r
- Adds an option to the optionName list</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/metadata/Option.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Option.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
-\r
-<BR>\r
- A default value of the option.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Option.html#getDescription()">getDescription</A></B>()</CODE>\r
-\r
-<BR>\r
- A long description of the Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
-\r
-<BR>\r
- The URL where further details about the option can be found</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Option.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
- Human readable name of the option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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="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/metadata/Option.html#getOptionNames()">getOptionNames</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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="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/metadata/Option.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
-\r
-<BR>\r
- List of possible optionNames</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/metadata/Option.html#isRequired()">isRequired</A></B>()</CODE>\r
-\r
-<BR>\r
- Flag that indicated that this option must be specified in the command
- line for an executable to run</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</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> defaultVal)</CODE>\r
-\r
-<BR>\r
- Sets one of the values defined in optionList as default.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setDescription(java.lang.String)">setDescription</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> description)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> furtherDetails)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setName(java.lang.String)">setName</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> name)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>> optionNames)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setRequired(boolean)">setRequired</A></B>(boolean isRequired)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</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> dValue)</CODE>\r
-\r
-<BR>\r
- Set default values for the parameter or an option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Option.html#toCommand(java.lang.String)">toCommand</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> nameValueSeparator)</CODE>\r
-\r
-<BR>\r
- Convert the option to the command string.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Option.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_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>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="description"><!-- --></A><H3>\r
-description</H3>\r
-<PRE>\r
-protected <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>description</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="name"><!-- --></A><H3>\r
-name</H3>\r
-<PRE>\r
-protected <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>name</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isRequired"><!-- --></A><H3>\r
-isRequired</H3>\r
-<PRE>\r
-protected boolean <B>isRequired</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="furtherDetails"><!-- --></A><H3>\r
-furtherDetails</H3>\r
-<PRE>\r
-protected <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> <B>furtherDetails</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="defaultValue"><!-- --></A><H3>\r
-defaultValue</H3>\r
-<PRE>\r
-protected <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>defaultValue</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\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="Option(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-Option</H3>\r
-<PRE>\r
-public <B>Option</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> name,\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> description)</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="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<PRE>\r
-public <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>getName</B>()</PRE>\r
-<DL>\r
-<DD>Human readable name of the option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
-setName</H3>\r
-<PRE>\r
-public void <B>setName</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> name)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDescription()"><!-- --></A><H3>\r
-getDescription</H3>\r
-<PRE>\r
-public <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>getDescription</B>()</PRE>\r
-<DL>\r
-<DD>A long description of the Option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDescription()">getDescription</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
-setDescription</H3>\r
-<PRE>\r
-public void <B>setDescription</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> description)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
-getFurtherDetails</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> <B>getFurtherDetails</B>()</PRE>\r
-<DL>\r
-<DD>The URL where further details about the option can be found\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setFurtherDetails(java.net.URL)"><!-- --></A><H3>\r
-setFurtherDetails</H3>\r
-<PRE>\r
-public void <B>setFurtherDetails</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> furtherDetails)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDefaultValue()"><!-- --></A><H3>\r
-getDefaultValue</H3>\r
-<PRE>\r
-public <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>getDefaultValue</B>()</PRE>\r
-<DL>\r
-<DD>A default value of the option. Defaults to command line argument name
- e.g. -auto\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
-setDefaultValue</H3>\r
-<PRE>\r
-public void <B>setDefaultValue</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> defaultVal)\r
- throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Sets one of the values defined in optionList as default. Attempting set
- the value not listed there will result in WrongParameter exception\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>defaultVal</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isRequired()"><!-- --></A><H3>\r
-isRequired</H3>\r
-<PRE>\r
-public boolean <B>isRequired</B>()</PRE>\r
-<DL>\r
-<DD>Flag that indicated that this option must be specified in the command
- line for an executable to run\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is the option is required, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRequired(boolean)"><!-- --></A><H3>\r
-setRequired</H3>\r
-<PRE>\r
-public void <B>setRequired</B>(boolean isRequired)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptionNames()"><!-- --></A><H3>\r
-getOptionNames</H3>\r
-<PRE>\r
-public <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="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>getOptionNames</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of option names</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
-setOptionNames</H3>\r
-<PRE>\r
-public void <B>setOptionNames</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>> optionNames)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
-addOptionNames</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>addOptionNames</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>... value)</PRE>\r
-<DL>\r
-<DD>Adds an option to the optionName list\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>value</CODE> - \r
-<DT><B>Returns:</B><DD>modified optionName list</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toCommand(java.lang.String)"><!-- --></A><H3>\r
-toCommand</H3>\r
-<PRE>\r
-public <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>toCommand</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> nameValueSeparator)</PRE>\r
-<DL>\r
-<DD>Convert the option to the command string.\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
- option names are defined, then the defaultValue is returned.
- Option must have a default value if there are many optionNames to
- be valid.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</H3>\r
-<PRE>\r
-public <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="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>getPossibleValues</B>()</PRE>\r
-<DL>\r
-<DD>List of possible optionNames\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
-setValue</H3>\r
-<PRE>\r
-public void <B>setValue</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> dValue)\r
- throws <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/metadata/Argument.html#setValue(java.lang.String)">Argument</A></CODE></B></DD>\r
-<DD>Set default values for the parameter or an option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>dValue</CODE> - the value to be set\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
- numeric parameter is the value defined outside it , for
- string type parameter, wrong value is the one which is not
- listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></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/Option.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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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Option.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Option.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <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: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Parameter\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Parameter";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/Parameter.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Parameter.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Parameter.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_compbio.metadata.Option">FIELD</A> | <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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Parameter<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">compbio.metadata.Option</A><T>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Parameter<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Parameter<T></B><DT>extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><T></DL>\r
-</PRE>\r
-\r
-<P>\r
-A single value containing an option supported by the web service e.g.
- seqType=protein. Where seqType is a optionName and protein is one of
- possibleValues\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 November 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>, \r
-<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></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.metadata.Option"><!-- --></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 class compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../compbio/metadata/Option.html#defaultValue">defaultValue</A>, <A HREF="../../compbio/metadata/Option.html#description">description</A>, <A HREF="../../compbio/metadata/Option.html#furtherDetails">furtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#isRequired">isRequired</A>, <A HREF="../../compbio/metadata/Option.html#name">name</A></CODE></TD>\r
-</TR>\r
-</TABLE>\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/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)">Parameter</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> name,\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> description)</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> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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/metadata/Parameter.html#addOptionNames(java.lang.String...)">addOptionNames</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>... value)</CODE>\r
-\r
-<BR>\r
- Adds an option to the optionName list</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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/metadata/Parameter.html#addPossibleValues(java.lang.String...)">addPossibleValues</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>... value)</CODE>\r
-\r
-<BR>\r
- </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/metadata/Parameter.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Parameter.html#getOptionName()">getOptionName</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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="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/metadata/Parameter.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
-\r
-<BR>\r
- List is more convenient to work with</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/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#getValidValue()">getValidValue</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</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> defaultVal)</CODE>\r
-\r
-<BR>\r
- Sets one of the values defined in optionList as default.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setOptionName(java.lang.String)">setOptionName</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> optionName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>> optionName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)">setPossibleValues</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>> possibleValues)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)">setValidValue</A></B>(<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> validValue)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Parameter.html#toCommand(java.lang.String)">toCommand</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> nameValueSeparator)</CODE>\r
-\r
-<BR>\r
- Convert the option to the command string.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Parameter.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_compbio.metadata.Option"><!-- --></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 compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../compbio/metadata/Option.html#getDefaultValue()">getDefaultValue</A>, <A HREF="../../compbio/metadata/Option.html#getDescription()">getDescription</A>, <A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#getName()">getName</A>, <A HREF="../../compbio/metadata/Option.html#getOptionNames()">getOptionNames</A>, <A HREF="../../compbio/metadata/Option.html#isRequired()">isRequired</A>, <A HREF="../../compbio/metadata/Option.html#setDescription(java.lang.String)">setDescription</A>, <A HREF="../../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A>, <A HREF="../../compbio/metadata/Option.html#setName(java.lang.String)">setName</A>, <A HREF="../../compbio/metadata/Option.html#setRequired(boolean)">setRequired</A>, <A HREF="../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></CODE></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="Parameter(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-Parameter</H3>\r
-<PRE>\r
-public <B>Parameter</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> name,\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> description)</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="getValidValue()"><!-- --></A><H3>\r
-getValidValue</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> <B>getValidValue</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setValidValue(compbio.metadata.ValueConstrain)"><!-- --></A><H3>\r
-setValidValue</H3>\r
-<PRE>\r
-public void <B>setValidValue</B>(<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> validValue)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toCommand(java.lang.String)"><!-- --></A><H3>\r
-toCommand</H3>\r
-<PRE>\r
-public <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>toCommand</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> nameValueSeparator)</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">Option</A></CODE></B></DD>\r
-<DD>Convert the option to the command string.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#toCommand(java.lang.String)">toCommand</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
- option names are defined, then the defaultValue is returned.
- Option must have a default value if there are many optionNames to
- be valid.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</H3>\r
-<PRE>\r
-public <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="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>getPossibleValues</B>()</PRE>\r
-<DL>\r
-<DD>List is more convenient to work with\r
-<P>\r
-<DD><DL>\r
-<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPossibleValues(java.util.Set)"><!-- --></A><H3>\r
-setPossibleValues</H3>\r
-<PRE>\r
-public void <B>setPossibleValues</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>> possibleValues)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addPossibleValues(java.lang.String...)"><!-- --></A><H3>\r
-addPossibleValues</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>addPossibleValues</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>... value)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
-setOptionNames</H3>\r
-<PRE>\r
-public void <B>setOptionNames</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>> optionName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
-addOptionNames</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A><<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>addOptionNames</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>... value)</PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">Option</A></CODE></B></DD>\r
-<DD>Adds an option to the optionName list\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>modified optionName list</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptionName()"><!-- --></A><H3>\r
-getOptionName</H3>\r
-<PRE>\r
-public <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>getOptionName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptionName(java.lang.String)"><!-- --></A><H3>\r
-setOptionName</H3>\r
-<PRE>\r
-public void <B>setOptionName</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> optionName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
-setDefaultValue</H3>\r
-<PRE>\r
-public void <B>setDefaultValue</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> defaultVal)\r
- throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD><B>Description copied from class: <CODE><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">Option</A></CODE></B></DD>\r
-<DD>Sets one of the values defined in optionList as default. Attempting set
- the value not listed there will result in WrongParameter exception\r
-<P>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></CODE> in class <CODE><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</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
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- <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/Parameter.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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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Parameter.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Parameter.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
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_compbio.metadata.Option">FIELD</A> | <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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-<A NAME="skip-navbar_bottom"></A>\r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Preset\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
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- parent.document.title="Preset";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <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/Preset.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
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Preset.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Preset.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class Preset<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Preset<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - executable type</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Preset<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Collection of Options and Parameters with their values\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 December 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>, \r
-<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\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/metadata/Preset.html#Preset()">Preset</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
-\r
-<BR>\r
- Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Preset.html#getDescription()">getDescription</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Preset.html#getName()">getName</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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="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/metadata/Preset.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setDescription(java.lang.String)">setDescription</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> description)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setName(java.lang.String)">setName</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> name)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Preset.html#setOptions(java.util.List)">setOptions</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> option)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/Preset.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="Preset()"><!-- --></A><H3>\r
-Preset</H3>\r
-<PRE>\r
-public <B>Preset</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="setOptions(java.util.List)"><!-- --></A><H3>\r
-setOptions</H3>\r
-<PRE>\r
-public void <B>setOptions</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="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> option)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
-setName</H3>\r
-<PRE>\r
-public void <B>setName</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> name)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
-setDescription</H3>\r
-<PRE>\r
-public void <B>setDescription</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> description)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptions()"><!-- --></A><H3>\r
-getOptions</H3>\r
-<PRE>\r
-public <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="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>getOptions</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>a List of Options as a String</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getName()"><!-- --></A><H3>\r
-getName</H3>\r
-<PRE>\r
-public <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>getName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- name of the Preset</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getDescription()"><!-- --></A><H3>\r
-getDescription</H3>\r
-<PRE>\r
-public <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>getDescription</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>- a long description of the Preset</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArguments(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-getArguments</H3>\r
-<PRE>\r
-public <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/metadata/Preset.html" title="type parameter in Preset">T</A>>> <B>getArguments</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)\r
- throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
-<DL>\r
-<DD>Converts list of options as String to type Option\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
-<DT><B>Returns:</B><DD>List of Options\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - if the value of the parameter is invalid @see
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</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
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Preset.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Preset.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-PresetManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="PresetManager";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/PresetManager.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/PresetManager.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="PresetManager.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <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: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class PresetManager<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.PresetManager<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable.</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>PresetManager<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\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>\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 December 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</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
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\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/metadata/PresetManager.html#PresetManager()">PresetManager</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> <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</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> presetName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/PresetManager.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</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/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)">setRunnerClassName</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> runnerClassName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/PresetManager.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)</CODE>\r
-\r
-<BR>\r
- Checks whether preset option and parameter are defined in RunnerConfig
- object.</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_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>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><H3>\r
-LOCAL_ENGINE_LIMIT_PRESET</H3>\r
-<PRE>\r
-public static final <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>LOCAL_ENGINE_LIMIT_PRESET</B></PRE>\r
-<DL>\r
-<DL>\r
-<DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET">Constant Field Values</A></DL>\r
-</DL>\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="PresetManager()"><!-- --></A><H3>\r
-PresetManager</H3>\r
-<PRE>\r
-public <B>PresetManager</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="getPresets()"><!-- --></A><H3>\r
-getPresets</H3>\r
-<PRE>\r
-public <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/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> <B>getPresets</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPresets(java.util.List)"><!-- --></A><H3>\r
-setPresets</H3>\r
-<PRE>\r
-public void <B>setPresets</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/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
-getRunnerClassName</H3>\r
-<PRE>\r
-public <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>getRunnerClassName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>fully qualified class name of type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
-setRunnerClassName</H3>\r
-<PRE>\r
-public void <B>setRunnerClassName</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> runnerClassName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPresetByName(java.lang.String)"><!-- --></A><H3>\r
-getPresetByName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> <B>getPresetByName</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> presetName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>presetName</CODE> - \r
-<DT><B>Returns:</B><DD>preset by its name, null if no preset found</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
-<DL>\r
-<DD>Checks whether preset option and parameter are defined in RunnerConfig
- object.
-
- TODO handle parameters with values properly!\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if preset is found to be invalid.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
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-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class ResultNotAvailableException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ResultNotAvailableException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ResultNotAvailableException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained. For cluster execution it hides lower level exceptions
- like DrmaaException\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin
-
- Date October 2009</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.ResultNotAvailableException">Serialized Form</A></DL>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
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-<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/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)">ResultNotAvailableException</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> message)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)">ResultNotAvailableException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)">ResultNotAvailableException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
-</TR>\r
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-</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="ResultNotAvailableException(java.lang.String)"><!-- --></A><H3>\r
-ResultNotAvailableException</H3>\r
-<PRE>\r
-public <B>ResultNotAvailableException</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> message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ResultNotAvailableException(java.lang.Throwable)"><!-- --></A><H3>\r
-ResultNotAvailableException</H3>\r
-<PRE>\r
-public <B>ResultNotAvailableException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-ResultNotAvailableException</H3>\r
-<PRE>\r
-public <B>ResultNotAvailableException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= 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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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-RunnerConfig\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="RunnerConfig";\r
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-}\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
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-compbio.metadata</FONT>\r
-<BR>\r
-Class RunnerConfig<T></H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.RunnerConfig<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of an Executable</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@NotThreadSafe\r
-</FONT>public class <B>RunnerConfig<T></B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\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.
- The lists is defined in and loaded from <ExecutableName>Parameters.xml file.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 October 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\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/metadata/RunnerConfig.html#RunnerConfig()">RunnerConfig</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
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-<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> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</CODE>\r
-\r
-<BR>\r
- Adds Option to the internal list of options</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</CODE>\r
-\r
-<BR>\r
- Adds parameter to the internal parameter list</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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>\r
-\r
-<BR>\r
- </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/metadata/RunnerConfig.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </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/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the argument by its name if found, NULL otherwise.</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/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</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> optionName)</CODE>\r
-\r
-<BR>\r
- Returns the argument by option name, NULL if the argument is not found</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
- runner</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the list of the Options supported by the executable of type T</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the list of parameters supported executable of type T.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/RunnerConfig.html#getPrmSeparator()">getPrmSeparator</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/RunnerConfig.html#getRunnerClassName()">getRunnerClassName</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/metadata/RunnerConfig.html#removeArgument(java.lang.String)">removeArgument</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> name)</CODE>\r
-\r
-<BR>\r
- Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.</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/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)">removeArgumentByOptionName</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> optionName)</CODE>\r
-\r
-<BR>\r
- Removes the argument which can be a Parameter or an Option instance by
- the value in <optionNames> element of the runner configuration
- descriptor.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</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/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
-\r
-<BR>\r
- Adds the list of options or parameters to the internal list of options</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</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/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
-\r
-<BR>\r
- Sets the list of parameters as internal list</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)">setPrmSeparator</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> prmSeparator)</CODE>\r
-\r
-<BR>\r
- Sets name value separator character</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)">setRunnerClassName</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> runnerClassName)</CODE>\r
-\r
-<BR>\r
- Set the name of a runner class</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/RunnerConfig.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#validate()">validate</A></B>()</CODE>\r
-\r
-<BR>\r
- Validate the value of the argument.</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="RunnerConfig()"><!-- --></A><H3>\r
-RunnerConfig</H3>\r
-<PRE>\r
-public <B>RunnerConfig</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="copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-copyAndValidateRConfig</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>copyAndValidateRConfig</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptions()"><!-- --></A><H3>\r
-getOptions</H3>\r
-<PRE>\r
-public <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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getOptions</B>()</PRE>\r
-<DL>\r
-<DD>Returns the list of the Options supported by the executable of type T\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by type T<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameter(compbio.metadata.Parameter)"><!-- --></A><H3>\r
-addParameter</H3>\r
-<PRE>\r
-public void <B>addParameter</B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</PRE>\r
-<DL>\r
-<DD>Adds parameter to the internal parameter list\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>param</CODE> - the <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> to add<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOption(compbio.metadata.Option)"><!-- --></A><H3>\r
-addOption</H3>\r
-<PRE>\r
-public void <B>addOption</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</PRE>\r
-<DL>\r
-<DD>Adds Option to the internal list of options\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>option</CODE> - the <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> to add</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArguments()"><!-- --></A><H3>\r
-getArguments</H3>\r
-<PRE>\r
-public <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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getArguments</B>()</PRE>\r
-<DL>\r
-<DD>Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
- runner\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPrmSeparator()"><!-- --></A><H3>\r
-getPrmSeparator</H3>\r
-<PRE>\r
-public <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>getPrmSeparator</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>name value separator character</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPrmSeparator(java.lang.String)"><!-- --></A><H3>\r
-setPrmSeparator</H3>\r
-<PRE>\r
-public void <B>setPrmSeparator</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> prmSeparator)</PRE>\r
-<DL>\r
-<DD>Sets name value separator character\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>prmSeparator</CODE> - the separator char</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
-setOptions</H3>\r
-<PRE>\r
-public void <B>setOptions</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/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>\r
-<DL>\r
-<DD>Adds the list of options or parameters to the internal list of options\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters to add</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
-getRunnerClassName</H3>\r
-<PRE>\r
-public <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>getRunnerClassName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>fully qualified class name for type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
-setRunnerClassName</H3>\r
-<PRE>\r
-public void <B>setRunnerClassName</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> runnerClassName)</PRE>\r
-<DL>\r
-<DD>Set the name of a runner class\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>runnerClassName</CODE> - the name of the executable wrapping class</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParameters(java.util.List)"><!-- --></A><H3>\r
-setParameters</H3>\r
-<PRE>\r
-public void <B>setParameters</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/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>\r
-<DL>\r
-<DD>Sets the list of parameters as internal list\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters()"><!-- --></A><H3>\r
-getParameters</H3>\r
-<PRE>\r
-public <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/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getParameters</B>()</PRE>\r
-<DL>\r
-<DD>Returns the list of parameters supported executable of type T. Where
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> is an <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> with value.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArgument(java.lang.String)"><!-- --></A><H3>\r
-getArgument</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgument</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> name)</PRE>\r
-<DL>\r
-<DD>Returns the argument by its name if found, NULL otherwise. Where the
- Argument is a common interface for <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>
- therefore this method can return either. If you need to retrieve the
- Option by its optionNames use @link
- <A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>getArgumentByOptionName(String)</CODE></A> method. The
- difference between option name and optionName is explained by the
- following example:
-
- <pre>
- <name>Sequence type</name>
- <description>
- --nuc - Assume the sequences are nucleotide.
- --amino - Assume the sequences are amino acid. </description>
- <optionNames>--amino</optionNames>
- <optionNames>--nuc</optionNames>
- <optionNames>--auto</optionNames>
- </pre>
-
- In the example, the "Sequence type" is a name whereas --amino, --nuc and
- --auto are all optionNames. This dichotomy only manifests in
- <code>Option</code> never in <code>Parameters</code> as the latter can
- only have single <optioNames> element\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the Parameter of Option name\r
-<DT><B>Returns:</B><DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeArgument(java.lang.String)"><!-- --></A><H3>\r
-removeArgument</H3>\r
-<PRE>\r
-public boolean <B>removeArgument</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> name)</PRE>\r
-<DL>\r
-<DD>Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found. Where Argument is either
- <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> or <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - of the argument\r
-<DT><B>Returns:</B><DD>true if argument was removed, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
-getArgumentByOptionName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgumentByOptionName</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> optionName)</PRE>\r
-<DL>\r
-<DD>Returns the argument by option name, NULL if the argument is not found\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - - the optionName. This is not the same as an Option name.
-
- For example:
-
- <pre>
- <name>Output sequences order</name>
- <description>--inputorder - Output order: same as input.
- --reorder - Output order: aligned. Default: same as input</description>
- <optionNames>--inputorder</optionNames>
- <optionNames>--reorder</optionNames>
- </pre>
-
- The name of the option in the example is
- "Output sequences order" whereas optionNames are
- "--inputorder" and "--reorder". If you need to retrieve the
- Option or Parameter by its names use
- <A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><CODE>getArgument(String)</CODE></A> method\r
-<DT><B>Returns:</B><DD>Option</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
-removeArgumentByOptionName</H3>\r
-<PRE>\r
-public boolean <B>removeArgumentByOptionName</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> optionName)</PRE>\r
-<DL>\r
-<DD>Removes the argument which can be a Parameter or an Option instance by
- the value in <optionNames> element of the runner configuration
- descriptor.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - the optionName of the option, do not confuse with the name!\r
-<DT><B>Returns:</B><DD>true if argument with optionName exists and was removed, false
- otherwise<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>for destinctions
- between optionNames and the name of the Option</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate()"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>()\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
-<DL>\r
-<DD>Validate the value of the argument. Checks whether the argument value is
- in the valid values range.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if any of the arguments found invalid which is when
- <dl>
- <li>Parameter value outside <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A> boundary</li>
- <li>Parameter name is not listed in possible values</li>
- </dl></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/RunnerConfig.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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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/RunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="RunnerConfig.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-UnsupportedRuntimeException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="UnsupportedRuntimeException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/UnsupportedRuntimeException.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
- <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/UnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="UnsupportedRuntimeException.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
-\r
-</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="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class UnsupportedRuntimeException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.UnsupportedRuntimeException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>UnsupportedRuntimeException</B><DT>extends <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Indicates that the server could not execute native executables. e.g. If Mafft
- (unix executable) is asked to be run on Windows. In context of JABAWS this
- exception indicates that the service is deployed but is not able to run.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin
-
- Date February 2010</DD>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.String)">UnsupportedRuntimeException</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> message)</CODE>\r
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-Enum ValueConstrain.Type</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ValueConstrain.Type</B>\r
-</PRE>\r
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-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>></DD>\r
-</DL>\r
-<DL>\r
-<DT><B>Enclosing class:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public static enum <B>ValueConstrain.Type</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>></DL>\r
-</PRE>\r
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-\r
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-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_summary"><!-- --></A>\r
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-<B>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#Float">Float</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#Integer">Integer</A></B></CODE>\r
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-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></A>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></TD>\r
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-<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
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-<B>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Integer"><!-- --></A><H3>\r
-Integer</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>Integer</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="Float"><!-- --></A><H3>\r
-Float</H3>\r
-<PRE>\r
-public static final <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>Float</B></PRE>\r
-<DL>\r
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-<A NAME="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared. This method may be used to iterate
-over the constants as follows:
-<pre>
-for (ValueConstrain.Type c : ValueConstrain.Type.values())
- System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>valueOf</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> name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type. (Extraneous whitespace characters are
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
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-compbio.metadata</FONT>\r
-<BR>\r
-Class ValueConstrain</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.ValueConstrain</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>ValueConstrain</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-The type and the lower and upper boundaries for numerical value.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 November 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- ======== NESTED CLASS SUMMARY ======== -->\r
-\r
-<A NAME="nested_class_summary"><!-- --></A>\r
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-<B>Nested Class Summary</B></FONT></TH>\r
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-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<B>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#ValueConstrain()">ValueConstrain</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getMax()">getMax</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getMin()">getMin</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> int</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#hashCode()">hashCode</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)">setMax</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> max)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)">setMin</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> min)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)">setType</A></B>(<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> type)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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/metadata/ValueConstrain.html#toString()">toString</A></B>()</CODE>\r
-\r
-<BR>\r
- </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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="ValueConstrain()"><!-- --></A><H3>\r
-ValueConstrain</H3>\r
-<PRE>\r
-public <B>ValueConstrain</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
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-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="getType()"><!-- --></A><H3>\r
-getType</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> <B>getType</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setType(compbio.metadata.ValueConstrain.Type)"><!-- --></A><H3>\r
-setType</H3>\r
-<PRE>\r
-public void <B>setType</B>(<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> type)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMax()"><!-- --></A><H3>\r
-getMax</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A> <B>getMax</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setMax(java.lang.String)"><!-- --></A><H3>\r
-setMax</H3>\r
-<PRE>\r
-public void <B>setMax</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> max)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getMin()"><!-- --></A><H3>\r
-getMin</H3>\r
-<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Number.html?is-external=true" title="class or interface in java.lang">Number</A> <B>getMin</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setMin(java.lang.String)"><!-- --></A><H3>\r
-setMin</H3>\r
-<PRE>\r
-public void <B>setMin</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> min)</PRE>\r
-<DL>\r
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-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<PRE>\r
-public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<PRE>\r
-public <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>toString</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
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-\r
-<A NAME="hashCode()"><!-- --></A><H3>\r
-hashCode</H3>\r
-<PRE>\r
-public int <B>hashCode</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
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-<TITLE>\r
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-\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.metadata</FONT>\r
-<BR>\r
-Class WrongParameterException</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">java.lang.Throwable</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">java.lang.Exception</A>\r
- <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.WrongParameterException</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>WrongParameterException</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A></DL>\r
-</PRE>\r
-\r
-<P>\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.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 October 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-<DT><B>See Also:</B><DD><A HREF="../../serialized-form.html#compbio.metadata.WrongParameterException">Serialized Form</A></DL>\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/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)">WrongParameterException</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> message)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)">WrongParameterException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)">WrongParameterException</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</CODE>\r
-\r
-<BR>\r
- </TD>\r
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- \r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#fillInStackTrace()" title="class or interface in java.lang">fillInStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getCause()" title="class or interface in java.lang">getCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getLocalizedMessage()" title="class or interface in java.lang">getLocalizedMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getMessage()" title="class or interface in java.lang">getMessage</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#getStackTrace()" title="class or interface in java.lang">getStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#initCause(java.lang.Throwable)" title="class or interface in java.lang">initCause</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace()" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintStream)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#printStackTrace(java.io.PrintWriter)" title="class or interface in java.lang">printStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#setStackTrace(java.lang.StackTraceElement[])" title="class or interface in java.lang">setStackTrace</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="WrongParameterException(compbio.metadata.Option)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="WrongParameterException(java.lang.String)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</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> message)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="WrongParameterException(java.lang.Throwable)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="WrongParameterException(java.lang.String, java.lang.Throwable)"><!-- --></A><H3>\r
-WrongParameterException</H3>\r
-<PRE>\r
-public <B>WrongParameterException</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> message,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang">Throwable</A> cause)</PRE>\r
-<DL>\r
-</DL>\r
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-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Interface compbio.metadata.Argument\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-}\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <SCRIPT type="text/javascript">\r
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-<B>Uses of Interface<br>compbio.metadata.Argument</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A></FONT></TH>\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.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
-Uses of <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that implement <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option<T></A></B></CODE>\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 ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></CODE>\r
-\r
-<BR>\r
- A single value containing an option supported by the web service e.g.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useArgument.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Argument.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
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-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ChunkHolder\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.ChunkHolder";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="ChunkHolder.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ChunkHolder</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</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
-</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
-Uses of <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></FONT></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>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)">pullExecStatistics</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,\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 <code>position</code>.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useChunkHolder.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="ChunkHolder.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.JobExecutionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.JobExecutionException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <SCRIPT type="text/javascript">\r
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-<A NAME="skip-navbar_top"></A>\r
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-<H2>\r
-<B>Uses of Class<br>compbio.metadata.JobExecutionException</B></H2>\r
-</CENTER>\r
-No usage of compbio.metadata.JobExecutionException\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="JobExecutionException.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
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.JobStatus\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.JobStatus";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="JobStatus.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
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.JobStatus</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</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.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
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></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/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)">getJobStatus</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 status of the job.</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
-Uses of <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
-<TD><CODE><B>JobStatus.</B><B><A HREF="../../../compbio/metadata/JobStatus.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>JobStatus.</B><B><A HREF="../../../compbio/metadata/JobStatus.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
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- </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="JobStatus.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
-\r
-</FONT></TD>\r
-</TR>\r
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-<A NAME="skip-navbar_bottom"></A>\r
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-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.JobSubmissionException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.JobSubmissionException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- </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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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.JobSubmissionException</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</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.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
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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> <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>MsaWS.</B><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="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>MsaWS.</B><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
- \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
-Uses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></CODE>\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 ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></CODE>\r
-\r
-<BR>\r
- Indicates that the server could not execute native executables.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useJobSubmissionException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="JobSubmissionException.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Limit\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.Limit";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
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- <A HREF="Limit.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Limit</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</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.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
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></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/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>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)">getLimit</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> presetName)</CODE>\r
-\r
-<BR>\r
- Get a Limit for a preset.</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
-Uses of <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></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/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getDefaultLimit()">getDefaultLimit</A></B>()</CODE>\r
-\r
-<BR>\r
- </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/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)">getLimitByName</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> presetName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#getLimits()">getLimits</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useLimit.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Limit.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.LimitExceededException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.LimitExceededException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="LimitExceededException.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
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- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-<A NAME="skip-navbar_top"></A>\r
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-\r
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-<H2>\r
-<B>Uses of Class<br>compbio.metadata.LimitExceededException</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</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.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
-Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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> <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>MsaWS.</B><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="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>MsaWS.</B><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
- \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
-Uses of <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></CODE></FONT></TD>\r
-<TD><CODE><B>LimitExceededException.</B><B><A HREF="../../../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)">newLimitExceeded</A></B>(<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><?> limit,\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/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> seqs)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useLimitExceededException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="LimitExceededException.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
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.LimitsManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.LimitsManager";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
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-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- </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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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="LimitsManager.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.LimitsManager</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</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
-</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
-Uses of <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A></FONT></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/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>MsaWS.</B><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
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useLimitsManager.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="LimitsManager.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Option\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.Option";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
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- <SCRIPT type="text/javascript">\r
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-<B>Uses of Class<br>compbio.metadata.Option</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</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.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
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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
-</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
-Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></CODE>\r
-\r
-<BR>\r
- A single value containing an option supported by the web service e.g.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></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/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the argument by its name if found, NULL otherwise.</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/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</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> optionName)</CODE>\r
-\r
-<BR>\r
- Returns the argument by option name, NULL if the argument is not found</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns list of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
- runner</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
-\r
-<BR>\r
- Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the list of the Options supported by the executable of type T</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</CODE>\r
-\r
-<BR>\r
- Adds Option to the internal list of options</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</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/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
-\r
-<BR>\r
- Adds the list of options or parameters to the internal list of options</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)">WrongParameterException</A></B>(<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?> option)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="Option.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
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-\r
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-</HTML>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Parameter\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
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-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
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-}\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useParameter.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Parameter.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
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Parameter</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\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.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
-Uses of <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the list of parameters supported executable of type T.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</CODE>\r
-\r
-<BR>\r
- Adds parameter to the internal parameter list</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</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/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
-\r
-<BR>\r
- Sets the list of parameters as internal list</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useParameter.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Parameter.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.Preset\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.Preset";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Preset.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.Preset</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</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.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
-Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> with parameters of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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
- \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
-Uses of <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></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/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)">getPresetByName</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> presetName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return types with arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#getPresets()">getPresets</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with type arguments of type <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#setPresets(java.util.List)">setPresets</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/metadata/Preset.html" title="class in compbio.metadata">Preset</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>>> presets)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-usePreset.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Preset.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.PresetManager\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.PresetManager";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-usePresetManager.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="PresetManager.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.PresetManager</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</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.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
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></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/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>MsaWS.</B><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
-</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
-Uses of <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>LimitsManager.</B><B><A HREF="../../../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)">validate</A></B>(<A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> presets)</CODE>\r
-\r
-<BR>\r
- Validate Limits</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-usePresetManager.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="PresetManager.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ResultNotAvailableException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.ResultNotAvailableException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="ResultNotAvailableException.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ResultNotAvailableException</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</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
-</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
-Uses of <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></FONT></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/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><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
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useResultNotAvailableException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="ResultNotAvailableException.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.RunnerConfig\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.RunnerConfig";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="RunnerConfig.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.RunnerConfig</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</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.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
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></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/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>MsaWS.</B><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
-</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
-Uses of <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></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/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A></FONT></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/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
-\r
-<BR>\r
- Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>PresetManager.</B><B><A HREF="../../../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)">validate</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> options)</CODE>\r
-\r
-<BR>\r
- Checks whether preset option and parameter are defined in RunnerConfig
- object.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useRunnerConfig.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="RunnerConfig.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.UnsupportedRuntimeException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.UnsupportedRuntimeException";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
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-</TD>\r
-</TR>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
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-<H2>\r
-<B>Uses of Class<br>compbio.metadata.UnsupportedRuntimeException</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</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
-</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
-Uses of <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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> <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>MsaWS.</B><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="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>MsaWS.</B><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
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/metadata/\class-useUnsupportedRuntimeException.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="UnsupportedRuntimeException.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.ValueConstrain.Type\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.metadata.ValueConstrain.Type";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="ValueConstrain.Type.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
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-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.metadata.ValueConstrain.Type</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\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.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
-Uses of <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></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/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.html#getType()">getType</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.Type.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.Type.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.Type.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>ValueConstrain.</B><B><A HREF="../../../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)">setType</A></B>(<A HREF="../../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A> type)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
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-<P>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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+++ /dev/null
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-<B>Uses of Class<br>compbio.metadata.ValueConstrain</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\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.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
-Uses of <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that return <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></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/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></CODE></FONT></TD>\r
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#getValidValue()">getValidValue</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> with parameters of type <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)">setValidValue</A></B>(<A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A> validValue)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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-</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 \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="ValueConstrain.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
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- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
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-</BODY>\r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.metadata.WrongParameterException\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
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- }\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
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-<B>Uses of Class<br>compbio.metadata.WrongParameterException</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</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.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
-Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\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>MsaWS.</B><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="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>MsaWS.</B><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
- \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
-Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/metadata/package-summary.html">compbio.metadata</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> <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/metadata/Preset.html" title="type parameter in Preset">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> rconfig)</CODE>\r
-\r
-<BR>\r
- Converts list of options as String to type Option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</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> defaultVal)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</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> defaultVal)</CODE>\r
-\r
-<BR>\r
- Sets one of the values defined in optionList as default.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>Argument.</B><B><A HREF="../../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</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> defaultValue)</CODE>\r
-\r
-<BR>\r
- Set default values for the parameter or an option</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</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> dValue)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="WrongParameterException.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
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-\r
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-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-compbio.metadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white">\r
-<FONT size="+1" CLASS="FrameTitleFont">\r
-<A HREF="../../compbio/metadata/package-summary.html" target="classFrame">compbio.metadata</A></FONT>\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Interfaces</FONT> \r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="Argument.html" title="interface in compbio.metadata" target="classFrame"><I>Argument</I></A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Classes</FONT> \r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="ChunkHolder.html" title="class in compbio.metadata" target="classFrame">ChunkHolder</A>\r
-<BR>\r
-<A HREF="Limit.html" title="class in compbio.metadata" target="classFrame">Limit</A>\r
-<BR>\r
-<A HREF="LimitsManager.html" title="class in compbio.metadata" target="classFrame">LimitsManager</A>\r
-<BR>\r
-<A HREF="Option.html" title="class in compbio.metadata" target="classFrame">Option</A>\r
-<BR>\r
-<A HREF="Parameter.html" title="class in compbio.metadata" target="classFrame">Parameter</A>\r
-<BR>\r
-<A HREF="Preset.html" title="class in compbio.metadata" target="classFrame">Preset</A>\r
-<BR>\r
-<A HREF="PresetManager.html" title="class in compbio.metadata" target="classFrame">PresetManager</A>\r
-<BR>\r
-<A HREF="RunnerConfig.html" title="class in compbio.metadata" target="classFrame">RunnerConfig</A>\r
-<BR>\r
-<A HREF="ValueConstrain.html" title="class in compbio.metadata" target="classFrame">ValueConstrain</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Enums</FONT> \r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="JobStatus.html" title="enum in compbio.metadata" target="classFrame">JobStatus</A>\r
-<BR>\r
-<A HREF="ValueConstrain.Type.html" title="enum in compbio.metadata" target="classFrame">ValueConstrain.Type</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-<TABLE BORDER="0" WIDTH="100%" SUMMARY="">\r
-<TR>\r
-<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">\r
-Exceptions</FONT> \r
-<FONT CLASS="FrameItemFont">\r
-<BR>\r
-<A HREF="JobExecutionException.html" title="class in compbio.metadata" target="classFrame">JobExecutionException</A>\r
-<BR>\r
-<A HREF="JobSubmissionException.html" title="class in compbio.metadata" target="classFrame">JobSubmissionException</A>\r
-<BR>\r
-<A HREF="LimitExceededException.html" title="class in compbio.metadata" target="classFrame">LimitExceededException</A>\r
-<BR>\r
-<A HREF="ResultNotAvailableException.html" title="class in compbio.metadata" target="classFrame">ResultNotAvailableException</A>\r
-<BR>\r
-<A HREF="UnsupportedRuntimeException.html" title="class in compbio.metadata" target="classFrame">UnsupportedRuntimeException</A>\r
-<BR>\r
-<A HREF="WrongParameterException.html" title="class in compbio.metadata" target="classFrame">WrongParameterException</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-compbio.metadata\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="compbio.metadata";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/data/sequence/package-summary.html"><B>PREV PACKAGE</B></A> \r
- <A HREF="../../compbio/ws/client/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/package-summary.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="package-summary.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.metadata\r
-</H2>\r
-A meta-data model for multiple sequence alignment web services
- Classes in this package have no dependencies to other sources in the project.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
- <A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\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>Interface Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument<T></A></B></TD>\r
-<TD>An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-\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>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A></B></TD>\r
-<TD>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 WIDTH="15%"><B><A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit<T></A></B></TD>\r
-<TD>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 WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager<T></A></B></TD>\r
-<TD>A collection of Limits</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option<T></A></B></TD>\r
-<TD>Command line option/flag or multiple exclusive options with no value.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter<T></A></B></TD>\r
-<TD>A single value containing an option supported by the web service e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset<T></A></B></TD>\r
-<TD>Collection of Options and Parameters with their values</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager<T></A></B></TD>\r
-<TD>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 WIDTH="15%"><B><A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig<T></A></B></TD>\r
-<TD>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 WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A></B></TD>\r
-<TD>The type and the lower and upper boundaries for numerical value.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-\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>Enum Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></B></TD>\r
-<TD>The status of the job.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-\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>Exception Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></B></TD>\r
-<TD>JobExecutionException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></B></TD>\r
-<TD>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 WIDTH="15%"><B><A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A></B></TD>\r
-<TD>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 WIDTH="15%"><B><A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></B></TD>\r
-<TD>ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A></B></TD>\r
-<TD>Indicates that the server could not execute native executables.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></B></TD>\r
-<TD>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
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.metadata Description\r
-</H2>\r
-\r
-<P>\r
-A meta-data model for multiple sequence alignment web services
- Classes in this package have no dependencies to other sources in the project.
- They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS)\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 January 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>Peter Troshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-Hierarchy For Package compbio.metadata\r
-</H2>\r
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-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="../../overview-tree.html">All Packages</A></DL>\r
-<HR>\r
-<H2>\r
-Class Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><T> (implements compbio.metadata.<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T>)\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><T></UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><T><LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
-<UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang"><B>Exception</B></A><UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A><UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A></UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A></UL>\r
-</UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A></UL>\r
-</UL>\r
-<H2>\r
-Interface Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><T></UL>\r
-<H2>\r
-Enum Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang"><B>Enum</B></A><E> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><T>, java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A><LI TYPE="circle">compbio.metadata.<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A></UL>\r
-</UL>\r
-</UL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../compbio/data/sequence/package-tree.html"><B>PREV</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
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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.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.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
- \r
-<P>\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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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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- <A HREF="package-use.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
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- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Jws2Client\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
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-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Jws2Client";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\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/Jws2Client.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- 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
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Class Jws2Client</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Jws2Client</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>Jws2Client</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-A command line client for JAva Bioinformatics Analysis Web Services\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</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>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</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> host,\r
- <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
-\r
-<BR>\r
- Connects to a web service by the host and the service name</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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/ws/client/Jws2Client.html#getHost(java.lang.String[])">getHost</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>[] cmd)</CODE>\r
-\r
-<BR>\r
- Extracts host name from the command line</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <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/ws/client/Jws2Client.html#getServiceName(java.lang.String[])">getServiceName</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>[] cmd)</CODE>\r
-\r
-<BR>\r
- Extracts service name from the command line</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#main(java.lang.String[])">main</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>[] args)</CODE>\r
-\r
-<BR>\r
- Starts command line client, if no parameter are supported print help.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)">validURL</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> urlstr)</CODE>\r
-\r
-<BR>\r
- Attempt to construct the URL object from the string</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></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="validURL(java.lang.String)"><!-- --></A><H3>\r
-validURL</H3>\r
-<PRE>\r
-public static boolean <B>validURL</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> urlstr)</PRE>\r
-<DL>\r
-<DD>Attempt to construct the URL object from the string\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>urlstr</CODE> - \r
-<DT><B>Returns:</B><DD>true if it succeed false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getServiceName(java.lang.String[])"><!-- --></A><H3>\r
-getServiceName</H3>\r
-<PRE>\r
-public static <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>getServiceName</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>[] cmd)</PRE>\r
-<DL>\r
-<DD>Extracts service name from the command line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>cmd</CODE> - command line options\r
-<DT><B>Returns:</B><DD>service name or null if it is not defined</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getHost(java.lang.String[])"><!-- --></A><H3>\r
-getHost</H3>\r
-<PRE>\r
-public static <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>getHost</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>[] cmd)</PRE>\r
-<DL>\r
-<DD>Extracts host name from the command line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>cmd</CODE> - command line options\r
-<DT><B>Returns:</B><DD>host name or null if it is not defined</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="connect(java.lang.String, compbio.ws.client.Services)"><!-- --></A><H3>\r
-connect</H3>\r
-<PRE>\r
-public static <T> <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T> <B>connect</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> host,\r
- <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/ws/WebServiceException.html?is-external=true" title="class or interface in javax.xml.ws">WebServiceException</A></PRE>\r
-<DL>\r
-<DD>Connects to a web service by the host and the service name\r
-<P>\r
-<DD><DL>\r
-<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>host</CODE> - <DD><CODE>service</CODE> - \r
-<DT><B>Returns:</B><DD>MsaWS<T>\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/ws/WebServiceException.html?is-external=true" title="class or interface in javax.xml.ws">WebServiceException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static void <B>main</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>[] args)</PRE>\r
-<DL>\r
-<DD>Starts command line client, if no parameter are supported print help. Two
- parameters are required for successfull call the JWS2 host name and a
- service name.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>args</CODE> - Usage: <Class or Jar file name> -h=host_and_context
- -s=serviceName ACTION [OPTIONS]
-
- -h=<host_and_context> - a full URL to the JWS2 web server
- including context path e.g. http://10.31.1.159:8080/ws
-
- -s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS,
- TcoffeeWS, ProbconsWS] ACTIONS:
-
- -i=<inputFile> - full path to fasta formatted sequence file,
- from which to align sequences
-
- -parameters - lists parameters supported by web service
-
- -presets - lists presets supported by web service
-
- -limits - lists web services limits Please note that if input
- file is specified other actions are ignored
-
- OPTIONS: (only for use with -i action):
-
- -r=<presetName> - name of the preset to use
-
- -o=<outputFile> - full path to the file where to write an
- alignment -f=<parameterInputFile> - the name of the file with
- the list of parameters to use. Please note that -r and -f
- options cannot be used together. Alignment is done with either
- preset or a parameters from the file, but not both!</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/Jws2Client.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV CLASS \r
- <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/client/Jws2Client.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Jws2Client.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- 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
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Services\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Services";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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/Services.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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/client/Services.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Services.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Enum Services</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">java.lang.Enum</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.Services</B>\r
-</PRE>\r
-<DL>\r
-<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>></DD>\r
-</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public enum <B>Services</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A><<A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>></DL>\r
-</PRE>\r
-\r
-<P>\r
-List of web services currently supported by JABAWS version 1\r
-<P>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== ENUM CONSTANT SUMMARY =========== -->\r
-\r
-<A NAME="enum_constant_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>Enum Constant Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#ClustalWS">ClustalWS</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#MafftWS">MafftWS</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#MuscleWS">MuscleWS</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#ProbconsWS">ProbconsWS</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#TcoffeeWS">TcoffeeWS</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>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#getService(java.lang.Class)">getService</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A> wsImplClass)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#getService(java.lang.String)">getService</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> servName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/Services.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Enum"><!-- --></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#compareTo(E)" title="class or interface in java.lang">compareTo</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#getDeclaringClass()" title="class or interface in java.lang">getDeclaringClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#name()" title="class or interface in java.lang">name</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#ordinal()" title="class or interface in java.lang">ordinal</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true#valueOf(java.lang.Class, java.lang.String)" title="class or interface in java.lang">valueOf</A></CODE></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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ ENUM CONSTANT DETAIL =========== -->\r
-\r
-<A NAME="enum_constant_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>Enum Constant Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="MafftWS"><!-- --></A><H3>\r
-MafftWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>MafftWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="MuscleWS"><!-- --></A><H3>\r
-MuscleWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>MuscleWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ClustalWS"><!-- --></A><H3>\r
-ClustalWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>ClustalWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="TcoffeeWS"><!-- --></A><H3>\r
-TcoffeeWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>TcoffeeWS</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="ProbconsWS"><!-- --></A><H3>\r
-ProbconsWS</H3>\r
-<PRE>\r
-public static final <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>ProbconsWS</B></PRE>\r
-<DL>\r
-<DL>\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="values()"><!-- --></A><H3>\r
-values</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>[] <B>values</B>()</PRE>\r
-<DL>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared. This method may be used to iterate
-over the constants as follows:
-<pre>
-for (Services c : Services.values())
- System.out.println(c);
-</pre>\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>an array containing the constants of this enum type, in
-the order they are declared</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="valueOf(java.lang.String)"><!-- --></A><H3>\r
-valueOf</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>valueOf</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> name)</PRE>\r
-<DL>\r
-<DD>Returns the enum constant of this type with the specified name.
-The string must match <I>exactly</I> an identifier used to declare an
-enum constant in this type. (Extraneous whitespace characters are
-not permitted.)\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the name of the enum constant to be returned.\r
-<DT><B>Returns:</B><DD>the enum constant with the specified name\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</A></CODE> - if this enum type has no constant
-with the specified name\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the argument is null</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getService(java.lang.String)"><!-- --></A><H3>\r
-getService</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>getService</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> servName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getService(java.lang.Class)"><!-- --></A><H3>\r
-getService</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> <B>getService</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A> wsImplClass)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</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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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\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/Services.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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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>NEXT CLASS</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/client/Services.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Services.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
-\r
-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#enum_constant_summary">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: <A HREF="#enum_constant_detail">ENUM CONSTANTS</A> | FIELD | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-WSTester\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="WSTester";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\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/WSTester.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>PREV CLASS</B></A> \r
- NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/client/WSTester.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="WSTester.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
-\r
-</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
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.ws.client</FONT>\r
-<BR>\r
-Class WSTester</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.ws.client.WSTester</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public class <B>WSTester</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-Class for testing web services\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 February 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\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/client/WSTester.html#WSTester()">WSTester</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>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> void</CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/ws/client/WSTester.html#main(java.lang.String[])">main</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>[] args)</CODE>\r
-\r
-<BR>\r
- Test JWS2 web services</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.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></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="WSTester()"><!-- --></A><H3>\r
-WSTester</H3>\r
-<PRE>\r
-public <B>WSTester</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="main(java.lang.String[])"><!-- --></A><H3>\r
-main</H3>\r
-<PRE>\r
-public static <T> void <B>main</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>[] args)\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
-<DL>\r
-<DD>Test JWS2 web services\r
-<P>\r
-<DD><DL>\r
-<DT><B>Type Parameters:</B><DD><CODE>T</CODE> - web service type<DT><B>Parameters:</B><DD><CODE>args</CODE> - -h=<Your web application server host name, port and JWS2
- context path>
-
- -s=<ServiceName> which is optional. If service name is not
- provided then all known JWS2 web services are tested\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></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
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- <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/WSTester.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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>PREV CLASS</B></A> \r
- NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/ws/client/WSTester.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="WSTester.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
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-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</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
-</TR>\r
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-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.Jws2Client\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.ws.client.Jws2Client";\r
- }\r
-}\r
-</SCRIPT>\r
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-\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.Jws2Client</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.client.Jws2Client\r
-<P>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- PREV \r
- NEXT</FONT></TD>\r
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- <A HREF="Jws2Client.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
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-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.Services\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.ws.client.Services";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="Services.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.Services</B></H2>\r
-</CENTER>\r
-\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
-Packages that use <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services. </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-<A NAME="compbio.ws.client"><!-- --></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
-Uses of <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A></FONT></TH>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> that return <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
-<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#getService(java.lang.Class)">getService</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A> wsImplClass)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
-<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#getService(java.lang.String)">getService</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> servName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></CODE></FONT></TD>\r
-<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#valueOf(java.lang.String)">valueOf</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the enum constant of this type with the specified name.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>[]</CODE></FONT></TD>\r
-<TD><CODE><B>Services.</B><B><A HREF="../../../../compbio/ws/client/Services.html#values()">values</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns an array containing the constants of this enum type, in
-the order they are declared.</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/client/package-summary.html">compbio.ws.client</A> with parameters of type <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B>Jws2Client.</B><B><A HREF="../../../../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)">connect</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> host,\r
- <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A> service)</CODE>\r
-\r
-<BR>\r
- Connects to a web service by the host and the service name</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\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="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </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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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="Services.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Uses of Class compbio.ws.client.WSTester\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Uses of Class compbio.ws.client.WSTester";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT> </TD>\r
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- <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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="WSTester.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
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
-<HR>\r
-<CENTER>\r
-<H2>\r
-<B>Uses of Class<br>compbio.ws.client.WSTester</B></H2>\r
-</CENTER>\r
-No usage of compbio.ws.client.WSTester\r
-<P>\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
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-Package compbio.ws.client\r
-</H2>\r
-A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services.\r
-<P>\r
-<B>See:</B>\r
-<BR>\r
- <A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\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>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A></B></TD>\r
-<TD>A command line client for JAva Bioinformatics Analysis Web Services</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></B></TD>\r
-<TD>Class for testing web services</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-\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>Enum Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A></B></TD>\r
-<TD>List of web services currently supported by JABAWS version 1</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.ws.client Description\r
-</H2>\r
-\r
-<P>\r
-A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 April 2010</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>Peter Troshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-\r
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-<UL>\r
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-<TD><A HREF="#compbio.ws.client"><B>compbio.ws.client</B></A></TD>\r
-<TD>A command line client and web services testing client for
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-compbio.data.*</FONT></TH>\r
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-<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
-<CODE>public static final char</CODE></FONT></TD>\r
-<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
-<TD ALIGN="right"><CODE>45</CODE></TD>\r
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-<TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>></TH>\r
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-<A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
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-<DL>\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AA"><B>AA</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Valid Amino acids\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option<T>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Adds Option to the internal list of options\r
-<DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Adds an option to the optionName list\r
-<DT><A HREF="../compbio/metadata/Parameter.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter<T>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Adds parameter to the internal parameter list\r
-<DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List<FastaSequence>)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Align a list of sequences with default settings.\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Multiple sequence alignment.<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)"><B>Alignment(List<FastaSequence>, Program, char)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><B>Alignment(List<FastaSequence>, AlignmentMetadata)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Alignment metadata e.g.<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)"><B>AlignmentMetadata(Program, char)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Same as AA pattern but with two additional letters - XU\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Ambiguous nucleotide\r
-<DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>> - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
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-<A NAME="_L_"><!-- --></A><H2>\r
-<B>L</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A><<A HREF="../compbio/metadata/Limit.html" title="type parameter in Limit">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A value object containing a maximum number of sequences and a maximum average
- sequence length for a preset.<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String)"><B>Limit(int, int, String)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>Instantiate the limit\r
-<DT><A HREF="../compbio/metadata/Limit.html#Limit(int, int, java.lang.String, boolean)"><B>Limit(int, int, String, boolean)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>This exception is thrown if the task larger in size that the limit that
- applies to the calculation.<DT><A HREF="../compbio/metadata/LimitExceededException.html#LimitExceededException(java.lang.String)"><B>LimitExceededException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><<A HREF="../compbio/metadata/LimitsManager.html" title="type parameter in LimitsManager">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A collection of Limits<DT><A HREF="../compbio/metadata/LimitsManager.html#LimitsManager()"><B>LimitsManager()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET"><B>LOCAL_ENGINE_LIMIT_PRESET</B></A> - \r
-Static variable in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
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+++ /dev/null
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-function windowTitle()\r
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- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-<A NAME="_M_"><!-- --></A><H2>\r
-<B>M</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Starts command line client, if no parameter are supported print help.\r
-<DT><A HREF="../compbio/ws/client/WSTester.html#main(java.lang.String[])"><B>main(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<DD>Test JWS2 web services\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><<A HREF="../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Multiple Sequence Alignment (MSA) Web Services Interface</DL>\r
-<HR>\r
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-\r
-</BODY>\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="N-Index";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<A NAME="_N_"><!-- --></A><H2>\r
-<B>N</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/Option.html#name"><B>name</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)"><B>newLimitExceeded(Limit<?>, List<FastaSequence>)</B></A> - \r
-Static method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_AA"><B>NON_AA</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>inversion of AA pattern\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE"><B>NON_NUCLEOTIDE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Non nucleotide\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NONWORD"><B>NONWORD</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Non word\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE"><B>NUCLEOTIDE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Nucleotides a, t, g, c, u\r
-</DL>\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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- <SCRIPT type="text/javascript">\r
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-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-O-Index\r
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-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
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-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="O-Index";\r
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-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-</TABLE>\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-12.html"><B>PREV LETTER</B></A> \r
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- <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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_O_"><!-- --></A><H2>\r
-<B>O</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><<A HREF="../compbio/metadata/Option.html" title="type parameter in Option">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Command line option/flag or multiple exclusive options with no value.<DT><A HREF="../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)"><B>Option(String, String)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
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-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-12.html"><B>PREV LETTER</B></A> \r
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- <A HREF="index-13.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
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
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-<A NAME="skip-navbar_bottom"></A>\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-P-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="P-Index";\r
- }\r
-}\r
-</SCRIPT>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <SCRIPT type="text/javascript">\r
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- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
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-</TR>\r
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-<A NAME="skip-navbar_top"></A>\r
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-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_P_"><!-- --></A><H2>\r
-<B>P</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><<A HREF="../compbio/metadata/Parameter.html" title="type parameter in Parameter">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>A single value containing an option supported by the web service e.g.<DT><A HREF="../compbio/metadata/Parameter.html#Parameter(java.lang.String, java.lang.String)"><B>Parameter(String, String)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><<A HREF="../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of Options and Parameters with their values<DT><A HREF="../compbio/metadata/Preset.html#Preset()"><B>Preset()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)"><B>presetAlign(List<FastaSequence>, Preset<T>)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Align a list of sequences with preset.\r
-<DT><A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><<A HREF="../compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Collection of presets and methods to manipulate them @see <A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata"><CODE>Preset</CODE></A><DT><A HREF="../compbio/metadata/PresetManager.html#PresetManager()"><B>PresetManager()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>The list of programmes that can produce alignments<DT><A HREF="../compbio/data/msa/MsaWS.html#pullExecStatistics(java.lang.String, long)"><B>pullExecStatistics(String, long)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Reads 1kb chunk from the statistics file which is specific to a given web
- service from the <code>position</code>.\r
-</DL>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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-<A NAME="_R_"><!-- --></A><H2>\r
-<B>R</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Read Clustal formatted alignment.\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Reads fasta sequences from inStream into the list of FastaSequence
- objects\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Removes the argument which can be a Parameter or an Option instance by
- the value in <optionNames> element of the runner configuration
- descriptor.\r
-<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>ResultNotAvailableException is thrown wherever the results of the calculation
- cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>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.<DT><A HREF="../compbio/metadata/RunnerConfig.html#RunnerConfig()"><B>RunnerConfig()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_S_"><!-- --></A><H2>\r
-<B>S</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Utility class for operations on sequences<DT><A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A> - Enum in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>List of web services currently supported by JABAWS version 1<DT><A HREF="../compbio/metadata/Option.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Sets one of the values defined in optionList as default.\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)"><B>setDefaultValue(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#setDescription(java.lang.String)"><B>setDescription(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#setFurtherDetails(java.net.URL)"><B>setFurtherDetails(URL)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMax(java.lang.String)"><B>setMax(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#setMin(java.lang.String)"><B>setMin(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#setName(java.lang.String)"><B>setName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#setOptionName(java.lang.String)"><B>setOptionName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#setOptionNames(java.util.Set)"><B>setOptionNames(Set<String>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#setOptions(java.util.List)"><B>setOptions(List<String>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)"><B>setOptions(List<Option<T>>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Adds the list of options or parameters to the internal list of options\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)"><B>setParameters(List<Parameter<T>>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Sets the list of parameters as internal list\r
-<DT><A HREF="../compbio/metadata/Parameter.html#setPossibleValues(java.util.Set)"><B>setPossibleValues(Set<String>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#setPresets(java.util.List)"><B>setPresets(List<Preset<T>>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)"><B>setPrmSeparator(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Sets name value separator character\r
-<DT><A HREF="../compbio/metadata/Option.html#setRequired(boolean)"><B>setRequired(boolean)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)"><B>setRunnerClassName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Set the name of a runner class\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#setType(compbio.metadata.ValueConstrain.Type)"><B>setType(ValueConstrain.Type)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#setValidValue(compbio.metadata.ValueConstrain)"><B>setValidValue(ValueConstrain)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Argument.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD>Set default values for the parameter or an option\r
-<DT><A HREF="../compbio/metadata/Option.html#setValue(java.lang.String)"><B>setValue(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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-\r
-</BODY>\r
-</HTML>\r
+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-T-Index\r
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-function windowTitle()\r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<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
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_T_"><!-- --></A><H2>\r
-<B>T</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/Option.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Convert the option to the command string.\r
-<DT><A HREF="../compbio/metadata/Parameter.html#toCommand(java.lang.String)"><B>toCommand(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Same as oneLineFasta\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#toString()"><B>toString()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-</DL>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-16.html"><B>PREV LETTER</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-U-Index\r
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-<META NAME="date" CONTENT="2010-11-24">\r
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-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="U-Index";\r
- }\r
-}\r
-</SCRIPT>\r
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-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-</TR>\r
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- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
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-</FONT></TD>\r
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-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_U_"><!-- --></A><H2>\r
-<B>U</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>UnknownFileFormatException</B></A> - Exception in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD> <DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException()"><B>UnknownFileFormatException()</B></A> - \r
-Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.io.File, java.lang.Throwable)"><B>UnknownFileFormatException(File, Throwable)</B></A> - \r
-Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String, java.lang.Throwable)"><B>UnknownFileFormatException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.String)"><B>UnknownFileFormatException(String)</B></A> - \r
-Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/UnknownFileFormatException.html#UnknownFileFormatException(java.lang.Throwable)"><B>UnknownFileFormatException(Throwable)</B></A> - \r
-Constructor for exception compbio.data.sequence.<A HREF="../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Indicates that the server could not execute native executables.<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.String)"><B>UnsupportedRuntimeException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/UnsupportedRuntimeException.html#UnsupportedRuntimeException(java.lang.Throwable)"><B>UnsupportedRuntimeException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
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-<A NAME="navbar_bottom"><!-- --></A>\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HTML>\r
-<HEAD>\r
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-<TITLE>\r
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-function windowTitle()\r
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-}\r
-</SCRIPT>\r
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-</TD>\r
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-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-18.html"><B>PREV LETTER</B></A> \r
- <A HREF="index-20.html"><B>NEXT LETTER</B></A></FONT></TD>\r
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- <A HREF="../index.html?index-filesindex-19.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="index-19.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_V_"><!-- --></A><H2>\r
-<B>V</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#validate(compbio.metadata.PresetManager)"><B>validate(PresetManager<T>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD>Validate Limits\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#validate(compbio.metadata.RunnerConfig)"><B>validate(RunnerConfig<T>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD>Checks whether preset option and parameter are defined in RunnerConfig
- object.\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#validate()"><B>validate()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Validate the value of the argument.\r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#validURL(java.lang.String)"><B>validURL(String)</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Attempt to construct the URL object from the string\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The type and the lower and upper boundaries for numerical value.<DT><A HREF="../compbio/metadata/ValueConstrain.html#ValueConstrain()"><B>ValueConstrain()</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD> <DT><A HREF="../compbio/data/sequence/Program.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/metadata/JobStatus.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/ws/client/Services.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
-<DD>Returns the enum constant of this type with the specified name.\r
-<DT><A HREF="../compbio/data/sequence/Program.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/metadata/JobStatus.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/metadata/ValueConstrain.Type.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata">ValueConstrain.Type</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-<DT><A HREF="../compbio/ws/client/Services.html#values()"><B>values()</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
-<DD>Returns an array containing the constants of this enum type, in
-the order they are declared.\r
-</DL>\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
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-18.html"><B>PREV LETTER</B></A> \r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
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-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-C-Index\r
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-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
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-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="C-Index";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-1.html"><B>PREV LETTER</B></A> \r
- <A HREF="index-3.html"><B>NEXT LETTER</B></A></FONT></TD>\r
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- <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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_C_"><!-- --></A><H2>\r
-<B>C</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Stop running the job <code>jobId</code> but leave its output untouched\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of a string data together with the position in a file for
- the next read operation.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
-Constructor for class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)"><B>cleanSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Removes all whitespace chars in the sequence string\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#closeSilently(java.util.logging.Logger, java.io.Closeable)"><B>closeSilently(Logger, Closeable)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Closes the Closable and logs the exception if any\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/ws/client/package-summary.html"><B>compbio.ws.client</B></A> - package compbio.ws.client<DD>A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Connects to a web service by the host and the service name\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig<?>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List<FastaSequence>, List<Option<T>>)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Align a list of sequences with options.\r
-</DL>\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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-</BODY>\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-W-Index\r
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-<META NAME="date" CONTENT="2010-11-24">\r
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-function windowTitle()\r
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- if (location.href.indexOf('is-external=true') == -1) {\r
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-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-</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
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-<A NAME="skip-navbar_top"></A>\r
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-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_W_"><!-- --></A><H2>\r
-<B>W</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE"><B>WHITE_SPACE</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>A whitespace character: [\t\n\x0B\f\r]\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(OutputStream, Alignment)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Write Clustal formatted alignment Limitations: does not record the
- consensus.\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)"><B>writeFasta(OutputStream, List<FastaSequence>, int)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)"><B>writeFasta(OutputStream, List<FastaSequence>)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Writes FastaSequence in the file, each sequence will take one line only\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><B>writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>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.<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(compbio.metadata.Option)"><B>WrongParameterException(Option<?>)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String)"><B>WrongParameterException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.Throwable)"><B>WrongParameterException(Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/WrongParameterException.html#WrongParameterException(java.lang.String, java.lang.Throwable)"><B>WrongParameterException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>Class for testing web services<DT><A HREF="../compbio/ws/client/WSTester.html#WSTester()"><B>WSTester()</B></A> - \r
-Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<DD> \r
-</DL>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- NEXT LETTER</FONT></TD>\r
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- <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
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-<A NAME="skip-navbar_bottom"></A>\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-D-Index\r
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-\r
-<META NAME="date" CONTENT="2010-11-24">\r
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-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="D-Index";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
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-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
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-<!-- ========= START OF TOP NAVBAR ======= -->\r
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-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
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-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
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- <A HREF="index-2.html"><B>PREV LETTER</B></A> \r
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- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<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
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_D_"><!-- --></A><H2>\r
-<B>D</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)"><B>deepCleanSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Removes all special characters and digits as well as whitespace chars
- from the sequence\r
-<DT><A HREF="../compbio/metadata/Option.html#defaultValue"><B>defaultValue</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#description"><B>description</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#DIGIT"><B>DIGIT</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>A digit\r
-</DL>\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
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-2.html"><B>PREV LETTER</B></A> \r
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- <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
-\r
-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-E-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="E-Index";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-3.html"><B>PREV LETTER</B></A> \r
- <A HREF="index-5.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../index.html?index-filesindex-4.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="index-4.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_E_"><!-- --></A><H2>\r
-<B>E</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD>Please note that this implementation does not take the order of sequences
- into account!\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-</DL>\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"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-3.html"><B>PREV LETTER</B></A> \r
- <A HREF="index-5.html"><B>NEXT LETTER</B></A></FONT></TD>\r
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- <A HREF="../index.html?index-filesindex-4.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="index-4.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-F-Index\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="F-Index";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
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-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
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- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-4.html"><B>PREV LETTER</B></A> \r
- <A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../index.html?index-filesindex-5.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="index-5.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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_F_"><!-- --></A><H2>\r
-<B>F</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>A FASTA formatted sequence.<DT><A HREF="../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)"><B>FastaSequence(String, String)</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Upon construction the any whitespace characters are removed from the
- sequence\r
-<DT><A HREF="../compbio/metadata/Option.html#furtherDetails"><B>furtherDetails</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-</DL>\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"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../overview-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="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-4.html"><B>PREV LETTER</B></A> \r
- <A HREF="index-6.html"><B>NEXT LETTER</B></A></FONT></TD>\r
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- <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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
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-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_G_"><!-- --></A><H2>\r
-<B>G</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar"><B>gapchar</B></A> - \r
-Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Dash char to be used as gap char in the alignments\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getActualNumberofSequences()"><B>getActualNumberofSequences()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><B>getArgument(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the argument by its name if found, NULL otherwise.\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><B>getArgumentByOptionName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the argument by option name, NULL if the argument is not found\r
-<DT><A HREF="../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)"><B>getArguments(RunnerConfig<T>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD>Converts list of options as String to type Option\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getArguments()"><B>getArguments()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
- runner\r
-<DT><A HREF="../compbio/metadata/Limit.html#getAvgSeqLength()"><B>getAvgSeqLength()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#getAvgSequenceLength(java.util.List)"><B>getAvgSequenceLength(List<FastaSequence>)</B></A> - \r
-Static method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>Calculates an average sequence length of the dataset\r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#getChunk()"><B>getChunk()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getDefaultLimit()"><B>getDefaultLimit()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getDefaultValue()"><B>getDefaultValue()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>A default value of the option.\r
-<DT><A HREF="../compbio/metadata/Argument.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>A long description of the Option\r
-<DT><A HREF="../compbio/metadata/Preset.html#getDescription()"><B>getDescription()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)"><B>getFormatedSequence(int)</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Format sequence per width letter in one string.\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getFormattedFasta()"><B>getFormattedFasta()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getFurtherDetails()"><B>getFurtherDetails()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>The URL where further details about the option can be found\r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getGapchar()"><B>getGapchar()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getHost(java.lang.String[])"><B>getHost(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts host name from the command line\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getId()"><B>getId()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Gets the value of id\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getJobStatus(java.lang.String)"><B>getJobStatus(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Return the status of the job.\r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getLength()"><B>getLength()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimit(java.lang.String)"><B>getLimit(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Get a Limit for a preset.\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimitByName(java.lang.String)"><B>getLimitByName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>List Limits supported by a web service.\r
-<DT><A HREF="../compbio/metadata/LimitsManager.html#getLimits()"><B>getLimits()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMax()"><B>getMax()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#getMetadata()"><B>getMetadata()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#getMin()"><B>getMin()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Argument.html#getName()"><B>getName()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Human readable name of the option\r
-<DT><A HREF="../compbio/metadata/Preset.html#getName()"><B>getName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#getNextPosition()"><B>getNextPosition()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getNumberOfSequencesAllowed()"><B>getNumberOfSequencesAllowed()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getOnelineFasta()"><B>getOnelineFasta()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#getOptionName()"><B>getOptionName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getOptionNames()"><B>getOptionNames()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#getOptions()"><B>getOptions()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getOptions()"><B>getOptions()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the list of the Options supported by the executable of type T\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getParameters()"><B>getParameters()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD>Returns the list of parameters supported executable of type T.\r
-<DT><A HREF="../compbio/metadata/Argument.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in interface compbio.metadata.<A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>List of possible optionNames\r
-<DT><A HREF="../compbio/metadata/Parameter.html#getPossibleValues()"><B>getPossibleValues()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD>List is more convenient to work with\r
-<DT><A HREF="../compbio/metadata/Limit.html#getPreset()"><B>getPreset()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getPresetByName(java.lang.String)"><B>getPresetByName(String)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Get presets supported by a web service\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getPresets()"><B>getPresets()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getPrmSeparator()"><B>getPrmSeparator()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#getProgram()"><B>getProgram()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getResult(java.lang.String)"><B>getResult(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Return the result of the job.\r
-<DT><A HREF="../compbio/metadata/PresetManager.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#getRunnerClassName()"><B>getRunnerClassName()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#getRunnerOptions()"><B>getRunnerOptions()</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
-<DD>Get options supported by a web service\r
-<DT><A HREF="../compbio/metadata/Limit.html#getSeqNumber()"><B>getSeqNumber()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#getSequence()"><B>getSequence()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD>Gets the value of sequence\r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtActual()"><B>getSequenceLenghtActual()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/LimitExceededException.html#getSequenceLenghtAllowed()"><B>getSequenceLenghtAllowed()</B></A> - \r
-Method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#getSequences()"><B>getSequences()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.String)"><B>getService(String)</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/client/Services.html#getService(java.lang.Class)"><B>getService(Class)</B></A> - \r
-Static method in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html#getServiceName(java.lang.String[])"><B>getServiceName(String[])</B></A> - \r
-Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
-<DD>Extracts service name from the command line\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#getSize()"><B>getSize()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#getType()"><B>getType()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#getValidValue()"><B>getValidValue()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
-\r
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- }\r
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-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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-<A NAME="skip-navbar_top"></A>\r
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-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_H_"><!-- --></A><H2>\r
-<B>H</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/Alignment.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/FastaSequence.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ChunkHolder.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Parameter.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Preset.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/ValueConstrain.html#hashCode()"><B>hashCode()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata">ValueConstrain</A>\r
-<DD> \r
-</DL>\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
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+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-<TITLE>\r
-I-Index\r
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-</TD>\r
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-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
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-<NOSCRIPT>\r
- <A HREF="../allclasses-noframe.html"><B>All Classes</B></A>\r
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-\r
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-</FONT></TD>\r
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-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
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-\r
-<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
-<A NAME="_I_"><!-- --></A><H2>\r
-<B>I</B></H2>\r
-<DL>\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Check whether the sequence confirms to amboguous protein sequence\r
-<DT><A HREF="../compbio/metadata/Limit.html#isDefault()"><B>isDefault()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List<FastaSequence>)</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
-<DD>Checks if the number of sequences or their average length in the dataset
- exceeds this limit.\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char\r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)"><B>isNucleotideSequence(FastaSequence)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD> \r
-<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#isRequired"><B>isRequired</B></A> - \r
-Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - \r
-Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
-<DD>Flag that indicated that this option must be specified in the command
- line for an executable to run\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - \r
-Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
-<DD>Please note this method closes the input stream provided as a parameter\r
-</DL>\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
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-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
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- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="index-7.html"><B>PREV LETTER</B></A> \r
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- cannot be obtained.<DT><A HREF="../compbio/metadata/JobExecutionException.html#JobExecutionException(java.lang.String)"><B>JobExecutionException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
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-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A>\r
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-<DT><A HREF="../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A> - Enum in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The status of the job.<DT><A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Exception for generic problems with JobSubmission it is often thrown as a
- wrapper for the lower level exceptions like IOException or DrmaaException.<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String)"><B>JobSubmissionException(String)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
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-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/metadata/JobSubmissionException.html#JobSubmissionException(java.lang.String, java.lang.Throwable)"><B>JobSubmissionException(String, Throwable)</B></A> - \r
-Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A>\r
-<DD> \r
-<DT><A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>A command line client for JAva Bioinformatics Analysis Web Services</DL>\r
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-JABAWS datamodel and client documentation\r
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-<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="20%"><B><A HREF="compbio/data/sequence/package-summary.html">compbio.data.sequence</A></B></TD>\r
-<TD>A data model for multiple sequence alignment web services and utility methods
- that work on the objects of this model.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="20%"><B><A HREF="compbio/metadata/package-summary.html">compbio.metadata</A></B></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
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="20%"><B><A HREF="compbio/ws/client/package-summary.html">compbio.ws.client</A></B></TD>\r
-<TD>A command line client and web services testing client for
- JAva Bioinformatics Analysis Web Services.</TD>\r
-</TR>\r
-</TABLE>\r
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- <SCRIPT type="text/javascript">\r
- <!--\r
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- document.writeln('<A HREF="allclasses-noframe.html"><B>All Classes</B></A>');\r
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+++ /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_21) on Wed Nov 24 12:17:19 GMT 2010 -->\r
-<TITLE>\r
-Class Hierarchy\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Class Hierarchy";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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-<HR>\r
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-<H2>\r
-Hierarchy For All Packages</H2>\r
-</CENTER>\r
-<DL>\r
-<DT><B>Package Hierarchies:</B><DD><A HREF="compbio/data/msa/package-tree.html">compbio.data.msa</A>, <A HREF="compbio/data/sequence/package-tree.html">compbio.data.sequence</A>, <A HREF="compbio/metadata/package-tree.html">compbio.metadata</A>, <A HREF="compbio/ws/client/package-tree.html">compbio.ws.client</A></DL>\r
-<HR>\r
-<H2>\r
-Class Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
-<LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>FastaSequence</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client"><B>Jws2Client</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Limit.html" title="class in compbio.metadata"><B>Limit</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>LimitsManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A><T> (implements compbio.metadata.<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T>)\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Parameter.html" title="class in compbio.metadata"><B>Parameter</B></A><T></UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Preset.html" title="class in compbio.metadata"><B>Preset</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata"><B>PresetManager</B></A><T><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A><T><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>SequenceUtil</B></A><LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Throwable.html?is-external=true" title="class or interface in java.lang"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
-<UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang"><B>Exception</B></A><UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata"><B>JobExecutionException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata"><B>JobSubmissionException</B></A><UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata"><B>LimitExceededException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata"><B>UnsupportedRuntimeException</B></A></UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence"><B>UnknownFileFormatException</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/WrongParameterException.html" title="class in compbio.metadata"><B>WrongParameterException</B></A></UL>\r
-</UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><B>ValueConstrain</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A></UL>\r
-</UL>\r
-<H2>\r
-Interface Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A><T><LI TYPE="circle">compbio.data.msa.<A HREF="compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>MsaWS</B></A><T></UL>\r
-<H2>\r
-Enum Hierarchy\r
-</H2>\r
-<UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang"><B>Object</B></A><UL>\r
-<LI TYPE="circle">java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang"><B>Enum</B></A><E> (implements java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A><T>, java.io.<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Serializable.html?is-external=true" title="class or interface in java.io">Serializable</A>)\r
-<UL>\r
-<LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><B>JobStatus</B></A><LI TYPE="circle">compbio.metadata.<A HREF="compbio/metadata/ValueConstrain.Type.html" title="enum in compbio.metadata"><B>ValueConstrain.Type</B></A><LI TYPE="circle">compbio.data.sequence.<A HREF="compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>Program</B></A><LI TYPE="circle">compbio.ws.client.<A HREF="compbio/ws/client/Services.html" title="enum in compbio.ws.client"><B>Services</B></A></UL>\r
-</UL>\r
-</UL>\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"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <A HREF="overview-tree.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
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-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
+++ /dev/null
-compbio.data.msa\r
-compbio.data.sequence\r
-compbio.metadata\r
-compbio.ws.client\r
+++ /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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
-<TITLE>\r
-Serialized Form\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2010-11-24">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="Serialized Form";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" 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_top_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"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Use</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-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
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- PREV \r
- NEXT</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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- <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
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<CENTER>\r
-<H1>\r
-Serialized Form</H1>\r
-</CENTER>\r
-<HR SIZE="4" NOSHADE>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="center"><FONT SIZE="+2">\r
-<B>Package</B> <B>compbio.data.sequence</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<A NAME="compbio.data.sequence.UnknownFileFormatException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">compbio.data.sequence.UnknownFileFormatException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID: </B>196629543695636854L\r
-\r
-<P>\r
-<A NAME="serializedForm"><!-- --></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>Serialized Fields</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<H3>\r
-file</H3>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A> <B>file</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR SIZE="4" NOSHADE>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="center"><FONT SIZE="+2">\r
-<B>Package</B> <B>compbio.metadata</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.JobExecutionException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">compbio.metadata.JobExecutionException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID: </B>-5477751361755778769L\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.JobSubmissionException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">compbio.metadata.JobSubmissionException</A> extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Exception.html?is-external=true" title="class or interface in java.lang">Exception</A> implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID: </B>607986894357895572L\r
-\r
-<P>\r
-\r
-<P>\r
-<A NAME="compbio.metadata.LimitExceededException"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class <A HREF="compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">compbio.metadata.LimitExceededException</A> extends <A HREF="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A> implements Serializable</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<P>\r
-<B>serialVersionUID: </B>15066952180013505L\r
-\r
-<P>\r
-<A NAME="serializedForm"><!-- --></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>Serialized Fields</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<H3>\r
-numberOfSequencesAllowed</H3>\r
-<PRE>\r
-int <B>numberOfSequencesAllowed</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-<H3>\r
-actualNumberofSequences</H3>\r
-<PRE>\r
-int <B>actualNumberofSequences</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-<H3>\r
-aSequenceLenghtAllowed</H3>\r
-<PRE>\r
-int <B>aSequenceLenghtAllowed</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-<H3>\r
-aSequenceLenghtActual</H3>\r
-<PRE>\r
-int <B>aSequenceLenghtActual</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
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git://source.jalview.org / jabaws.git / commitdiff
