--- /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 Tue Dec 21 18:32:59 GMT 2010 -->\r
+<TITLE>\r
+Metadata\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2010-12-21">\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="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="#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/Metadata.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/msa/JManagement.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/Metadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Metadata.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_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 Metadata<T></H2>\r
+<DL>\r
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A><T>, <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A><T></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>Metadata<T></B></DL>\r
+</PRE>\r
+\r
+<P>\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="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.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/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.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/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.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/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../compbio/data/msa/Metadata.html" title="type parameter in Metadata">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/msa/Metadata.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
+\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="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/Metadata.html" title="type parameter in Metadata">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/Metadata.html" title="type parameter in Metadata">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/Metadata.html" title="type parameter in Metadata">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/Metadata.html" title="type parameter in Metadata">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/Metadata.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/msa/JManagement.html" title="interface in compbio.data.msa"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../index.html?compbio/data/msa/Metadata.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Metadata.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