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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / compbio / runner / _impl / NetNglyc.html
diff --git a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html
new file mode 100644 (file)
index 0000000..b6f4bca
--- /dev/null
+++ b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html
@@ -0,0 +1,574 @@
+<!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_24) on Wed Dec 07 12:30:41 GMT 2011 -->\r
+<TITLE>\r
+NetNglyc\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\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="NetNglyc";\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>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/NetNglyc.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</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
+&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
+&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../../../index.html?compbio/runner/_impl/NetNglyc.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="NetNglyc.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
+&nbsp;<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:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+DETAIL:&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_detail">CONSTR</A>&nbsp;|&nbsp;<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.runner._impl</FONT>\r
+<BR>\r
+Class NetNglyc</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.runner._impl.NetNglyc</B>\r
+</PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>NetNglyc</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/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+<!-- ======== NESTED CLASS SUMMARY ======== -->\r
+\r
+<A NAME="nested_class_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>Nested Class Summary</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+&nbsp;<A NAME="nested_classes_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Nested classes/interfaces inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+&nbsp;\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/runner/_impl/NetNglyc.html#NetNglyc()">NetNglyc</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+</TABLE>\r
+&nbsp;\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>&nbsp;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#addParameters(java.util.List)">addParameters</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;parameters)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds parameter to the list of parameters for a native executable</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="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/runner/_impl/NetNglyc.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="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/runner/_impl/NetNglyc.html#getCommandName()">getCommandName</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getCreatedFiles()">getCreatedFiles</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="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/runner/_impl/NetNglyc.html#getError()">getError</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="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/runner/_impl/NetNglyc.html#getInput()">getInput</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.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>&nbsp;presetName)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="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/runner/_impl/NetNglyc.html#getOutput()">getOutput</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
+<TR ALIGN="right" VALIGN="">\r
+<TD NOWRAP><FONT SIZE="-1">\r
+<CODE>&lt;V&gt; V</CODE></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getResults(java.lang.String)">getResults</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>&nbsp;directory)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;<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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#getTestArgs()">getTestArgs</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;<A HREF="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/runner/_impl/NetNglyc.html#getTestCommand()">getTestCommand</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/runner/_impl/NetNglyc.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+</TABLE>\r
+&nbsp;<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#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#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
+&nbsp;\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="NetNglyc()"><!-- --></A><H3>\r
+NetNglyc</H3>\r
+<PRE>\r
+public <B>NetNglyc</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="getParameters(compbio.engine.client.Executable.ExecProvider)"><!-- --></A><H3>\r
+getParameters</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <B>getParameters</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getParameters(compbio.engine.client.Executable.ExecProvider)">getParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getTestArgs()"><!-- --></A><H3>\r
+getTestArgs</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt; <B>getTestArgs</B>()</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="addParameters(java.util.List)"><!-- --></A><H3>\r
+addParameters</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A> <B>addParameters</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt;&nbsp;parameters)</PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
+<DD>Adds parameter to the list of parameters for a native executable\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">addParameters</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>this Executable</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getTestCommand()"><!-- --></A><H3>\r
+getTestCommand</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>getTestCommand</B>()</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="getCommandName()"><!-- --></A><H3>\r
+getCommandName</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>getCommandName</B>()</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="getCreatedFiles()"><!-- --></A><H3>\r
+getCreatedFiles</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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&gt; <B>getCreatedFiles</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getCreatedFiles()">getCreatedFiles</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getInput()"><!-- --></A><H3>\r
+getInput</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>getInput</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getResults(java.lang.String)"><!-- --></A><H3>\r
+getResults</H3>\r
+<PRE>\r
+public &lt;V&gt; V <B>getResults</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>&nbsp;directory)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="loadRunConfiguration(compbio.engine.client.RunConfiguration)"><!-- --></A><H3>\r
+loadRunConfiguration</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt; <B>loadRunConfiguration</B>(<A HREF="../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconfig)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOutput()"><!-- --></A><H3>\r
+getOutput</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>getOutput</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getError()"><!-- --></A><H3>\r
+getError</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>getError</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
+getLimit</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <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>&nbsp;presetName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimits()"><!-- --></A><H3>\r
+getLimits</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt; <B>getLimits</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
+getClusterJobSettings</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>getClusterJobSettings</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;<A HREF="../../../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>&gt;</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>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="class-use/NetNglyc.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</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
+&nbsp;<A HREF="../../../compbio/runner/_impl/Mcl.html" title="class in compbio.runner._impl"><B>PREV CLASS</B></A>&nbsp;\r
+&nbsp;<A HREF="../../../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl"><B>NEXT CLASS</B></A></FONT></TD>\r
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+  if(window==top) {\r
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+  SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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