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+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:43 GMT 2011 -->\r
+<TITLE>\r
+Uses of Class compbio.runner.msa.Probcons\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
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+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Uses of Class compbio.runner.msa.Probcons";\r
+ }\r
+}\r
+</SCRIPT>\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="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.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
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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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+ PREV \r
+ NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../../../index.html?compbio/runner/msa/\class-useProbcons.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Probcons.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
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+<HR>\r
+<CENTER>\r
+<H2>\r
+<B>Uses of Class<br>compbio.runner.msa.Probcons</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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
+<TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
+<TD> </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.runner.msa"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Uses of <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.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/runner/msa/package-summary.html">compbio.runner.msa</A> that return <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></CODE></FONT></TD>\r
+<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#setInput(java.lang.String)">setInput</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> inFile)</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/runner/msa/package-summary.html">compbio.runner.msa</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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/Class.html?is-external=true" title="class or interface in java.lang">Class</A><<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>></CODE></FONT></TD>\r
+<TD><CODE><B>Probcons.</B><B><A HREF="../../../../compbio/runner/msa/Probcons.html#getType()">getType</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.ws.server"><!-- --></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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</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/server/package-summary.html">compbio.ws.server</A> that return types with arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>></CODE></FONT></TD>\r
+<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.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
+ </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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>></CODE></FONT></TD>\r
+<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.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="../../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>></CODE></FONT></TD>\r
+<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.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="../../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>></CODE></FONT></TD>\r
+<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.html#getRunnerOptions()">getRunnerOptions</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/ws/server/package-summary.html">compbio.ws.server</A> with type arguments of type <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</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>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>>> options)</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>ProbconsWS.</B><B><A HREF="../../../../compbio/ws/server/ProbconsWS.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/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>> preset)</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
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.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
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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+ <A HREF="Probcons.html" target="_top"><B>NO FRAMES</B></A> \r
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+</HTML>\r