--- /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_24) on Wed Dec 07 12:08:24 GMT 2011 -->\r
+<TITLE>\r
+ScoreManager\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="ScoreManager";\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/ScoreManager.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/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.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/ScoreManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ScoreManager.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: <A HREF="#nested_class_summary">NESTED</A> | <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_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 ScoreManager</H2>\r
+<PRE>\r
+java.lang.Object\r
+ <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.ScoreManager</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>ScoreManager</B><DT>extends java.lang.Object</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
+<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/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\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 java.lang.String</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</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> java.util.Map<java.lang.String,java.util.TreeSet<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#asMap()">asMap</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> java.util.Set<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#asSet()">asSet</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/data/sequence/ScoreManager.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object 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/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence(java.lang.String)">getAnnotationForSequence</A></B>(java.lang.String seqId)</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/ScoreManager.html#getNumberOfSeq()">getNumberOfSeq</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/ScoreManager.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>static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)">newInstance</A></B>(java.util.Map<java.lang.String,java.util.Set<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</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/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)">newInstanceSingleScore</A></B>(java.util.Map<java.lang.String,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</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/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)">newInstanceSingleSequence</A></B>(java.util.Set<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</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/data/sequence/ScoreManager.html#writeOut(java.io.Writer)">writeOut</A></B>(java.io.Writer outStream)</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.Object</B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE>getClass, notify, notifyAll, toString, wait, wait, wait</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="SINGLE_ENTRY_KEY"><!-- --></A><H3>\r
+SINGLE_ENTRY_KEY</H3>\r
+<PRE>\r
+public static final java.lang.String <B>SINGLE_ENTRY_KEY</B></PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY">Constant Field Values</A></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="newInstance(java.util.Map)"><!-- --></A><H3>\r
+newInstance</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstance</B>(java.util.Map<java.lang.String,java.util.Set<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="newInstanceSingleScore(java.util.Map)"><!-- --></A><H3>\r
+newInstanceSingleScore</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstanceSingleScore</B>(java.util.Map<java.lang.String,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="newInstanceSingleSequence(java.util.Set)"><!-- --></A><H3>\r
+newInstanceSingleSequence</H3>\r
+<PRE>\r
+public static <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A> <B>newInstanceSingleSequence</B>(java.util.Set<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="asMap()"><!-- --></A><H3>\r
+asMap</H3>\r
+<PRE>\r
+public java.util.Map<java.lang.String,java.util.TreeSet<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> <B>asMap</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="asSet()"><!-- --></A><H3>\r
+asSet</H3>\r
+<PRE>\r
+public java.util.Set<<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>asSet</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getNumberOfSeq()"><!-- --></A><H3>\r
+getNumberOfSeq</H3>\r
+<PRE>\r
+public int <B>getNumberOfSeq</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getAnnotationForSequence(java.lang.String)"><!-- --></A><H3>\r
+getAnnotationForSequence</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A> <B>getAnnotationForSequence</B>(java.lang.String seqId)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="writeOut(java.io.Writer)"><!-- --></A><H3>\r
+writeOut</H3>\r
+<PRE>\r
+public void <B>writeOut</B>(java.io.Writer outStream)\r
+ throws java.io.IOException</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE>java.io.IOException</CODE></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>hashCode</CODE> in class <CODE>java.lang.Object</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>(java.lang.Object obj)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</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/ScoreManager.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/Score.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
+ <A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.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/ScoreManager.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="ScoreManager.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: <A HREF="#nested_class_summary">NESTED</A> | <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
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