<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:03 BST 2011 -->\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="2011-08-12">\r
+<META NAME="date" CONTENT="2011-12-07">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
\r
<BR>\r
Class ScoreManager</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
+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 <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
+<DT><PRE>public class <B>ScoreManager</B><DT>extends java.lang.Object</DL>\r
</PRE>\r
\r
<P>\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
+<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
</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/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>></CODE></FONT></TD>\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
</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="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\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
<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>(<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
+<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 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> seqId)</CODE>\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 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</CODE>\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 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</CODE>\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 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>(<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="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</CODE>\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 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A> outStream)</CODE>\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
<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
+<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</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#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
+<TD><CODE>getClass, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
</TR>\r
</TABLE>\r
\r
<A NAME="SINGLE_ENTRY_KEY"><!-- --></A><H3>\r
SINGLE_ENTRY_KEY</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>SINGLE_ENTRY_KEY</B></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
<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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<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="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> data)</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
<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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> seqScoresMap)</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
<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>(<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="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> data)</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
<A NAME="asMap()"><!-- --></A><H3>\r
asMap</H3>\r
<PRE>\r
-public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>>> <B>asMap</B>()</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
<A NAME="asSet()"><!-- --></A><H3>\r
asSet</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="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>asSet</B>()</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
<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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> seqId)</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
<A NAME="writeOut(java.io.Writer)"><!-- --></A><H3>\r
writeOut</H3>\r
<PRE>\r
-public void <B>writeOut</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A> outStream)\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
+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><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><CODE>java.io.IOException</CODE></DL>\r
</DD>\r
</DL>\r
<HR>\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
+<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
</DD>\r
<DD><DL>\r
</DL>\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
+public boolean <B>equals</B>(java.lang.Object 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
+<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
</DD>\r
<DD><DL>\r
</DL>\r