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web pages updates to point to new download location also the redirect servlet
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / Score.html
diff --git a/website/dm_javadoc/compbio/data/sequence/Score.html b/website/dm_javadoc/compbio/data/sequence/Score.html
index 4d0f191..bd2db3b 100644 (file)
--- a/website/dm_javadoc/compbio/data/sequence/Score.html
+++ b/website/dm_javadoc/compbio/data/sequence/Score.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:58 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:03 BST 2011 -->\r
 <TITLE>\r
 Score\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-12-21">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -55,8 +55,8 @@ function windowTitle()
 \r
 <TR>\r
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+&nbsp;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
+&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.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/Score.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 &nbsp;<A HREF="Score.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
@@ -95,14 +95,18 @@ Class Score</H2>
 <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.data.sequence.Score</B>\r
 </PRE>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</DD>\r
+</DL>\r
 <HR>\r
 <DL>\r
 <DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public class <B>Score</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
+</FONT>public class <B>Score</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="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</DL>\r
 </PRE>\r
 \r
 <P>\r
-A value class for AACon annotation results storage\r
+A value class for AACon annotation results storage. The objects of this type
+ are immutable\r
 <P>\r
 \r
 <P>\r
@@ -123,12 +127,34 @@ A value class for AACon annotation results storage
 <B>Constructor Summary</B></FONT></TH>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(compbio.data.sequence.ConservationMethod, java.util.List)">Score</A></B>(<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>&nbsp;method,\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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+      <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Instantiate the Score</TD>\r
 </TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+      <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores,\r
+      <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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</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><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, float[])">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+      float[]&nbsp;scores)</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><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#Score(java.lang.Enum, java.util.TreeSet)">Score</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+      <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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</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
@@ -141,6 +167,14 @@ A value class for AACon annotation results storage
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#compareTo(compbio.data.sequence.Score)">compareTo</A></B>(<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&nbsp;o)</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;boolean</CODE></FONT></TD>\r
 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.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>&nbsp;obj)</CODE>\r
 \r
@@ -149,7 +183,7 @@ A value class for AACon annotation results storage
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A></CODE></FONT></TD>\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/data/sequence/Score.html#getMethod()">getMethod</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -157,7 +191,15 @@ A value class for AACon annotation results storage
 </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/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getRanges()">getRanges</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Return Ranges if any Collections.EMPTY_SET otherwise</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/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;</CODE></FONT></TD>\r
 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getScores()">getScores</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -173,6 +215,14 @@ A value class for AACon annotation results storage
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#setRanges(java.util.TreeSet)">setRanges</A></B>(<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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</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/data/sequence/Score.html#toString()">toString</A></B>()</CODE>\r
 \r
@@ -182,8 +232,8 @@ A value class for AACon annotation results storage
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#write(java.util.Set, java.io.OutputStream)">write</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>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
-      <A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;output)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)">write</A></B>(<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>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
+      <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>&nbsp;writer)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Outputs the List of Score objects into the Output stream.</TD>\r
@@ -211,11 +261,11 @@ A value class for AACon annotation results storage
 </TR>\r
 </TABLE>\r
 \r
-<A NAME="Score(compbio.data.sequence.ConservationMethod, java.util.List)"><!-- --></A><H3>\r
+<A NAME="Score(java.lang.Enum, java.util.ArrayList)"><!-- --></A><H3>\r
 Score</H3>\r
 <PRE>\r
-public <B>Score</B>(<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A>&nbsp;method,\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>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores)</PRE>\r
+public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+             <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores)</PRE>\r
 <DL>\r
 <DD>Instantiate the Score\r
 <P>\r
@@ -224,6 +274,39 @@ public <B>Score</B>(<A HREF="../../../compbio/data/sequence/ConservationMethod.h
             calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
             alignment</DL>\r
 </DL>\r
+<HR>\r
+\r
+<A NAME="Score(java.lang.Enum, java.util.ArrayList, java.util.TreeSet)"><!-- --></A><H3>\r
+Score</H3>\r
+<PRE>\r
+public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+             <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt;&nbsp;scores,\r
+             <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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>Parameters:</B><DD><CODE>method</CODE> - the ConservationMethod with which <code>scores</code> were
+            calculated<DD><CODE>scores</CODE> - the actual conservation values for each column of the
+            alignment<DD><CODE>ranges</CODE> - The set of ranges i.e. parts of the sequence with specific
+            function, usually can be calculated based on scores</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Score(java.lang.Enum, java.util.TreeSet)"><!-- --></A><H3>\r
+Score</H3>\r
+<PRE>\r
+public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+             <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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</PRE>\r
+<DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="Score(java.lang.Enum, float[])"><!-- --></A><H3>\r
+Score</H3>\r
+<PRE>\r
+public <B>Score</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Enum.html?is-external=true" title="class or interface in java.lang">Enum</A>&lt;?&gt;&nbsp;method,\r
+             float[]&nbsp;scores)</PRE>\r
+<DL>\r
+</DL>\r
 \r
 <!-- ============ METHOD DETAIL ========== -->\r
 \r
@@ -238,11 +321,14 @@ public <B>Score</B>(<A HREF="../../../compbio/data/sequence/ConservationMethod.h
 <A NAME="getMethod()"><!-- --></A><H3>\r
 getMethod</H3>\r
 <PRE>\r
-public <A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A> <B>getMethod</B>()</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>getMethod</B>()</PRE>\r
 <DL>\r
 <DD>Returns the ConservationMethod\r
 <P>\r
 <DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
 \r
 <DT><B>Returns:</B><DD>the ConservationMethod</DL>\r
 </DD>\r
@@ -252,17 +338,51 @@ public <A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="e
 <A NAME="getScores()"><!-- --></A><H3>\r
 getScores</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/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt; <B>getScores</B>()</PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/ArrayList.html?is-external=true" title="class or interface in java.util">ArrayList</A>&lt;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Float.html?is-external=true" title="class or interface in java.lang">Float</A>&gt; <B>getScores</B>()</PRE>\r
 <DL>\r
 <DD>The column scores for the alignment\r
 <P>\r
 <DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
 \r
 <DT><B>Returns:</B><DD>the column scores for the alignment</DL>\r
 </DD>\r
 </DL>\r
 <HR>\r
 \r
+<A NAME="getRanges()"><!-- --></A><H3>\r
+getRanges</H3>\r
+<PRE>\r
+public <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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt; <B>getRanges</B>()</PRE>\r
+<DL>\r
+<DD>Return Ranges if any Collections.EMPTY_SET otherwise\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>ordered set of Range</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setRanges(java.util.TreeSet)"><!-- --></A><H3>\r
+setRanges</H3>\r
+<PRE>\r
+public void <B>setRanges</B>(<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>&lt;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>&gt;&nbsp;ranges)</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="toString()"><!-- --></A><H3>\r
 toString</H3>\r
 <PRE>\r
@@ -305,11 +425,11 @@ public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java
 </DL>\r
 <HR>\r
 \r
-<A NAME="write(java.util.Set, java.io.OutputStream)"><!-- --></A><H3>\r
+<A NAME="write(java.util.TreeSet, java.io.Writer)"><!-- --></A><H3>\r
 write</H3>\r
 <PRE>\r
-public static void <B>write</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>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
-                         <A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;output)\r
+public static void <B>write</B>(<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>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&nbsp;scores,\r
+                         <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>&nbsp;writer)\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
 <DL>\r
 <DD>Outputs the List of Score objects into the Output stream. The output
@@ -328,12 +448,29 @@ public static void <B>write</B>(<A HREF="http://java.sun.com/javase/6/docs/api/j
  The maximum precision for values is 3 digits, but can be less.\r
 <P>\r
 <DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>scores</CODE> - the list of scores to output<DD><CODE>output</CODE> - the stream to output the data to\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>scores</CODE> - the list of scores to output<DD><CODE>writer</CODE> - \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> - if the OutputStream cannot be written into\r
 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE> - if the output stream is null</DL>\r
 </DD>\r
 </DL>\r
+<HR>\r
+\r
+<A NAME="compareTo(compbio.data.sequence.Score)"><!-- --></A><H3>\r
+compareTo</H3>\r
+<PRE>\r
+public int <B>compareTo</B>(<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&nbsp;o)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true#compareTo(T)" title="class or interface in java.lang">compareTo</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Comparable.html?is-external=true" title="class or interface in java.lang">Comparable</A>&lt;<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
 <!-- ========= END OF CLASS DATA ========= -->\r
 <HR>\r
 \r
@@ -365,8 +502,8 @@ public static void <B>write</B>(<A HREF="http://java.sun.com/javase/6/docs/api/j
 \r
 <TR>\r
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+&nbsp;<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
+&nbsp;<A HREF="../../../compbio/data/sequence/ScoreManager.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/Score.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 &nbsp;<A HREF="Score.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r