+++ /dev/null
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-<TITLE>\r
-Score\r
-</TITLE>\r
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- <A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
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-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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-<!-- ======== START OF CLASS DATA ======== -->\r
-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class Score</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.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><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></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><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><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></DL>\r
-</PRE>\r
-\r
-<P>\r
-A value class for AACon annotation results storage. The objects of this type
- are immutable\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\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/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><?> 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><<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>> scores)</CODE>\r
-\r
-<BR>\r
- 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><?> 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><<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>> 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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</CODE>\r
-\r
-<BR>\r
- </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><?> method,\r
- float[] scores)</CODE>\r
-\r
-<BR>\r
- </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><?> 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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</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> 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> o)</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/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> 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="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
- Returns the ConservationMethod</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/util/TreeSet.html?is-external=true" title="class or interface in java.util">TreeSet</A><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getRanges()">getRanges</A></B>()</CODE>\r
-\r
-<BR>\r
- 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> <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><<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>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Score.html#getScores()">getScores</A></B>()</CODE>\r
-\r
-<BR>\r
- The column scores for the alignment</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/Score.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> 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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> ranges)</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><A HREF="../../../compbio/data/sequence/Score.html#toString()">toString</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 void</CODE></FONT></TD>\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><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> 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> writer)</CODE>\r
-\r
-<BR>\r
- Outputs the List of Score objects into the Output stream.</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.<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#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#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
- \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="Score(java.lang.Enum, java.util.ArrayList)"><!-- --></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><?> 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><<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>> scores)</PRE>\r
-<DL>\r
-<DD>Instantiate the Score\r
-<P>\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</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><?> 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><<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>> 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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> 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><?> 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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> 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><?> method,\r
- float[] scores)</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="getMethod()"><!-- --></A><H3>\r
-getMethod</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>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
-</DL>\r
-<HR>\r
-\r
-<A NAME="getScores()"><!-- --></A><H3>\r
-getScores</H3>\r
-<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><<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>> <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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> <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><<A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>> 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
-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>toString</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#toString()" title="class or interface in java.lang">toString</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
-</DD>\r
-<DD><DL>\r
-</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><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
-</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>(<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
-<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
-</DD>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\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/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>> 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> 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
- format is as follows:
-
- <pre>
- <code>#MethodName <space separated list of values>
-
- For example:
-
- #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
- #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
- </code>
- </pre>
-
- The maximum precision for values is 3 digits, but can be less.\r
-<P>\r
-<DD><DL>\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> 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><<A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></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/Score.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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-</EM>\r
-</TD>\r
-</TR>\r
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-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
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- <A HREF="../../../index.html?compbio/data/sequence/Score.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Score.html" target="_top"><B>NO FRAMES</B></A> \r
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git://source.jalview.org / jabaws.git / blobdiff