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<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:28 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="2010-12-09">\r
+<META NAME="date" CONTENT="2011-08-12">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
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<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\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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<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></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><<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
<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.Method, java.util.List)">Score</A></B>(<A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> 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><<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
+<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
<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
</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/Method.html" title="enum in compbio.data.sequence">Method</A></CODE></FONT></TD>\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
- </TD>\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/List.html?is-external=true" title="class or interface in java.util">List</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
+<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
- </TD>\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
</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>\r
</TABLE>\r
\r
-<A NAME="Score(compbio.data.sequence.Method, 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="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="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</A> 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><<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
+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
<A NAME="getMethod()"><!-- --></A><H3>\r
getMethod</H3>\r
<PRE>\r
-public <A HREF="../../../compbio/data/sequence/Method.html" title="enum in compbio.data.sequence">Method</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
</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/List.html?is-external=true" title="class or interface in java.util">List</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
+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
</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
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<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A> \r
- <A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\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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