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| date | Mon, 03 Oct 2016 07:26:10 -0400 |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd"> <!--NewPage--> <HTML> <HEAD> <!-- Generated by javadoc on Fri Feb 13 17:31:23 CET 2004 --> <META http-equiv="Content-Type" content="text/html; charset=windows-1252"> <TITLE> SearchMatrix </TITLE> <META NAME="keywords" CONTENT="jspp.SearchMatrix,SearchMatrix class"> <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style"> </HEAD> <SCRIPT> function asd() { parent.document.title="SearchMatrix"; } </SCRIPT> <BODY BGCOLOR="white" onload="asd();"> <!-- ========== START OF NAVBAR ========== --> <A NAME="navbar_top"><!-- --></A> <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0"> <TR> <TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A NAME="navbar_top_firstrow"><!-- --></A> <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3"> <TR ALIGN="center" VALIGN="top"> <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD> <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD> <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD> <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD> <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD> <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD> </TR> </TABLE> </TD> <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM> </EM> </TD> </TR> <TR> <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2"> <A HREF="../jspp/JSPP.html"><B>PREV CLASS</B></A> <A HREF="../jspp/SignalPChecker.html"><B>NEXT CLASS</B></A></FONT></TD> <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2"> <A HREF="../index.html" TARGET="_top"><B>FRAMES</B></A> <A HREF="SearchMatrix.html" TARGET="_top"><B>NO FRAMES</B></A> <SCRIPT> <!-- if(window==top) { document.writeln('<A HREF="../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>'); } //--> </SCRIPT> <NOSCRIPT> <A HREF="../allclasses-noframe.html" TARGET=""><B>All Classes</B></A> </NOSCRIPT> </FONT></TD> </TR> <TR> <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2"> SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD> <TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2"> DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD> </TR> </TABLE> <!-- =========== END OF NAVBAR =========== --> <HR> <!-- ======== START OF CLASS DATA ======== --> <H2> <FONT SIZE="-1"> jspp</FONT> <BR> Class SearchMatrix</H2> <PRE> java.lang.Object | +--<B>jspp.SearchMatrix</B> </PRE> <DL> <DT><B>All Implemented Interfaces:</B> <DD>java.io.Serializable</DD> </DL> <HR> <DL> <DT>public class <B>SearchMatrix</B><DT>extends java.lang.Object<DT>implements java.io.Serializable</DL> <P> <DL> <DT><B>See Also:</B><DD><A HREF="../serialized-form.html" TARGET="jspp.SearchMatrix">Serialized Form</A></DL> <HR> <P> <!-- ======== NESTED CLASS SUMMARY ======== --> <!-- =========== FIELD SUMMARY =========== --> <!-- ======== CONSTRUCTOR SUMMARY ======== --> <A NAME="constructor_summary"><!-- --></A> <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> <TD COLSPAN=2><FONT SIZE="+2"> <B>Constructor Summary</B></FONT></TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#SearchMatrix(int, int)">SearchMatrix</A></B>(int sequencelength, int cleavageposition)</CODE> <BR> constructs an empty SearchMatrix</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#SearchMatrix(java.lang.String[], int)">SearchMatrix</A></B>(java.lang.String[] alignedsequences, int cleavageposition)</CODE> <BR> constructs a new SearchMatrix</TD> </TR> </TABLE> <!-- ========== METHOD SUMMARY =========== --> <A NAME="method_summary"><!-- --></A> <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> <TD COLSPAN=2><FONT SIZE="+2"> <B>Method Summary</B></FONT></TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#addSearchMatrix(jspp.SearchMatrix)">addSearchMatrix</A></B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> matrix)</CODE> <BR> Adds a complete SearchMatrix object to this SearchMatrixThe length of both SearchMatrix must be the same, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#addSequence(java.lang.String)">addSequence</A></B>(java.lang.String sequence)</CODE> <BR> Adds new sequences to the SearchMatrix. </TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> int</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getCleavagePosition()">getCleavagePosition</A></B>()</CODE> <BR> Returns the cleavage position.</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> double</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getCutOffScore()">getCutOffScore</A></B>()</CODE> <BR> Returns the cutoff score</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> double</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getInformation(int)">getInformation</A></B>(int position)</CODE> <BR> Returns the information contents of the specified position</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> int[][]</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getMatrix()">getMatrix</A></B>()</CODE> <BR> Returns the alignment matrix</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> double</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getRawScore(java.lang.String)">getRawScore</A></B>(java.lang.String sequence)</CODE> <BR> Returns the raw score</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> double</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getScore(java.lang.String)">getScore</A></B>(java.lang.String sequence)</CODE> <BR> Returns the normalized score.</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> int</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#getSequenceLength()">getSequenceLength</A></B>()</CODE> <BR> </TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> double</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#raw2normalizedScore(double)">raw2normalizedScore</A></B>(double rawscore)</CODE> <BR> Transfers a raw score to a normalized score</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#removeSequence(java.lang.String)">removeSequence</A></B>(java.lang.String sequence)</CODE> <BR> Removes a sequence from the SearchMatrix The sequence length must be the same as the initial weight matrix size, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#setFrequencyMatrix(jspp.SearchMatrix)">setFrequencyMatrix</A></B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> sequences)</CODE> <BR> Method for considering the amino acid background</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#setFrequencyMatrix(java.lang.String[])">setFrequencyMatrix</A></B>(java.lang.String[] sequences)</CODE> <BR> Method for considering the amino acid background</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#setLimits(double, double)">setLimits</A></B>(double cutoff, double uppercutoff)</CODE> <BR> Sets the limits for score normalization.</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SearchMatrix.html#writeMatrix(java.io.File)">writeMatrix</A></B>(java.io.File file)</CODE> <BR> Writes the content of this object as tabulator seperated values in a file</TD> </TR> </TABLE> <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A> <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor"> <TD><B>Methods inherited from class java.lang.Object</B></TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD> </TR> </TABLE> <P> <!-- ============ FIELD DETAIL =========== --> <!-- ========= CONSTRUCTOR DETAIL ======== --> <A NAME="constructor_detail"><!-- --></A> <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> <TD COLSPAN=1><FONT SIZE="+2"> <B>Constructor Detail</B></FONT></TD> </TR> </TABLE> <A NAME="SearchMatrix(java.lang.String[], int)"><!-- --></A><H3> SearchMatrix</H3> <PRE> public <B>SearchMatrix</B>(java.lang.String[] alignedsequences, int cleavageposition)</PRE> <DL> <DD>constructs a new SearchMatrix <P> <DT><B>Parameters:</B><DD><CODE>alignedsequences</CODE> - String-Array of aligned sequences<DD><CODE>cleavageposition</CODE> - cleavage position inside the aligned sequences</DL> <HR> <A NAME="SearchMatrix(int, int)"><!-- --></A><H3> SearchMatrix</H3> <PRE> public <B>SearchMatrix</B>(int sequencelength, int cleavageposition)</PRE> <DL> <DD>constructs an empty SearchMatrix <P> <DT><B>Parameters:</B><DD><CODE>sequencelength</CODE> - length of sequences (signalpeptide+mature protein)<DD><CODE>cleavageposition</CODE> - cleavageposition, normally the same length as signalpeptide</DL> <!-- ============ METHOD DETAIL ========== --> <A NAME="method_detail"><!-- --></A> <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%"> <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor"> <TD COLSPAN=1><FONT SIZE="+2"> <B>Method Detail</B></FONT></TD> </TR> </TABLE> <A NAME="getSequenceLength()"><!-- --></A><H3> getSequenceLength</H3> <PRE> public int <B>getSequenceLength</B>()</PRE> <DL> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Returns:</B><DD>the sequence length of the aligned sequences</DL> </DD> </DL> <HR> <A NAME="addSequence(java.lang.String)"><!-- --></A><H3> addSequence</H3> <PRE> public void <B>addSequence</B>(java.lang.String sequence) throws jspp.SequenceLengthException</PRE> <DL> <DD>Adds new sequences to the SearchMatrix. <p>The sequence length must be the same as the initial weight matrix size, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </p> <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence to add to the matrix <DT><B>Throws:</B> <DD><CODE>jspp.SequenceLengthException</CODE></DL> </DD> </DL> <HR> <A NAME="addSearchMatrix(jspp.SearchMatrix)"><!-- --></A><H3> addSearchMatrix</H3> <PRE> public void <B>addSearchMatrix</B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> matrix) throws jspp.SequenceLengthException</PRE> <DL> <DD>Adds a complete SearchMatrix object to this SearchMatrix<p>The length of both SearchMatrix must be the same, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </p> <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>matrix</CODE> - SearchMatrix to add to this SearchMatrix <DT><B>Throws:</B> <DD><CODE>jspp.SequenceLengthException</CODE></DL> </DD> </DL> <HR> <A NAME="removeSequence(java.lang.String)"><!-- --></A><H3> removeSequence</H3> <PRE> public void <B>removeSequence</B>(java.lang.String sequence) throws jspp.SequenceLengthException</PRE> <DL> <DD>Removes a sequence from the SearchMatrix <p>The sequence length must be the same as the initial weight matrix size, otherwise a <CODE>SequenceLengthException</CODE> will be thrown </p> <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - Sequence to remove from the SearchMatrix <DT><B>Throws:</B> <DD><CODE>jspp.SequenceLengthException</CODE></DL> </DD> </DL> <HR> <A NAME="getCleavagePosition()"><!-- --></A><H3> getCleavagePosition</H3> <PRE> public int <B>getCleavagePosition</B>()</PRE> <DL> <DD>Returns the cleavage position. <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Returns:</B><DD>the cleavage position.</DL> </DD> </DL> <HR> <A NAME="setLimits(double, double)"><!-- --></A><H3> setLimits</H3> <PRE> public void <B>setLimits</B>(double cutoff, double uppercutoff)</PRE> <DL> <DD>Sets the limits for score normalization.<p>Scores are normalized in a linear manner, where cutoff is normalized to 0.5 and uppercuttoff is normalized to 1.0.</p> <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>cutoff</CODE> - cutoff-score will be normalized to 0.5.<DD><CODE>uppercutoff</CODE> - upper-limit will be normalized to 1.0.</DL> </DD> </DL> <HR> <A NAME="getScore(java.lang.String)"><!-- --></A><H3> getScore</H3> <PRE> public double <B>getScore</B>(java.lang.String sequence) throws jspp.SequenceLengthException</PRE> <DL> <DD>Returns the normalized score.<p>Method <A HREF="../jspp/SearchMatrix.html#setLimits(double, double)"><CODE>setLimits()</CODE></A> should be called before.</p> <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - sequence for score calculation <DT><B>Returns:</B><DD>a normalized score for <CODE>sequence</CODE> <DT><B>Throws:</B> <DD><CODE>jspp.SequenceLengthException</CODE></DL> </DD> </DL> <HR> <A NAME="getRawScore(java.lang.String)"><!-- --></A><H3> getRawScore</H3> <PRE> public double <B>getRawScore</B>(java.lang.String sequence) throws jspp.SequenceLengthException</PRE> <DL> <DD>Returns the raw score <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - sequence for score calculation <DT><B>Returns:</B><DD>the raw score <DT><B>Throws:</B> <DD><CODE>jspp.SequenceLengthException</CODE></DL> </DD> </DL> <HR> <A NAME="getCutOffScore()"><!-- --></A><H3> getCutOffScore</H3> <PRE> public double <B>getCutOffScore</B>()</PRE> <DL> <DD>Returns the cutoff score <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Returns:</B><DD>the cutoff score</DL> </DD> </DL> <HR> <A NAME="raw2normalizedScore(double)"><!-- --></A><H3> raw2normalizedScore</H3> <PRE> public double <B>raw2normalizedScore</B>(double rawscore)</PRE> <DL> <DD>Transfers a raw score to a normalized score <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>rawscore</CODE> - the raw score <DT><B>Returns:</B><DD>the normalized score</DL> </DD> </DL> <HR> <A NAME="getInformation(int)"><!-- --></A><H3> getInformation</H3> <PRE> public double <B>getInformation</B>(int position) throws jspp.SequenceLengthException</PRE> <DL> <DD>Returns the information contents of the specified position <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>position</CODE> - the weight matrix position <DT><B>Returns:</B><DD>the information content of specified weight matrix position <DT><B>Throws:</B> <DD><CODE>jspp.SequenceLengthException</CODE></DL> </DD> </DL> <HR> <A NAME="getMatrix()"><!-- --></A><H3> getMatrix</H3> <PRE> public int[][] <B>getMatrix</B>()</PRE> <DL> <DD>Returns the alignment matrix <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Returns:</B><DD>the alignment matrix</DL> </DD> </DL> <HR> <A NAME="setFrequencyMatrix(java.lang.String[])"><!-- --></A><H3> setFrequencyMatrix</H3> <PRE> public void <B>setFrequencyMatrix</B>(java.lang.String[] sequences)</PRE> <DL> <DD>Method for considering the amino acid background <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - array of Strings containing sequences of dependent organism / group</DL> </DD> </DL> <HR> <A NAME="setFrequencyMatrix(jspp.SearchMatrix)"><!-- --></A><H3> setFrequencyMatrix</H3> <PRE> public void <B>setFrequencyMatrix</B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> sequences)</PRE> <DL> <DD>Method for considering the amino acid background <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequences</CODE> - sequences stored in a SearchMatrix object</DL> </DD> </DL> <HR> <A NAME="writeMatrix(java.io.File)"><!-- --></A><H3> writeMatrix</H3> <PRE> public void <B>writeMatrix</B>(java.io.File file) throws java.io.IOException</PRE> <DL> <DD>Writes the content of this object as tabulator seperated values in a file <P> <DD><DL> </DL> </DD> <DD><DL> <DT><B>Parameters:</B><DD><CODE>file</CODE> - the output file <DT><B>Throws:</B> 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