Mercurial > repos > eduardo > predsi
diff doc/jspp/SearchMatrix.html @ 0:cfd8864953c9 draft
planemo upload
| author | eduardo |
|---|---|
| date | Thu, 29 Sep 2016 12:00:13 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/doc/jspp/SearchMatrix.html Thu Sep 29 12:00:13 2016 -0400 @@ -0,0 +1,636 @@ +<!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> +<DD><CODE>java.io.IOException</CODE></DL> +</DD> +</DL> +<!-- ========= END OF CLASS DATA ========= --> +<HR> + +<!-- ========== START OF NAVBAR ========== --> +<A NAME="navbar_bottom"><!-- --></A> +<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" 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