Mercurial > repos > eduardo > predsi
view doc/jspp/SignalPeptidePredictor.html @ 5:f66c6b1a7930 draft default tip
planemo upload
| author | eduardo |
|---|---|
| date | Mon, 03 Oct 2016 07:26:10 -0400 |
| parents | cfd8864953c9 |
| children |
line wrap: on
line source
<!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> SignalPeptidePredictor </TITLE> <META NAME="keywords" CONTENT="jspp.SignalPeptidePredictor,SignalPeptidePredictor class"> <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style"> </HEAD> <SCRIPT> function asd() { parent.document.title="SignalPeptidePredictor"; } </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/SignalPDataParser.html"><B>PREV CLASS</B></A> <A HREF="../jspp/TrainingSet.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="SignalPeptidePredictor.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 SignalPeptidePredictor</H2> <PRE> java.lang.Object | +--<B>jspp.SignalPeptidePredictor</B> </PRE> <HR> <DL> <DT>public class <B>SignalPeptidePredictor</B><DT>extends java.lang.Object</DL> <P> <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/SignalPeptidePredictor.html#SignalPeptidePredictor(jspp.SearchMatrix)">SignalPeptidePredictor</A></B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> positive)</CODE> <BR> Constructs a SignalPeptidePredictor</TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#SignalPeptidePredictor(java.lang.String[], java.lang.String[], int)">SignalPeptidePredictor</A></B>(java.lang.String[] positive, java.lang.String[] negative, int clpos)</CODE> <BR> Constructs a SignalPeptidePredictor object</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> double</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#getRawScore()">getRawScore</A></B>()</CODE> <BR> Returns the raw score of the analyzed sequence. </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/SignalPeptidePredictor.html#getScore()">getScore</A></B>()</CODE> <BR> Returns the normalized score of the analyzed sequence. </TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE> boolean</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#isSignalPeptide()">isSignalPeptide</A></B>()</CODE> <BR> True if analyzed sequence contains a predicted signal sequence, otherwise false. </TD> </TR> <TR BGCOLOR="white" CLASS="TableRowColor"> <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1"> <CODE>static void</CODE></FONT></TD> <TD><CODE><B><A HREF="../jspp/SignalPeptidePredictor.html#main(java.lang.String[])">main</A></B>(java.lang.String[] args)</CODE> <BR> </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/SignalPeptidePredictor.html#predictEnhancedPosition(java.lang.String)">predictEnhancedPosition</A></B>(java.lang.String sequence)</CODE> <BR> Predicts the most probable cleavage position inside the sequence</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/SignalPeptidePredictor.html#predictPosition(java.lang.String)">predictPosition</A></B>(java.lang.String sequence)</CODE> <BR> </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="SignalPeptidePredictor(java.lang.String[], java.lang.String[], int)"><!-- --></A><H3> SignalPeptidePredictor</H3> <PRE> public <B>SignalPeptidePredictor</B>(java.lang.String[] positive, java.lang.String[] negative, int clpos)</PRE> <DL> <DD>Constructs a SignalPeptidePredictor object <P> <DT><B>Parameters:</B><DD><CODE>positive</CODE> - String-array of aligned sequences containing a leader peptide for the sec pathway<DD><CODE>negative</CODE> - String array of negative sequences lacking a leader peptide for the sec pathway<DD><CODE>clpos</CODE> - cleavage position</DL> <HR> <A NAME="SignalPeptidePredictor(jspp.SearchMatrix)"><!-- --></A><H3> SignalPeptidePredictor</H3> <PRE> public <B>SignalPeptidePredictor</B>(<A HREF="../jspp/SearchMatrix.html">SearchMatrix</A> positive)</PRE> <DL> <DD>Constructs a SignalPeptidePredictor <P> <DT><B>Parameters:</B><DD><CODE>positive</CODE> - a SearchMatrix</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="predictEnhancedPosition(java.lang.String)"><!-- --></A><H3> predictEnhancedPosition</H3> <PRE> public int <B>predictEnhancedPosition</B>(java.lang.String sequence)</PRE> <DL> <DD>Predicts the most probable cleavage position inside the sequence <P> <DD><DL> <DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence to test <DT><B>Returns:</B><DD>the most probable cleavage position</DL> </DD> </DL> <HR> <A NAME="predictPosition(java.lang.String)"><!-- --></A><H3> predictPosition</H3> <PRE> public int <B>predictPosition</B>(java.lang.String sequence)</PRE> <DL> <DD><DL> </DL> </DD> </DL> <HR> <A NAME="getRawScore()"><!-- --></A><H3> getRawScore</H3> <PRE> public double <B>getRawScore</B>()</PRE> <DL> <DD>Returns the raw score of the analyzed sequence. Only call this method after running predictEnhancedPosition ! <P> <DD><DL> <DT><B>Returns:</B><DD>the raw score</DL> </DD> </DL> <HR> <A NAME="getScore()"><!-- --></A><H3> getScore</H3> <PRE> public double <B>getScore</B>()</PRE> <DL> <DD>Returns the normalized score of the analyzed sequence. Only call this method after running predictEnhancedPosition ! <P> <DD><DL> <DT><B>Returns:</B><DD>the normalized score</DL> </DD> </DL> <HR> <A NAME="isSignalPeptide()"><!-- --></A><H3> isSignalPeptide</H3> <PRE> public boolean <B>isSignalPeptide</B>()</PRE> <DL> <DD>True if analyzed sequence contains a predicted signal sequence, otherwise false. Only call this method after running predictEnhancedPosition ! <P> <DD><DL> <DT><B>Returns:</B><DD>true or false</DL> </DD> </DL> <HR> <A NAME="main(java.lang.String[])"><!-- --></A><H3> main</H3> <PRE> public static void <B>main</B>(java.lang.String[] args)</PRE> <DL> <DD><DL> </DL> </DD> </DL> <!-- ========= END OF CLASS DATA ========= --> <HR> <!-- ========== START OF NAVBAR ========== --> <A NAME="navbar_bottom"><!-- --></A> <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0"> <TR> <TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A NAME="navbar_bottom_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/SignalPDataParser.html"><B>PREV CLASS</B></A> <A HREF="../jspp/TrainingSet.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="SignalPeptidePredictor.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> </BODY> </HTML>