Mercurial > repos > eduardo > predsi
diff doc/jspp/SignalPeptidePredictor.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/SignalPeptidePredictor.html Thu Sep 29 12:00:13 2016 -0400 @@ -0,0 +1,368 @@ +<!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 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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>