trans.main
Class IntervalGFFPrinter

java.lang.Object
  trans.main.IntervalGFFPrinter

public class IntervalGFFPrinter

extends java.lang.Object

Prints intervals as a GFF3 File.

Constructor Summary

IntervalGFFPrinter(java.lang.String[] args)

Method Summary

static void	gff(BindingPeak peak, Interval i, java.lang.String name, int peakNumber, java.lang.StringBuffer s) Appends a GFF3 line for a BindingPeak
void	gff(Interval i, int rank, java.lang.String name, java.lang.StringBuffer s) Appends a GFF3 line for an Interval.
void	gff(Interval i, java.lang.String name, java.lang.StringBuffer s) Appends a GFF3 line for a Window.
static void	gff(Oligo o, Interval i, java.lang.String name, int oligoNumber, java.lang.StringBuffer s) Appends a GFF3 line for an Oligo.
static void	gff(SubWindow sub, Interval i, java.lang.String name, java.lang.StringBuffer s) Appends a GFF3 line for a SubWindow.
static void	main(java.lang.String[] args)
static void	printDocs()
void	printGFF()
void	processArgs(java.lang.String[] args) This method will process each argument and assign any new varibles

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IntervalGFFPrinter

public IntervalGFFPrinter(java.lang.String[] args)

Method Detail

printGFF

public void printGFF()

gff

public static void gff(Oligo o,
                       Interval i,
                       java.lang.String name,
                       int oligoNumber,
                       java.lang.StringBuffer s)

Appends a GFF3 line for an Oligo. Summary Score is a log2Ratio

gff

public static void gff(BindingPeak peak,
                       Interval i,
                       java.lang.String name,
                       int peakNumber,
                       java.lang.StringBuffer s)

Appends a GFF3 line for a BindingPeak

gff

public static void gff(SubWindow sub,
                       Interval i,
                       java.lang.String name,
                       java.lang.StringBuffer s)

Appends a GFF3 line for a SubWindow. Summary score is median ratio

gff

public void gff(Interval i,
                int rank,
                java.lang.String name,
                java.lang.StringBuffer s)

Appends a GFF3 line for an Interval.

gff

public void gff(Interval i,
                java.lang.String name,
                java.lang.StringBuffer s)

Appends a GFF3 line for a Window.

printDocs

public static void printDocs()

processArgs

public void processArgs(java.lang.String[] args)

This method will process each argument and assign any new varibles

main

public static void main(java.lang.String[] args)