net.sf.snver.pileup.loader
Class Peeker

java.lang.Object
  net.sf.snver.pileup.loader.Peeker

All Implemented Interfaces:

java.lang.Comparable<Peeker>

public class Peeker
extends java.lang.Object
implements java.lang.Comparable<Peeker>

Robust iterator for Bam to integrate with reference and filter

Created by IntelliJ IDEA. User: weicheng hu Date: 11/1/11 Time: 6:05 PM

Constructor Summary

Peeker(FastaReader ref, Filter f, net.sf.samtools.SAMFileReader reader, java.util.Properties prop, java.lang.String name)
Constructor

Peeker(FastaReader ref, java.util.Properties properties)
Constructor

Method Summary

int	compareTo(Peeker peeker)
java.lang.String	getFileIndex() Get file index
Filter	getFilter() Filter Getter
int	getPosition() Get current position
java.util.Properties	getProperties() Properties Getter
char	getRef() Return the current reference base pair
boolean	hasNext() Check if has next element
SnverMeta	next() Return the next element
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Peeker

public Peeker(FastaReader ref,
              Filter f,
              net.sf.samtools.SAMFileReader reader,
              java.util.Properties prop,
              java.lang.String name)

Constructor

Parameters:

ref - FastaReader

f - Filter

reader - SAMFileReader

prop - Properties

name - String

Peeker

public Peeker(FastaReader ref,
              java.util.Properties properties)
       throws java.io.IOException

Constructor

Parameters:

ref - FastaReader

properties - Properties

Throws:

java.io.IOException - Error when read fasta file

Method Detail

hasNext

public boolean hasNext()

Check if has next element

Returns:

boolean

next

public SnverMeta next()

Return the next element

Returns:

SnverMeta

getRef

public char getRef()

Return the current reference base pair

Returns:

compareTo

public int compareTo(Peeker peeker)

Specified by:

compareTo in interface java.lang.Comparable<Peeker>

Parameters:

peeker -

Returns:

See Also:

Comparable.compareTo(Object)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

See Also:

Object.toString()

getFileIndex

public java.lang.String getFileIndex()

Get file index

Returns:

String

getPosition

public int getPosition()

Get current position

Returns:

int

getProperties

public java.util.Properties getProperties()

Properties Getter

Returns:

Properties

getFilter

public Filter getFilter()

Filter Getter

Returns:

Filter