net.sf.snver.pileup.meta
Class SnverMeta

java.lang.Object
  net.sf.snver.pileup.meta.SnverMeta

All Implemented Interfaces:

java.lang.Comparable<SnverMeta>

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

Position based countable object for result Created by IntelliJ IDEA. User: weicheng hu Date: 10/27/11 Time: 4:44 PM

Constructor Summary

SnverMeta()
Null parameter constructor

SnverMeta(java.lang.String name, int index, char ref, int indel, java.lang.String seq, java.lang.String score)
Constructor

Method Summary

int	compareTo(SnverMeta snverMeta)
java.lang.String	getChromosome() Get chromosome name
double	getCorrectedWeitghtedErrorEstimate(int correct)
int	getCount(char base) Return the count number of base from both sequence
double	getErrorEstimate() Return estimated error
int	getForwardBaseNum(char base) Get the base count from forward sequence
char	getGnomeChar(int i) Return the base character
int	getIndel() Retunr the indel number
int	getIndex() Get the index of chromosome
char	getMostAltBase() Get the mose alt base
char	getMostBase() Get the mose base including ref, if indel is most, return 0
double	getRatio() Return the alt/ref ratio
java.lang.String	getRatioString() Return the alt/ref type
char	getRef() Get reference
int	getReverseBaseNum(char base) Get the base count from reverse sequence
int	getTotal() Return the total number of base, not including indel
boolean	isEmpty() Check is empty
boolean	isNoAlternate() Deprecated.
boolean	isOnlyRef() Check there is only ref
boolean	isReference(char base) Check the base is a ref
java.lang.String	printCount() Print count information
java.lang.String	printVcfObject(java.io.PrintWriter out) Deprecated.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SnverMeta

public SnverMeta(java.lang.String name,
                 int index,
                 char ref,
                 int indel,
                 java.lang.String seq,
                 java.lang.String score)

Constructor

Parameters:

name - String

index - int

ref - char

indel - int

seq - String

score - String

SnverMeta

public SnverMeta()

Null parameter constructor

Method Detail

getChromosome

public java.lang.String getChromosome()

Get chromosome name

Returns:

String

getIndex

public int getIndex()

Get the index of chromosome

Returns:

int

getRef

public char getRef()

Get reference

Returns:

char

getErrorEstimate

public double getErrorEstimate()

Return estimated error

Returns:

double

getCorrectedWeitghtedErrorEstimate

public double getCorrectedWeitghtedErrorEstimate(int correct)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

printCount

public java.lang.String printCount()

Print count information

Returns:

printVcfObject

@Deprecated
public java.lang.String printVcfObject(java.io.PrintWriter out)
                                throws org.apache.commons.math.MathException

Deprecated.

Throws:

org.apache.commons.math.MathException

getMostAltBase

public char getMostAltBase()

Get the mose alt base

Returns:

char

getMostBase

public char getMostBase()

Get the mose base including ref, if indel is most, return 0

Returns:

char

isNoAlternate

@Deprecated
public boolean isNoAlternate()

Deprecated.

isEmpty

public boolean isEmpty()

Check is empty

Returns:

boolean

getForwardBaseNum

public int getForwardBaseNum(char base)

Get the base count from forward sequence

Parameters:

base - char

Returns:

int

getReverseBaseNum

public int getReverseBaseNum(char base)

Get the base count from reverse sequence

Parameters:

base - char

Returns:

int

isReference

public boolean isReference(char base)

Check the base is a ref

Parameters:

base - char

Returns:

int

getCount

public int getCount(char base)

Return the count number of base from both sequence

Parameters:

base -

Returns:

getTotal

public int getTotal()

Return the total number of base, not including indel

Returns:

compareTo

public int compareTo(SnverMeta snverMeta)

Specified by:

compareTo in interface java.lang.Comparable<SnverMeta>

getRatioString

public java.lang.String getRatioString()

Return the alt/ref type

Returns:

String

getRatio

public double getRatio()

Return the alt/ref ratio

Returns:

double

getGnomeChar

public char getGnomeChar(int i)

Return the base character

Parameters:

i - int

Returns:

char

getIndel

public int getIndel()

Retunr the indel number

Returns:

int

isOnlyRef

public boolean isOnlyRef()

Check there is only ref

Returns:

boolean