pedviz.haplotype
Class Haplotypes

java.lang.Object
  pedviz.haplotype.Haplotypes

Direct Known Subclasses:

MerlinHaplotypes

public class Haplotypes
extends java.lang.Object

Contains haplotypes for each node in a graph.

Author:

Luki

Constructor Summary

Haplotypes()
Creates a Haplotypes object.

Method Summary

java.util.Vector<HaplotypeItem>	getData(java.lang.Object id) Returns the HaplotypeItem for the node with the given id.
java.util.HashMap<java.lang.Object,MerlinError>	getErrors() Returns all errors for the node with the given id.
java.util.Vector<java.lang.String>	getMarkers() Returns a collection of all markers in this haplotype.
java.util.Vector<java.lang.String>	getPos() Returns a collection of all chrom. positions.
int	getSize() Returns the number of all markers.
int	getVisibleSize() Returns the number of visible markers.
void	hideAllMarkers() Hides all markers.
boolean	isMarkerVisible(int marker) Returns true, if the given marker is visible.
void	showAllMarkers() Shows all markers.
void	showMarker(int marker) Shows the given marker.

Methods inherited from class java.lang.Object

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

Constructor Detail

Haplotypes

public Haplotypes()

Creates a Haplotypes object.

Method Detail

getData

public java.util.Vector<HaplotypeItem> getData(java.lang.Object id)

Returns the HaplotypeItem for the node with the given id.

Parameters:

id -

Returns:

Collection of all HaplotypeItem for the node with the given id.

getMarkers

public java.util.Vector<java.lang.String> getMarkers()

Returns a collection of all markers in this haplotype.

Returns:

collection of all markers.

isMarkerVisible

public boolean isMarkerVisible(int marker)

Returns true, if the given marker is visible.

Parameters:

marker -

Returns:

true, if the given marker is visible.

getVisibleSize

public int getVisibleSize()

Returns the number of visible markers.

Returns:

number of visible markers.

hideAllMarkers

public void hideAllMarkers()

Hides all markers.

showAllMarkers

public void showAllMarkers()

Shows all markers.

showMarker

public void showMarker(int marker)

Shows the given marker.

Parameters:

marker - marker.

getSize

public int getSize()

Returns the number of all markers.

Returns:

number of all markers.

getPos

public java.util.Vector<java.lang.String> getPos()

Returns a collection of all chrom. positions.

Returns:

a collection of all chrom. positions

getErrors

public java.util.HashMap<java.lang.Object,MerlinError> getErrors()

Returns all errors for the node with the given id.

Returns:

all errors for the node with the given id.