pedviz.haplotype
Class MerlinHaplotypes

java.lang.Object
  pedviz.haplotype.Haplotypes
      pedviz.haplotype.MerlinHaplotypes

public class MerlinHaplotypes
extends Haplotypes

The haplotype visualization is based on the Merlin data format . The Merlin error output file (MerlinErrorChecking) can be used to highlight errors in the haplotype/genotype data.

Author:

Luki

Constructor Summary

MerlinHaplotypes(java.lang.String filename, java.lang.String map)
Imports the haplotype information from the given *.chr and *.map file.

MerlinHaplotypes(java.lang.String filename, java.lang.String map, boolean resource)
Imports the haplotype information from the given *.chr and *.map file.

Method Summary

void	setErrors(java.util.HashMap<java.lang.Object,MerlinError> errors) Sets a collection of errors (MerlinErrorChecking).

Methods inherited from class pedviz.haplotype.Haplotypes

getData, getErrors, getMarkers, getPos, getSize, getVisibleSize, hideAllMarkers, isMarkerVisible, showAllMarkers, showMarker

Methods inherited from class java.lang.Object

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

Constructor Detail

MerlinHaplotypes

public MerlinHaplotypes(java.lang.String filename,
                        java.lang.String map)

Imports the haplotype information from the given *.chr and *.map file.

Parameters:

filename - *.chr file

map - *.map file

MerlinHaplotypes

public MerlinHaplotypes(java.lang.String filename,
                        java.lang.String map,
                        boolean resource)

Imports the haplotype information from the given *.chr and *.map file.

Parameters:

filename - *.chr file

map - *.map file

resource - load files from a resource.

Method Detail

setErrors

public void setErrors(java.util.HashMap<java.lang.Object,MerlinError> errors)

Sets a collection of errors (MerlinErrorChecking).

Parameters:

errors - a collection of errors.