public final class PedPerson extends Object
.ped
) file.
A pedigree file is a TSV file and contains information about multiple indivdidual. Each line is a record and
describes an individual. The files have six core columns that have to be present:
pedigree
name
father
mother
sex
disease
extraFields
.
The PedPerson
class describes a record from a pedigree file. This introduces some limitations. For
example, the record stores the id of the parents but not references to the parent objects. The class Person
provides a more Java-programmer oriented version of this information.Constructor and Description |
---|
PedPerson(String pedigree,
String name,
String father,
String mother,
Sex sex,
Disease disease)
Initialize object with the given data.
|
PedPerson(String pedigree,
String name,
String father,
String mother,
Sex sex,
Disease disease,
Collection<String> extraFields)
Initialize object with the given data.
|
Modifier and Type | Method and Description |
---|---|
boolean |
equals(Object obj) |
Disease |
getDisease() |
com.google.common.collect.ImmutableList<String> |
getExtraFields() |
String |
getFather() |
String |
getMother() |
String |
getName() |
String |
getPedigree() |
Sex |
getSex() |
int |
hashCode() |
boolean |
isFounder() |
String |
toString() |
public PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease, Collection<String> extraFields)
public String getPedigree()
public String getName()
public String getFather()
"0"
if father not in pedigreepublic String getMother()
"0"
if father not in pedigreepublic Sex getSex()
public Disease getDisease()
public com.google.common.collect.ImmutableList<String> getExtraFields()
public boolean isFounder()
true
if the person is a founder (both mother and father are "0"
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