picard.pedigree

Class PedFile

java.lang.Object

java.util.AbstractMap<K,V>

java.util.TreeMap<java.lang.String,PedFile.PedTrio>

picard.pedigree.PedFile

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.util.Map<java.lang.String,PedFile.PedTrio>, java.util.NavigableMap<java.lang.String,PedFile.PedTrio>, java.util.SortedMap<java.lang.String,PedFile.PedTrio>

public class PedFile
extends java.util.TreeMap<java.lang.String,PedFile.PedTrio>

Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	PedFile.PedTrio

Nested classes/interfaces inherited from class java.util.AbstractMap

java.util.AbstractMap.SimpleEntry<K,V>, java.util.AbstractMap.SimpleImmutableEntry<K,V>

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.Number	NO_PHENO
static Sex	UNKNOWN_SEX

Constructor Summary

Constructors

Constructor and Description
PedFile(boolean isTabMode)

Method Summary

Modifier and Type	Method and Description
void	add(PedFile.PedTrio trio) Adds a trio to the PedFile keyed by the individual id.
static PedFile	fromFile(java.io.File file, boolean isTabMode) Attempts to read a pedigree file into memory.
static PedFile	fromSexMap(java.util.Map<java.lang.String,Sex> sampleSexes) Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
PedFile	removeIncompleteTrios() Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
void	write(java.io.File file) Writes a set of pedigrees out to disk.

Methods inherited from class java.util.TreeMap

ceilingEntry, ceilingKey, clear, clone, comparator, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, forEach, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, navigableKeySet, pollFirstEntry, pollLastEntry, put, putAll, remove, replace, replace, replaceAll, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap

equals, hashCode, isEmpty, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, remove

Field Detail

NO_PHENO

public static final java.lang.Number NO_PHENO

UNKNOWN_SEX

public static final Sex UNKNOWN_SEX

Constructor Detail

PedFile

public PedFile(boolean isTabMode)

Method Detail

add

public void add(PedFile.PedTrio trio)

Adds a trio to the PedFile keyed by the individual id.

write

public void write(java.io.File file)

Writes a set of pedigrees out to disk.

fromFile

public static PedFile fromFile(java.io.File file,
                               boolean isTabMode)

Attempts to read a pedigree file into memory.

removeIncompleteTrios

public PedFile removeIncompleteTrios()

Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.

fromSexMap

public static PedFile fromSexMap(java.util.Map<java.lang.String,Sex> sampleSexes)

Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.

Parameters:

sampleSexes - a map from sample-name to its sex

Returns:

a PedFile object that contains data.