Serializable, Cloneable, Map<String,PedFile.PedTrio>, NavigableMap<String,PedFile.PedTrio>, SortedMap<String,PedFile.PedTrio>public class PedFile extends TreeMap<String,PedFile.PedTrio>
| Modifier and Type | Class | Description |
|---|---|---|
class |
PedFile.PedTrio |
AbstractMap.SimpleEntry<K extends Object,V extends Object>, AbstractMap.SimpleImmutableEntry<K extends Object,V extends Object>| Modifier and Type | Field | Description |
|---|---|---|
static Number |
NO_PHENO |
|
static Sex |
UNKNOWN_SEX |
| Constructor | Description |
|---|---|
PedFile(boolean isTabMode) |
| Modifier and Type | Method | Description |
|---|---|---|
void |
add(PedFile.PedTrio trio) |
Adds a trio to the PedFile keyed by the individual id.
|
static PedFile |
fromFile(File file,
boolean isTabMode) |
Attempts to read a pedigree file into memory.
|
static PedFile |
fromSexMap(Map<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(File file) |
Writes a set of pedigrees out to disk.
|
equals, hashCode, isEmpty, toStringcompute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, removefinalize, getClass, notify, notifyAll, wait, wait, waitceilingEntry, 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, valuespublic static final Number NO_PHENO
public static final Sex UNKNOWN_SEX
public void add(PedFile.PedTrio trio)
public void write(File file)
public static PedFile fromFile(File file, boolean isTabMode)
public PedFile removeIncompleteTrios()