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, toString
compute, computeIfAbsent, computeIfPresent, entry, equals, getOrDefault, hashCode, isEmpty, merge, of, of, of, of, of, of, of, of, of, of, of, ofEntries, putIfAbsent, remove
finalize, getClass, notify, notifyAll, wait, wait, wait
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
public 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()