Represents a set of relationships between individuals in a family
| Type | Name and description |
|---|---|
java.util.List<java.lang.String> |
affected |
java.lang.String |
idUnique identifier for the family |
java.util.List<Subject> |
individualsList of subjects belonging to the family |
java.util.List<java.lang.Integer> |
phenoTypes |
java.util.List<java.lang.String> |
samples |
java.util.List<java.lang.String> |
unaffected |
| Type Params | Return Type | Name and description |
|---|---|---|
|
Subject |
copySubject(java.lang.String fromId, java.lang.String toId) |
|
Subject |
fatherOf(java.lang.String id) |
|
java.util.List<Subject> |
findMaximalUnrelatedSet()Compute the largest set of samples within the pedigree who are unrelated. |
|
java.util.List<java.lang.String> |
getAffected() |
|
Subject |
getAt(java.lang.String id) |
|
java.util.List<java.lang.Object> |
getPedData(Subject subject) |
|
java.util.List<java.lang.String> |
getSamples() |
|
java.util.List<java.lang.String> |
getUnaffected() |
|
Subject |
motherOf(java.lang.String id) |
|
void |
renameSubject(java.lang.String fromId, java.lang.String toId) |
|
void |
reset() |
|
void |
setSamples(java.util.List<java.lang.String> samples) |
|
java.lang.String |
toJson() |
|
void |
toPed(java.io.Writer w) |
|
java.lang.String |
toString() |
|
void |
validate()Verify that the samples in the pedigree are internally consistent ie: mother must be female, father male, sample cannot be mother of itself, etc. |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long, int), java.lang.Object#wait(long), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Unique identifier for the family
List of subjects belonging to the family
Compute the largest set of samples within the pedigree who are unrelated. Typically this will be the topmost set of parents in the pedigree, however the method actually brute forces the answer by iterating every combination of samples and keeping only the sets that do not contain related individuals.
Verify that the samples in the pedigree are internally consistent ie: mother must be female, father male, sample cannot be mother of itself, etc.