Property Detail

• static final java.util.Set<java.lang.String> NULL_VALUES

• static final java.util.List PED_COLUMNS

• java.util.Map<java.lang.String, gngs.Pedigree> families

  Lookup table to find family by family Id

• java.util.Map<java.lang.String, gngs.Pedigree> subjects

  Look up table to find pedigree by subject Ids

Constructor Detail

• Pedigrees()

Method Detail

• Pedigrees add(Pedigrees other)

• void add(gngs.Pedigree ped)

  Add the pedigree to this Pedigrees object

  Parameters:

  ped

• Subject fatherOf(java.lang.String id)

• java.util.List<Subject> findMaximalUnrelatedSet(java.lang.String sampleId)

  Find the largest possible set of samples that are unrelated to the given sample. If null is passed, the maximal set of unrelated samples from the entire set will be computed. @return

• static Pedigrees fromSingletons(java.util.List<java.lang.String> sampleIds)

  A convenience method that creates a set of pedigrees from set of unrelated singletons. Such a pedigree is not very useful, but it allows code expecting a pedigree to work with unrelated samples.

• java.util.List<java.lang.String> getAffected()

• java.util.List<Subject> getAllSubjects()

• Subject getAt(java.lang.String id)

  Get Subject by their id @return

  Parameters:

  id

• java.util.List<java.lang.String> getFemales()

• java.util.List<java.lang.String> getMales()

• java.util.List<java.lang.String> getSubjectsBySex(Sex sex)

• java.util.List<java.lang.String> getUnaffected()

• Subject motherOf(java.lang.String id)

• static Pedigrees parse(java.lang.String pedFileName, groovy.lang.Closure c)

  Parse a PED file to create a set of pedigrees from it See parse(Reader,Closure) @return

  Parameters:

  pedFileName - path to file

  c - filtering closure

• static Pedigrees parse(java.io.Reader r, groovy.lang.Closure c)

  Parse a PED file from the given reader, with optional filtering via the provided closure

  Parameters:

  r - the reader to read the PED file from

  c - an optional Closure that will be called for each line (see PED_COLUMNS) which will cause samples to be skipped from parsing if it returns false

  Returns:

  a Pedigrees object representing the families parsed from the PED file

• void removeFamily(java.lang.String id)

• void renameFamily(java.lang.String id, java.lang.String newId)

• void renameSubject(java.lang.String fromId, java.lang.String toId)

• void save(java.lang.String fileName)

• void save(java.io.Writer w)

• java.lang.String toJson()

• void validate()