net.maizegenetics.pangenome.hapCalling

Class HapIdMultiset

net.maizegenetics.pangenome.hapCalling.HapIdMultiset

public class HapIdMultiset

Guava like Multiset which will store a sorted set of hapids as the key and how many reads hit that exact subset of ids.

Constructor Detail

HapIdMultiset

public HapIdMultiset()

Guava like Multiset which will store a sorted set of hapids as the key and how many reads hit that exact subset of ids.

Method Detail

getMultiset

@NotNull
public java.util.Map<java.util.SortedSet,java.lang.Integer> getMultiset()

setMultiset

public void setMultiset(@NotNull
                        java.util.Map<java.util.SortedSet,java.lang.Integer> p)

add

public void add(@NotNull
                java.util.Set<java.lang.Integer> hapIds)

Method to increment the count for a given hapId set

count

public int count(@NotNull
                 java.util.Set<java.lang.Integer> hapIds)

Method to return the count for a given hapId set. We sort the hapId set again just to be safe.

clear

public void clear()

Method to clear out the multiset and create a new empty one.

getMap

@NotNull
public java.util.Map<java.util.SortedSet,java.lang.Integer> getMap()

Method to get out the backing Map. This can be more easily worked with once everything is added to the Multiset.