umcg.genetica.genomicboundaries

Class GenomicBoundaries<V>

java.lang.Object

umcg.genetica.genomicboundaries.GenomicBoundaries<V>

All Implemented Interfaces:

Iterable<GenomicBoundary<V>>

public class GenomicBoundaries<V>
extends Object
implements Iterable<GenomicBoundary<V>>

Author:

PatrickDeelen

Constructor Summary

Constructors

Constructor and Description
GenomicBoundaries() Empty constructor that only creates an empty structure for saving Genomic Boundaries.
GenomicBoundaries(String genomicsBoundarysFilePath) Constructor for building Genomic Boundaries from a file.
GenomicBoundaries(String genomicsBoundarysFilePath, int margin)

Method Summary

Modifier and Type	Method and Description
void	addBoundary(String chromosome, Integer beginPoint, int endPoint) Method to add a Genomic Boundary to the Genmoic Boundaries set.
void	addBoundary(String chromosome, Integer beginPoint, int endPoint, V annotation) Method to add a Genomic Boundary to the Genmoic Boundaries set.
int	getBoudaryCount() This method returns the count of Boundary objects.
GenomicBoundary	getBoundary(String chromosome, int position, int listIndex) This method returns a Boundary object from a chromosome at a specific position.
int	getBoundaryCountChromosome(String chromosome)
Set<String>	getChromosomes()
HashMap<String,TreeMap<Integer,ArrayList<GenomicBoundary<V>>>>	getGenomicBoundaries() Returns the GenomicBoundaries
Collection<ArrayList<GenomicBoundary<V>>>	getGenomicBoundaries(String chromosome) Returns the GenomicBoundaries
TreeMap<Integer,ArrayList<GenomicBoundary<V>>>	getGenomicBoundariesMap(String chromosome) Returns a TreeMap> if the provided chromosome is present with genomicsBoundaries.
boolean	isChromosomeInBoundary(String chromosome) Method to check if a chromosome is contained in the Genomic Boundaries.
boolean	isInBoundary(String chromosome, int position, int listIndex)
Iterator<GenomicBoundary<V>>	iterator()
void	mergeGenomicBoundaries(GenomicBoundaries otherGenomicBoundariesSet) Merges GenomicBoundaries by adding
void	mergeOverlappingBoundaries() Method that merges overlapping Boundaries.
void	removeSubBoundaries() Method to remove boundaries that are sub boundaries of other boundaries.
void	writeBoundariesToBedFile(String bedFilePath, String trackName) Write the data of the Boundary objects to a BED file, specified by @param bedFilePath.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

GenomicBoundaries

public GenomicBoundaries(String genomicsBoundarysFilePath)
                  throws FileNotFoundException,
                         IOException

Constructor for building Genomic Boundaries from a file.

Parameters:

genomicsBoundarysFilePath -

Throws:

FileNotFoundException

IOException

GenomicBoundaries

public GenomicBoundaries()

Empty constructor that only creates an empty structure for saving Genomic Boundaries.

GenomicBoundaries

public GenomicBoundaries(String genomicsBoundarysFilePath,
                         int margin)
                  throws FileNotFoundException,
                         IOException

Throws:

FileNotFoundException

IOException

Method Detail

addBoundary

public final void addBoundary(String chromosome,
                              Integer beginPoint,
                              int endPoint)

Method to add a Genomic Boundary to the Genmoic Boundaries set.

Parameters:

chromosome -

beginPoint -

endPoint -

removeSubBoundaries

public final void removeSubBoundaries()

Method to remove boundaries that are sub boundaries of other boundaries.

mergeOverlappingBoundaries

public final void mergeOverlappingBoundaries()

Method that merges overlapping Boundaries.

isChromosomeInBoundary

public boolean isChromosomeInBoundary(String chromosome)

Method to check if a chromosome is contained in the Genomic Boundaries.

Parameters:

chromosome -

Returns:

getChromosomes

public Set<String> getChromosomes()

Returns:

isInBoundary

public boolean isInBoundary(String chromosome,
                            int position,
                            int listIndex)

getBoundary

public GenomicBoundary getBoundary(String chromosome,
                                   int position,
                                   int listIndex)

This method returns a Boundary object from a chromosome at a specific position.

Parameters:

chromosome -

position -

Returns:

iterator

public Iterator<GenomicBoundary<V>> iterator()

Specified by:

iterator in interface Iterable<GenomicBoundary<V>>

getBoundaryCountChromosome

public int getBoundaryCountChromosome(String chromosome)

getBoudaryCount

public int getBoudaryCount()

This method returns the count of Boundary objects.

Returns:

writeBoundariesToBedFile

public void writeBoundariesToBedFile(String bedFilePath,
                                     String trackName)
                              throws IOException

Write the data of the Boundary objects to a BED file, specified by @param bedFilePath.

Parameters:

bedFilePath -

trackName -

Throws:

IOException

getGenomicBoundariesMap

public TreeMap<Integer,ArrayList<GenomicBoundary<V>>> getGenomicBoundariesMap(String chromosome)
                                                                       throws Exception

Returns a TreeMap> if the provided chromosome is present with genomicsBoundaries. Otherwise an exception is thrown.

Parameters:

chromosome -

Returns:

Throws:

Exception

getGenomicBoundaries

public Collection<ArrayList<GenomicBoundary<V>>> getGenomicBoundaries(String chromosome)
                                                               throws Exception

Returns the GenomicBoundaries

Parameters:

chromosome -

Returns:

Throws:

Exception

mergeGenomicBoundaries

public void mergeGenomicBoundaries(GenomicBoundaries otherGenomicBoundariesSet)

Merges GenomicBoundaries by adding

Parameters:

otherGenomicBoundariesSet -

getGenomicBoundaries

public HashMap<String,TreeMap<Integer,ArrayList<GenomicBoundary<V>>>> getGenomicBoundaries()

Returns the GenomicBoundaries

Returns:

addBoundary

public final void addBoundary(String chromosome,
                              Integer beginPoint,
                              int endPoint,
                              V annotation)

Method to add a Genomic Boundary to the Genmoic Boundaries set.

Parameters:

chromosome -

beginPoint -

endPoint -