org.dishevelled.bio.feature.bed

Class BedRecord

java.lang.Object

org.dishevelled.bio.feature.bed.BedRecord

@Immutable
public final class BedRecord
extends Object

BED record. Supports the same BED formats as bedtools2.

• BED3: A BED file where each feature is described by chrom, start, and end. For example: chr1 11873 14409
• BED4: A BED file where each feature is described by chrom, start, end, and name. For example: chr1 11873 14409 uc001aaa.3
• BED5: A BED file where each feature is described by chrom, start, end, name, and score. For example: chr1 11873 14409 uc001aaa.3 0
• BED6: A BED file where each feature is described by chrom, start, end, name, score, and strand. For example: chr1 11873 14409 uc001aaa.3 0 +
• BED12: A BED file where each feature is described by all twelve columns listed above. For example: chr1 11873 14409 uc001aaa.3 0 + 11873 11873 0 3 354,109,1189, 0,739,1347,

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor and Description
BedRecord(String chrom, long start, long end) Create a new BED3 record.
BedRecord(String chrom, long start, long end, String name) Create a new BED4 record.
BedRecord(String chrom, long start, long end, String name, String score) Create a new BED5 record.
BedRecord(String chrom, long start, long end, String name, String score, String strand) Create a new BED6 record.
BedRecord(String chrom, long start, long end, String name, String score, String strand, long thickStart, long thickEnd, String itemRgb, int blockCount, long[] blockSizes, long[] blockStarts) Create a new BED12 record.

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object o)
int	getBlockCount() Return the block count for this BED record.
long[]	getBlockSizes() Return the block sizes for this BED record.
long[]	getBlockStarts() Return the block starts for this BED record.
String	getChrom() Return the chrom for this BED record.
long	getEnd() Return the end for this BED record in 0-based coordinate system, closed open range.
BedFormat	getFormat() Return the format of this BED record.
String	getItemRgb() Return the item RGB for this BED record, if any.
String	getName() Return the name for this BED record, if any.
String	getScore() Return the score for this BED record, if any.
long	getStart() Return the start for this BED record in 0-based coordinate system, closed open range.
String	getStrand() Return the strand for this BED record, if any.
long	getThickEnd() Return the thick end for this BED record in 0-based coordinate system, closed open range.
long	getThickStart() Return the thick start for this BED record in 0-based coordinate system, closed open range.
int	hashCode()
com.google.common.collect.Range<Long>	toRange() Return this BED record as a 0-based coordinate system, closed open range.
String	toString()
static BedRecord	valueOf(String value) Return a new BED record parsed from the specified value.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

BedRecord

public BedRecord(String chrom,
                 long start,
                 long end)

Create a new BED3 record.

Parameters:

chrom - chrom, must not be null

start - start, must be at least zero

end - end, must be at least zero, and greater than or equal to start

BedRecord

public BedRecord(String chrom,
                 long start,
                 long end,
                 String name)

Create a new BED4 record.

Parameters:

chrom - chrom, must not be null

start - start, must be at least zero

end - end, must be at least zero, and greater than or equal to start

name - name

BedRecord

public BedRecord(String chrom,
                 long start,
                 long end,
                 String name,
                 String score)

Create a new BED5 record.

Parameters:

chrom - chrom, must not be null

start - start, must be at least zero

end - end, must be at least zero, and greater than or equal to start

name - name

score - score

BedRecord

public BedRecord(String chrom,
                 long start,
                 long end,
                 String name,
                 String score,
                 String strand)

Create a new BED6 record.

Parameters:

chrom - chrom, must not be null

start - start, must be at least zero

end - end, must be at least zero, and greater than or equal to start

name - name

score - score

strand - strand, if present must be either - or +

BedRecord

public BedRecord(String chrom,
                 long start,
                 long end,
                 String name,
                 String score,
                 String strand,
                 long thickStart,
                 long thickEnd,
                 String itemRgb,
                 int blockCount,
                 long[] blockSizes,
                 long[] blockStarts)

Create a new BED12 record.

Parameters:

chrom - chrom, must not be null

start - start, must be at least zero

end - end, must be at least zero, and greater than or equal to start

name - name

score - score

strand - strand, if present must be either - or +

thickStart - thick start, must be at least zero

thickEnd - thick end, must be at least zero and greater than or equal to thick start

itemRgb - item RGB, if present, must be in R,G,B format, e.g. 255,0,0

blockCount - block count, must be at least zero

blockSizes - block sizes, must be the same length as block count

blockStarts - block starts, must be the same length as block count

Method Detail

getChrom

public String getChrom()

Return the chrom for this BED record.

Returns:

the chrom for this BED record

getStart

public long getStart()

Return the start for this BED record in 0-based coordinate system, closed open range.

Returns:

the start for this BED record in 0-based coordinate system, closed open range

getEnd

public long getEnd()

Return the end for this BED record in 0-based coordinate system, closed open range.

Returns:

the end for this BED record in 0-based coordinate system, closed open range

getName

public String getName()

Return the name for this BED record, if any.

Returns:

the name for this BED record, if any

getScore

public String getScore()

Return the score for this BED record, if any.

Returns:

the score for this BED record, if any

getStrand

public String getStrand()

Return the strand for this BED record, if any.

Returns:

the strand for this BED record, if any

getThickStart

public long getThickStart()

Return the thick start for this BED record in 0-based coordinate system, closed open range.

Returns:

the thick start for this BED record in 0-based coordinate system, closed open range

getThickEnd

public long getThickEnd()

Return the thick end for this BED record in 0-based coordinate system, closed open range.

Returns:

the thick end for this BED record in 0-based coordinate system, closed open range

getItemRgb

public String getItemRgb()

Return the item RGB for this BED record, if any.

Returns:

the item RGB for this BED record, if any

getBlockCount

public int getBlockCount()

Return the block count for this BED record.

Returns:

the block count for this BED record

getBlockSizes

public long[] getBlockSizes()

Return the block sizes for this BED record.

Returns:

the block sizes for this BED record

getBlockStarts

public long[] getBlockStarts()

Return the block starts for this BED record.

Returns:

the block starts for this BED record

getFormat

public BedFormat getFormat()

Return the format of this BED record.

Returns:

the format of this BED record

toRange

public com.google.common.collect.Range<Long> toRange()

Return this BED record as a 0-based coordinate system, closed open range.

Returns:

this BED record as a 0-based coordinate system, closed open range

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

valueOf

public static BedRecord valueOf(String value)

Return a new BED record parsed from the specified value.

Parameters:

value - value to parse

Returns:

a new BED record parsed from the specified value

Throws:

IllegalArgumentException - if the value is not valid BED[3,4,5,6,12] format

NullPointerException - if a required field is missing

NumberFormatException - if a long valued field cannot be parsed as a long