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B

BED12 - org.dishevelled.bio.feature.bed.BedFormat

BED12 format, chrom start end name score strand thickStart thickEnd itemRgb blockCount blockSizes blockStarts.

BED3 - org.dishevelled.bio.feature.bed.BedFormat

BED3 format, chrom start end.

BED4 - org.dishevelled.bio.feature.bed.BedFormat

BED4 format, chrom start end name.

BED5 - org.dishevelled.bio.feature.bed.BedFormat

BED5 format, chrom start end name score.

BED6 - org.dishevelled.bio.feature.bed.BedFormat

BED6 format, chrom start end name score strand.

BedFormat - Enum in org.dishevelled.bio.feature.bed

BED formats.

BedListener - Interface in org.dishevelled.bio.feature.bed

BED listener.

BedReader - Class in org.dishevelled.bio.feature.bed

BED format reader.

BedRecord - Class in org.dishevelled.bio.feature.bed

BED record.

BedRecord(String, long, long) - Constructor for class org.dishevelled.bio.feature.bed.BedRecord

Create a new BED3 record.

BedRecord(String, long, long, String) - Constructor for class org.dishevelled.bio.feature.bed.BedRecord

Create a new BED4 record.

BedRecord(String, long, long, String, String) - Constructor for class org.dishevelled.bio.feature.bed.BedRecord

Create a new BED5 record.

BedRecord(String, long, long, String, String, String) - Constructor for class org.dishevelled.bio.feature.bed.BedRecord

Create a new BED6 record.

BedRecord(String, long, long, String, String, String, long, long, String, int, long[], long[]) - Constructor for class org.dishevelled.bio.feature.bed.BedRecord

Create a new BED12 record.

BedWriter - Class in org.dishevelled.bio.feature.bed

BED writer.

E

equals(Object) - Method in class org.dishevelled.bio.feature.bed.BedRecord

equals(Object) - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

G

getAttributes() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the attributes for this GFF3 record.

getBlockCount() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the block count for this BED record.

getBlockSizes() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the block sizes for this BED record.

getBlockStarts() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the block starts for this BED record.

getChrom() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the chrom for this BED record.

getEnd() - Method in class org.dishevelled.bio.feature.bed.BedRecord

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

getEnd() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the end for this GFF3 record in 0-based coordinate system, closed open range.

getFeatureType() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the feature type for this GFF3 record.

getFormat() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the format of this BED record.

getItemRgb() - Method in class org.dishevelled.bio.feature.bed.BedRecord

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

getName() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the name for this BED record, if any.

getPhase() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the phase for this GFF3 record, if any.

getScore() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the score for this BED record, if any.

getScore() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the score for this GFF3 record, if any.

getSeqid() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the seqid for this GFF3 record.

getSource() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the source for this GFF3 record.

getStart() - Method in class org.dishevelled.bio.feature.bed.BedRecord

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

getStart() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the start for this GFF3 record in 0-based coordinate system, closed open range.

getStrand() - Method in class org.dishevelled.bio.feature.bed.BedRecord

Return the strand for this BED record, if any.

getStrand() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return the strand for this GFF3 record.

getThickEnd() - Method in class org.dishevelled.bio.feature.bed.BedRecord

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

getThickStart() - Method in class org.dishevelled.bio.feature.bed.BedRecord

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

Gff3Listener - Interface in org.dishevelled.bio.feature.gff3

GFF3 listener.

Gff3Reader - Class in org.dishevelled.bio.feature.gff3

GFF3 format reader.

Gff3Record - Class in org.dishevelled.bio.feature.gff3

GFF3 record.

Gff3Record(String, String, String, long, long, Double, String, Integer, ListMultimap<String, String>) - Constructor for class org.dishevelled.bio.feature.gff3.Gff3Record

Create a new GFF3 record.

Gff3Writer - Class in org.dishevelled.bio.feature.gff3

GFF3 writer.

H

hashCode() - Method in class org.dishevelled.bio.feature.bed.BedRecord

hashCode() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

I

isAtLeastBED12() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is at least BED12.

isAtLeastBED3() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is at least BED3.

isAtLeastBED4() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is at least BED4.

isAtLeastBED5() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is at least BED5.

isAtLeastBED6() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is at least BED6.

isBED12() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is BED12.

isBED3() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is BED3.

isBED4() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is BED4.

isBED5() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is BED5.

isBED6() - Method in enum org.dishevelled.bio.feature.bed.BedFormat

Return true if this BED format is BED6.

isMissingValue(String) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return true if the specified value is the missing value (".").

O

org.dishevelled.bio.feature - package org.dishevelled.bio.feature

Sequence features.

org.dishevelled.bio.feature.bed - package org.dishevelled.bio.feature.bed

Sequence features in BED format.

org.dishevelled.bio.feature.gff3 - package org.dishevelled.bio.feature.gff3

Sequence features in GFF3 format.

P

parseAttributes(String) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Record

Parse the GFF3 attributes column into a list multimap of <String, String> entries.

R

read(Readable) - Static method in class org.dishevelled.bio.feature.bed.BedReader

Read zero or more BED records from the specified readable.

read(Readable) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Reader

Read zero or more GFF3 records from the specified readable.

record(BedRecord) - Method in interface org.dishevelled.bio.feature.bed.BedListener

Notify this BED listener of a BED record.

record(Gff3Record) - Method in interface org.dishevelled.bio.feature.gff3.Gff3Listener

Notify this GFF3 listener of a GFF3 record.

S

stream(Readable, BedListener) - Static method in class org.dishevelled.bio.feature.bed.BedReader

Stream zero or more BED records from the specified readable.

stream(Readable, Gff3Listener) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Reader

Stream zero or more GFF3 records from the specified readable.

T

toRange() - Method in class org.dishevelled.bio.feature.bed.BedRecord

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

toRange() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return this GFF3 record as a 0-based coordinate system, closed open range.

toString() - Method in class org.dishevelled.bio.feature.bed.BedRecord

toString() - Method in class org.dishevelled.bio.feature.gff3.Gff3Record

V

valueOf(String) - Static method in enum org.dishevelled.bio.feature.bed.BedFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in class org.dishevelled.bio.feature.bed.BedRecord

Return a new BED record parsed from the specified value.

valueOf(String) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Record

Return a new GFF3 record parsed from the specified value.

values() - Static method in enum org.dishevelled.bio.feature.bed.BedFormat

Returns an array containing the constants of this enum type, in the order they are declared.

W

write(Iterable<BedRecord>, PrintWriter) - Static method in class org.dishevelled.bio.feature.bed.BedWriter

Write zero or more BED records with the specified print writer.

write(Iterable<Gff3Record>, PrintWriter) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Writer

Write zero or more GFF3 records with the specified print writer.

write(BedRecord, PrintWriter) - Static method in class org.dishevelled.bio.feature.bed.BedWriter

Write the specified BED record with the specified print writer.

write(Gff3Record, PrintWriter) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Writer

Write the specified GFF3 record with the specified print writer.

writeAttributes(ListMultimap<String, String>) - Static method in class org.dishevelled.bio.feature.gff3.Gff3Record

Write the list multimap of <String, String> entries as GFF3 attributes column format.

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