Constant Field Values

Contents

• com.milaboratory.*

com.milaboratory.*

com.milaboratory.core.alignment.AffineGapAlignmentScoring<S extends Sequence<S>>

Modifier and Type	Constant Field	Value
public static final int	IGBLAST_NUCLEOTIDE_SCORING_THRESHOLD	150

com.milaboratory.core.alignment.AlignerCustom

Modifier and Type	Constant Field	Value
public static final int	MIN_VALUE	-1073741824

com.milaboratory.core.alignment.BandedMatrix

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_VALUE	-1073741824

com.milaboratory.core.alignment.blast.Blast

Modifier and Type	Constant Field	Value
public static final String	CMD_BLASTDBCMD	"blastdbcmd"
public static final String	CMD_BLASTN	"blastn"
public static final String	CMD_BLASTP	"blastp"
public static final String	CMD_MAKEBLASTDB	"makeblastdb"

com.milaboratory.core.alignment.kaligner1.KMapper

Modifier and Type	Constant Field	Value
public static final int	SEED_NOT_FOUND_OFFSET	-2147483647

com.milaboratory.core.alignment.kaligner2.KMapper2

Modifier and Type	Constant Field	Value
public static final int	SEED_NOT_FOUND_OFFSET	-2147483647

com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator

Modifier and Type	Constant Field	Value
public static final int	DROPPED_CLUSTER	-274653
public static final int	FIRST_RECORD_ID	0
public static final int	LAST_INDEX	6
public static final int	LAST_RECORD_ID	1
public static final int	LAST_VALUE	5
public static final int	MAX_VALUE	4
public static final int	MIN_VALUE	3
public static final int	OUTPUT_RECORD_SIZE	3
public static final int	RECORD_SIZE	7
public static final int	SCORE	2
public static final int	STRETCH_INDEX_MARK	-1610612736
public static final int	STRETCH_INDEX_MASK	-536870912

com.milaboratory.core.io.sequence.fasta.FastaWriter<S extends Sequence<S>>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_LENGTH	75

com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_INDEX_STEP	4096
public static final int	FILE_POSITION_OFFSET	20
public static final String	INDEX_SUFFIX	".mifdx"
public static final long	SKIP_MASK	1048575L

com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader<S extends Sequence<S>>

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BUFFER_SIZE	4096

com.milaboratory.core.io.sequence.fastq.SingleFastqReader

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BUFFER_SIZE	524288

com.milaboratory.core.io.sequence.fastq.SingleFastqWriter

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_BUFFER_SIZE	131072

com.milaboratory.core.io.util.FileIndex

Modifier and Type	Constant Field	Value
public static final int	MAGIC	-1659399333

com.milaboratory.core.merger.MergerParameters

Modifier and Type	Constant Field	Value
public static final int	DEFAULT_MAX_QUALITY_VALUE	50

com.milaboratory.core.merger.MismatchOnlyPairedReadMerger

Modifier and Type	Constant Field	Value
public static final int	MIN_SCORE_VALUE	0

com.milaboratory.core.merger.PairedReadMergingResult

Modifier and Type	Constant Field	Value
public static final int	MATCH_SCORE	2
public static final int	MISMATCH_SCORE	-5

com.milaboratory.core.mutations.Mutation

Modifier and Type	Constant Field	Value
public static final int	FROM_OFFSET	7
public static final int	LETTER_MASK	31
public static final int	MAX_POSITION_VALUE	1048575
public static final int	MUTATION_POSITION_MASK	-4096
public static final int	MUTATION_TYPE_MASK	96
public static final int	MUTATION_TYPE_OFFSET	5
public static final int	NON_MUTATION	0
public static final int	NON_MUTATION_1	1
public static final int	POSITION_OFFSET	12
public static final int	RAW_MUTATION_TYPE_DELETION	64
public static final int	RAW_MUTATION_TYPE_INSERTION	96
public static final int	RAW_MUTATION_TYPE_RESERVED	0
public static final int	RAW_MUTATION_TYPE_SUBSTITUTION	32

com.milaboratory.core.sequence.AminoAcidAlphabet

Modifier and Type	Constant Field	Value
public static final byte	A	1
public static final byte	B	23
public static final byte	C	2
public static final byte	D	3
public static final byte	E	4
public static final byte	F	5
public static final byte	G	6
public static final byte	H	7
public static final byte	I	8
public static final byte	INCOMPLETE_CODON	21
public static final byte	J	24
public static final byte	K	9
public static final byte	L	10
public static final byte	M	11
public static final byte	N	12
public static final byte	P	13
public static final byte	Q	14
public static final byte	R	15
public static final byte	S	16
public static final byte	STOP	0
public static final byte	T	17
public static final byte	V	18
public static final byte	W	19
public static final byte	X	22
public static final byte	Y	20
public static final byte	Z	25

com.milaboratory.core.sequence.NucleotideAlphabet

Modifier and Type	Constant Field	Value
public static final byte	A	0
public static final byte	B	11
public static final byte	C	2
public static final byte	D	12
public static final byte	G	1
public static final byte	H	13
public static final byte	K	9
public static final byte	M	10
public static final byte	N	4
public static final byte	R	5
public static final byte	S	7
public static final byte	T	3
public static final byte	V	14
public static final byte	W	8
public static final byte	Y	6

com.milaboratory.core.sequence.SequenceQuality

Modifier and Type	Constant Field	Value
public static final byte	BAD_QUALITY_VALUE	0
public static final byte	GOOD_QUALITY_VALUE	34
public static final byte	MAX_QUALITY_VALUE	58

com.milaboratory.util.AbstractLongProcessReporter

Modifier and Type	Constant Field	Value
public static final long	DEFAULT_REPORTING_INTERVAL	1000000000L
public static final double	DEFAULT_REPORTING_PROGRESS_DELTA	0.1

com.milaboratory.util.HashFunctions

Modifier and Type	Constant Field	Value
public static final long	FNV_BASIS	-2128831035L
public static final long	FNV_PRIME_32	16777619L
public static final long	FNV_PRIME_64	1099511628211L