A C D G M P R S T V

A

accept(SingleRead) - Method in class com.milaboratory.mitools.trimmer.ReadLengthFilter

C

CheckAction - Class in com.milaboratory.mitools.cli

CheckAction() - Constructor for class com.milaboratory.mitools.cli.CheckAction

CheckAction.AParameters - Class in com.milaboratory.mitools.cli

CheckAction.AParameters() - Constructor for class com.milaboratory.mitools.cli.CheckAction.AParameters

chunkSize - Variable in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

com.milaboratory.mitools.cli - package com.milaboratory.mitools.cli

com.milaboratory.mitools.processors - package com.milaboratory.mitools.processors

com.milaboratory.mitools.trimmer - package com.milaboratory.mitools.trimmer

com.milaboratory.mitools.util - package com.milaboratory.mitools.util

command() - Method in class com.milaboratory.mitools.cli.CheckAction

command() - Method in class com.milaboratory.mitools.cli.CutAction

command() - Method in class com.milaboratory.mitools.cli.MergeAction

command() - Method in class com.milaboratory.mitools.cli.RandomizeAction

command() - Method in class com.milaboratory.mitools.cli.RCAction

command() - Method in class com.milaboratory.mitools.cli.RenameAction

command() - Method in class com.milaboratory.mitools.cli.SplitAction

command() - Method in class com.milaboratory.mitools.cli.TrimAction

convert(String) - Method in class com.milaboratory.mitools.cli.MiCLIUtil.FileConverter

createSingleReader(String, boolean) - Static method in class com.milaboratory.mitools.cli.MiCLIUtil

createSingleWriter(String) - Static method in class com.milaboratory.mitools.cli.MiCLIUtil

CutAction - Class in com.milaboratory.mitools.cli

CutAction() - Constructor for class com.milaboratory.mitools.cli.CutAction

CutAction.AParams - Class in com.milaboratory.mitools.cli

CutAction.AParams() - Constructor for class com.milaboratory.mitools.cli.CutAction.AParams

CutSide - Enum in com.milaboratory.mitools.processors

D

doOutput() - Method in class com.milaboratory.mitools.cli.CheckAction.AParameters

G

generateSize(RandomGenerator, int, int) - Method in class com.milaboratory.mitools.cli.SplitAction

getHeaderPatternR1() - Method in class com.milaboratory.mitools.cli.CheckAction.AParameters

getHeaderPatternR2() - Method in class com.milaboratory.mitools.cli.CheckAction.AParameters

getInput() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

getInput() - Method in class com.milaboratory.mitools.cli.RCAction.RCParameters

getInput() - Method in class com.milaboratory.mitools.cli.RenameAction.RenameParameters

getInputStream(String) - Method in class com.milaboratory.mitools.cli.CheckAction

getMaxLengt() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

getMinLengt() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

getOutput() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

getOutput() - Method in class com.milaboratory.mitools.cli.MergeAction.MergingParameters

getOutput() - Method in class com.milaboratory.mitools.cli.RCAction.RCParameters

getOutput() - Method in class com.milaboratory.mitools.cli.RenameAction.RenameParameters

getOutputFileName(int, int) - Method in class com.milaboratory.mitools.cli.SplitAction

getOutputFiles() - Method in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

getPosition() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

getQualityMergingAlgorithm() - Method in class com.milaboratory.mitools.cli.MergeAction.MergingParameters

getR1() - Method in class com.milaboratory.mitools.cli.MergeAction.MergingParameters

getR2() - Method in class com.milaboratory.mitools.cli.MergeAction.MergingParameters

getReader() - Method in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

getSeed() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

getSeed() - Method in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

getSequenceReader() - Method in class com.milaboratory.mitools.cli.SplitAction

getSequenceWriter(int) - Method in class com.milaboratory.mitools.cli.SplitAction

getTotalTrimmedReads() - Method in class com.milaboratory.mitools.trimmer.SequenceTrimmer

getTrimmedNucleotidesLeft() - Method in class com.milaboratory.mitools.trimmer.SequenceTrimmer

getTrimmedNucleotidesRight() - Method in class com.milaboratory.mitools.trimmer.SequenceTrimmer

getTrimmedReadsLeft() - Method in class com.milaboratory.mitools.trimmer.SequenceTrimmer

getTrimmedReadsRight() - Method in class com.milaboratory.mitools.trimmer.SequenceTrimmer

getWriter() - Method in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.CheckAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.CutAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.MergeAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.RandomizeAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.RCAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.RenameAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.SplitAction

go(ActionHelper) - Method in class com.milaboratory.mitools.cli.TrimAction

M

Main - Class in com.milaboratory.mitools.cli

Main() - Constructor for class com.milaboratory.mitools.cli.Main

main(String[]) - Static method in class com.milaboratory.mitools.cli.Main

MergeAction - Class in com.milaboratory.mitools.cli

MergeAction() - Constructor for class com.milaboratory.mitools.cli.MergeAction

MergeAction.MergingParameters - Class in com.milaboratory.mitools.cli

MergeAction.MergingParameters() - Constructor for class com.milaboratory.mitools.cli.MergeAction.MergingParameters

MiCLIUtil - Class in com.milaboratory.mitools.cli

MiCLIUtil() - Constructor for class com.milaboratory.mitools.cli.MiCLIUtil

MiCLIUtil.FileConverter - Class in com.milaboratory.mitools.cli

MiCLIUtil.FileConverter() - Constructor for class com.milaboratory.mitools.cli.MiCLIUtil.FileConverter

MiCLIUtil.FileValidator - Class in com.milaboratory.mitools.cli

MiCLIUtil.FileValidator() - Constructor for class com.milaboratory.mitools.cli.MiCLIUtil.FileValidator

MiCLIUtil.FileValueValidator - Class in com.milaboratory.mitools.cli

MiCLIUtil.FileValueValidator() - Constructor for class com.milaboratory.mitools.cli.MiCLIUtil.FileValueValidator

MiCLIUtil.List2Validator - Class in com.milaboratory.mitools.cli

MiCLIUtil.List2Validator() - Constructor for class com.milaboratory.mitools.cli.MiCLIUtil.List2Validator

P

parameters - Variable in class com.milaboratory.mitools.cli.CheckAction.AParameters

parameters - Variable in class com.milaboratory.mitools.cli.CutAction.AParams

parameters - Variable in class com.milaboratory.mitools.cli.MergeAction.MergingParameters

parameters - Variable in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

parameters - Variable in class com.milaboratory.mitools.cli.RCAction.RCParameters

parameters - Variable in class com.milaboratory.mitools.cli.RenameAction.RenameParameters

parameters - Variable in class com.milaboratory.mitools.cli.SplitAction.AParameters

params() - Method in class com.milaboratory.mitools.cli.CheckAction

params() - Method in class com.milaboratory.mitools.cli.CutAction

params() - Method in class com.milaboratory.mitools.cli.MergeAction

params() - Method in class com.milaboratory.mitools.cli.RandomizeAction

params() - Method in class com.milaboratory.mitools.cli.RCAction

params() - Method in class com.milaboratory.mitools.cli.RenameAction

params() - Method in class com.milaboratory.mitools.cli.SplitAction

params() - Method in class com.milaboratory.mitools.cli.TrimAction

partIndexToString(int) - Method in class com.milaboratory.mitools.cli.SplitAction

process(SingleRead) - Method in class com.milaboratory.mitools.processors.RandomCutter

process(SingleRead) - Method in class com.milaboratory.mitools.trimmer.SequenceTrimmer

R

RandomCutter - Class in com.milaboratory.mitools.processors

RandomCutter(CutSide, int, int) - Constructor for class com.milaboratory.mitools.processors.RandomCutter

RandomCutter(CutSide, int, int, long) - Constructor for class com.milaboratory.mitools.processors.RandomCutter

RandomizeAction - Class in com.milaboratory.mitools.cli

RandomizeAction() - Constructor for class com.milaboratory.mitools.cli.RandomizeAction

RandomizeAction.AParameters - Class in com.milaboratory.mitools.cli

RandomizeAction.AParameters() - Constructor for class com.milaboratory.mitools.cli.RandomizeAction.AParameters

RCAction - Class in com.milaboratory.mitools.cli

RCAction() - Constructor for class com.milaboratory.mitools.cli.RCAction

RCAction.RCParameters - Class in com.milaboratory.mitools.cli

RCAction.RCParameters() - Constructor for class com.milaboratory.mitools.cli.RCAction.RCParameters

ReadLengthFilter - Class in com.milaboratory.mitools.trimmer

ReadLengthFilter(int) - Constructor for class com.milaboratory.mitools.trimmer.ReadLengthFilter

RenameAction - Class in com.milaboratory.mitools.cli

RenameAction() - Constructor for class com.milaboratory.mitools.cli.RenameAction

RenameAction.RenameParameters - Class in com.milaboratory.mitools.cli

RenameAction.RenameParameters() - Constructor for class com.milaboratory.mitools.cli.RenameAction.RenameParameters

S

seed - Variable in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

SequenceTrimmer - Class in com.milaboratory.mitools.trimmer

SequenceTrimmer(int, boolean, boolean) - Constructor for class com.milaboratory.mitools.trimmer.SequenceTrimmer

SimpleReadsStatisticsPortWrapper<R extends com.milaboratory.core.io.sequence.SequenceRead> - Class in com.milaboratory.mitools.cli

SimpleReadsStatisticsPortWrapper(OutputPort<R>) - Constructor for class com.milaboratory.mitools.cli.SimpleReadsStatisticsPortWrapper

SplitAction - Class in com.milaboratory.mitools.cli

SplitAction() - Constructor for class com.milaboratory.mitools.cli.SplitAction

SplitAction.AParameters - Class in com.milaboratory.mitools.cli

SplitAction.AParameters() - Constructor for class com.milaboratory.mitools.cli.SplitAction.AParameters

T

take() - Method in class com.milaboratory.mitools.cli.SimpleReadsStatisticsPortWrapper

tmpDir - Variable in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

TrimAction - Class in com.milaboratory.mitools.cli

TrimAction() - Constructor for class com.milaboratory.mitools.cli.TrimAction

V

validate() - Method in class com.milaboratory.mitools.cli.CheckAction.AParameters

validate() - Method in class com.milaboratory.mitools.cli.CutAction.AParams

validate() - Method in class com.milaboratory.mitools.cli.MergeAction.MergingParameters

validate(String, String) - Method in class com.milaboratory.mitools.cli.MiCLIUtil.FileValidator

validate(String, File) - Method in class com.milaboratory.mitools.cli.MiCLIUtil.FileValueValidator

validate(String, List) - Method in class com.milaboratory.mitools.cli.MiCLIUtil.List2Validator

validate() - Method in class com.milaboratory.mitools.cli.RandomizeAction.AParameters

validate() - Method in class com.milaboratory.mitools.cli.RCAction.RCParameters

validate() - Method in class com.milaboratory.mitools.cli.RenameAction.RenameParameters

validate() - Method in class com.milaboratory.mitools.cli.SplitAction.AParameters

valueOf(String) - Static method in enum com.milaboratory.mitools.processors.CutSide

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

values() - Static method in enum com.milaboratory.mitools.processors.CutSide

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

VersionInfoUtils - Class in com.milaboratory.mitools.util

Created by dbolotin on 12/07/16.

VersionInfoUtils() - Constructor for class com.milaboratory.mitools.util.VersionInfoUtils

A C D G M P R S T V