Index (jmzQC 1.0.0-RC2 API)

A B C D E F G H I L M N O P Q R S T U V
All Classes and Interfaces|All Packages

A

accession() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns the value of the accession record component.
accession() - Method in record class org.lifstools.jmzqc.CvParameter: Returns the value of the accession record component.
accession() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns the value of the accession record component.
addFileInputOption(Options) - Static method in class org.lifstools.jmzqc.CmdLineParser
addHelpOption(Options) - Static method in class org.lifstools.jmzqc.CmdLineParser
addOutputToFileOption(Options) - Static method in class org.lifstools.jmzqc.CmdLineParser
addVersionOption(Options) - Static method in class org.lifstools.jmzqc.CmdLineParser
analysisSoftware() - Method in record class org.lifstools.jmzqc.Metadata: Returns the value of the analysisSoftware record component.
AnalysisSoftware - Record Class in org.lifstools.jmzqc: Base element for a term that is defined in a controlled vocabulary, with OPTIONAL value.
AnalysisSoftware(String, String, String, Object, URI, String) - Constructor for record class org.lifstools.jmzqc.AnalysisSoftware: Creates an instance of a AnalysisSoftware record class.

B

BaseQuality - Record Class in org.lifstools.jmzqc: Element containing metadata and qualityMetrics for a single run.
BaseQuality(Metadata, List<QualityMetric>) - Constructor for record class org.lifstools.jmzqc.BaseQuality: Creates an instance of a BaseQuality record class.

C

CmdLineParser - Class in org.lifstools.jmzqc: Create a new command line parser for parsing of lipid names.
CmdLineParser() - Constructor for class org.lifstools.jmzqc.CmdLineParser
contactAddress() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the contactAddress record component.
contactName() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the contactName record component.
controlledVocabularies() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the controlledVocabularies record component.
ControlledVocabulary - Record Class in org.lifstools.jmzqc: Element describing a controlled vocabulary used to refer to the source of the used CV terms in qualityMetric objects (and others).
ControlledVocabulary(String, URI, String) - Constructor for record class org.lifstools.jmzqc.ControlledVocabulary: Creates an instance of a ControlledVocabulary record class.
Converter - Class in org.lifstools.jmzqc: Provides convenience functions to parse date and time strings and to serialize and deserialize mzQC from and to a variety of sources.
Converter() - Constructor for class org.lifstools.jmzqc.Converter
Coordinate - Record Class in org.lifstools.jmzqc: JSON schema specifying the mzQC format v1.0.0 developed by the HUPO-PSI Quality Control working group (http://psidev.info/groups/quality-control).
Coordinate(MzQC) - Constructor for record class org.lifstools.jmzqc.Coordinate: Creates an instance of a Coordinate record class.
creationDate() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the creationDate record component.
CvParameter - Record Class in org.lifstools.jmzqc: Base element for a term that is defined in a controlled vocabulary, with OPTIONAL value.
CvParameter(String, String, String, Object) - Constructor for record class org.lifstools.jmzqc.CvParameter: Creates an instance of a CvParameter record class.
cvParameterArrayValue() - Method in record class org.lifstools.jmzqc.Unit: Returns the value of the cvParameterArrayValue record component.
cvParameters() - Method in record class org.lifstools.jmzqc.Metadata: Returns the value of the cvParameters record component.
cvParameterValue() - Method in record class org.lifstools.jmzqc.Unit: Returns the value of the cvParameterValue record component.

D

description() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns the value of the description record component.
description() - Method in record class org.lifstools.jmzqc.CvParameter: Returns the value of the description record component.
description() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the description record component.
description() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns the value of the description record component.

E

equals(Object) - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.BaseQuality: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.ControlledVocabulary: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.Coordinate: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.CvParameter: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.InputFile: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.Metadata: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.MzQC: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.QualityMetric: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in record class org.lifstools.jmzqc.Unit: Indicates whether some other object is "equal to" this one.

F

fileFormat() - Method in record class org.lifstools.jmzqc.InputFile: Returns the value of the fileFormat record component.
fileProperties() - Method in record class org.lifstools.jmzqc.InputFile: Returns the value of the fileProperties record component.

G

getRunQualityMetrics(int) - Method in record class org.lifstools.jmzqc.MzQC: Returns a reference to the internal list of quality metrics for the given run.
getRunQualityMetricsByAccession(int, String) - Method in record class org.lifstools.jmzqc.MzQC: Returns a reference to the internal list of quality metrics for the given run.

H

hashCode() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.BaseQuality: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.ControlledVocabulary: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.Coordinate: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.CvParameter: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.InputFile: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.Metadata: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.MzQC: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns a hash code value for this object.
hashCode() - Method in record class org.lifstools.jmzqc.Unit: Returns a hash code value for this object.

I

InputFile - Record Class in org.lifstools.jmzqc: Input file used to generate the QC metrics.
InputFile(CvParameter, List<CvParameter>, URI, String) - Constructor for record class org.lifstools.jmzqc.InputFile: Creates an instance of a InputFile record class.
inputFiles() - Method in record class org.lifstools.jmzqc.Metadata: Returns the value of the inputFiles record component.

L

label() - Method in record class org.lifstools.jmzqc.Metadata: Returns the value of the label record component.
location() - Method in record class org.lifstools.jmzqc.InputFile: Returns the value of the location record component.

M

main(String[]) - Static method in class org.lifstools.jmzqc.CmdLineParser: Runs the command line validation for jmzqc.
metadata() - Method in record class org.lifstools.jmzqc.BaseQuality: Returns the value of the metadata record component.
Metadata - Record Class in org.lifstools.jmzqc: Metadata describing the QC analysis.
Metadata(List<AnalysisSoftware>, List<CvParameter>, List<InputFile>, String) - Constructor for record class org.lifstools.jmzqc.Metadata: Creates an instance of a Metadata record class.
mzQC() - Method in record class org.lifstools.jmzqc.Coordinate: Returns the value of the mzQC record component.
MzQC - Record Class in org.lifstools.jmzqc: Root element of an mzQC file.
MzQC(String, String, List<ControlledVocabulary>, OffsetDateTime, String, List<BaseQuality>, List<BaseQuality>, String) - Constructor for record class org.lifstools.jmzqc.MzQC: Creates an instance of a MzQC record class.

N

name() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns the value of the name record component.
name() - Method in record class org.lifstools.jmzqc.ControlledVocabulary: Returns the value of the name record component.
name() - Method in record class org.lifstools.jmzqc.CvParameter: Returns the value of the name record component.
name() - Method in record class org.lifstools.jmzqc.InputFile: Returns the value of the name record component.
name() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns the value of the name record component.

O

of(File) - Static method in class org.lifstools.jmzqc.Converter: Return a Coordinate holding an MzQC object from a file.
of(String) - Static method in class org.lifstools.jmzqc.Converter: Return a Coordinate holding an MzQC object from a string holding the JSON representation of an mzQC data.
of(URL) - Static method in class org.lifstools.jmzqc.Converter: Return a Coordinate holding an MzQC object from a URL.
org.lifstools.jmzqc - package org.lifstools.jmzqc: Base package for MzQC Java implementation.

P

parseDateTimeString(String) - Static method in class org.lifstools.jmzqc.Converter: Parse a date and time string using the default date and time formatter.
parseTimeString(String) - Static method in class org.lifstools.jmzqc.Converter: Parse a time string using the default time formatter.

Q

QualityMetric - Record Class in org.lifstools.jmzqc: Element containing the value and description of a QC metric defined in a controlled vocabulary.
QualityMetric(String, String, String, Object, Unit) - Constructor for record class org.lifstools.jmzqc.QualityMetric: Creates an instance of a QualityMetric record class.
qualityMetrics() - Method in record class org.lifstools.jmzqc.BaseQuality: Returns the value of the qualityMetrics record component.

R

runQualities() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the runQualities record component.

S

setQualities() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the setQualities record component.

T

toDouble() - Method in record class org.lifstools.jmzqc.QualityMetric
toInteger() - Method in record class org.lifstools.jmzqc.QualityMetric
toJsonFile(MzQC, File) - Static method in class org.lifstools.jmzqc.Converter: Serialize the MzQC object to a file containing the data as a JSON string.
toJsonString(MzQC) - Static method in class org.lifstools.jmzqc.Converter: Serialize the MzQC object to a JSON string.
toLong() - Method in record class org.lifstools.jmzqc.QualityMetric
toString() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.BaseQuality: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.ControlledVocabulary: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.Coordinate: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.CvParameter: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.InputFile: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.Metadata: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.MzQC: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns a string representation of this record class.
toString() - Method in record class org.lifstools.jmzqc.Unit: Returns a string representation of this record class.

U

unit() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns the value of the unit record component.
Unit - Record Class in org.lifstools.jmzqc: One or more controlled vocabulary elements describing the unit of the metric.
Unit(CvParameter, List<CvParameter>) - Constructor for record class org.lifstools.jmzqc.Unit: Creates an instance of a Unit record class.
uri() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns the value of the uri record component.
uri() - Method in record class org.lifstools.jmzqc.ControlledVocabulary: Returns the value of the uri record component.

V

validate(File) - Static method in class org.lifstools.jmzqc.Converter: Validate a mzQC JSON file.
validate(String) - Static method in class org.lifstools.jmzqc.Converter: Validate a mzQC JSON string.
validate(URL) - Static method in class org.lifstools.jmzqc.Converter: Validate a mzQC JSON URL.
validate(MzQC) - Static method in class org.lifstools.jmzqc.Converter: Validate a mzQC Object.
value() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns the value of the value record component.
value() - Method in record class org.lifstools.jmzqc.CvParameter: Returns the value of the value record component.
value() - Method in record class org.lifstools.jmzqc.QualityMetric: Returns the value of the value record component.
version() - Method in record class org.lifstools.jmzqc.AnalysisSoftware: Returns the value of the version record component.
version() - Method in record class org.lifstools.jmzqc.ControlledVocabulary: Returns the value of the version record component.
version() - Method in record class org.lifstools.jmzqc.MzQC: Returns the value of the version record component.

A B C D E F G H I L M N O P Q R S T U V
All Classes and Interfaces|All Packages