Package de.isas.mztab2.io.serialization

Class Serializers

java.lang.Object

de.isas.mztab2.io.serialization.Serializers

public class Serializers
extends Object

Utility class providing helper methods for other serializers.

Since:

11/30/17

Author:

nilshoffmann

Constructor Summary

Constructors

Constructor	Description
Serializers()

Method Summary

Modifier and Type	Method	Description
static <T extends de.isas.mztab2.model.IndexedElement> void	addIndexedLine(com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, String prefix, Object element, List<T> indexedElementList)	addIndexedLine for elements like assay[1] that have an id and a list of additional property elements
static <T extends de.isas.mztab2.model.IndexedElement> void	addIndexedLine(com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, String prefix, Object element, T indexedElement)	addIndexedLine for elements like assay[1] that have an id and one additional property element
static void	addLine(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, Object... value)	addLine.
static void	addLineWithMetadataProperty(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, MetadataProperty property, Object element, Object... value)	addLineWithMetadataProperty.
static void	addLineWithNullProperty(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, String propertyName, Object element)	addLineWithNullProperty.
static void	addLineWithParameters(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, List<de.isas.mztab2.model.Parameter> parameterList)	addLineWithParameters.
static void	addLineWithProperty(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, String propertyName, Object element, Object... value)	addLineWithProperty.
static void	addLineWithPropertyParameters(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, String propertyName, Object element, List<de.isas.mztab2.model.Parameter> value)	addLineWithPropertyParameters.
static void	addSubElementParameter(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, String subElementName, de.isas.mztab2.model.Parameter subElement)	addSubElementParameter.
static void	addSubElementParameters(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, String subElementName, List<de.isas.mztab2.model.Parameter> subElements, boolean oneLine)	addSubElementParameters.
static void	addSubElementStrings(com.fasterxml.jackson.core.JsonGenerator jg, String prefix, Object element, String subElementName, List<?> subElements, boolean oneLine)	addSubElementStrings.
static Map<String,Object>	asMap(Object element)	asMap.
static String	camelCaseToUnderscoreLowerCase(String camelCase)	camelCaseToUnderscoreLowerCase.
static boolean	checkForNull(Object element, List<?> subElements, String subElementName)	checkForNull.
static void	checkIndexedElement(de.isas.mztab2.model.IndexedElement element)
static Optional<String>	getElementName(Object element)	getElementName.
static List<String>	getPropertyNames(Object element)	getPropertyNames.
static String	getReference(Object element, Integer idx)	getReference.
static String	printAbundanceAssay(de.isas.mztab2.model.Assay a)	printAbundanceAssay.
static String	printAbundanceCoeffVarStudyVar(de.isas.mztab2.model.StudyVariable sv)	printAbundanceCoeffVarStudyVar.
static String	printAbundanceStudyVar(de.isas.mztab2.model.StudyVariable sv)	printAbundanceStudyVar.
static String	printOptColumnMapping(de.isas.mztab2.model.OptColumnMapping ocm)	printOptColumnMapping.
static void	writeAsNumberArray(String columnName, com.fasterxml.jackson.core.JsonGenerator jg, List<? extends Number> elements)	writeAsNumberArray.
static void	writeAsNumberArray(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, List<? extends Number> elements)	writeAsNumberArray.
static void	writeAsStringArray(com.fasterxml.jackson.core.JsonGenerator jg, List<String> elements)	writeAsStringArray.
static void	writeAsStringArray(String columnName, com.fasterxml.jackson.core.JsonGenerator jg, List<String> elements)	writeAsStringArray.
static void	writeAsStringArray(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, List<String> elements)	writeAsStringArray.
static void	writeIndexedDoubles(String prefix, com.fasterxml.jackson.core.JsonGenerator jg, List<Double> values)	writeIndexedValues.
static void	writeNumber(com.fasterxml.jackson.core.JsonGenerator jg, Double value)	writeNumber.
static void	writeNumber(com.fasterxml.jackson.core.JsonGenerator jg, Integer value)	writeNumber.
static void	writeNumber(String columnName, com.fasterxml.jackson.core.JsonGenerator jg, Double value)	writeNumber.
static void	writeNumber(String columnName, com.fasterxml.jackson.core.JsonGenerator jg, Integer value)	writeNumber.
static void	writeNumber(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, Double value)	writeNumber.
static void	writeNumber(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, Integer value)	writeNumber.
static void	writeObject(String columnName, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, Object value)	writeObject.
static void	writeObject(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, Object value)	writeObject.
static void	writeOptColumnMappings(List<de.isas.mztab2.model.OptColumnMapping> optColumnMappings, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp)	writeOptColumnMappings.
static void	writeString(String columnName, com.fasterxml.jackson.core.JsonGenerator jg, String value)	writeString.
static void	writeString(IMZTabColumn column, com.fasterxml.jackson.core.JsonGenerator jg, String value)	writeString.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Serializers

public Serializers()

Method Detail

getReference

public static String getReference(Object element,
                                  Integer idx)

getReference.

Parameters:

element - a Object object.

idx - a Integer object.

Returns:

a String object.

printAbundanceAssay

public static String printAbundanceAssay(de.isas.mztab2.model.Assay a)

printAbundanceAssay.

Parameters:

a - a Assay object.

Returns:

a String object.

printAbundanceStudyVar

public static String printAbundanceStudyVar(de.isas.mztab2.model.StudyVariable sv)

printAbundanceStudyVar.

Parameters:

sv - a StudyVariable object.

Returns:

a String object.

printAbundanceCoeffVarStudyVar

public static String printAbundanceCoeffVarStudyVar(de.isas.mztab2.model.StudyVariable sv)

printAbundanceCoeffVarStudyVar.

Parameters:

sv - a StudyVariable object.

Returns:

a String object.

printOptColumnMapping

public static String printOptColumnMapping(de.isas.mztab2.model.OptColumnMapping ocm)

printOptColumnMapping.

Parameters:

ocm - a OptColumnMapping object.

Returns:

a String object.

addIndexedLine

public static <T extends de.isas.mztab2.model.IndexedElement> void addIndexedLine(com.fasterxml.jackson.core.JsonGenerator jg,
                                                                                  com.fasterxml.jackson.databind.SerializerProvider sp,
                                                                                  String prefix,
                                                                                  Object element,
                                                                                  T indexedElement)

addIndexedLine for elements like assay[1] that have an id and one additional property element

Type Parameters:

T - the type of IndexedElement.

Parameters:

jg - a JsonGenerator object.

sp - a SerializerProvider object.

prefix - a String object.

element - a Object object.

indexedElement - a Parameter object.

addIndexedLine

public static <T extends de.isas.mztab2.model.IndexedElement> void addIndexedLine(com.fasterxml.jackson.core.JsonGenerator jg,
                                                                                  com.fasterxml.jackson.databind.SerializerProvider sp,
                                                                                  String prefix,
                                                                                  Object element,
                                                                                  List<T> indexedElementList)

addIndexedLine for elements like assay[1] that have an id and a list of additional property elements

Type Parameters:

T - the type of IndexedElement.

Parameters:

jg - a JsonGenerator object.

sp - a SerializerProvider object.

prefix - a String object.

element - a Object object.

indexedElementList - a List object.

addLineWithParameters

public static void addLineWithParameters(com.fasterxml.jackson.core.JsonGenerator jg,
                                         String prefix,
                                         Object element,
                                         List<de.isas.mztab2.model.Parameter> parameterList)

addLineWithParameters.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

element - a Object object.

parameterList - a List object.

addLineWithPropertyParameters

public static void addLineWithPropertyParameters(com.fasterxml.jackson.core.JsonGenerator jg,
                                                 String prefix,
                                                 String propertyName,
                                                 Object element,
                                                 List<de.isas.mztab2.model.Parameter> value)

addLineWithPropertyParameters.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

propertyName - a String object.

element - a Object object.

value - a List object.

addLineWithMetadataProperty

public static void addLineWithMetadataProperty(com.fasterxml.jackson.core.JsonGenerator jg,
                                               String prefix,
                                               MetadataProperty property,
                                               Object element,
                                               Object... value)

addLineWithMetadataProperty.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

property - a MetadataProperty object.

element - a Object object.

value - a Object object.

addLineWithNullProperty

public static void addLineWithNullProperty(com.fasterxml.jackson.core.JsonGenerator jg,
                                           String prefix,
                                           String propertyName,
                                           Object element)

addLineWithNullProperty.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

propertyName - a String object.

element - a Object object.

addLineWithProperty

public static void addLineWithProperty(com.fasterxml.jackson.core.JsonGenerator jg,
                                       String prefix,
                                       String propertyName,
                                       Object element,
                                       Object... value)

addLineWithProperty.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

propertyName - a String object.

element - a Object object.

value - a Object object.

addLine

public static void addLine(com.fasterxml.jackson.core.JsonGenerator jg,
                           String prefix,
                           Object element,
                           Object... value)

addLine.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

element - a Object object.

value - a Object object.

getElementName

public static Optional<String> getElementName(Object element)

getElementName.

Parameters:

element - a Object object.

Returns:

a Optional object.

getPropertyNames

public static List<String> getPropertyNames(Object element)

getPropertyNames.

Parameters:

element - a Object object.

Returns:

a List object.

asMap

public static Map<String,Object> asMap(Object element)

asMap.

Parameters:

element - a Object object.

Returns:

a Map object.

camelCaseToUnderscoreLowerCase

public static String camelCaseToUnderscoreLowerCase(String camelCase)

camelCaseToUnderscoreLowerCase.

Parameters:

camelCase - a String object.

Returns:

a String object.

addSubElementStrings

public static void addSubElementStrings(com.fasterxml.jackson.core.JsonGenerator jg,
                                        String prefix,
                                        Object element,
                                        String subElementName,
                                        List<?> subElements,
                                        boolean oneLine)

addSubElementStrings.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

element - a Object object.

subElementName - a String object.

subElements - a List object.

oneLine - a boolean.

addSubElementParameter

public static void addSubElementParameter(com.fasterxml.jackson.core.JsonGenerator jg,
                                          String prefix,
                                          Object element,
                                          String subElementName,
                                          de.isas.mztab2.model.Parameter subElement)

addSubElementParameter.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

element - a Object object.

subElementName - a String object.

subElement - a Parameter object.

addSubElementParameters

public static void addSubElementParameters(com.fasterxml.jackson.core.JsonGenerator jg,
                                           String prefix,
                                           Object element,
                                           String subElementName,
                                           List<de.isas.mztab2.model.Parameter> subElements,
                                           boolean oneLine)

addSubElementParameters.

Parameters:

jg - a JsonGenerator object.

prefix - a String object.

element - a Object object.

subElementName - a String object.

subElements - a List object.

oneLine - a boolean.

checkForNull

public static boolean checkForNull(Object element,
                                   List<?> subElements,
                                   String subElementName)

checkForNull.

Parameters:

element - a Object object.

subElements - a List object.

subElementName - a String object.

Returns:

a boolean.

writeString

public static void writeString(String columnName,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               String value)
                        throws IOException

writeString.

Parameters:

columnName - a String object.

jg - a JsonGenerator object.

value - a String object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeString

public static void writeString(IMZTabColumn column,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               String value)
                        throws IOException

writeString.

Parameters:

column - a IMZTabColumn object.

jg - a JsonGenerator object.

value - a String object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeObject

public static void writeObject(String columnName,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               com.fasterxml.jackson.databind.SerializerProvider sp,
                               Object value)
                        throws IOException

writeObject.

Parameters:

columnName - a String object.

jg - a JsonGenerator object.

sp - a SerializerProvider object.

value - a Object object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeObject

public static void writeObject(IMZTabColumn column,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               com.fasterxml.jackson.databind.SerializerProvider sp,
                               Object value)
                        throws IOException

writeObject.

Parameters:

column - a IMZTabColumn object.

jg - a JsonGenerator object.

sp - a SerializerProvider object.

value - a Object object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeAsNumberArray

public static void writeAsNumberArray(IMZTabColumn column,
                                      com.fasterxml.jackson.core.JsonGenerator jg,
                                      List<? extends Number> elements)

writeAsNumberArray.

Parameters:

column - a IMZTabColumn object.

jg - a JsonGenerator object.

elements - a List object.

writeAsNumberArray

public static void writeAsNumberArray(String columnName,
                                      com.fasterxml.jackson.core.JsonGenerator jg,
                                      List<? extends Number> elements)

writeAsNumberArray.

Parameters:

columnName - a String object.

jg - a JsonGenerator object.

elements - a List object.

writeAsStringArray

public static void writeAsStringArray(IMZTabColumn column,
                                      com.fasterxml.jackson.core.JsonGenerator jg,
                                      List<String> elements)

writeAsStringArray.

Parameters:

column - a IMZTabColumn object.

jg - a JsonGenerator object.

elements - a List object.

writeAsStringArray

public static void writeAsStringArray(com.fasterxml.jackson.core.JsonGenerator jg,
                                      List<String> elements)

writeAsStringArray.

Parameters:

jg - a JsonGenerator object.

elements - a List object.

writeAsStringArray

public static void writeAsStringArray(String columnName,
                                      com.fasterxml.jackson.core.JsonGenerator jg,
                                      List<String> elements)

writeAsStringArray.

Parameters:

columnName - a String object.

jg - a JsonGenerator object.

elements - a List object.

writeNumber

public static void writeNumber(String columnName,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               Integer value)
                        throws IOException

writeNumber.

Parameters:

columnName - a String object.

jg - a JsonGenerator object.

value - a Integer object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeNumber

public static void writeNumber(IMZTabColumn column,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               Integer value)
                        throws IOException

writeNumber.

Parameters:

column - a IMZTabColumn object.

jg - a JsonGenerator object.

value - a Integer object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeNumber

public static void writeNumber(String columnName,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               Double value)
                        throws IOException

writeNumber.

Parameters:

columnName - a String object.

jg - a JsonGenerator object.

value - a Double object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeNumber

public static void writeNumber(IMZTabColumn column,
                               com.fasterxml.jackson.core.JsonGenerator jg,
                               Double value)
                        throws IOException

writeNumber.

Parameters:

column - a IMZTabColumn object.

jg - a JsonGenerator object.

value - a Double object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeNumber

public static void writeNumber(com.fasterxml.jackson.core.JsonGenerator jg,
                               Integer value)
                        throws IOException

writeNumber.

Parameters:

jg - a JsonGenerator object.

value - a Integer object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeNumber

public static void writeNumber(com.fasterxml.jackson.core.JsonGenerator jg,
                               Double value)
                        throws IOException

writeNumber.

Parameters:

jg - a JsonGenerator object.

value - a Double object.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeOptColumnMappings

public static void writeOptColumnMappings(List<de.isas.mztab2.model.OptColumnMapping> optColumnMappings,
                                          com.fasterxml.jackson.core.JsonGenerator jg,
                                          com.fasterxml.jackson.databind.SerializerProvider sp)
                                   throws IOException

writeOptColumnMappings.

Parameters:

optColumnMappings - a List object.

jg - a JsonGenerator object.

sp - the serialization provider.

Throws:

IOException - if an operation on the JsonGenerator object fails.

writeIndexedDoubles

public static void writeIndexedDoubles(String prefix,
                                       com.fasterxml.jackson.core.JsonGenerator jg,
                                       List<Double> values)

writeIndexedValues.

Parameters:

prefix - a String object.

jg - a JsonGenerator object.

values - a List object.

checkIndexedElement

public static void checkIndexedElement(de.isas.mztab2.model.IndexedElement element)