ambit2.export.isa

Class ISAExportConfig

java.lang.Object

ambit2.export.isa.ISAExportConfig

Direct Known Subclasses:

ISAJsonExportConfig

public class ISAExportConfig
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
ISALocation	bundleDescriptionLoc
String	bundleDescriptionLocString
ISALocation	bundleTitleLoc
String	bundleTitleLocString
ISAConst.DataFileFormat	dataFileFormat
ISALocation	effectRecordLoc
String	effectRecordLocString
ISAConst.DataFileFormat	extDataFileType
boolean	FlagAllCompositionInOneProcess
boolean	FlagDescriptionAdditiveContent
boolean	FlagExportContentAsConstituentCharacteristics
boolean	FlagExportFormulaAsConstituentCharacteristics
boolean	FlagExportInchiAsConstituentCharacteristics
boolean	FlagExportInchiKeyAsConstituentCharacteristics
boolean	FlagExportRelationAsConstituentCharacteristics
boolean	FlagExportSmilesAsConstituentCharacteristics
boolean	FlagExportStrucTypeAsConstituentCharacteristics
boolean	FlagSaveCompositionAsExtensionMaterial
boolean	FlagSaveCompositionAsStudy
boolean	FlagUseAbsolutePathForExternalDataFileLocation
boolean	FlagUseDeafultExtDataFileHeader
ISAConst.ISAFormat	isaFormat
ISAConst.ISAVersion	isaVersion
protected static Logger	logger
ISALocation	protocolParamLoc
String	protocolParamLocString

Constructor Summary

Constructors

Constructor and Description
ISAExportConfig()

Method Summary

Modifier and Type	Method and Description
static void	fillDefaultISAConfig(ISAExportConfig cfg)
void	parseISALocations()
protected ISALocation	parseISALocationString(String isaLocStr, String contexInfo)
void	parseJSONConfig(com.fasterxml.jackson.databind.JsonNode rootNode)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final Logger logger

isaFormat

public ISAConst.ISAFormat isaFormat

isaVersion

public ISAConst.ISAVersion isaVersion

dataFileFormat

public ISAConst.DataFileFormat dataFileFormat

protocolParamLoc

public ISALocation protocolParamLoc

protocolParamLocString

public String protocolParamLocString

effectRecordLoc

public ISALocation effectRecordLoc

effectRecordLocString

public String effectRecordLocString

bundleDescriptionLoc

public ISALocation bundleDescriptionLoc

bundleDescriptionLocString

public String bundleDescriptionLocString

bundleTitleLoc

public ISALocation bundleTitleLoc

bundleTitleLocString

public String bundleTitleLocString

FlagSaveCompositionAsStudy

public boolean FlagSaveCompositionAsStudy

FlagSaveCompositionAsExtensionMaterial

public boolean FlagSaveCompositionAsExtensionMaterial

FlagAllCompositionInOneProcess

public boolean FlagAllCompositionInOneProcess

FlagDescriptionAdditiveContent

public boolean FlagDescriptionAdditiveContent

FlagExportFormulaAsConstituentCharacteristics

public boolean FlagExportFormulaAsConstituentCharacteristics

FlagExportSmilesAsConstituentCharacteristics

public boolean FlagExportSmilesAsConstituentCharacteristics

FlagExportContentAsConstituentCharacteristics

public boolean FlagExportContentAsConstituentCharacteristics

FlagExportInchiAsConstituentCharacteristics

public boolean FlagExportInchiAsConstituentCharacteristics

FlagExportInchiKeyAsConstituentCharacteristics

public boolean FlagExportInchiKeyAsConstituentCharacteristics

FlagExportRelationAsConstituentCharacteristics

public boolean FlagExportRelationAsConstituentCharacteristics

FlagExportStrucTypeAsConstituentCharacteristics

public boolean FlagExportStrucTypeAsConstituentCharacteristics

FlagUseDeafultExtDataFileHeader

public boolean FlagUseDeafultExtDataFileHeader

FlagUseAbsolutePathForExternalDataFileLocation

public boolean FlagUseAbsolutePathForExternalDataFileLocation

extDataFileType

public ISAConst.DataFileFormat extDataFileType

Constructor Detail

ISAExportConfig

public ISAExportConfig()

Method Detail

parseJSONConfig

public void parseJSONConfig(com.fasterxml.jackson.databind.JsonNode rootNode)
                     throws Exception

Throws:

Exception

parseISALocations

public void parseISALocations()
                       throws Exception

Throws:

Exception

parseISALocationString

protected ISALocation parseISALocationString(String isaLocStr,
                                             String contexInfo)
                                      throws Exception

Throws:

Exception

fillDefaultISAConfig

public static void fillDefaultISAConfig(ISAExportConfig cfg)