Package com.actelion.research.chem.io

Class ODEFileParser

java.lang.Object

com.actelion.research.chem.io.CompoundFileParser

com.actelion.research.chem.io.ODEFileParser

All Implemented Interfaces:

DescriptorConstants, CompoundTableConstants

public class ODEFileParser
extends CompoundFileParser
implements CompoundTableConstants, DescriptorConstants

Field Summary

Fields inherited from interface com.actelion.research.chem.io.CompoundTableConstants

cAllowLogModeForNegativeOrZeroValues, cAutoStartMacro, cColumnName, cColumnNameRowList, cColumnProperty, cColumnPropertyBinBase, cColumnPropertyBinIsDate, cColumnPropertyBinIsLog, cColumnPropertyBinSize, cColumnPropertyCommentDepartment, cColumnPropertyCommentUploadStatus, cColumnPropertyCyclicDataMax, cColumnPropertyDataMax, cColumnPropertyDataMin, cColumnPropertyDescriptorVersion, cColumnPropertyDetailCount, cColumnPropertyDetailName, cColumnPropertyDetailSeparator, cColumnPropertyDetailSource, cColumnPropertyDetailType, cColumnPropertyDisplayGroup, cColumnPropertyEnd, cColumnPropertyFormula, cColumnPropertyGroupName, cColumnPropertyImagePath, cColumnPropertyIsClusterNo, cColumnPropertyIsDisplayable, cColumnPropertyIsFragment, cColumnPropertyLaunchAllowMultiple, cColumnPropertyLaunchCommand, cColumnPropertyLaunchCount, cColumnPropertyLaunchDecoration, cColumnPropertyLaunchName, cColumnPropertyLaunchOption, cColumnPropertyLookupCount, cColumnPropertyLookupDetailURL, cColumnPropertyLookupEncode, cColumnPropertyLookupFilter, cColumnPropertyLookupFilterRemoveMinus, cColumnPropertyLookupName, cColumnPropertyLookupURL, cColumnPropertyOpenExternalName, cColumnPropertyOpenExternalPath, cColumnPropertyOrbitType, cColumnPropertyParentColumn, cColumnPropertyReactionPart, cColumnPropertyReferencedColumn, cColumnPropertyReferenceStrengthColumn, cColumnPropertyReferenceType, cColumnPropertyReferenceTypeRedundant, cColumnPropertyReferenceTypeTopDown, cColumnPropertyRelatedCatalystColumn, cColumnPropertyRelatedIdentifierColumn, cColumnPropertySpecialType, cColumnPropertyStart, cColumnPropertySuperpose, cColumnPropertySuperposeAlign, cColumnPropertySuperposeMolecule, cColumnPropertyUseThumbNail, cColumnRelationTypes, cColumnType2DCoordinates, cColumnType3DCoordinates, cColumnTypeAtomColorInfo, cColumnTypeIDCode, cColumnTypeReactionMapping, cColumnTypeReactionObjects, cColumnTypeRXNCode, cColumnUnassignedCode, cColumnUnassignedItemText, cDataDependentPropertiesEnd, cDataDependentPropertiesStart, cDataTypeAutomatic, cDataTypeCode, cDataTypeDate, cDataTypeFloat, cDataTypeInteger, cDataTypeString, cDataTypeText, cDefaultDetailSeparator, cDetailDataEnd, cDetailDataStart, cDetailID, cDetailIndexSeparator, cEntrySeparator, cEntrySeparatorBytes, cExtensionNameFileExplanation, cExtensionNameMacroList, cFileExplanationEnd, cFileExplanationStart, cHitlistData, cHitlistDataEnd, cHitlistDataStart, cHitlistName, cLineSeparator, cLineSeparatorByte, cMacroListEnd, cMacroListStart, cMaxDateOrDoubleCategoryCount, cMaxTextCategoryCount, cNativeFileCreated, cNativeFileHeaderEnd, cNativeFileHeaderStart, cNativeFileRowCount, cNativeFileVersion, cParentSpecialColumnTypes, cPropertiesEnd, cPropertiesStart, cRangeNotAvailable, cRangeSeparation, cReactionHiliteModeCode, cReactionHiliteModeNone, cReactionHiliteModeReactionCenter, cReactionHiliteModeText, cReactionPartDelimiter, cReactionPartProducts, cReactionPartReactants, cReactionPartReaction, cStructureHiliteModeCode, cStructureHiliteModeCurrentRow, cStructureHiliteModeFilter, cStructureHiliteModeNone, cStructureHiliteModeText, cSummaryModeCode, cSummaryModeMaximum, cSummaryModeMean, cSummaryModeMedian, cSummaryModeMinimum, cSummaryModeNormal, cSummaryModeSum, cSummaryModeText, cSuperposeAlignValueShape, cSuperposeValueReferenceRow, cTemplateTagName, cTextExclusionTypeContains, cTextExclusionTypeEndsWith, cTextExclusionTypeEquals, cTextExclusionTypeRegEx, cTextExclusionTypeStartsWith, cTextMultipleCategories, cViewConfigTagName, cViewNameEnd, cViewNameStart, NEWLINE_REGEX, NEWLINE_STRING, TAB_STRING

Fields inherited from interface com.actelion.research.chem.descriptor.DescriptorConstants

DESCRIPTOR_BINARY_SKELETONSPHERES, DESCRIPTOR_CenteredSkeletonFragments, DESCRIPTOR_EXTENDED_LIST, DESCRIPTOR_FFP512, DESCRIPTOR_Flexophore, DESCRIPTOR_FULL_FRAGMENT_SET, DESCRIPTOR_HashedCFp, DESCRIPTOR_IntegerVector, DESCRIPTOR_LIST, DESCRIPTOR_MAX_COMMON_SUBSTRUCT, DESCRIPTOR_OrganicFunctionalGroups, DESCRIPTOR_PFP512, DESCRIPTOR_PhysicoChemicalProperties, DESCRIPTOR_PTREE, DESCRIPTOR_ReactionFP, DESCRIPTOR_ShapeAlign, DESCRIPTOR_ShapeAlignSingleConf, DESCRIPTOR_SkeletonSpheres, DESCRIPTOR_SUBSTRUCT_QUERY_IN_BASE, DESCRIPTOR_TopoPPHistDist, DESCRIPTOR_TYPE_MOLECULE, DESCRIPTOR_TYPE_REACTION, DESCRIPTOR_TYPE_UNKNOWN

Constructor Summary

Constructors

Constructor	Description
ODEFileParser(java.io.File file)
ODEFileParser(java.io.Reader reader)
ODEFileParser(java.lang.String fileName)

Method Summary

Modifier and Type	Method	Description
protected boolean	advanceToNext()	Dont't call this method directly.
static java.lang.String	extractValue(java.lang.String theLine)
java.lang.String	getCoordinates()	Either getIDCode and this method or getMolecule() must be overwritten!!!
java.lang.String	getFieldData(int no)	Returns the cell content of the current row.
java.lang.String[]	getFieldNames()	Compiles all column names that contain alpha-numerical information.
java.lang.String	getIDCode()	Either this method and getCoordinates() or getMolecule() must be overwritten!!!
java.lang.String	getIndex()
java.lang.String	getMoleculeName()
int	getRowCount()	Depending on data source returns the total row count or -1 if unknown
boolean	moreRecordsAvailable()

Methods inherited from class com.actelion.research.chem.io.CompoundFileParser

close, createParser, getDescriptor, getDescriptorHandlerFactory, getFieldIndex, getMolecule, isOpen, next, setDescriptorHandlerFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

ODEFileParser

public ODEFileParser(java.lang.String fileName)

ODEFileParser

public ODEFileParser(java.io.File file)

ODEFileParser

public ODEFileParser(java.io.Reader reader)

Method Detail

getFieldNames

public java.lang.String[] getFieldNames()

Description copied from class: CompoundFileParser

Compiles all column names that contain alpha-numerical information. Columns containing chemistry objects, coordinates or descriptors don't appear in the list.

Specified by:

getFieldNames in class CompoundFileParser

Returns:

columns name array in the order of appearance

advanceToNext

protected boolean advanceToNext()

Description copied from class: CompoundFileParser

Dont't call this method directly. Use next() instead.

Specified by:

advanceToNext in class CompoundFileParser

Returns:

false if there is no next row

getMoleculeName

public java.lang.String getMoleculeName()

Specified by:

getMoleculeName in class CompoundFileParser

Returns:

name/id of (primary) chemical structure of the current row

getRowCount

public int getRowCount()

Description copied from class: CompoundFileParser

Depending on data source returns the total row count or -1 if unknown

Specified by:

getRowCount in class CompoundFileParser

Returns:

number of rows or -1

moreRecordsAvailable

public boolean moreRecordsAvailable()

getIDCode

public java.lang.String getIDCode()

Description copied from class: CompoundFileParser

Either this method and getCoordinates() or getMolecule() must be overwritten!!!

Overrides:

getIDCode in class CompoundFileParser

Returns:

idcode of first chemical structure column of the current row

getCoordinates

public java.lang.String getCoordinates()

Description copied from class: CompoundFileParser

Either getIDCode and this method or getMolecule() must be overwritten!!!

Overrides:

getCoordinates in class CompoundFileParser

Returns:

idcoords of first chemical structure column of the current row

getIndex

public java.lang.String getIndex()

getFieldData

public java.lang.String getFieldData(int no)

Description copied from class: CompoundFileParser

Returns the cell content of the current row. Multi-line cell entries are separated by a '\n' character.

Specified by:

getFieldData in class CompoundFileParser

Parameters:

no - refers to alpha-numerical columns only, as getFieldNames()

Returns:

extractValue

public static java.lang.String extractValue(java.lang.String theLine)