Package com.actelion.research.chem.io
Class ODEFileParser
- java.lang.Object
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- com.actelion.research.chem.io.CompoundFileParser
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- com.actelion.research.chem.io.ODEFileParser
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- All Implemented Interfaces:
DescriptorConstants
,CompoundTableConstants
public class ODEFileParser extends CompoundFileParser implements CompoundTableConstants, DescriptorConstants
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Field Summary
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Fields inherited from interface com.actelion.research.chem.io.CompoundTableConstants
cAllowLogModeForNegativeOrZeroValues, cAutoStartMacro, cColumnName, cColumnNameRowList, cColumnProperty, cColumnProperty3DFragmentSplit, cColumnPropertyBinBase, cColumnPropertyBinIsDate, cColumnPropertyBinIsLog, cColumnPropertyBinSize, cColumnPropertyCalculated, 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, cColumnPropertyNaturalLigand, cColumnPropertyOpenExternalName, cColumnPropertyOpenExternalPath, cColumnPropertyOrbitType, cColumnPropertyParentColumn, cColumnPropertyProteinCavity, cColumnPropertyReactionPart, cColumnPropertyReferencedColumn, cColumnPropertyReferenceStrengthColumn, cColumnPropertyReferenceType, cColumnPropertyReferenceTypeRedundant, cColumnPropertyReferenceTypeTopDown, cColumnPropertyRelatedCatalystColumn, cColumnPropertyRelatedIdentifierColumn, cColumnPropertyShowNaturalLigand, cColumnPropertySpecialType, cColumnPropertyStart, cColumnPropertySuperpose, cColumnPropertySuperposeAlign, cColumnPropertySuperposeMolecule, cColumnPropertyUseThumbNail, cColumnRelationTypes, cColumnType2DCoordinates, cColumnType3DCoordinates, cColumnTypeAtomColorInfo, cColumnTypeFlagColors, cColumnTypeIDCode, cColumnTypeNegRecImage, cColumnTypeReactionMapping, cColumnTypeReactionObjects, cColumnTypeRXNCode, cColumnTypeTransformation, cColumnUnassignedCode, cColumnUnassignedItemText, cDataDependentPropertiesEnd, cDataDependentPropertiesStart, cDataTypeAutomatic, cDataTypeCode, cDataTypeDate, cDataTypeFloat, cDataTypeInteger, cDataTypeString, cDataTypeText, cDefaultDetailSeparator, cDetailDataEnd, cDetailDataStart, cDetailID, cDetailIndexSeparator, cEntrySeparator, cEntrySeparatorBytes, cExtensionNameFileExplanation, cExtensionNameMacroList, cFileExplanationEnd, cFileExplanationStart, cFlagColor, cHitlistData, cHitlistDataEnd, cHitlistDataStart, cHitlistName, cLineSeparator, cLineSeparatorByte, cMacroListEnd, cMacroListStart, cMaxDateOrDoubleCategoryCount, cMaxTextCategoryCount, cNativeFileCreated, cNativeFileHeaderEnd, cNativeFileHeaderStart, cNativeFileRowCount, cNativeFileVersion, cParentSpecialColumnTypes, cPropertiesEnd, cPropertiesStart, cRangeNotAvailable, cRangeSeparation, cReactionHiliteModeCode, cReactionHiliteModeMapping, 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
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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
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Constructor Summary
Constructors Constructor Description ODEFileParser(java.io.File file)
ODEFileParser(java.io.Reader reader)
ODEFileParser(java.lang.String fileName)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 unknownboolean
moreRecordsAvailable()
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Methods inherited from class com.actelion.research.chem.io.CompoundFileParser
close, createParser, getDescriptor, getDescriptorHandlerFactory, getFieldIndex, getMolecule, isOpen, next, setDescriptorHandlerFactory
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Method Detail
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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 classCompoundFileParser
- Returns:
- columns name array in the order of appearance
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advanceToNext
protected boolean advanceToNext()
Description copied from class:CompoundFileParser
Dont't call this method directly. Use next() instead.- Specified by:
advanceToNext
in classCompoundFileParser
- Returns:
- false if there is no next row
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getMoleculeName
public java.lang.String getMoleculeName()
- Specified by:
getMoleculeName
in classCompoundFileParser
- Returns:
- name/id of (primary) chemical structure of the current row
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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 classCompoundFileParser
- Returns:
- number of rows or -1
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moreRecordsAvailable
public boolean moreRecordsAvailable()
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getIDCode
public java.lang.String getIDCode()
Description copied from class:CompoundFileParser
Either this method and getCoordinates() or getMolecule() must be overwritten!!!- Overrides:
getIDCode
in classCompoundFileParser
- Returns:
- idcode of first chemical structure column of the current row
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getCoordinates
public java.lang.String getCoordinates()
Description copied from class:CompoundFileParser
Either getIDCode and this method or getMolecule() must be overwritten!!!- Overrides:
getCoordinates
in classCompoundFileParser
- Returns:
- idcoords of first chemical structure column of the current row
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getIndex
public java.lang.String getIndex()
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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 classCompoundFileParser
- Parameters:
no
- refers to alpha-numerical columns only, as getFieldNames()- Returns:
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extractValue
public static java.lang.String extractValue(java.lang.String theLine)
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