ambit2.core.io

Class IteratingDelimitedFileReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.IteratingFilesWithHeaderReader<COLUMN>

ambit2.core.io.IteratingDelimitedFileReaderComplexHeader<String>

ambit2.core.io.IteratingDelimitedFileReader

All Implemented Interfaces:

Closeable, AutoCloseable, Iterator, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.iterator.IIteratingChemObjectReader

Direct Known Subclasses:

MalariaHTSDataDelimitedReader, ToxcastAssayReader

public class IteratingDelimitedFileReader
extends IteratingDelimitedFileReaderComplexHeader<String>
implements org.openscience.cdk.io.iterator.IIteratingChemObjectReader

Iterating reader for delimited files.

Author:

Nina Jeliazkova Modified 2005-9-5

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields inherited from class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader

casTransformer, commentChar, format, values

Fields inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

defaultSMILESHeader, header, inchiFactory, inchiIndex, logger, numberOfHeaderLines, optionalSMILESHeader, smilesIndex, sp, timeout

Fields inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
IteratingDelimitedFileReader(InputStream in)
IteratingDelimitedFileReader(InputStream in, DelimitedFileFormat format)
IteratingDelimitedFileReader(Reader in)
IteratingDelimitedFileReader(Reader in, DelimitedFileFormat format)

Method Summary

Modifier and Type	Method and Description
protected String	createPropertyByColumnName(String name)
protected String	getSmilesHeader(int index)

Methods inherited from class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader

close, createHeader, extractRowKeyAndData, getCommentChar, getFormat, getReference, hasNext, next, processComment, processHeader, remove, removeStringDelimiters, setCommentChar, setReader, setReader, skipLines, toString

Methods inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

addHeaderColumn, getHeaderColumn, getNumberOfColumns, getNumberOfHeaderLines, getOptionalSMILESHeader, getTimeout, isHeaderEmpty, setHeaderColumn, setNumberOfHeaderLines, setOptionalSMILESHeader, setTimeout, updateHeaderColumn

Methods inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

accepts, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.io.IChemObjectReader

handleError, handleError, handleError, handleError, setErrorHandler, setReader, setReader, setReaderMode

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

accepts, addChemObjectIOListener, addSetting, addSettings, close, getFormat, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from interface java.util.Iterator

forEachRemaining, hasNext, next, remove

Constructor Detail

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(Reader in)
                             throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(Reader in,
                                    DelimitedFileFormat format)
                             throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(InputStream in)
                             throws UnsupportedEncodingException,
                                    org.openscience.cdk.exception.CDKException

Throws:

UnsupportedEncodingException

org.openscience.cdk.exception.CDKException

IteratingDelimitedFileReader

public IteratingDelimitedFileReader(InputStream in,
                                    DelimitedFileFormat format)
                             throws UnsupportedEncodingException,
                                    org.openscience.cdk.exception.CDKException

Throws:

UnsupportedEncodingException

org.openscience.cdk.exception.CDKException

Method Detail

getSmilesHeader

protected String getSmilesHeader(int index)

Specified by:

getSmilesHeader in class IteratingDelimitedFileReaderComplexHeader<String>

createPropertyByColumnName

protected String createPropertyByColumnName(String name)

Specified by:

createPropertyByColumnName in class IteratingDelimitedFileReaderComplexHeader<String>