ambit2.core.io

Class ToxcastAssayReader

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

ambit2.core.io.ToxcastAssayReader

All Implemented Interfaces:

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

public class ToxcastAssayReader
extends IteratingDelimitedFileReader

ToxCast assay data are TXT tab delimited files.
Lines starting with # are comments.
The column SOURCE_NAME_SID contains DSSTOX_RID (DSSTOX record ID) , prependend with "DSSTOX_" string, e.g. DSSTOX_40307

Author:

nina

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	DSSTox_RID
protected int	DSSTOX_RID_index
protected boolean	isToxCastAssayFile
protected static String	prefix
protected static String	ToxCast_signature

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
ToxcastAssayReader(InputStream in)
ToxcastAssayReader(Reader in)

Method Summary

Modifier and Type	Method and Description
protected void	addHeaderColumn(String name)
void	extractRowKeyAndData(String line) Extract values from a line
protected void	processComment(String line)
protected void	processHeader(BufferedReader in)

Methods inherited from class ambit2.core.io.IteratingDelimitedFileReader

createPropertyByColumnName, getSmilesHeader

Methods inherited from class ambit2.core.io.IteratingDelimitedFileReaderComplexHeader

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

Methods inherited from class ambit2.core.io.IteratingFilesWithHeaderReader

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

Field Detail

prefix

protected static final String prefix

See Also:

Constant Field Values

DSSTox_RID

protected static final String DSSTox_RID

See Also:

Constant Field Values

ToxCast_signature

protected static final String ToxCast_signature

See Also:

Constant Field Values

isToxCastAssayFile

protected boolean isToxCastAssayFile

DSSTOX_RID_index

protected int DSSTOX_RID_index

Constructor Detail

ToxcastAssayReader

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

Throws:

UnsupportedEncodingException

org.openscience.cdk.exception.CDKException

ToxcastAssayReader

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

Throws:

org.openscience.cdk.exception.CDKException

Method Detail

processComment

protected void processComment(String line)

Overrides:

processComment in class IteratingDelimitedFileReaderComplexHeader<String>

addHeaderColumn

protected void addHeaderColumn(String name)

Overrides:

addHeaderColumn in class IteratingFilesWithHeaderReader<String>

processHeader

protected void processHeader(BufferedReader in)

Overrides:

processHeader in class IteratingDelimitedFileReaderComplexHeader<String>

extractRowKeyAndData

public void extractRowKeyAndData(String line)

Description copied from class: IteratingDelimitedFileReaderComplexHeader

Extract values from a line

Overrides:

extractRowKeyAndData in class IteratingDelimitedFileReaderComplexHeader<String>