ambit2.core.io

Class IteratingDelimitedFileReaderComplexHeader<COLUMN>

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

ambit2.core.io.IteratingFilesWithHeaderReader<COLUMN>

ambit2.core.io.IteratingDelimitedFileReaderComplexHeader<COLUMN>

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:

IteratingDelimitedFileReader

public abstract class IteratingDelimitedFileReaderComplexHeader<COLUMN>
extends IteratingFilesWithHeaderReader<COLUMN>

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 CASProcessor	casTransformer
protected String	commentChar
protected DelimitedFileFormat	format
protected Object[]	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
IteratingDelimitedFileReaderComplexHeader(InputStream in)
IteratingDelimitedFileReaderComplexHeader(InputStream in, DelimitedFileFormat format)
IteratingDelimitedFileReaderComplexHeader(Reader in)
IteratingDelimitedFileReaderComplexHeader(Reader in, DelimitedFileFormat format)

Method Summary

Modifier and Type	Method and Description
void	close()
protected ArrayList<COLUMN>	createHeader()
protected abstract COLUMN	createPropertyByColumnName(String name)
void	extractRowKeyAndData(String line) Extract values from a line
String	getCommentChar()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
protected LiteratureEntry	getReference()
protected abstract String	getSmilesHeader(int index)
boolean	hasNext()
Object	next()
protected void	processComment(String line)
protected void	processHeader(BufferedReader in)
void	remove()
protected String	removeStringDelimiters(String key)
void	setCommentChar(String commentChar)
void	setReader(InputStream in)
void	setReader(Reader reader)
protected void	skipLines(int numlines)
String	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.IChemObjectIO

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

commentChar

protected String commentChar

format

protected DelimitedFileFormat format

values

protected Object[] values

casTransformer

protected CASProcessor casTransformer

Constructor Detail

IteratingDelimitedFileReaderComplexHeader

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

Throws:

org.openscience.cdk.exception.CDKException

IteratingDelimitedFileReaderComplexHeader

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

Throws:

org.openscience.cdk.exception.CDKException

IteratingDelimitedFileReaderComplexHeader

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

Throws:

UnsupportedEncodingException

org.openscience.cdk.exception.CDKException

IteratingDelimitedFileReaderComplexHeader

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

Throws:

UnsupportedEncodingException

org.openscience.cdk.exception.CDKException

Method Detail

getCommentChar

public String getCommentChar()

setCommentChar

public void setCommentChar(String commentChar)

setReader

public void setReader(InputStream in)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(Reader reader)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

getReference

protected LiteratureEntry getReference()

Specified by:

getReference in class IteratingFilesWithHeaderReader<COLUMN>

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

hasNext

public boolean hasNext()

next

public Object next()

close

public void close()
           throws IOException

Throws:

IOException

remove

public void remove()

Specified by:

remove in interface Iterator

Overrides:

remove in class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

processComment

protected void processComment(String line)

processHeader

protected void processHeader(BufferedReader in)

getSmilesHeader

protected abstract String getSmilesHeader(int index)

removeStringDelimiters

protected String removeStringDelimiters(String key)

extractRowKeyAndData

public void extractRowKeyAndData(String line)

Extract values from a line

toString

public String toString()

Overrides:

toString in class Object

createHeader

protected ArrayList<COLUMN> createHeader()

Specified by:

createHeader in class IteratingFilesWithHeaderReader<COLUMN>

createPropertyByColumnName

protected abstract COLUMN createPropertyByColumnName(String name)

Specified by:

createPropertyByColumnName in class IteratingFilesWithHeaderReader<COLUMN>

skipLines

protected void skipLines(int numlines)
                  throws IOException

Throws:

IOException