ambit2.core.io

Class FileInputState

java.lang.Object

ambit2.core.io.FileState

ambit2.core.io.FileInputState

All Implemented Interfaces:

IInputOutputState, IInputState, Serializable

public class FileInputState
extends FileState
implements IInputState

Use getReader(InputStream, String) to get a reader of the right type.

Author:

Nina Jeliazkova nina@acad.bg Modified June 13, 2013

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class ambit2.core.io.FileState

FileState._FILE_TYPE

Field Summary

Fields

Modifier and Type	Field and Description
String	optionalInChIHeader
String	optionalInChIKeyHeader
String	optionalSMILESHeader

Fields inherited from class ambit2.core.io.FileState

currentRecord, extensionDescriptions, file, fileFormat, filename, hashCode, lastModified, length, MSG_CANTCREATEFILE, MSG_ERRORSAVE, MSG_FILEDONOTEXISTS, MSG_OPEN, MSG_UNSUPPORTEDFORMAT, offset, responseType, supportedExtensions

Constructor Summary

Constructors

Constructor and Description
FileInputState()
FileInputState(File file)
FileInputState(String filename)

Method Summary

Modifier and Type	Method and Description
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getI5DReader(File file)
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getI5DReader(InputStream in)
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getI5ZReader(File file)
String	getOptionalInChIHeader()
String	getOptionalInChIKeyHeader()
String	getOptionalSMILESHeader()
static IRawReader<IStructureRecord>	getRawReader(InputStream stream, String extension, org.openscience.cdk.io.formats.IChemFormat format)
org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getReader()
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getReader(File file)
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getReader(File file, org.openscience.cdk.io.formats.IChemFormat format)
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getReader(InputStream stream, String ext)
static org.openscience.cdk.io.iterator.IIteratingChemObjectReader	getReader(InputStream stream, String extension, org.openscience.cdk.io.formats.IChemFormat format)
void	setOptionalInChIHeader(String optionalInChIHeader)
void	setOptionalInChIKeyHeader(String optionalInChIKeyHeader)
void	setOptionalSMILESHeader(String optionalSMILESHeader)

Methods inherited from class ambit2.core.io.FileState

createFile, equals, getCurrentRecord, getExtensionDescriptions, getExtensions, getFile, getFileFormat, getFilename, getHashCode, getLastModified, getLength, getOffset, getResponseType, getSupportedExtDescriptions, getSupportedExtensions, match, match, setCurrentRecord, setFile, setFile, setFilename, setHashCode, setLastModified, setLength, setOffset, setResponseType, setSupportedExtDescriptions, setSupportedExtensions, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface ambit2.core.io.IInputState

getFileFormat

Methods inherited from interface ambit2.base.interfaces.IInputOutputState

getCurrentRecord, getResponseType, setCurrentRecord, setResponseType

Field Detail

optionalSMILESHeader

public String optionalSMILESHeader

optionalInChIKeyHeader

public String optionalInChIKeyHeader

optionalInChIHeader

public String optionalInChIHeader

Constructor Detail

FileInputState

public FileInputState()

FileInputState

public FileInputState(String filename)

FileInputState

public FileInputState(File file)

Method Detail

getOptionalInChIKeyHeader

public String getOptionalInChIKeyHeader()

setOptionalInChIKeyHeader

public void setOptionalInChIKeyHeader(String optionalInChIKeyHeader)

getOptionalInChIHeader

public String getOptionalInChIHeader()

setOptionalInChIHeader

public void setOptionalInChIHeader(String optionalInChIHeader)

getOptionalSMILESHeader

public String getOptionalSMILESHeader()

setOptionalSMILESHeader

public void setOptionalSMILESHeader(String optionalSMILESHeader)

getReader

public org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader()
                                                                     throws AmbitIOException

Specified by:

getReader in interface IInputState

Throws:

AmbitIOException

getReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(File file)
                                                                            throws FileNotFoundException,
                                                                                   AmbitIOException,
                                                                                   org.openscience.cdk.exception.CDKException

Throws:

FileNotFoundException

AmbitIOException

org.openscience.cdk.exception.CDKException

getReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(InputStream stream,
                                                                                   String ext)
                                                                            throws AmbitIOException,
                                                                                   org.openscience.cdk.exception.CDKException

Throws:

AmbitIOException

org.openscience.cdk.exception.CDKException

getReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(File file,
                                                                                   org.openscience.cdk.io.formats.IChemFormat format)
                                                                            throws AmbitIOException,
                                                                                   org.openscience.cdk.exception.CDKException,
                                                                                   FileNotFoundException

Throws:

AmbitIOException

org.openscience.cdk.exception.CDKException

FileNotFoundException

getI5ZReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getI5ZReader(File file)
                                                                               throws FileNotFoundException,
                                                                                      AmbitIOException,
                                                                                      org.openscience.cdk.exception.CDKException

Parameters:

file -

Returns:

Throws:

FileNotFoundException

AmbitIOException

org.openscience.cdk.exception.CDKException

getI5DReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getI5DReader(InputStream in)
                                                                               throws AmbitIOException,
                                                                                      org.openscience.cdk.exception.CDKException

Parameters:

in -

Returns:

Throws:

FileNotFoundException

AmbitIOException

org.openscience.cdk.exception.CDKException

getI5DReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getI5DReader(File file)
                                                                               throws FileNotFoundException,
                                                                                      AmbitIOException,
                                                                                      org.openscience.cdk.exception.CDKException

Throws:

FileNotFoundException

AmbitIOException

org.openscience.cdk.exception.CDKException

getRawReader

public static IRawReader<IStructureRecord> getRawReader(InputStream stream,
                                                        String extension,
                                                        org.openscience.cdk.io.formats.IChemFormat format)
                                                 throws org.openscience.cdk.exception.CDKException,
                                                        AmbitIOException

Throws:

org.openscience.cdk.exception.CDKException

AmbitIOException

getReader

public static org.openscience.cdk.io.iterator.IIteratingChemObjectReader getReader(InputStream stream,
                                                                                   String extension,
                                                                                   org.openscience.cdk.io.formats.IChemFormat format)
                                                                            throws AmbitIOException,
                                                                                   org.openscience.cdk.exception.CDKException

Throws:

AmbitIOException

org.openscience.cdk.exception.CDKException