chemaxon.marvin.io

Class MRecordImporter

java.lang.Object

chemaxon.marvin.io.MRecordImporter

@PublicAPI
public class MRecordImporter
extends java.lang.Object

Marvin molecule file reader. By default, in case of machines with multiple processors processing is concurrent, otherwise single-threaded. By default, the number of worker threads is the number of processors - the number of concurrent threads can be set in setThreadCount(int).

Since:

Marvin 5.0, 05/07/2007

Version:

5.3, 09/17/2009

Author:

Peter Csizmadia, Szilveszter Juhos

Constructor Summary

Constructors

Constructor and Description
MRecordImporter(MolInputStream in, java.lang.String opts) Creates a reader for the specified molecule input stream in concurrent mode.

Method Summary

Modifier and Type	Method and Description
void	close() Closes the input stream.
static MolImportModule	createImportMod(MolInputStream mis) Creates an importer for the specified molecule input stream.
static MolImportModule	createImportMod(java.lang.String fmt) Creates an importer for the specified molecule format.
Molecule	createMol() Creates an empty target molecule for import.
Molecule	createMolIfNeeded() Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.
long	getFilePointer() Gets the current position in the input file.
java.lang.String	getFormat() Gets the file format.
MPropertyContainer	getGlobalProperties() Gets the global properties.
int	getLineCount() Gets the current line number in the input file.
java.lang.String	getMoleculeString() Gets the last molecule as a string.
MolImportModule	getMolImportModule()
java.lang.String	getOptions() Gets the options for the import module.
boolean	getQueryMode() Gets the query mode.
MRecordReader	getRecordReader() Gets the record reader.
boolean	isSeekable() Tests whether the record reader is seekable.
long	length() Gets the length of the input file.
MDocument	readDoc() Reads the next document.
Molecule	readMol(Molecule mol) Reads the next molecule.
MDocument	readMolMovie(MDocument doc) Reads molecules as a movie.
Molecule	readMultiSet(Molecule m) Reads molecules as one multi-set molecule.
java.lang.String	readRecordAsText() Reads the next record.
void	seek(long p, int lcount, int k) Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.
void	setOptions(java.lang.String opts) Sets the options for the import module.
void	setProgressMonitor(MProgressMonitor pmon) Sets the progress monitor.
void	setQueryMode(boolean q) Sets the query mode.
void	setThreadCount(int threadCount) Sets the number of threads for concurrent processing.
MRecord	skipRecord() Skips the next document.

Methods inherited from class java.lang.Object

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

Constructor Detail

MRecordImporter

public MRecordImporter(MolInputStream in,
                       java.lang.String opts)
                throws MolFormatException,
                       java.io.IOException

Creates a reader for the specified molecule input stream in concurrent mode.

Parameters:

in - the molecule input stream

opts - input options or null

Throws:

MolFormatException - If the format is not recognizable

java.io.IOException - If I/O error occurred

java.nio.charset.IllegalCharsetNameException - if illegal encoding is used

java.nio.charset.UnsupportedCharsetException - if unsupported encoding is used

Method Detail

setThreadCount

public void setThreadCount(int threadCount)
                    throws java.lang.IllegalStateException

Sets the number of threads for concurrent processing. Default: the number of CPUs, single-threaded processing if there is 1 CPU. Note, that in concurrent mode the import is not rewindable.

Parameters:

threadCount - the number of threads, set 0 for the number of CPUs, 1 for single-threaded mode

Throws:

java.lang.IllegalStateException - if called after isSeekable() or readMol(chemaxon.struc.Molecule) or readDoc().

Since:

Marvin 5.3

setProgressMonitor

public void setProgressMonitor(MProgressMonitor pmon)

Sets the progress monitor.

Parameters:

pmon - the progress monitor

createImportMod

public static MolImportModule createImportMod(MolInputStream mis)
                                       throws java.io.IOException,
                                              MolFormatException

Creates an importer for the specified molecule input stream.

Parameters:

mis - the molecule input stream

Throws:

MolFormatException - If the format is not recognizable

java.io.IOException - If I/O error occurred

createImportMod

public static MolImportModule createImportMod(java.lang.String fmt)
                                       throws java.io.IOException,
                                              MolFormatException

Creates an importer for the specified molecule format.

Parameters:

fmt - the molecule format

Throws:

MolFormatException - If the format is not recognizable

java.io.IOException - If I/O error occurred

Since:

Marvin 5.2

getOptions

public java.lang.String getOptions()

Gets the options for the import module.

Returns:

the import options

setOptions

public void setOptions(java.lang.String opts)

Sets the options for the import module.

Parameters:

opts - options passed to the import module or null

Throws:

java.lang.IllegalStateException - if called after readMol(chemaxon.struc.Molecule) or readDoc().

readDoc

public MDocument readDoc()
                  throws MRecordParseException,
                         MolFormatException,
                         java.io.IOException

Reads the next document.

Returns:

the document or null at end of file

Throws:

MRecordParseException - If the record could not be parsed

MolFormatException - If the file format is invalid

java.io.IOException - If I/O error occurred

readMol

public Molecule readMol(Molecule mol)
                 throws MRecordParseException,
                        MolFormatException,
                        java.io.IOException

Reads the next molecule. If the 'mol' parameter is not null then processing is single-threaded.

Parameters:

mol - target object or null

Returns:

the molecule or null at end of file

Throws:

MRecordParseException - If the record could not be parsed

MolFormatException - If the file format is invalid

java.io.IOException - If I/O error occurred

readMultiSet

public Molecule readMultiSet(Molecule m)
                      throws MRecordParseException,
                             MolFormatException,
                             java.io.IOException

Reads molecules as one multi-set molecule. Processing is single-threaded.

Parameters:

m - the output molecule object

Returns:

the molecule in case of success, null otherwise

Throws:

java.io.IOException - cannot read molecule (bad format or I/O error)

MRecordParseException

MolFormatException

readMolMovie

public MDocument readMolMovie(MDocument doc)
                       throws MolFormatException,
                              java.io.IOException

Reads molecules as a movie. Processing is single-threaded.

Parameters:

doc - the output document object or null

Returns:

the document if success, null otherwise

Throws:

MolFormatException - invalid molecule file

java.io.IOException - cannot read molecule (bad format or I/O error)

Since:

Marvin 5.2, 02/12/2009

readRecordAsText

public java.lang.String readRecordAsText()
                                  throws MRecordParseException,
                                         java.io.IOException

Reads the next record. Processing is single-threaded.

Returns:

the record or null at end of file

Throws:

MRecordParseException - If the record could not be parsed

java.io.IOException - If I/O error occurred

java.lang.IllegalStateException - if the concurrent processor is already running

getGlobalProperties

public MPropertyContainer getGlobalProperties()

Gets the global properties.

Returns:

the global properties or null

isSeekable

public boolean isSeekable()

Tests whether the record reader is seekable. In concurrent mode always returns false. Therefore this method should not be called before calling setThreadCount(int).

Returns:

true if it is seekable, false otherwise

See Also:

setThreadCount(int)

getFormat

public java.lang.String getFormat()

Gets the file format.

Returns:

the format

getQueryMode

public boolean getQueryMode()

Gets the query mode. SMILES strings are imported as SMARTS if query mode is set.

Returns:

query mode

setQueryMode

public void setQueryMode(boolean q)

Sets the query mode. SMILES strings are imported as SMARTS if query mode is set. IMPORTANT: call this before any call to readDoc() or readMol(chemaxon.struc.Molecule).

Parameters:

q - query mode

Throws:

java.lang.IllegalStateException - if the concurrent processor is already running

getFilePointer

public long getFilePointer()

Gets the current position in the input file.

Returns:

the position

Throws:

java.lang.IllegalStateException - if the concurrent processor is running

length

public long length()
            throws java.io.IOException

Gets the length of the input file.

Returns:

the length

Throws:

java.io.IOException - if the length cannot be determined

getLineCount

public int getLineCount()

Gets the current line number in the input file.

Returns:

the position

seek

public void seek(long p,
                 int lcount,
                 int k)
          throws java.io.IOException

Sets the file-pointer offset, measured from the beginning of this file, at which the next read or write occurs.

Parameters:

p - the file pointer

lcount - the line count at the specified position

k - the record count at the specified position

Throws:

java.io.IOException - if pos is less than 0 or if an I/O error occurs.

java.lang.UnsupportedOperationException - if the concurrent processor is running

skipRecord

public MRecord skipRecord()
                   throws MRecordParseException,
                          MolFormatException,
                          java.io.IOException

Skips the next document. Not implemented for concurrent processing, in this case returns the next complete record.

Returns:

incomplete record info containing only the start and end positions, or null if there are no more records

Throws:

java.io.IOException - If I/O error occurred

MRecordParseException

MolFormatException

close

public void close()
           throws java.io.IOException

Closes the input stream. IMPORTANT: call this after reading molecules to close concurrent processing properly.

Throws:

java.io.IOException - If I/O error occurred

getMolImportModule

public MolImportModule getMolImportModule()

getMoleculeString

public java.lang.String getMoleculeString()

Gets the last molecule as a string.

Returns:

the molecule as a string

createMolIfNeeded

public Molecule createMolIfNeeded()

Creates an empty target molecule for import if non-concurrent mode, returns null if concurrent mode.

Returns:

an empty molecule or null

Since:

Marvin 5.3

createMol

public Molecule createMol()

Creates an empty target molecule for import.

Returns:

an empty molecule

getRecordReader

public MRecordReader getRecordReader()

Gets the record reader.

Returns:

the record reader