chemaxon.marvin.io
Class MRecordImporter

java.lang.Object
  chemaxon.marvin.io.MRecordImporter

public class MRecordImporter
extends java.lang.Object

Marvin molecule file reader.

Since:

Marvin 5.0, 05/07/2007

Version:

5.0.2, 03/13/2008

Author:

Peter Csizmadia, Szilveszter Juhos

Constructor Summary

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

Method Summary

void	close() Closes the input stream.
static MolImportModule	createImportMod(MolInputStream mis, java.lang.String[] opts) Creates an importer for the specified molecule input stream.
Molecule	createMol() Creates an empty target molecule for import.
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.
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.
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.
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.

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 occured

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

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

Method Detail

setProgressMonitor

public void setProgressMonitor(MProgressMonitor pmon)

Sets the progress monitor.

Parameters:

pmon - the progress monitor

createImportMod

public static MolImportModule createImportMod(MolInputStream mis,
                                              java.lang.String[] opts)
                                       throws java.io.IOException,
                                              MolFormatException

Creates an importer for the specified molecule input stream.

Parameters:

mis - the molecule input stream

opts - one-element array containing the input options, may be changed by this function

Throws:

MolFormatException - If the format is not recognizable

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

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

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 occured

readMol

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

Reads the next molecule.

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 occured

readMultiSet

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

Reads molecules as one multi-set molecule.

Parameters:

m - the output molecule object

Returns:

the molecule if success, null if cannot read any atom set

Throws:

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

MRecordParseException

MolFormatException

readRecordAsText

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

Reads the next record.

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 occured

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.

Returns:

true if it is seekable, false otherwise

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.

Parameters:

q - query mode

getFilePointer

public long getFilePointer()

Gets the current position in the input file.

Returns:

the position

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.

skipRecord

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

Skips the next document.

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 occured

MRecordParseException

MolFormatException

close

public void close()
           throws java.io.IOException

Closes the input stream.

Throws:

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

getMoleculeString

public java.lang.String getMoleculeString()

Gets the last molecule as a string.

Returns:

the molecule as a string

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