chemaxon.marvin.io
Interface MRecordReader

All Known Implementing Classes:

AbstractMRecordReader

public interface MRecordReader

Marvin record reader.

Since:

Marvin 5.0, 04/06/2006

Version:

5.0.2, 03/13/2008

Author:

Peter Csizmadia

Nested Class Summary

static class

MRecordReader.Position Position in the input file.

Method Summary

void	close() Closes the input stream.
chemaxon.util.LongVector	detectRecordPositions(chemaxon.util.IntVector linenums) Detects positions of records in the input stream.
MRecordReader	getEncapsulatedReader() Gets the encapsulated record reader if it exists.
long	getFilePointer() Gets the current position in the input file.
java.lang.String	getFooterAsString() Gets the footer of the file as a string.
java.lang.String	getHeaderAsString() Gets the header of the file as a string.
int	getLineCount() Get the current line number.
MolInputStream	getMolInputStream() Gets the molecule input stream.
java.lang.String	getOptions() Gets the import options.
java.lang.String	getRecognizedFormat() Gets the recognized file format.
boolean	isPropertyRecord()
boolean	isSeekable() Tests whether the record reader is seekable.
MRecord	nextRecord() 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	setProgressMonitor(MProgressMonitor pmon) Sets the progress monitor.
MRecord	skipRecord() Skips the next record.

Method Detail

setProgressMonitor

public void setProgressMonitor(MProgressMonitor pmon)

Sets the progress monitor.

Parameters:

pmon - the progress monitor

nextRecord

public MRecord nextRecord()
                   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

skipRecord

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

Skips the next record.

Returns:

incomplete record information, only the record start and end positions are guaranteed to be set

Throws:

MRecordParseException - If the record could not be parsed

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

getRecognizedFormat

public java.lang.String getRecognizedFormat()

Gets the recognized file format.

Returns:

the input file format

getHeaderAsString

public java.lang.String getHeaderAsString()

Gets the header of the file as a string.

Returns:

the header or empty string if there is no header

Since:

Marvin 5.0.2, 03/11/2008

getFooterAsString

public java.lang.String getFooterAsString()

Gets the footer of the file as a string.

Returns:

the footer or empty string if there is no footer or not yet read

Since:

Marvin 5.0.2, 03/11/2008

getOptions

public java.lang.String getOptions()

Gets the import options.

Returns:

the import options

close

public void close()
           throws java.io.IOException

Closes the input stream.

Throws:

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

getEncapsulatedReader

public MRecordReader getEncapsulatedReader()

Gets the encapsulated record reader if it exists. For example, in case of a GZIPped, BASE64 encoded molfile, the GzipRecordReader has an encapsulated Base64RecordReader instance.

Returns:

the encapsulated record reader or null

getMolInputStream

public MolInputStream getMolInputStream()

Gets the molecule input stream.

Returns:

the molecule input stream

getFilePointer

public long getFilePointer()

Gets the current position in the input file.

Returns:

the position

getLineCount

public int getLineCount()

Get the current line number.

Returns:

the line number

isSeekable

public boolean isSeekable()

Tests whether the record reader is seekable.

Returns:

true if it is seekable, false otherwise

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.

isPropertyRecord

public boolean isPropertyRecord()

detectRecordPositions

public chemaxon.util.LongVector detectRecordPositions(chemaxon.util.IntVector linenums)
                                               throws MolFormatException

Detects positions of records in the input stream. Optionally returns also with the line number of records.

Parameters:

linenums - If not null, stores start line numbers of records in this container.

Returns:

container with start and end positions of records (inpair elements describe starting, pairs the ending positions).

Throws:

MolFormatException