chemaxon.marvin.io.formats

Class AbstractMRecordReader

java.lang.Object

chemaxon.marvin.io.formats.AbstractMRecordReader

All Implemented Interfaces:

MRecordReader

@PublicAPI
public abstract class AbstractMRecordReader
extends java.lang.Object
implements MRecordReader

Abstract record reader class. It is able to read lines and to create line number mappings for the records.

Since:

Marvin 5.0, 04/26/2007

Version:

5.1.3, 10/18/2008

Author:

Peter Csizmadia, Szilveszter Juhos

Nested Class Summary

Nested classes/interfaces inherited from interface chemaxon.marvin.io.MRecordReader

MRecordReader.Position

Constructor Summary

Constructors

Modifier	Constructor and Description
	AbstractMRecordReader(java.io.InputStream istr, java.lang.String opts) Constructs an abstract record reader.
protected	AbstractMRecordReader(java.io.InputStream istr, java.lang.String opts, java.lang.String path)

Method Summary

Modifier and Type	Method and Description
protected void	appendLine(java.lang.StringBuffer sb, java.lang.String line) Appends line to string buffer with closing '\n' character.
protected void	appendLines(java.lang.StringBuffer sb, java.lang.String l) Appends lines to string buffer with closing '\n' character if it is not yet present.
void	close() Interrupts parsing.
chemaxon.common.util.LongVector	detectRecordPositions(chemaxon.common.util.IntVector linenums) Detects positions of records in the input stream.
protected int[]	endRecord(boolean skip) It must be called at the end of record.
MRecordReader	getEncapsulatedReader() Gets the encapsulated record reader if it exists.
long	getFilePointer() Get the file pointer.
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.
protected MRecordReader.Position	getPosition() Gets the current position.
java.lang.String	getRecognizedFormat() Gets the recognized file format.
boolean	isPropertyRecord()
boolean	isSeekable() Tests whether the record reader is seekable.
protected void	putBackLine() Puts back the previous line to the input stream.
protected java.lang.String	readLine() Reads the next line.
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.
protected boolean	skipLine() Skips the next line.

Methods inherited from class java.lang.Object

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

Methods inherited from interface chemaxon.marvin.io.MRecordReader

nextRecord, skipRecord

Constructor Detail

AbstractMRecordReader

public AbstractMRecordReader(java.io.InputStream istr,
                             java.lang.String opts)
                      throws java.io.IOException

Constructs an abstract record reader.

Parameters:

istr - the input stream

opts - format and options

Throws:

java.io.IOException

AbstractMRecordReader

protected AbstractMRecordReader(java.io.InputStream istr,
                                java.lang.String opts,
                                java.lang.String path)
                         throws java.io.IOException

Throws:

java.io.IOException

Method Detail

setProgressMonitor

public void setProgressMonitor(MProgressMonitor pmon)

Sets the progress monitor. The default implementation does nothing.

Specified by:

setProgressMonitor in interface MRecordReader

Parameters:

pmon - the progress monitor

getRecognizedFormat

public java.lang.String getRecognizedFormat()

Gets the recognized file format.

Specified by:

getRecognizedFormat in interface MRecordReader

Returns:

the input file format

getHeaderAsString

public java.lang.String getHeaderAsString()

Gets the header of the file as a string.

Specified by:

getHeaderAsString in interface MRecordReader

Returns:

empty string in the default implementation

Since:

Marvin 5.0.2, 03/11/2008

getFooterAsString

public java.lang.String getFooterAsString()

Gets the footer of the file as a string.

Specified by:

getFooterAsString in interface MRecordReader

Returns:

empty string in the default implementation

Since:

Marvin 5.0.2, 03/11/2008

getOptions

public java.lang.String getOptions()

Gets the import options.

Specified by:

getOptions in interface MRecordReader

Returns:

the import options

readLine

protected java.lang.String readLine()
                             throws java.io.IOException

Reads the next line.

Returns:

the next line

Throws:

java.io.IOException

skipLine

protected boolean skipLine()
                    throws java.io.IOException

Skips the next line. The skipped line is not stored and cannot put be back into the stream.

Returns:

true if a line was skipped successfully, false at end of file

Throws:

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

Since:

Marvin 5.1.3, 10/18/2008

putBackLine

protected void putBackLine()
                    throws java.io.IOException

Puts back the previous line to the input stream.

Throws:

java.io.IOException

endRecord

protected int[] endRecord(boolean skip)

It must be called at the end of record.

Parameters:

skip - whether to skip the record

Returns:

the line number mapping

close

public void close()

Interrupts parsing.

Specified by:

close in interface MRecordReader

getEncapsulatedReader

public MRecordReader getEncapsulatedReader()

Gets the encapsulated record reader if it exists.

Specified by:

getEncapsulatedReader in interface MRecordReader

Returns:

the encapsulated record reader or null

getMolInputStream

public MolInputStream getMolInputStream()

Gets the molecule input stream.

Specified by:

getMolInputStream in interface MRecordReader

Returns:

the molecule input stream

getFilePointer

public long getFilePointer()

Get the file pointer.

Specified by:

getFilePointer in interface MRecordReader

Returns:

the file pointer

getLineCount

public int getLineCount()

Get the current line number.

Specified by:

getLineCount in interface MRecordReader

Returns:

the line number

isSeekable

public boolean isSeekable()

Tests whether the record reader is seekable.

Specified by:

isSeekable in interface MRecordReader

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.

Specified by:

seek in interface MRecordReader

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.

getPosition

protected MRecordReader.Position getPosition()

Gets the current position.

Returns:

the position

appendLines

protected void appendLines(java.lang.StringBuffer sb,
                           java.lang.String l)

Appends lines to string buffer with closing '\n' character if it is not yet present.

Parameters:

sb - the string buffer

l - the lines

appendLine

protected void appendLine(java.lang.StringBuffer sb,
                          java.lang.String line)

Appends line to string buffer with closing '\n' character.

Parameters:

sb - the string buffer

line - the line

isPropertyRecord

public boolean isPropertyRecord()

Specified by:

isPropertyRecord in interface MRecordReader

detectRecordPositions

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

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

Specified by:

detectRecordPositions in interface MRecordReader

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