chemaxon.marvin.io

Class MRecord

java.lang.Object

chemaxon.marvin.io.MRecord

public class MRecord
extends Object

Record in a multi-molecule file.

Since:

Marvin 5.0, 04/06/2006

Version:

5.0.3, 03/20/2008

Author:

Peter Csizmadia

Field Summary

Fields

Modifier and Type	Field and Description
static int	F_MOL_MISSING Molecule (or reaction) is missing from the record.
protected long	fileEndPosition
protected long	fileStartPosition
protected MPropertyContainer	properties

Constructor Summary

Constructors

Constructor and Description
MRecord() Default constructor.
MRecord(long start, long end, int lineno, String s, MPropertyContainer p, int[] lmap) Creates a record.
MRecord(long start, long end, int lineno, String s, MPropertyContainer p, int[] lmap, int descflags) Creates a record.
MRecord(long start, long end, int lineno, String s, MPropertyContainer p, int[] lmap, int descflags, String moleculeName) Creates a record.

Method Summary

Methods

Modifier and Type	Method and Description
String	getEncoding() Gets the encoding.
int	getEndLineCount() Gets the line number at the ending point.
long	getEndPosition() Gets the end position in the input file.
int	getFlags() Gets the record descriptor flags.
String	getFormat() Gets the full format string of the record.
int	getHeaderNewLineCount() Gets the number of new lines in the molecule header part.
String	getInputFormat() Gets the input format.
int[]	getLineNumberMap() Gets the line number to original line number mapping.
byte[]	getMolBytes() Gets the molecule bytes, with preprended header and appended footer if appropriate.
String	getMoleculeName() Returns the name of the molecule in the record.
String	getMolString() Gets the molecule string, with preprended header and appended footer if appropriate.
MPropertyContainer	getPropertyContainer() Gets the properties.
int	getStartLineCount() Gets the line number at the starting point.
long	getStartPosition() Gets the start position in the input file.
String	getString() Gets the record text as string.
void	setMolBytes(byte[] molBytes) Sets the molecule bytes.

Methods inherited from class java.lang.Object

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

Field Detail

F_MOL_MISSING

public static final int F_MOL_MISSING

Molecule (or reaction) is missing from the record. This record descriptor flag is set if the molecule part of the record contains only a registry number ("MIREG", "MEREG", "RIREG" or "REREG") in case of an RDfile.

Since:

Marvin 5.0.3, 03/20/2008

See Also:

getFlags(), Constant Field Values

fileStartPosition

protected long fileStartPosition

fileEndPosition

protected long fileEndPosition

properties

protected MPropertyContainer properties

Constructor Detail

MRecord

public MRecord()

Default constructor.

Since:

Marvin 5.2

MRecord

public MRecord(long start,
       long end,
       int lineno,
       String s,
       MPropertyContainer p,
       int[] lmap)

Creates a record.

Parameters:

start - the start position in input file

end - the end position in input file

lineno - the line number at the starting point

s - the record string

p - the properties

lmap - original line numbers

MRecord

public MRecord(long start,
       long end,
       int lineno,
       String s,
       MPropertyContainer p,
       int[] lmap,
       int descflags)

Creates a record.

Parameters:

start - the start position in input file

end - the end position in input file

lineno - the line number at the starting point

s - the record string

p - the properties

lmap - original line numbers

descflags - extra record descriptor flags

MRecord

public MRecord(long start,
       long end,
       int lineno,
       String s,
       MPropertyContainer p,
       int[] lmap,
       int descflags,
       String moleculeName)

Creates a record.

Parameters:

start - the start position in input file

end - the end position in input file

lineno - the line number at the starting point

s - the record string

p - the properties

lmap - original line numbers

descflags - extra record descriptor flags

moleculeName - name of the molecule

Since:

Marvin 5.0.3, 03/20/2008

Method Detail

getEncoding

public String getEncoding()

Gets the encoding.

Returns:

the encoding

Since:

Marvin 5.3

getMolString

public String getMolString()

Gets the molecule string, with preprended header and appended footer if appropriate. This string can be imported to get a valid molecule.

Returns:

the molecule string

Since:

Marvin 5.3

setMolBytes

public void setMolBytes(byte[] molBytes)

Sets the molecule bytes. Used for binary formats, otherwise setMolString(java.lang.String) is called to set the mol string.

Parameters:

molBytes - the molecule bytes

getMolBytes

public byte[] getMolBytes()

Gets the molecule bytes, with preprended header and appended footer if appropriate. This byte array can be imported to get a valid molecule. Only used for binary formats, otherwise call getMolString().

Returns:

the molecule string

Since:

Marvin 5.4

getHeaderNewLineCount

public int getHeaderNewLineCount()

Gets the number of new lines in the molecule header part.

Returns:

the number of new lines in the molecule header part

Since:

Marvin 5.3

getFormat

public String getFormat()

Gets the full format string of the record. E.g. for a gzipped mrv it returns "gzip:mrv".

Returns:

the format of the record as a string.

getInputFormat

public String getInputFormat()

Gets the input format. This the format of the file. E.g for a gzipped mrv it returns "mrv"

Returns:

the input format

Since:

Marvin 5.3

getString

public String getString()

Gets the record text as string. Note that the returned string is not guaranteed to be a valid molecule file. Prepend the molecule file header and append the footer to get an importable file.

Returns:

the text

See Also:

MRecordReader.getHeaderAsString(), MRecordReader.getFooterAsString(), getMolString()

getPropertyContainer

public MPropertyContainer getPropertyContainer()

Gets the properties.

Returns:

the properties

getLineNumberMap

public int[] getLineNumberMap()

Gets the line number to original line number mapping.

Returns:

the mapping

getStartPosition

public long getStartPosition()

Gets the start position in the input file.

Returns:

the position

getEndPosition

public long getEndPosition()

Gets the end position in the input file.

Returns:

the position

getStartLineCount

public int getStartLineCount()

Gets the line number at the starting point.

Returns:

the line number

getEndLineCount

public int getEndLineCount()

Gets the line number at the ending point.

Returns:

the line number

Since:

Marvin 5.3

getFlags

public int getFlags()

Gets the record descriptor flags.

Returns:

the record descriptor flags

Since:

Marvin 5.0.3, 03/20/2008

See Also:

F_MOL_MISSING

getMoleculeName

public String getMoleculeName()

Returns the name of the molecule in the record.

Returns:

the name or an empty string if it's not specified

Since:

Marvin 6.3