chemaxon.formats
Class MFileFormat

java.lang.Object
  chemaxon.formats.MFileFormat

public class MFileFormat
extends java.lang.Object

File format descriptor class.

Since:

Marvin 5.0, 05/23/2007

Version:

5.1, 07/29/2008

Author:

Peter Csizmadia

Field Summary

static MFileFormat	ABBREVGROUP ChemAxon SMILES Abbreviated Groups.
static MFileFormat	AWT_IMAGE Image object (java.awt.Image).
static MFileFormat	BASE64 BASE64 encoded file.
static MFileFormat	CML Chemical Markup Language.
static MFileFormat	CSMDL_IN ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
static MFileFormat	CSMOL_OUT ChemAxon Compressed Molfiles and Rgfiles.
static MFileFormat	CSRDF ChemAxon Compressed RDfiles.
static MFileFormat	CSRXN_OUT ChemAxon Compressed Rxnfiles.
static MFileFormat	CSSDF_OUT ChemAxon Compressed SDfiles.
static MFileFormat	CXSMARTS ChemAxon Extended SMARTS.
static MFileFormat	CXSMILES ChemAxon Extended SMILES.
static MFileFormat	EMF Windows Enhanced Metafiles.
static long	F_ARCHIVE General archive format that stores a file in another format.
static long	F_BINARY Import/export module handles binary (byte array) data.
static long	F_COORDS The format can store atom coordinates if this flag is set.
static long	F_EXPORT Export is possible if this flag is set.
static long	F_GRAPHICS File format readable by a graphics program (image viewer, ray tracer etc.).
static long	F_IMAGE 2D image file format, readable by image viewers.
static long	F_IMPORT Import is possible if this flag is set.
static long	F_MIXED Storage of records in different formats is possible if this flag is set.
static long	F_MOLECULE The format can store molecule(s) if this flag is set.
static long	F_MULTIPLE_RECORDS_LEGAL The format is designed to store multiple records if this flag is set.
static long	F_MULTIPLE_RECORDS_POSSIBLE The import/export modules can handle files with multiple records if this flag is set.
static long	F_OBJECT Import/export module creates or reads a java object.
static long	F_REACTION The format can store reaction(s) if this flag is set.
static long	F_RECOGNIZER Format recognizer exists if this flag is set.
static long	F_SINGLE_LINE Format uses one line per structure.
static long	F_USER_DEFINED User defined format.
static long	F_XML The format is XML based if this flag is set.
static MFileFormat	GAUSSIAN_CUBE Gaussian Cube files.
static MFileFormat	GAUSSIAN_INPUT Gaussian Input Format.
static MFileFormat	GZIP GZIPped file.
static MFileFormat	INCHI IUPAC InChI files.
static MFileFormat	JPEG JPEG format.
static MFileFormat	JTF JChem Table Format.
static MFileFormat	MOL MDL Molfiles and Rgfiles.
static MFileFormat	MOL_V3_OUT MDL Extended Molfiles and Rgfiles.
static MFileFormat	MOL2 Tripos Mol2 files.
static MFileFormat	MRV Chemaxon Marvin Document.
static MFileFormat	MSBMP Windows Bitmap format.
static MFileFormat	NAME IUPAC Name files.
static MFileFormat	PDB Protein Data Bank format.
static MFileFormat	PDF Portable Document Format.
static MFileFormat	PEPTIDE_IN Peptide Sequence.
static MFileFormat	PEPTIDE1_OUT Peptide Sequence (1-letter).
static MFileFormat	PEPTIDE3_OUT Peptide Sequence (3-letter).
static MFileFormat	PNG Portable Network Graphics.
static MFileFormat	POVRAY POVRay file.
static MFileFormat	PPM Portable Pixmap format.
static MFileFormat	RDF MDL RDfiles.
static MFileFormat	RXN MDL Rxnfiles.
static MFileFormat	RXN_V3_OUT MDL Extended Rxnfiles.
static MFileFormat	SDF MDL SDfiles.
static MFileFormat	SMARTS SMARTS.
static MFileFormat	SMILES SMILES.
static MFileFormat	SVG Scalable Vector Graphics.
static MFileFormat	SYBYLMOL Tripos SYBYL molfiles.
static MFileFormat	XYZ XYZ files.

Constructor Summary

MFileFormat(java.lang.String desc, java.lang.String format, java.lang.String mime, java.lang.String exts, java.lang.String rrname, java.lang.String impname, java.lang.String expname, java.lang.String recogn, long f)
Creates a format descriptor.

Method Summary

MolExportModule	createExportModule() Creates the export module.
MolImportModule	createImportModule() Creates the molecule import module.
Recognizer	createRecognizer(java.lang.String fmt) Creates a recognizer module.
MRecordReader	createRecordReader(MolInputStream mis, java.lang.String opts) Creates the record reader.
MFileFormat	getAssociatedNonQueryFormat() Gets the associated non-query format.
MFileFormat	getAssociatedQueryFormat() Gets the associated query format.
java.lang.String	getDescription() Gets the format description.
java.lang.String[]	getExtensions() Gets the extension list.
long	getFlags() Gets the format descriptor flags.
java.lang.String	getMIMEType() Gets the MIME type.
java.lang.String	getName() Gets the codename of the format.
java.lang.String[]	getNames() Gets all the codename of the format.
int	getPriority(java.lang.String subfmt) Gets the priority determining format recognition order.
boolean	isFlagSet(long flag) Checks whether the format has a given (set of) flag(s) set.
boolean	matches(java.lang.String fmt, long f, long mask) Tests whether the format matches the specified pattern.
java.lang.String	toString() Overrides Object.toString() to ease debugging.

Methods inherited from class java.lang.Object

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

Field Detail

MRV

public static final MFileFormat MRV

Chemaxon Marvin Document.

CML

public static final MFileFormat CML

Chemical Markup Language.

MOL

public static final MFileFormat MOL

MDL Molfiles and Rgfiles.

MOL_V3_OUT

public static final MFileFormat MOL_V3_OUT

MDL Extended Molfiles and Rgfiles.

RXN

public static final MFileFormat RXN

MDL Rxnfiles.

RXN_V3_OUT

public static final MFileFormat RXN_V3_OUT

MDL Extended Rxnfiles.

SDF

public static final MFileFormat SDF

MDL SDfiles.

RDF

public static final MFileFormat RDF

MDL RDfiles.

JTF

public static final MFileFormat JTF

JChem Table Format.

CSMDL_IN

public static final MFileFormat CSMDL_IN

ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles. Format object for import only.

CSMOL_OUT

public static final MFileFormat CSMOL_OUT

ChemAxon Compressed Molfiles and Rgfiles.

CSRXN_OUT

public static final MFileFormat CSRXN_OUT

ChemAxon Compressed Rxnfiles.

CSSDF_OUT

public static final MFileFormat CSSDF_OUT

ChemAxon Compressed SDfiles.

CSRDF

public static final MFileFormat CSRDF

ChemAxon Compressed RDfiles.

SMILES

public static final MFileFormat SMILES

SMILES.

SMARTS

public static final MFileFormat SMARTS

SMARTS.

CXSMILES

public static final MFileFormat CXSMILES

ChemAxon Extended SMILES.

CXSMARTS

public static final MFileFormat CXSMARTS

ChemAxon Extended SMARTS.

ABBREVGROUP

public static final MFileFormat ABBREVGROUP

ChemAxon SMILES Abbreviated Groups.

INCHI

public static final MFileFormat INCHI

IUPAC InChI files.

NAME

public static final MFileFormat NAME

IUPAC Name files.

PEPTIDE_IN

public static final MFileFormat PEPTIDE_IN

Peptide Sequence.

PEPTIDE1_OUT

public static final MFileFormat PEPTIDE1_OUT

Peptide Sequence (1-letter).

PEPTIDE3_OUT

public static final MFileFormat PEPTIDE3_OUT

Peptide Sequence (3-letter).

XYZ

public static final MFileFormat XYZ

XYZ files.

GAUSSIAN_CUBE

public static final MFileFormat GAUSSIAN_CUBE

Gaussian Cube files.

GAUSSIAN_INPUT

public static final MFileFormat GAUSSIAN_INPUT

Gaussian Input Format.

SYBYLMOL

public static final MFileFormat SYBYLMOL

Tripos SYBYL molfiles.

MOL2

public static final MFileFormat MOL2

Tripos Mol2 files.

PDB

public static final MFileFormat PDB

Protein Data Bank format.

GZIP

public static final MFileFormat GZIP

GZIPped file.

BASE64

public static final MFileFormat BASE64

BASE64 encoded file.

AWT_IMAGE

public static final MFileFormat AWT_IMAGE

Image object (java.awt.Image).

JPEG

public static final MFileFormat JPEG

JPEG format.

PNG

public static final MFileFormat PNG

Portable Network Graphics.

PPM

public static final MFileFormat PPM

Portable Pixmap format.

MSBMP

public static final MFileFormat MSBMP

Windows Bitmap format.

PDF

public static final MFileFormat PDF

Portable Document Format.

SVG

public static final MFileFormat SVG

Scalable Vector Graphics.

EMF

public static final MFileFormat EMF

Windows Enhanced Metafiles.

POVRAY

public static final MFileFormat POVRAY

POVRay file.

F_EXPORT

public static final long F_EXPORT

Export is possible if this flag is set.

See Also:

Constant Field Values

F_IMPORT

public static final long F_IMPORT

Import is possible if this flag is set.

See Also:

Constant Field Values

F_RECOGNIZER

public static final long F_RECOGNIZER

Format recognizer exists if this flag is set. Automatically set by the constructor if the recognizer argument is not null.

See Also:

Constant Field Values

F_BINARY

public static final long F_BINARY

Import/export module handles binary (byte array) data.

See Also:

Constant Field Values

F_OBJECT

public static final long F_OBJECT

Import/export module creates or reads a java object.

See Also:

Constant Field Values

F_MOLECULE

public static final long F_MOLECULE

The format can store molecule(s) if this flag is set.

See Also:

Constant Field Values

F_REACTION

public static final long F_REACTION

The format can store reaction(s) if this flag is set.

See Also:

Constant Field Values

F_ARCHIVE

public static final long F_ARCHIVE

General archive format that stores a file in another format.

See Also:

Constant Field Values

F_GRAPHICS

public static final long F_GRAPHICS

File format readable by a graphics program (image viewer, ray tracer etc.).

See Also:

Constant Field Values

F_IMAGE

public static final long F_IMAGE

2D image file format, readable by image viewers.

See Also:

Constant Field Values

F_COORDS

public static final long F_COORDS

The format can store atom coordinates if this flag is set.

See Also:

Constant Field Values

F_MULTIPLE_RECORDS_LEGAL

public static final long F_MULTIPLE_RECORDS_LEGAL

The format is designed to store multiple records if this flag is set.

See Also:

Constant Field Values

F_MULTIPLE_RECORDS_POSSIBLE

public static final long F_MULTIPLE_RECORDS_POSSIBLE

The import/export modules can handle files with multiple records if this flag is set.

See Also:

Constant Field Values

F_MIXED

public static final long F_MIXED

Storage of records in different formats is possible if this flag is set.

See Also:

Constant Field Values

F_XML

public static final long F_XML

The format is XML based if this flag is set.

See Also:

Constant Field Values

F_USER_DEFINED

public static final long F_USER_DEFINED

User defined format.

See Also:

Constant Field Values

F_SINGLE_LINE

public static final long F_SINGLE_LINE

Format uses one line per structure.

Since:

Marvin 5.1

See Also:

Constant Field Values

Constructor Detail

MFileFormat

public MFileFormat(java.lang.String desc,
                   java.lang.String format,
                   java.lang.String mime,
                   java.lang.String exts,
                   java.lang.String rrname,
                   java.lang.String impname,
                   java.lang.String expname,
                   java.lang.String recogn,
                   long f)

Creates a format descriptor. The recogn argument specifies the recognizer module name and the priority of the format, separated by a space. If the format has more than one subformats, then their priorities are specified here in the form "format1=priority1 format2=priority2 ...".

Parameters:

desc - the format description

format - the format

mime - the MIME type or null if unknown

exts - the file extensions separated by spaces

rrname - name of the record reader module

impname - name of the import module

expname - name of the export module

recogn - the file format recognizer module name and the priority (nonnegative integer)

f - the flags

Method Detail

getName

public java.lang.String getName()

Gets the codename of the format.

Returns:

the codename.

getNames

public java.lang.String[] getNames()

Gets all the codename of the format.

Returns:

the codename.

getDescription

public java.lang.String getDescription()

Gets the format description.

Returns:

the description.

getExtensions

public java.lang.String[] getExtensions()

Gets the extension list.

Returns:

the extension list

getMIMEType

public java.lang.String getMIMEType()

Gets the MIME type.

Returns:

the MIME type or null if unknown

getFlags

public long getFlags()

Gets the format descriptor flags.

Returns:

the flags

getAssociatedQueryFormat

public MFileFormat getAssociatedQueryFormat()

Gets the associated query format.

Returns:

the associated format or null

getAssociatedNonQueryFormat

public MFileFormat getAssociatedNonQueryFormat()

Gets the associated non-query format.

Returns:

the associated format or null

getPriority

public int getPriority(java.lang.String subfmt)

Gets the priority determining format recognition order.

Parameters:

subfmt - the name of the subformat or null

Returns:

zero or a positive number

Throws:

java.lang.IllegalArgumentException - if priority for the specified subformat is not defined

Since:

Marvin 5.1, 07/29/2008

matches

public boolean matches(java.lang.String fmt,
                       long f,
                       long mask)

Tests whether the format matches the specified pattern.

Parameters:

fmt - the format name or null if not important

f - these flags must be set

mask - only bits specified here are taken into account

Returns:

true if it matches, false otherwise

isFlagSet

public boolean isFlagSet(long flag)

Checks whether the format has a given (set of) flag(s) set.

Parameters:

flag - the flag (or set of flags) to be test

Returns:

true if (all of) the given flag(s) is set, false otherwise

Since:

Marvin 5.1

createRecordReader

public MRecordReader createRecordReader(MolInputStream mis,
                                        java.lang.String opts)
                                 throws MolFormatException

Creates the record reader.

Parameters:

mis - the molecule input stream

opts - the options or null

Returns:

the record reader or null if there is no record reader for this format

Throws:

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

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

java.lang.SecurityException - if the module cannot be loaded because of a firewall problem

MolFormatException

See Also:

MFileFormatUtil.createRecordReader(InputStream, String)

createImportModule

public MolImportModule createImportModule()
                                   throws MolFormatException

Creates the molecule import module.

Returns:

the molecule import module or null if there is no importer for this format

Throws:

java.lang.SecurityException - if the module cannot be loaded because of a firewall problem

MolFormatException

createExportModule

public MolExportModule createExportModule()
                                   throws MolExportException

Creates the export module.

Returns:

the molecul export module or null if there is no exporter for this format

Throws:

java.lang.SecurityException - if the module cannot be loaded because of a firewall problem

MolExportException

See Also:

MFileFormatUtil.createExportModule(String)

createRecognizer

public Recognizer createRecognizer(java.lang.String fmt)
                            throws MolFormatException

Creates a recognizer module.

Parameters:

fmt - the (sub)format's codename

Returns:

the recognizer module or null if there is no recognizer for this format

Throws:

java.lang.SecurityException - if the module cannot be loaded because of a firewall problem

MolFormatException - if the recognizer module cannot be created

toString

public java.lang.String toString()

Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', the unsigned hexadecimal representation of the hash code of the object and the format name(s) in square brackets.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of the object