MFileFormatUtil (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.formats.MFileFormatUtil

```
public class MFileFormatUtil
extends Object
```
File format related utility functions.

Since:

Marvin 4.1, 12/15/2005

Version:

5.3, 07/06/2009

Author:

Daniel Zatonyi

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`MOLMOVIE` Read multi-molecule files as movies.
`static int`	`MULTISET` The multi-molecule file really contains multiple atom sets of one molecule.
`static int`	`NOMOLMOVIE` Do not read multi-molecule XYZ files as movies.

Constructor Summary

Constructors
Constructor and Description

MFileFormatUtil()

Constructors
Constructor and Description
`MFileFormatUtil()`

Method Summary

Methods
Modifier and Type	Method and Description
`static String[]`	`convertToSmilingFormat(Molecule m)` Tries to convert a molecule to a SMILES related format.
`static String[]`	`convertToSmilingFormat(MProp p)` Try to convert a property to text with a SMILES related format argument.
`static MolExportModule`	`createExportModule(String fmt)` Creates an export module for the specified format.
`static MolExportModule`	`createExportModule(String fmt, String enc)` Creates an export module for the specified format with the specified encoding.
`static MRecordReader`	`createRecordReader(InputStream is, String opts)` Creates a record reader for an input stream.
`static MRecordReader`	`createRecordReader(InputStream is, String opts, String enc, String path)` Creates a record reader for an input stream.
`static MFileFormat[]`	`findFormats(String fmt, long flags, long mask)` Gets a list of formats.
`static String[]`	`getEncodingFromOptions(String fmtopts)` Gets the encoding that was explicitly given as an import option.
`static String`	`getFileExtensionLC(File f)` Gets the file extension in lower case.
`static String`	`getFileExtensionLC(String fname)` Gets the file extension in lower case.
`static MFileFormat`	`getFormat(String fmt)` Gets the file format descriptor for the specified codename.
`static List<String>`	`getFormatNamesWithExtension(String fileName)`
`static String`	`getKnownExtension(String fname)` Returns the file extension if it is a known extension.
`static String[]`	`getMolfileExtensions()` Gets the array of known molecule file extensions.
`static String[]`	`getMolfileFormats()` Gets the array of known molecule file formats.
`static String`	`getMostLikelyMolFormat(String fname)` Gets the most likey molecule file format from the file name extension.
`static String`	`getUnguessableFormat(String fname)` Gets the file format from the file name extension for formats that are not guessable from the file content.
`static boolean`	`isOutputCleanable(String fmt)` Tests whether the specified output format is cleanable.
`static boolean`	`isSubFormatOf(String f, String other)` Tests whether a format is a sub-format of another format.
`static boolean`	`isURLOrFileName(String s)` Tests whether the specified string is an URL (absolute or relative) or file name.
`static int`	`preprocessFormatAndOptions(String[] fmtopts)` Parses options like "MULTISET", "MOLMOVIE" or "NOMOLMOVIE".
`static String`	`recognizeOneLineFormat(String s)` Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
`static void`	`registerFormat(MFileFormat mff)` Registers a user defined file format.
`static String[]`	`splitFileAndOptions(String arg)` Parses "file{options}" strings used in molecule file import.
`static String[]`	`splitFormatAndOptions(String opts)` Parses "format:options" strings used in molecule file import and export.
`static void`	`testEncoding(String enc)` Tests whether the given charset name is supported by this JVM

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - MULTISET
```
public static final int MULTISET
```
    The multi-molecule file really contains multiple atom sets of one molecule.
    
    See Also:
    Constant Field Values
  - MOLMOVIE
```
public static final int MOLMOVIE
```
    Read multi-molecule files as movies.
    
    Since:
    
    Marvin 5.2, 02/12/2009
    
    See Also:
    Constant Field Values
  - NOMOLMOVIE
```
public static final int NOMOLMOVIE
```
    Do not read multi-molecule XYZ files as movies.
    
    Since:
    
    Marvin 5.2, 02/12/2009
    
    See Also:
    Constant Field Values
- Constructor Detail
  - MFileFormatUtil
```
public MFileFormatUtil()
```
- Method Detail
  - isSubFormatOf
```
public static boolean isSubFormatOf(String f,
                    String other)
```
    Tests whether a format is a sub-format of another format.
    
    Parameters:
    f - the format codename
    other - the other format
    
    Returns:
    true if it is a format variant of f
    Since:
    
    Marvin 4.1, 04/07/2006
  - splitFileAndOptions
```
public static String[] splitFileAndOptions(String arg)
```
    Parses "file{options}" strings used in molecule file import.
    
    Parameters:
    arg - string containing the filename and the options (if there are)
    
    Returns:
    a two-element array containing the filename and the options.
  - splitFormatAndOptions
```
public static String[] splitFormatAndOptions(String opts)
```
    Parses "format:options" strings used in molecule file import and export. Examples:
```
 splitFormatAndOptions("xyz:f1.4") returns {"xyz", "f1.4"}
 splitFormatAndOptions("f1.4") returns {null, "f1.4"}
 splitFormatAndOptions("xyz:") returns {"xyz", ""}
 splitFormatAndOptions("gzip:xyz:f1.4") returns {"gzip", "xyz:f1.4"}
 
```
    The semicolon can be omitted in case if Marvin's built-in input formats. Example:
```
 splitFormatAndOptions("xyz") returns { "xyz", ""}
 
```
    Parameters:
    opts - string containing the format and the options
    
    Returns:
    an array containing the format(s) and the options.
  - preprocessFormatAndOptions
```
public static int preprocessFormatAndOptions(String[] fmtopts)
```
    Parses options like "MULTISET", "MOLMOVIE" or "NOMOLMOVIE". Example:
```
 String[] fmtopts = splitFormatAndOptions("gzip:xyz:MULTISET,f1.4");
 // fmtopts == {"gzip", "xyz:MULTISET,f.14"}
 int result = preprocessFormatAndOptions(fmtopts);
 // fmtopts == {"gzip", "xyz:f.14"}, results == MULTISET
 
```
    Parameters:
    fmtopts - two-element array containing the format and the options
    
    Returns:
    flags corresponding to the options
    See Also:
    splitFormatAndOptions(java.lang.String), MULTISET, MOLMOVIE, NOMOLMOVIE
  - getEncodingFromOptions
```
public static String[] getEncodingFromOptions(String fmtopts)
```
    Gets the encoding that was explicitly given as an import option. The format is enc{name}, where name is a JAVA supported name of the charset.
    
    Parameters:
    fmtopts - the input format and options
    
    Returns:
    two element array, the first element is the encoding, the second contains the remaining import options.
    
    Throws:
    
    IllegalCharsetNameException - if the encoding is illegal
    
    UnsupportedCharsetException - if the encoding is unsupported
  - testEncoding
```
public static void testEncoding(String enc)
                         throws IllegalArgumentException
```
    Tests whether the given charset name is supported by this JVM
    
    Parameters:
    enc - the name of the charset
    
    Throws:
    
    IllegalArgumentException
  - getUnguessableFormat
```
public static String getUnguessableFormat(String fname)
```
    Gets the file format from the file name extension for formats that are not guessable from the file content. Used to distinguish SMARTS and SMILES.
    
    Parameters:
    fname - the filename
    
    Returns:
    the file format or null if the file contents can be used to recognize the format
  - getFileExtensionLC
```
public static String getFileExtensionLC(File f)
```
    Gets the file extension in lower case.
    
    Parameters:
    f - the file
    
    Returns:
    the extension in lower case
  - getFileExtensionLC
```
public static String getFileExtensionLC(String fname)
```
    Gets the file extension in lower case.
    
    Parameters:
    fname - the filename
    
    Returns:
    the extension in lower case
  - getMostLikelyMolFormat
```
public static String getMostLikelyMolFormat(String fname)
```
    Gets the most likey molecule file format from the file name extension.
    
    Parameters:
    fname - the filename
    
    Returns:
    the file format or null if the format cannot be determined from the file name
  - getKnownExtension
```
public static String getKnownExtension(String fname)
```
    Returns the file extension if it is a known extension. Known extensions are the following: mrv t gz mol mol2 rgf rxn csmol csrgf csrxn sdf cssdf rdf smi smiles sma smarts cml xml xyz txt html htm cgi gif jpg jpeg msbmp png svg svgz
    
    Parameters:
    fname - the filename
    
    Returns:
    the extension
  - getMolfileExtensions
```
public static String[] getMolfileExtensions()
```
    Gets the array of known molecule file extensions.
    
    Returns:
    the array of known molecule file extensions
  - getMolfileFormats
```
public static String[] getMolfileFormats()
```
    Gets the array of known molecule file formats.
    
    Returns:
    the array of known molecule file formats
  - isOutputCleanable
```
public static boolean isOutputCleanable(String fmt)
                                 throws SecurityException
```
    Tests whether the specified output format is cleanable. For a non-cleanable output format, cleaning is meaningless because coordinates are not stored.
    
    Parameters:
    fmt - the format string
    
    Returns:
    true if the specified output format is non-cleanable, false otherwise
    
    Throws:
    
    SecurityException
    Since:
    
    Marvin 4.1, 02/13/2006
  - registerFormat
```
public static void registerFormat(MFileFormat mff)
```
    Registers a user defined file format. The MFileFormat.F_USER_DEFINED flag is automatically set.
    
    Parameters:
    mff - the file format
    Since:
    
    Marvin 5.0, 05/23/2007
  - getFormat
```
public static MFileFormat getFormat(String fmt)
```
    Gets the file format descriptor for the specified codename.
    
    Parameters:
    fmt - the format codename
    
    Returns:
    the descriptor or null if not found
    Since:
    
    Marvin 5.0, 05/23/2007
  - findFormats
```
public static MFileFormat[] findFormats(String fmt,
                        long flags,
                        long mask)
```
    Gets a list of formats.
    
    Parameters:
    fmt - the format name or null if not important
    flags - select formats of which the specified flags are set
    mask - only bits specified here are taken into account
    
    Returns:
    the list
    Since:
    
    Marvin 5.0, 05/24/2007
  - createRecordReader
```
public static MRecordReader createRecordReader(InputStream is,
                               String opts)
                                        throws MolFormatException,
                                               IOException
```
    Creates a record reader for an input stream.
    
    Parameters:
    is - the input stream
    opts - input options or null
    
    Returns:
    the record reader or null if the format was not recognized
    
    Throws:
    
    IllegalCharsetNameException - if illegal encoding is used
    
    UnsupportedCharsetException - if unsupported encoding is used
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolFormatException
    
    IOException
    Since:
    
    Marvin 5.0, 06/03/2007
    
    See Also:
    MFileFormat.createRecordReader(MolInputStream, String)
  - createRecordReader
```
public static MRecordReader createRecordReader(InputStream is,
                               String opts,
                               String enc,
                               String path)
                                        throws MolFormatException,
                                               IOException
```
    Creates a record reader for an input stream.
    
    Parameters:
    is - the input stream
    opts - input options or null
    enc - the input encoding or null
    path - the file path (it can also be an URL) or null
    
    Returns:
    the record reader or null if the format was not recognized
    
    Throws:
    
    IllegalCharsetNameException - if illegal encoding is used
    
    UnsupportedCharsetException - if unsupported encoding is used
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolFormatException
    
    IOException
    Since:
    
    Marvin 5.0, 06/03/2007, Marvin 5.3
    
    See Also:
    MFileFormat.createRecordReader(MolInputStream, String)
  - createExportModule
```
public static MolExportModule createExportModule(String fmt)
                                          throws MolExportException
```
    Creates an export module for the specified format.
    
    Parameters:
    fmt - the format name
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolExportException
    See Also:
    MFileFormat.createExportModule()
  - createExportModule
```
public static MolExportModule createExportModule(String fmt,
                                 String enc)
                                          throws MolExportException
```
    Creates an export module for the specified format with the specified encoding.
    
    Parameters:
    fmt - the format name
    enc - the encoding
    
    Throws:
    
    SecurityException - if the module cannot be loaded because of a firewall problem
    
    MolExportException
    See Also:
    MFileFormat.createExportModule()
  - convertToSmilingFormat
```
public static String[] convertToSmilingFormat(Molecule m)
                                       throws MolExportException
```
    Tries to convert a molecule to a SMILES related format. SMILES, SMARTS, CxSMILES and CxSMARTS are tried in this order.
    
    Returns:
    the result of the first successful conversion, the 0th array element is the converted text, the 1st element is the format
    
    Throws:
    
    MolExportException - if conversion was not successful
    Since:
    
    Marvin 5.0, 11/11/2007
  - convertToSmilingFormat
```
public static String[] convertToSmilingFormat(MProp p)
                                       throws MolExportException
```
    Try to convert a property to text with a SMILES related format argument. SMILES, SMARTS, CxSMILES and CxSMARTS are tried in this order.
    
    Returns:
    the result of the first successful conversion, the 0th array element is the converted text, the 1st element is the format
    
    Throws:
    
    MolExportException - if conversion was not successful
    Since:
    
    Marvin 5.0, 11/11/2007
  - recognizeOneLineFormat
```
public static String recognizeOneLineFormat(String s)
```
    Recognize a one-line string as CxSMILES, CxSMARTS, AbbrevGroup, Peptide or IUPAC name.
    
    Parameters:
    s - the input string
    
    Returns:
    the most probable format or null
    Since:
    
    Marvin 4.1, 04/06/2006
  - isURLOrFileName
```
public static boolean isURLOrFileName(String s)
```
    Tests whether the specified string is an URL (absolute or relative) or file name.
    
    Parameters:
    s - the string
    
    Returns:
    true if it is an URL or file name, false otherwise
  - getFormatNamesWithExtension
```
public static List<String> getFormatNamesWithExtension(String fileName)
```

Class MFileFormatUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MULTISET

MOLMOVIE

NOMOLMOVIE

Constructor Detail

MFileFormatUtil

Method Detail

isSubFormatOf

splitFileAndOptions

splitFormatAndOptions

preprocessFormatAndOptions

getEncodingFromOptions

testEncoding

getUnguessableFormat

getFileExtensionLC

getFileExtensionLC

getMostLikelyMolFormat

getKnownExtension

getMolfileExtensions

getMolfileFormats

isOutputCleanable

registerFormat

getFormat

findFormats

createRecordReader

createRecordReader

createExportModule

createExportModule

convertToSmilingFormat

convertToSmilingFormat

recognizeOneLineFormat

isURLOrFileName

getFormatNamesWithExtension