chemaxon.formats

Class MolInputStream

java.lang.Object

java.io.InputStream

java.io.FilterInputStream

java.io.BufferedInputStream

chemaxon.marvin.io.PositionedInputStream

chemaxon.formats.MolInputStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

@PublicAPI
public class MolInputStream
extends PositionedInputStream

Molecule input stream that has the ability to determine the input file format.

Version:

5.3, 09/17/2009

Author:

Peter Csizmadia, Szilard Dorant, Szilveszter Juhos

Field Summary

Fields inherited from class chemaxon.marvin.io.PositionedInputStream

encoding, keeporiginalLineEnding, lineByteBuffer, lineCurrentColumn

Fields inherited from class java.io.BufferedInputStream

buf, count, marklimit, markpos, pos

Fields inherited from class java.io.FilterInputStream

in

Constructor Summary

Constructors

Constructor and Description
MolInputStream(java.io.InputStream is) Create a molecule input stream from an ordinary one, and determine the format.
MolInputStream(java.io.InputStream is, java.lang.String fmt) Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(java.io.InputStream is, java.lang.String fmt, java.lang.String enc) Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.
MolInputStream(java.io.InputStream is, java.lang.String fmt, java.lang.String enc, java.lang.String path) Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically.

Method Summary

Modifier and Type	Method and Description
java.lang.String	getFormat() Get the molecule file format.
java.lang.String	getPath() Gets the path or URL of the file.
void	setFormat(java.lang.String fmt) Sets the molecule file format.

Methods inherited from class chemaxon.marvin.io.PositionedInputStream

bufincRead, endGrabLines, getEncoding, getFilePointer, getGrabbedLines, getLastEOL, getLineCount, getWord, isSeekable, length, putBackLine, putBackLine, read, read, readLine, reset, resetFilePointer, seek, setByteOrder, setDesiredBufferSize, setEncoding, setEncoding, setWord, skip, skipLine, startGrabLines

Methods inherited from class java.io.BufferedInputStream

available, close, mark, markSupported

Methods inherited from class java.io.FilterInputStream

read

Methods inherited from class java.lang.Object

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

Constructor Detail

MolInputStream

public MolInputStream(java.io.InputStream is)
               throws java.io.IOException

Create a molecule input stream from an ordinary one, and determine the format.

Parameters:

is - the original input stream

Throws:

java.io.IOException - error occurred while trying to guess the file format

MolInputStream

public MolInputStream(java.io.InputStream is,
                      java.lang.String fmt)
               throws java.io.IOException

Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically. If "mol" or "csmol" is specified, then the file format is determined from the first line as "mol", "csmol", "rxn", "csrxn", "rgf" or "csrgf".

Parameters:

is - the original input stream

fmt - the input file format or null

Throws:

java.io.IOException - error occurred while trying to guess the file format

MolInputStream

public MolInputStream(java.io.InputStream is,
                      java.lang.String fmt,
                      java.lang.String enc)
               throws java.io.IOException

Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically. If "mol" or "csmol" is specified, then the file format is determined from the first line as "mol", "csmol", "rxn", "csrxn", "rgf" or "csrgf".

Parameters:

is - the original input stream

fmt - the input file format or null

enc - the input encoding or null

Throws:

java.io.IOException - error occurred while trying to guess the file format

Since:

Marvin 3.5.5

MolInputStream

public MolInputStream(java.io.InputStream is,
                      java.lang.String fmt,
                      java.lang.String enc,
                      java.lang.String path)
               throws java.io.IOException

Create a molecule input stream from an ordinary one, If null is specified as the fmt argument, then the file format is determined automatically. If "mol" or "csmol" is specified, then the file format is determined from the first line as "mol", "csmol", "rxn", "csrxn", "rgf" or "csrgf". If the file format cannot be determined from the contents and the file name is not null, then the file extension is used to guess the format.

Parameters:

is - the original input stream

fmt - the input file format or null

enc - the input encoding or null

path - the file path (it can also be an URL) or null

Throws:

java.io.IOException - error occurred while trying to guess the file format

Since:

Marvin 4.1, 01/03/2006

Method Detail

getFormat

public java.lang.String getFormat()

Get the molecule file format.

Returns:

"mrv", "mol", "mol:V3", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz" or "cube" or "inchi", "gzip" or "chemaxon.struc.Molecule" if imported from ObjectInputStream (serialized molecule)

setFormat

public void setFormat(java.lang.String fmt)

Sets the molecule file format.

Parameters:

fmt - the format

Since:

Marvin 5.0, 05/25/2007

getPath

public java.lang.String getPath()

Gets the path or URL of the file.

Returns:

the path or null if unknown

Since:

Marvin 5.3, 09/17/2009