chemaxon.formats
Class MolInputStream

java.lang.Object
  java.io.InputStream
      java.io.FilterInputStream
          java.io.BufferedInputStream
              chemaxon.marvin.io.PositionedInputStream
                  chemaxon.formats.MolInputStream

public class MolInputStream

extends chemaxon.marvin.io.PositionedInputStream

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

Version:

4.1, 06/29/2006

Author:

Peter Csizmadia, Szilard Dorant

Field Summary

Fields inherited from class chemaxon.marvin.io.PositionedInputStream

lineBuf, lineCurrentColumn

Fields inherited from class java.io.BufferedInputStream

buf, count, marklimit, markpos, pos

Fields inherited from class java.io.FilterInputStream

in

Constructor Summary

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 fname)
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

static boolean	canBeAbbrevgroup(java.lang.String line) Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeAbbrevgroup(String) must be used instead
static boolean	canBeBase64(java.lang.String line) Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeBase64(String) must be used instead
static boolean	canBeChime(java.lang.String s) Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeChime(String) must be used instead
static boolean	canBeJTF(java.lang.String line) Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeJTF(String) must be used instead
static boolean	canBeSMARTS(java.lang.String s) Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeSMARTS(String) must be used instead
static boolean	canBeSMILES(java.lang.String s) Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeSMILES(String) must be used instead
java.lang.String	getFormat() Get the molecule file format.
static java.util.Vector	getJtfFields(java.lang.String line) Deprecated. as of Marvin 4.1, MFileFormatUtil.getJTFFields(String) must be used instead

Methods inherited from class chemaxon.marvin.io.PositionedInputStream

bufincRead, endGrabLines, getEncoding, getFilePointer, getGrabbedLines, getLineCount, isSeekable, length, putBackLine, read, read, readLine, reset, resetFilePointer, seek, setDesiredBufferSize, setEncoding, skip, 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 occured 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 occured 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 occured 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 fname)
               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

fname - the file name (it can also be a path or URL) or null

Throws:

java.io.IOException - error occured 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:

the format

canBeBase64

public static boolean canBeBase64(java.lang.String line)

Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeBase64(String) must be used instead

canBeChime

public static boolean canBeChime(java.lang.String s)

Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeChime(String) must be used instead

canBeSMARTS

public static boolean canBeSMARTS(java.lang.String s)

Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeSMARTS(String) must be used instead

canBeSMILES

public static boolean canBeSMILES(java.lang.String s)

Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeSMILES(String) must be used instead

canBeAbbrevgroup

public static boolean canBeAbbrevgroup(java.lang.String line)

Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeAbbrevgroup(String) must be used instead

canBeJTF

public static boolean canBeJTF(java.lang.String line)

Deprecated. as of Marvin 4.1, MFileFormatUtil.canBeJTF(String) must be used instead

Since:

Marvin 2.9.9

getJtfFields

public static java.util.Vector getJtfFields(java.lang.String line)

Deprecated. as of Marvin 4.1, MFileFormatUtil.getJTFFields(String) must be used instead

Since:

Marvin 2.9.9