Package chemaxon.formats
Class MolInputStream
- java.lang.Object
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- java.io.InputStream
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- java.io.FilterInputStream
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- java.io.BufferedInputStream
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- chemaxon.marvin.io.PositionedInputStream
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- chemaxon.formats.MolInputStream
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- All Implemented Interfaces:
Closeable
,AutoCloseable
@PublicAPI public class MolInputStream extends PositionedInputStream
Molecule input stream that has the ability to determine the input file format.
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Field Summary
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Fields inherited from class chemaxon.marvin.io.PositionedInputStream
encoding, keeporiginalLineEnding, lineByteBuffer, lineCurrentColumn
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Fields inherited from class java.io.FilterInputStream
in
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Constructor Summary
Constructors Constructor Description MolInputStream(InputStream is)
Create a molecule input stream from an ordinary one, and determine the format.MolInputStream(InputStream is, 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(InputStream is, String fmt, 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(InputStream is, String fmt, String enc, 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.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String
getFormat()
Get the molecule file format.String
getPath()
Gets the path or URL of the file.void
setFormat(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
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Methods inherited from class java.io.BufferedInputStream
available, close, mark, markSupported
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Methods inherited from class java.io.FilterInputStream
read
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Methods inherited from class java.io.InputStream
nullInputStream, readAllBytes, readNBytes, readNBytes, transferTo
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Constructor Detail
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MolInputStream
public MolInputStream(InputStream is) throws IOException
Create a molecule input stream from an ordinary one, and determine the format.- Parameters:
is
- the original input stream- Throws:
IOException
- error occurred while trying to guess the file format
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MolInputStream
public MolInputStream(InputStream is, String fmt) throws 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 streamfmt
- the input file format or null- Throws:
IOException
- error occurred while trying to guess the file format
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MolInputStream
public MolInputStream(InputStream is, String fmt, String enc) throws 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 streamfmt
- the input file format or nullenc
- the input encoding or null- Throws:
IOException
- error occurred while trying to guess the file format- Since:
- Marvin 3.5.5
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MolInputStream
public MolInputStream(InputStream is, String fmt, String enc, String path) throws 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 streamfmt
- the input file format or nullenc
- the input encoding or nullpath
- the file path (it can also be an URL) ornull
- Throws:
IOException
- error occurred while trying to guess the file format- Since:
- Marvin 4.1, 01/03/2006
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Method Detail
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getFormat
public 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)
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setFormat
public void setFormat(String fmt)
Sets the molecule file format.- Parameters:
fmt
- the format- Since:
- Marvin 5.0, 05/25/2007
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getPath
public String getPath()
Gets the path or URL of the file.- Returns:
- the path or
null
if unknown - Since:
- Marvin 5.3, 09/17/2009
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