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joelib.io.types
Class JCAMP  

java.lang.Object
  joelib.io.types.JCAMP

All Implemented Interfaces:

joelib.io.MoleculeFileType

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public class JCAMP

extends java.lang.Object

implements joelib.io.MoleculeFileType

A class to interpret JCAMP-DX data (JCAMP-CS is not implemented yet). The supported data types are XYPAIRS, XYDATA=(X++(Y..Y)), PEAK TABLE and LINK.
If you want load a file with multiple blocks or inner blocks you must use JCampMultipleFile.
This class can only load separated single blocks with one TITLE and END label !

• ... The International Union of Pure and Applied Chemistry (IUPAC) took over responsibility from the Joint Commitee on Atomic and Molecular Physical Data (JCAMP) in 1995 ...
  I U P A C
  Committee on Printed and Electronic Publications
  Working Party on Spectroscopic Data Standards (JCAMP-DX)
  
  
• The Department of Chemistry at the University of the West Indies

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Field Summary
private static java.lang.String	description
private static java.lang.String[]	extensions
private  joelib.jcamp.JCAMPData	jcamp
private  java.lang.String	JCAMP_CHEMICAL_STRUCTURE
private  java.lang.String	JCAMP_SPECTRA
private  java.lang.String	JCAMP_START
private  java.lang.String	JCAMP_STOP
private  int	jcampCount
private  java.lang.String	LINK_TYPE
private  java.lang.String	LINK_TYPE_DATA
private  java.io.LineNumberReader	lnr
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  cformat.PrintfStream	ps

 

Constructor Summary

JCAMP()           Constructor for the Undefined object

 

Method Summary
private  boolean	addDataBlock(joelib.jcamp.JCAMPDataBlock block)           Adds a JCAMP block.
void	closeReader()           Description of the Method
void	closeWriter()           Description of the Method
java.lang.String	getJCAMPData()
void	initReader(java.io.InputStream is)           Description of the Method
void	initWriter(java.io.OutputStream os)           Description of the Method
java.lang.String	inputDescription()           Description of the Method
java.lang.String[]	inputFileExtensions()           Description of the Method
java.lang.String	outputDescription()           Description of the Method
java.lang.String[]	outputFileExtensions()           Description of the Method
java.lang.String	read()           Reads an molecule entry as (unparsed) String representation.
boolean	read(joelib.molecule.JOEMol mol)           Description of the Method
boolean	read(joelib.molecule.JOEMol mol, java.lang.String title)           Description of the Method
boolean	readable()           Description of the Method
private  joelib.jcamp.JCAMPDataBlock	resolveJCAMPBlocks(int _depth, java.lang.String previousLine, int blockID)           Gets the single JCAMP data blocks.
boolean	skipReaderEntry()           Skips an molecule or the rest of a molecule entry to grant the next read(JOEMol mol) invocation a proper starting position.
boolean	skipReaderEntry(int actualDepth)           Description of the Method
boolean	write(joelib.molecule.JOEMol mol)           Description of the Method
boolean	write(joelib.molecule.JOEMol mol, java.lang.String title)           Description of the Method
boolean	writeable()           Description of the Method

 

Methods inherited from class java.lang.Object

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

 

Field Detail

logger

private static org.apache.log4j.Category logger

Obtain a suitable logger.

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description

private static final java.lang.String description

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extensions

private static final java.lang.String[] extensions

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JCAMP_CHEMICAL_STRUCTURE

private final java.lang.String JCAMP_CHEMICAL_STRUCTURE

See Also:

Constant Field Values

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JCAMP_SPECTRA

private final java.lang.String JCAMP_SPECTRA

See Also:

Constant Field Values

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JCAMP_START

private final java.lang.String JCAMP_START

See Also:

Constant Field Values

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JCAMP_STOP

private final java.lang.String JCAMP_STOP

See Also:

Constant Field Values

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LINK_TYPE

private final java.lang.String LINK_TYPE

See Also:

Constant Field Values

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LINK_TYPE_DATA

private final java.lang.String LINK_TYPE_DATA

See Also:

Constant Field Values

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jcamp

private joelib.jcamp.JCAMPData jcamp

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lnr

private java.io.LineNumberReader lnr

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ps

private cformat.PrintfStream ps

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jcampCount

private int jcampCount

Constructor Detail

JCAMP

public JCAMP()

Constructor for the Undefined object

Method Detail

getJCAMPData

public java.lang.String getJCAMPData()

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closeReader

public void closeReader()
                 throws java.io.IOException

Description of the Method

Specified by:

closeReader in interface joelib.io.MoleculeFileType

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closeWriter

public void closeWriter()
                 throws java.io.IOException

Description of the Method

Specified by:

closeWriter in interface joelib.io.MoleculeFileType

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initReader

public void initReader(java.io.InputStream is)
                throws java.io.IOException

Description of the Method

Specified by:

initReader in interface joelib.io.MoleculeFileType

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initWriter

public void initWriter(java.io.OutputStream os)
                throws java.io.IOException

Description of the Method

Specified by:

initWriter in interface joelib.io.MoleculeFileType

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inputDescription

public java.lang.String inputDescription()

Description of the Method

Specified by:

inputDescription in interface joelib.io.MoleculeFileType

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inputFileExtensions

public java.lang.String[] inputFileExtensions()

Description of the Method

Specified by:

inputFileExtensions in interface joelib.io.MoleculeFileType

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outputDescription

public java.lang.String outputDescription()

Description of the Method

Specified by:

outputDescription in interface joelib.io.MoleculeFileType

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outputFileExtensions

public java.lang.String[] outputFileExtensions()

Description of the Method

Specified by:

outputFileExtensions in interface joelib.io.MoleculeFileType

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read

public java.lang.String read()
                      throws java.io.IOException

Reads an molecule entry as (unparsed) String representation.

Specified by:

read in interface joelib.io.MoleculeFileType

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read

public boolean read(joelib.molecule.JOEMol mol)
             throws java.io.IOException

Description of the Method

Specified by:

read in interface joelib.io.MoleculeFileType

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read

public boolean read(joelib.molecule.JOEMol mol,
                    java.lang.String title)
             throws java.io.IOException

Description of the Method

Specified by:

read in interface joelib.io.MoleculeFileType

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readable

public boolean readable()

Description of the Method

Specified by:

readable in interface joelib.io.MoleculeFileType

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skipReaderEntry

public boolean skipReaderEntry()
                        throws java.io.IOException

Description copied from interface: joelib.io.MoleculeFileType

Skips an molecule or the rest of a molecule entry to grant the next read(JOEMol mol) invocation a proper starting position. This method should always be called if you plan to throw an MoleculeIOException.

Specified by:

skipReaderEntry in interface joelib.io.MoleculeFileType

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skipReaderEntry

public boolean skipReaderEntry(int actualDepth)
                        throws java.io.IOException

Description of the Method

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write

public boolean write(joelib.molecule.JOEMol mol)
              throws java.io.IOException

Description of the Method

Specified by:

write in interface joelib.io.MoleculeFileType

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write

public boolean write(joelib.molecule.JOEMol mol,
                     java.lang.String title)
              throws java.io.IOException

Description of the Method

Specified by:

write in interface joelib.io.MoleculeFileType

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writeable

public boolean writeable()

Description of the Method

Specified by:

writeable in interface joelib.io.MoleculeFileType

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addDataBlock

private boolean addDataBlock(joelib.jcamp.JCAMPDataBlock block)

Adds a JCAMP block.

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resolveJCAMPBlocks

private joelib.jcamp.JCAMPDataBlock resolveJCAMPBlocks(int _depth,
                                                       java.lang.String previousLine,
                                                       int blockID)
                                                throws java.io.IOException

Gets the single JCAMP data blocks.

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Home >> All >> joelib >> io >> [ types overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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