Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> io >> [ types overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---

joelib.io.types
Class Flat  

java.lang.Object
  joelib.io.types.Flat

All Implemented Interfaces:

joelib.io.MoleculeFileType

---

public class Flat

extends java.lang.Object

implements joelib.io.MoleculeFileType

Flat file format support.

---

Field Summary
private  java.lang.String	delimiter
private static java.lang.String	description
private static java.lang.String[]	extensions
boolean	firstLineLoaded
private  boolean	firstLineWritten
private  java.lang.String	inputDelim
private  java.util.Vector	lineStructure
private  java.io.LineNumberReader	lnr
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  java.lang.String	outputDelim
private  cformat.PrintfStream	ps
private  boolean	storeLineInfo
private  int	titlePosition

 

Constructor Summary

Flat()           Constructor for the Smiles object

 

Method Summary
void	closeReader()           Description of the Method
void	closeWriter()           Description of the Method
boolean	getStoreLineInfo()           Gets the storeLineInfo attribute of the Smiles object
void	initParser()           Description of the Method
void	initReader(java.io.InputStream is)           Description of the Method
void	initReader(java.io.InputStream is, boolean _firstLineLoaded)
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	parseFirstLineReadNext(java.lang.String line)
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)           Loads an molecule in SMILES format and sets the title.
boolean	readable()           Description of the Method
void	setStoreLineInfo(boolean _flag)           Sets the storeLineInfo attribute of the Smiles object
boolean	skipReaderEntry()           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.

---

description

private static final java.lang.String description

---

extensions

private static final java.lang.String[] extensions

---

firstLineLoaded

public boolean firstLineLoaded

---

lnr

private java.io.LineNumberReader lnr

---

ps

private cformat.PrintfStream ps

---

delimiter

private java.lang.String delimiter

---

inputDelim

private java.lang.String inputDelim

---

outputDelim

private java.lang.String outputDelim

---

lineStructure

private java.util.Vector lineStructure

---

firstLineWritten

private boolean firstLineWritten

---

storeLineInfo

private boolean storeLineInfo

---

titlePosition

private int titlePosition

Constructor Detail

Flat

public Flat()

Constructor for the Smiles object

Method Detail

setStoreLineInfo

public void setStoreLineInfo(boolean _flag)

Sets the storeLineInfo attribute of the Smiles object

---

getStoreLineInfo

public boolean getStoreLineInfo()

Gets the storeLineInfo attribute of the Smiles object

---

closeReader

public void closeReader()
                 throws java.io.IOException

Description of the Method

Specified by:

closeReader in interface joelib.io.MoleculeFileType

---

closeWriter

public void closeWriter()
                 throws java.io.IOException

Description of the Method

Specified by:

closeWriter in interface joelib.io.MoleculeFileType

---

initParser

public void initParser()
                throws java.io.IOException

Description of the Method

---

initReader

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

Description of the Method

Specified by:

initReader in interface joelib.io.MoleculeFileType

---

initReader

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

---

initWriter

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

Description of the Method

Specified by:

initWriter in interface joelib.io.MoleculeFileType

---

inputDescription

public java.lang.String inputDescription()

Description of the Method

Specified by:

inputDescription in interface joelib.io.MoleculeFileType

---

inputFileExtensions

public java.lang.String[] inputFileExtensions()

Description of the Method

Specified by:

inputFileExtensions in interface joelib.io.MoleculeFileType

---

outputDescription

public java.lang.String outputDescription()

Description of the Method

Specified by:

outputDescription in interface joelib.io.MoleculeFileType

---

outputFileExtensions

public java.lang.String[] outputFileExtensions()

Description of the Method

Specified by:

outputFileExtensions in interface joelib.io.MoleculeFileType

---

parseFirstLineReadNext

public java.lang.String parseFirstLineReadNext(java.lang.String line)
                                        throws java.io.IOException

---

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

---

read

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

Description of the Method

Specified by:

read in interface joelib.io.MoleculeFileType

---

read

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

Loads an molecule in SMILES format and sets the title. If title is null the title line in the molecule file is used.

Specified by:

read in interface joelib.io.MoleculeFileType

---

readable

public boolean readable()

Description of the Method

Specified by:

readable in interface joelib.io.MoleculeFileType

---

skipReaderEntry

public boolean skipReaderEntry()
                        throws java.io.IOException

Description of the Method

Specified by:

skipReaderEntry in interface joelib.io.MoleculeFileType

---

write

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

Description of the Method

Specified by:

write in interface joelib.io.MoleculeFileType

---

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

---

writeable

public boolean writeable()

Description of the Method

Specified by:

writeable in interface joelib.io.MoleculeFileType

---

Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> io >> [ types overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

---