chemaxon.descriptors
Class MDReader

java.lang.Object
  chemaxon.descriptors.MDReader

Direct Known Subclasses:

MDArrayReader, MDDBReader, MDFileReader

public abstract class MDReader
extends java.lang.Object

Base class definitions for MDSet input streams. Different descriptors types (as fingerprints, pharmacophore fingerprints) are handled in the same, a transparent manner. Derived classes may differ in the source of initial data they handle: standard molecular structure file, chemical descriptor set file (written by an MDWrite derivative), or database.
Each element read can either get a unique identifier (ID) from the source it comes from, or alternatively an ID can also be generated by the reader.
An MDSet object is returned by the reader in each call. This set can either be re-used or a new instance can be created. This behaviour is determined by setCloneResult( boolean ).

Since:

JChem 2.0

Author:

Miklos Vargyas

Field Summary

protected boolean	cloneResult indicates if mdSet is cloned or not in next()
protected int	firstId starting value of id
protected boolean	generateDescriptor Generates descriptor from molecule if true, direct read otherwise.
protected boolean	generateId generate unique identifiers
protected int	id unique identifier (ID) of the current element read
protected java.lang.String	idTagName name of the tag in the SDfile input which stored the unique structure id
protected Molecule	lastReadMolecule the molecule last read from the structure table
protected MDSet	mdSet the schema mdSet if descriptors are generated on-the-fly
protected java.util.ArrayList	takeTags names of tags that have to be taken from the input Molecule

Constructor Summary

protected	MDReader() Creates an new, empty object.
protected	MDReader(MDSet mdSet) Creates a molecular structure file or database table reader.

Method Summary

abstract void	close() Closes down the descriptor stream.
protected void	createMDSetComponent(int i, java.lang.String type, java.lang.String settings) Creates and sets the given component of the internal MDSet object of the given type and specified parameter settings.
boolean	getCloneResult() Gets the current value of the cloning policy flag.
MDSet	getMDSet() Gets the molecular descriptor set.
Molecule	getMolecule() Gets the current molecular structure as read from the input file (that is before any transformation were applied).
abstract MDSet	next() Reads the next element from the input and stores it in the MDSet object passed as parameter.
void	reset() Initializes the MDSet input stream.
void	setCloneResult(boolean cloneResult) Sets the cloning policy of the next() method.
void	setFirstId(int firstId) Sets the ID of the first MDSet.
void	setGenerateId(boolean generateId) Sets whether ID-s are generated or not.
void	setIdTagName(java.lang.String tagName) Sets the name of the ID tag in the SDfile.
void	setTakeTag(int cdSetComponent, java.lang.String tagName) Sets the tag name of a MDSet component.

Methods inherited from class java.lang.Object

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

Field Detail

id

protected int id

unique identifier (ID) of the current element read

firstId

protected int firstId

starting value of id

generateId

protected boolean generateId

generate unique identifiers

generateDescriptor

protected boolean generateDescriptor

Generates descriptor from molecule if true, direct read otherwise.

lastReadMolecule

protected Molecule lastReadMolecule

the molecule last read from the structure table

mdSet

protected MDSet mdSet

the schema mdSet if descriptors are generated on-the-fly

cloneResult

protected boolean cloneResult

indicates if mdSet is cloned or not in next()

takeTags

protected java.util.ArrayList takeTags

names of tags that have to be taken from the input Molecule

idTagName

protected java.lang.String idTagName

name of the tag in the SDfile input which stored the unique structure id

Constructor Detail

MDReader

protected MDReader(MDSet mdSet)

Creates a molecular structure file or database table reader. The reader generates descriptors from the molecule read according to the MDSet parameter passed.

Parameters:

mdSet - a sample MDSet object that defines what should be read from the input source

MDReader

protected MDReader()

Creates an new, empty object.

Method Detail

setGenerateId

public void setGenerateId(boolean generateId)

Sets whether ID-s are generated or not. Generated ID-s are positive integers.

Parameters:

generateId - ID-s are generated if true, otherwise ID-s are read from the input source

setTakeTag

public void setTakeTag(int cdSetComponent,
                       java.lang.String tagName)

Sets the tag name of a MDSet component. If the name is not null, the value of the tag is taken from an SDfile input, otherwise, or in the case when the tag named does not exists in the input file, the desciptor of the specified component is generated.

Parameters:

cdSetComponent - index of a component of the MDSet

tagName - name of the tag to take the value of the descriptor from

setIdTagName

public void setIdTagName(java.lang.String tagName)

Sets the name of the ID tag in the SDfile. Unique indentifier is read from that tag if exists, otherwise the value of the identifier is undefined.

Parameters:

tagName - name of the ID tag

setFirstId

public void setFirstId(int firstId)

Sets the ID of the first MDSet. If not set, ID numeration starts from 1.

Parameters:

firstId - value of the of the ID of the first MDSet

setCloneResult

public void setCloneResult(boolean cloneResult)

Sets the cloning policy of the next() method. If set to true returned MDSet objects are new ones, otherswise always the same object is reused and returned (typically, this is passed in the constructor of the class derived from MDReader). By default, cloning policy is set to true. This is the safer option, though it might result in slower operation.

Parameters:

cloneResult - indicates cloning behaviour

getCloneResult

public boolean getCloneResult()

Gets the current value of the cloning policy flag.

Returns:

indicator of cloning policy

getMDSet

public MDSet getMDSet()

Gets the molecular descriptor set. This method is provided in order to allow the used intervene into descriptor generation (for instance by overriding parameter settings).

Returns:

the MDSet object

reset

public void reset()
           throws MDReaderException

Initializes the MDSet input stream. If the stream is not empty, the subsequent call to next( MDSet cds ) returns the first element.

Throws:

MDReaderException - when failed to reset the reader

next

public abstract MDSet next()
                    throws MDReaderException

Reads the next element from the input and stores it in the MDSet object passed as parameter. This method should be called by the next( ) method of the derived class as the first statement. It clones the internal MDSet instance if needed and increments the id (if id-s are generated).

Returns:

the MDSet to be filled in with the next descriptor

Throws:

MDReaderException - when failed reading the next descriptor set

getMolecule

public Molecule getMolecule()
                     throws MDReaderException

Gets the current molecular structure as read from the input file (that is before any transformation were applied). Not all MDReader subclasses can implement this method in a meaningful way, therefore it is not an abstract method (just for the sake of ease).

Returns:

always null, see subclasses for meaningful implementation

Throws:

MDReaderException

close

public abstract void close()
                    throws MDReaderException

Closes down the descriptor stream. After this, no more operation is permitted on the stream.

Throws:

MDReaderException - when failed to close the input stream

createMDSetComponent

protected void createMDSetComponent(int i,
                                    java.lang.String type,
                                    java.lang.String settings)
                             throws MDParametersException

Creates and sets the given component of the internal MDSet object of the given type and specified parameter settings.

Parameters:

i - index of the component

type - class name of the component

settings - parameter settings

Throws:

MDParametersException