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joelib.desc
Class ResultFactory  

java.lang.Object
  joelib.data.JOEGlobalDataBase
      joelib.desc.ResultFactory

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public class ResultFactory

extends joelib.data.JOEGlobalDataBase

Factory class to get descriptor results and faciliate the parsing of descriptor entries. The definition file can be defined in the joelib.data.ResultFactory.resourceFile property in the wsi.ra.tool.PropertyHolder. The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default.

Let's have a look at a knownResults.txt example file:

 $JOELIB_RESULT$ joelib.desc.result.IntResult
 #
 # PETRA descriptors
 #
 E_CHARGE
 E_DELTAHF
 E_HASH
 E_POLARIZABILITY
 #
 # Molconn Z 350
 #
 id
 nvx
 nrings
 ncirc
 nelem
 $REGEXP$ nas\p{Upper}\p{Lower}*
 $REGEXP$ nd\d
 $REGEXP$ ne\d+
 

This means all descriptors of the type nd1, nd2, nd3, ..., nd9 are joelib.desc.result.IntResult descriptors. Also the E_CHARGE, E_DELTAHF, E_HASH, E_POLARIZABILITY, id, nvx, ... descriptors.
For a detailed description for regular expressions patterns have a look at the java.util.regex.Pattern class.

Speed optimization (for external descriptors):

• Use as much explicit descriptor name entries as possible. They will be stored in a look up table (java.util.Hashtable) with fast access predicates.
• Use regular expressions only if there can be a lot of descriptors described with these expressions. Still, there will be all regular expressions checked, until the first one, which matches the given descriptor, will be found. But this will be always much more expensier than getting descriptor result (representation classes for descriptor values) directly from the java.util.Hashtable.

External descriptors will be descriptors, which are known in JOELib, but can not be calculated. All internal descriptor result classes will be always stored explicitly.

Default:
joelib.desc.ResultFactory.resourceFile=joelib/data/plain/knownResults.txt

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Field Summary
private  java.lang.String	actRep
private static java.lang.String	DEFAULT_RESOURCE
private static java.lang.String	IDENTIFIER
private static ResultFactory	instance
private static org.apache.log4j.Category	logger
private  java.util.Vector	regExp
private static java.lang.String	REGEXP
private  java.util.Hashtable	representation

 

Fields inherited from class joelib.data.JOEGlobalDataBase

initialized, resourceFile

 

Constructor Summary
private	ResultFactory()           Constructor for the ResultFactory.

 

Method Summary
DescResult	getDescResult(java.lang.String descName)           Gets the descResult attribute of the ResultFactory class
protected  java.lang.String	guessDescResult(java.lang.String descName)           Get descriptor result ype by using regular expressions.
static ResultFactory	instance()           Description of the Method
void	parseLine(java.lang.String buffer)           Description of the Method
joelib.data.JOEPairData	parsePairData(joelib.molecule.JOEMol mol, java.lang.String descName, joelib.data.JOEGenericData data)           Description of the Method

 

Methods inherited from class joelib.data.JOEGlobalDataBase

finalize, getLineCounter, init

 

Methods inherited from class java.lang.Object

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

 

Field Detail

logger

private static org.apache.log4j.Category logger

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DEFAULT_RESOURCE

private static final java.lang.String DEFAULT_RESOURCE

See Also:

Constant Field Values

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IDENTIFIER

private static final java.lang.String IDENTIFIER

See Also:

Constant Field Values

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REGEXP

private static final java.lang.String REGEXP

See Also:

Constant Field Values

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instance

private static ResultFactory instance

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representation

private java.util.Hashtable representation

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actRep

private java.lang.String actRep

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regExp

private java.util.Vector regExp

Constructor Detail

ResultFactory

private ResultFactory()

Constructor for the ResultFactory.

Method Detail

instance

public static ResultFactory instance()

Description of the Method

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getDescResult

public DescResult getDescResult(java.lang.String descName)
                         throws DescriptorException

Gets the descResult attribute of the ResultFactory class

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parseLine

public void parseLine(java.lang.String buffer)

Description of the Method

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parsePairData

public joelib.data.JOEPairData parsePairData(joelib.molecule.JOEMol mol,
                                             java.lang.String descName,
                                             joelib.data.JOEGenericData data)

Description of the Method

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guessDescResult

protected java.lang.String guessDescResult(java.lang.String descName)

Get descriptor result ype by using regular expressions.

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