Package edu.msu.cme.rdp.classifier.utils

Class ClassifierFactory

java.lang.Object

edu.msu.cme.rdp.classifier.utils.ClassifierFactory

public class ClassifierFactory
extends java.lang.Object

A factory to create a classifier with the training information defined by the property file.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	FUNGALITS_unite_GENE
static java.lang.String	FUNGALITS_warcup_GENE
static java.lang.String	FUNGALLSU_GENE
static java.lang.String	RRNA_16S_GENE

Method Summary

Modifier and Type	Method	Description
Classifier	createClassifier()	Creates a new classifier.
java.lang.String	getClassifierVersion()	Returns the version of the classifier.
static ClassifierFactory	getFactory(java.lang.String gene)	Returns a factory with the training information.
HierarchyVersion	getHierarchyTrainsetNo()	Returns the info of the taxonomy hierarchy from of the training file.
java.lang.String	getHierarchyVersion()	Returns the version of the taxonomical hierarchy.
HierarchyTree	getRoot()
java.lang.String	getTrainRank()
static void	resetDefaultDataProp()	Resets the data property file to the default data property file.
static void	setDataProp(java.lang.String properties, boolean relative)	Sets the property file which contains the mapping of the training files.

Methods inherited from class java.lang.Object

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

Field Detail

RRNA_16S_GENE

public static final java.lang.String RRNA_16S_GENE

See Also:

Constant Field Values

FUNGALLSU_GENE

public static final java.lang.String FUNGALLSU_GENE

See Also:

Constant Field Values

FUNGALITS_warcup_GENE

public static final java.lang.String FUNGALITS_warcup_GENE

See Also:

Constant Field Values

FUNGALITS_unite_GENE

public static final java.lang.String FUNGALITS_unite_GENE

See Also:

Constant Field Values

Method Detail

resetDefaultDataProp

public static void resetDefaultDataProp()

Resets the data property file to the default data property file.

setDataProp

public static void setDataProp(java.lang.String properties,
                               boolean relative)

Sets the property file which contains the mapping of the training files. The actually training data files should be in the same directory as this property file. To override the default property location, this method must be called before the first ClassifierFactory.getFactory() call.

getFactory

public static ClassifierFactory getFactory(java.lang.String gene)
                                    throws java.io.IOException,
                                           TrainingDataException

Returns a factory with the training information. This method initialize all the training information. Note: the ClassifierFactory.setDataProp() static method must be called before this method if default property file will not be used.

Throws:

java.io.IOException

TrainingDataException

createClassifier

public Classifier createClassifier()

Creates a new classifier.

getHierarchyVersion

public java.lang.String getHierarchyVersion()

Returns the version of the taxonomical hierarchy.

getHierarchyTrainsetNo

public HierarchyVersion getHierarchyTrainsetNo()

Returns the info of the taxonomy hierarchy from of the training file.

getClassifierVersion

public java.lang.String getClassifierVersion()

Returns the version of the classifier.

getRoot

public HierarchyTree getRoot()

getTrainRank

public java.lang.String getTrainRank()