A B C D E F G I K L M N P R S T U V W X

A

ABSENT_OPTION - Static variable in class uk.ac.ed.inf.enzml.mulan.MulanAttributeFactory

ABSENT_OPTION - Static variable in class uk.ac.ed.inf.enzml.weka.AttributeFactory

addEvaluationResultsToTableRow(TableRow, Evaluation) - Static method in class uk.ac.ed.inf.enzml.mulan.learn.ResultsFormatter

adds the evaluation results to a table row object

ALGORITHM - Static variable in class uk.ac.ed.inf.enzml.mulan.learn.ExperimentTable

the name for the algorithm table column

AllArffTests - Class in test

Class

AllArffTests() - Constructor for class test.AllArffTests

AllDataTests - Class in test.dataharness

Data harness for arff file generation and learning tests.

AllDataTests() - Constructor for class test.dataharness.AllDataTests

AllMulanArffTests - Class in test

Class

AllMulanArffTests() - Constructor for class test.AllMulanArffTests

AllMulanLearningTests - Class in test

Class

AllMulanLearningTests() - Constructor for class test.AllMulanLearningTests

AllMulanPredictionTests - Class in test

Class

AllMulanPredictionTests() - Constructor for class test.AllMulanPredictionTests

AllMulanTests - Class in test

Class

AllMulanTests() - Constructor for class test.AllMulanTests

AllPreliminaryTests - Class in test

Class

AllPreliminaryTests() - Constructor for class test.AllPreliminaryTests

AllTests - Class in test

All tests

AllTests() - Constructor for class test.AllTests

AllTrainTestsTests - Class in test

Class

AllTrainTestsTests() - Constructor for class test.AllTrainTestsTests

AllUtilsTests - Class in test

AllUtilsTests() - Constructor for class test.AllUtilsTests

Arff - Class in uk.ac.ed.inf.enzml.weka

Creates an ARFF file: checks file properties, loads data from database, fills and writes to file the ARFF attributes, classes and instances, generates auxiliary files if needed.

Arff(String, String) - Constructor for class uk.ac.ed.inf.enzml.weka.Arff

Apache logger

arff_EC_Instance1 - Static variable in class test.mulan.MulanArffTest

ARFF_FILE_PATH_PROP - Static variable in class uk.ac.ed.inf.enzml.weka.ArffProperties

the file path where the ARFF file will be written, inclusive of file name.

ARFF_ID_COLUMN - Static variable in class uk.ac.ed.inf.enzml.weka.ArffPropsTable

ARFF_PROPS_ARCHAEA - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_BACTERIA - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_EUKARIA - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_FUNGI - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_HUMAN - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_INVERTEBRATES - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_NOT_HUMAN - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

all swissprot-kegg agree records, except human

ARFF_PROPS_PATH - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_PLANTS - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_100 - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_ARCHAEA - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_BACTERIA - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_EUKARIA - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_FUNGI - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_INVERTEBRATES - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_PLANTS - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_RANDOM_VERTEBRATES - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_SWISSKEGG - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_TREMBL_KEGG - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_PROPS_VERTEBRATES - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

ARFF_TABLE - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters

The name of the table to save the arff file details to

arffEmptyInstance - Static variable in class test.dataharness.DataOne

arffEmptyInstance - Static variable in class test.dataharness.DataTwo

ArffGeneratorForFilterTests - Class in test.mulan.attributesfilter

ArffGeneratorForFilterTests() - Constructor for class test.mulan.attributesfilter.ArffGeneratorForFilterTests

arffInstance1 - Static variable in class test.dataharness.DataOne

arffInstance1 - Static variable in class test.dataharness.DataTwo

arffInstance1 - Static variable in class test.mulan.MulanArffTest

arffInstance1b - Static variable in class test.dataharness.DataOne

arffInstance1b - Static variable in class test.dataharness.DataTwo

arffInstance2 - Static variable in class test.dataharness.DataOne

arffInstance2 - Static variable in class test.dataharness.DataTwo

arffInstance2 - Static variable in class test.mulan.MulanArffTest

arffInstance4 - Static variable in class test.dataharness.DataOne

arffInstance4 - Static variable in class test.dataharness.DataTwo

arffInstance4 - Static variable in class test.mulan.MulanArffTest

arffInstanceAttributeVoid - Static variable in class test.mulan.MulanArffTest

arffInstanceAttVoid - Static variable in class test.dataharness.DataOne

arffInstanceAttVoid - Static variable in class test.dataharness.DataTwo

arffInstanceClassAttributeVoid - Static variable in class test.mulan.MulanArffTest

arffInstanceClassVoid - Static variable in class test.dataharness.DataOne

arffInstanceClassVoid - Static variable in class test.dataharness.DataTwo

arffInstanceClassVoid - Static variable in class test.mulan.MulanArffTest

ArffProperties - Class in uk.ac.ed.inf.enzml.weka

Contains the properties for a Weka ARFF file It contains: 1.

ArffProperties(String) - Constructor for class uk.ac.ed.inf.enzml.weka.ArffProperties

Constructor loads the properties from file

ArffPropsFilesTest - Class in test.dataharness

Test the ARFF properties files used in the test harness and their content.

ArffPropsFilesTest() - Constructor for class test.dataharness.ArffPropsFilesTest

ArffPropsOneTest - Class in test.dataharness

Get the arff data properties from file

ArffPropsOneTest() - Constructor for class test.dataharness.ArffPropsOneTest

ArffPropsQueriesOneTest - Class in test.dataharness

Class

ArffPropsQueriesOneTest() - Constructor for class test.dataharness.ArffPropsQueriesOneTest

ArffPropsQueriesTest - Class in test.dataharness

Checks the results of the queries contained in the arff properties files

ArffPropsQueriesTest() - Constructor for class test.dataharness.ArffPropsQueriesTest

ArffPropsQueriesTwoTest - Class in test.dataharness

Class

ArffPropsQueriesTwoTest() - Constructor for class test.dataharness.ArffPropsQueriesTwoTest

ArffPropsTable - Class in uk.ac.ed.inf.enzml.weka

Class to keep the name and column types for the database table to store the ARFF file parameters (the data files for Weka or Mulan machine learning)

ArffPropsTable() - Constructor for class uk.ac.ed.inf.enzml.weka.ArffPropsTable

ArffPropsTableManager - Class in uk.ac.ed.inf.enzml.weka

Writes into a database table the pointers needed to build an arff file (the name of the arff file, the query to select instances, attributes, class values etc) TODO integrate arff recording to database with mulan experiment recording

ArffPropsTableManager(Arff) - Constructor for class uk.ac.ed.inf.enzml.weka.ArffPropsTableManager

Constructor 1: initialises the table manager to point to the arff table.

ArffPropsTableManager(DbManager) - Constructor for class uk.ac.ed.inf.enzml.weka.ArffPropsTableManager

Constructor 2: initialises the table manager to point to the arff table.

ArffPropsTableManagerTest - Class in test.weka

Class

ArffPropsTableManagerTest() - Constructor for class test.weka.ArffPropsTableManagerTest

ArffPropsTableReader - Class in uk.ac.ed.inf.enzml.weka

Reads properties from the table where the arff records are collected.

ArffPropsTableReader(DbManager) - Constructor for class uk.ac.ed.inf.enzml.weka.ArffPropsTableReader

ArffPropsTableReaderTest - Class in test.weka

Class

ArffPropsTableReaderTest() - Constructor for class test.weka.ArffPropsTableReaderTest

ArffPropsTableTest - Class in test.weka

Class

ArffPropsTableTest() - Constructor for class test.weka.ArffPropsTableTest

ArffPropsTwoTest - Class in test.dataharness

Class

ArffPropsTwoTest() - Constructor for class test.dataharness.ArffPropsTwoTest

ArffTest - Class in test.weka

Class

ArffTest() - Constructor for class test.weka.ArffTest

ATT1 - Static variable in class test.dataharness.DataOne

ATT1_TO_STRING - Static variable in class test.dataharness.DataOne

ATT1_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT2 - Static variable in class test.dataharness.DataOne

ATT2_TO_STRING - Static variable in class test.dataharness.DataOne

ATT2_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT3 - Static variable in class test.dataharness.DataOne

ATT3_TO_STRING - Static variable in class test.dataharness.DataOne

ATT3_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT4 - Static variable in class test.dataharness.DataOne

ATT4_TO_STRING - Static variable in class test.dataharness.DataOne

ATT4_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT5 - Static variable in class test.dataharness.DataOne

ATT5_TO_STRING - Static variable in class test.dataharness.DataOne

ATT5_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_1111_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_111_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_11_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_1_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_2222_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_222_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_22_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATT_EC_2_TO_STRING - Static variable in class test.mulan.MulanArffTest

ATTRIBUTE_FIELD - Static variable in class test.dataharness.CreateDataTable

ATTRIBUTE_ID - Static variable in class uk.ac.ed.inf.enzml.mulan.predict.MulanPredict

ATTRIBUTE_NAME - Static variable in class uk.ac.ed.inf.enzml.mulan.predict.MulanPredict

AttributeFactory - Class in uk.ac.ed.inf.enzml.weka

The attribute factory produces binary and nominal Weka attributes.

AttributeFactory(DataSetGenerator) - Constructor for class uk.ac.ed.inf.enzml.weka.AttributeFactory

Takes the attribute names from the dataset generator object.

AttributeFactoryTest - Class in test.weka

Class

AttributeFactoryTest() - Constructor for class test.weka.AttributeFactoryTest

attributeIsValid(Attribute) - Static method in class uk.ac.ed.inf.enzml.weka.AttributeFactory

Check if an attribute is valid (not null, non-empty name)

attributesColumn() - Static method in class test.dataharness.DataOne

AttributesFilter - Class in uk.ac.ed.inf.enzml.mulan.attributesfilter

This class filters the attributes of a dataset (the test set) to make it compatible with another dataset (the train set).

AttributesFilter(int, int, String, String) - Constructor for class uk.ac.ed.inf.enzml.mulan.attributesfilter.AttributesFilter

AttributesFilteredArff - Class in uk.ac.ed.inf.enzml.mulan.attributesfilter

AttributesFilteredArff(String, String, TreeSet<String>, AttributesFilter, int) - Constructor for class uk.ac.ed.inf.enzml.mulan.attributesfilter.AttributesFilteredArff

AttributesFilteredArffTest - Class in test.mulan.attributesfilter

AttributesFilteredArffTest() - Constructor for class test.mulan.attributesfilter.AttributesFilteredArffTest

AttributesFilteredAttributeFactory - Class in uk.ac.ed.inf.enzml.mulan.attributesfilter

Takes the list of attributes from AttributesFilteredDataSetGenerator, instead of taking it from the instances-attributes map.

AttributesFilteredAttributeFactory(AttributesFilteredDataSetGenerator) - Constructor for class uk.ac.ed.inf.enzml.mulan.attributesfilter.AttributesFilteredAttributeFactory

AttributesFilteredDataSetGenerator - Class in uk.ac.ed.inf.enzml.mulan.attributesfilter

Get passed a list of attributes, instead of taking it from instances-attributes map.

AttributesFilteredDataSetGenerator(AttributesFilteredDataSetManager, OneToManyMap<String, String>, OneToManyMap<String, String>, TreeSet<String>) - Constructor for class uk.ac.ed.inf.enzml.mulan.attributesfilter.AttributesFilteredDataSetGenerator

AttributesFilteredDataSetGeneratorTest - Class in test.mulan.attributesfilter

AttributesFilteredDataSetGeneratorTest() - Constructor for class test.mulan.attributesfilter.AttributesFilteredDataSetGeneratorTest

AttributesFilteredDataSetManager - Class in uk.ac.ed.inf.enzml.mulan.attributesfilter

Get passed a list of attributes, instead of taking it from instances-attributes map.

AttributesFilteredDataSetManager(AttributesFilteredArff) - Constructor for class uk.ac.ed.inf.enzml.mulan.attributesfilter.AttributesFilteredDataSetManager

AttributesFilterTest - Class in test.mulan.attributesfilter

AttributesFilterTest() - Constructor for class test.mulan.attributesfilter.AttributesFilterTest

attributesSection(Instances) - Method in class uk.ac.ed.inf.enzml.weka.DataSetWriter

attributesValues() - Static method in class test.dataharness.DataOne

Results of a select distinct instance, attribute query

AttributeUtils - Class in uk.ac.ed.inf.enzml.mulan

AttributeUtils() - Constructor for class uk.ac.ed.inf.enzml.mulan.AttributeUtils

AUTHOR - Static variable in class uk.ac.ed.inf.enzml.ProjectParameters