Menu
▾
▴
[Cdk-commits] SF.net SVN: cdk:[14322] cdk-taverna/trunk/src/test/java/org/openscience/cdk /applications/taverna/qsar/model/weka
|
From: <tho...@us...> - 2009-03-02 20:33:37
|
Revision: 14322
http://cdk.svn.sourceforge.net/cdk/?rev=14322&view=rev
Author: thomaskuhn
Date: 2009-03-02 20:33:24 +0000 (Mon, 02 Mar 2009)
Log Message:
-----------
Remove unit test for deleted classes
Removed Paths:
-------------
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateDensityBasedClustererModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMClusterTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanClusterTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateLinearRegressionWModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateMultilayerPerceptronModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateNaiveBayesModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateSMOModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateSMOregModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateSimpleLinearRegressionModelTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/WFilterSupervisedResampleTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/WFilterUnSupervisedRandomizeTest.java
cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/WFilterUnSupervisedResampleTest.java
Deleted: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateDensityBasedClustererModelTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateDensityBasedClustererModelTest.java 2009-03-02 20:32:21 UTC (rev 14321)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateDensityBasedClustererModelTest.java 2009-03-02 20:33:24 UTC (rev 14322)
@@ -1,220 +0,0 @@
-/*
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2006 by Mario Baseda <mar...@us...>
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-package org.openscience.cdk.applications.taverna.qsar.model.weka;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegree;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomValence;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.BondsToAtom;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.CovalentRadius;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.PiElectronegativity;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.ProtonTotalPartialCharge;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AtomCount;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.BCUT;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.Weight;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.XLogP;
-
-/**
- * TestSuite that runs a test for the GenerateDensityBasedClustererModel
- *
- * @author Mario Baseda
- * @cdk.module taverna test-qsar
- */
-public class GenerateDensityBasedClustererModelTest extends CDKTavernaTestCases{
-// CMLChemFile which contains the original data for the calculation of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List<CMLChemFile> inputList = null;
- // map for the local worker input
- private Map<String, DataThing> inputMap = null;
- // map for the local worker result
- private Map<String, DataThing> resultMap = null;
- // Lists which contains the calculated results of the local worker
- private List<CMLChemFile> resultList = null;
- private List<CMLChemFile> newResultList = null;
- // String[] contains the descriptor titles of which the descriptor values should be select
- private String[] attributs = {"org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor",
- "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.BCUT",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor"};
- // String[] contains the dependent values in the same order like the CML Chemfiles
- private String[] y = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Aromat", "Amin", "Alkan", "Alkohol", "Amin"};
- // String[] contains the possible class attributes
- private String[] classAttribs = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Amin"};
-
- /**
- * Constructor of the GenerateDensityBasedClustererModelTest
- */
- public GenerateDensityBasedClustererModelTest(){}
-
- /**
- * A unit test suite for JUnit
- *
- * @return The test suite
- */
- public static Test suite() {
- return new TestSuite(GenerateDensityBasedClustererModelTest.class);
- }
-
- /** Generate a model of the given CML Chemfiles
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public void test_LocalWorkerGenerateDensityBasedClustererModel()throws Exception {
- boolean hasAnError = false;
- GenerateDensityBasedClustererModel gdbcm = new GenerateDensityBasedClustererModel();
- gdbcm.setY(y);
- gdbcm.setClassAttributs(classAttribs);
- Map<String, DataThing> resultMap = generate(gdbcm);
-
- if (resultMap.get(gdbcm.outputNames()[0])!= null){
- List<Double> tmp = (List<Double>) ((DataThing)(resultMap.get(gdbcm.outputNames()[0]))).getDataObject();
- if (tmp.size() == 0) hasAnError = true;
- } else hasAnError = true;
- if (resultMap.get(gdbcm.outputNames()[1])!= null){
- List<List<Double>> tmp = (List<List<Double>>) ((DataThing)(resultMap.get(gdbcm.outputNames()[1]))).getDataObject();
- if (tmp.size() == 0) hasAnError = true;
- } else hasAnError = true;
- if (resultMap.get(gdbcm.outputNames()[2])!= null){
- List<Double> tmp = (List<Double>) ((DataThing)(resultMap.get(gdbcm.outputNames()[2]))).getDataObject();
- if (tmp.size() == 0) hasAnError = true;
- } else hasAnError = true;
- if (resultMap.get(gdbcm.outputNames()[3])!= null){
- List<List<Double>> tmp = (List<List<Double>>) ((DataThing)(resultMap.get(gdbcm.outputNames()[3]))).getDataObject();
- if (tmp.size() == 0) hasAnError = true;
- } else hasAnError = true;
- if (resultMap.get(gdbcm.outputNames()[4])!= null){
- List<List<Double>> tmp = (List<List<Double>>) ((DataThing)(resultMap.get(gdbcm.outputNames()[4]))).getDataObject();
- if (tmp.size() == 0) hasAnError = true;
- } else hasAnError = true;
- assertEquals(hasAnError, false);
- }
-
- /** This method lets calculate the descriptor values for the molecules
- * @param gdbcm The model which should be built
- * @return Map A Map with specific model parameters
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public Map<String, DataThing> generate(GenerateDensityBasedClustererModel gdbcm) throws Exception{
- resultMap = new HashMap<String, DataThing>();
- inputMap = new HashMap<String, DataThing>();
- AtomCount atomcount = new AtomCount();
- XLogP xLogP = new XLogP();
- AtomDegree ad = new AtomDegree();
- Weight weight = new Weight();
- BondsToAtom bondsToAtom = new BondsToAtom();
- BCUT bcut = new BCUT();
- ProtonTotalPartialCharge ptpc = new ProtonTotalPartialCharge();
- PiElectronegativity piE = new PiElectronegativity();
- AtomValence aVa = new AtomValence();
- CovalentRadius coRadius = new CovalentRadius();
- Selection selection = new Selection();
- Standardise standardise = new Standardise();
- standardise.setMinMax(0.1, 0.9);
- selection.setDescriptor(attributs);
- Map<String, Integer> cases = new HashMap<String, Integer>();
- for (int i = 0; i < attributs.length; i++){
- switch (i)
- {
- case 3: cases.put(attributs[i], 1);
- break;
- case 4: cases.put(attributs[i], 2);
- break;
- case 5: cases.put(attributs[i], 3);
- break;
- case 6: cases.put(attributs[i], 4);
- break;
- case 7: cases.put(attributs[i], 5);
- break;
- case 8: cases.put(attributs[i], 6);
- break;
- default:
- break;
- }
- }
- standardise.setCases(cases);
- inputList = new ArrayList<CMLChemFile>();
- resultList = new ArrayList<CMLChemFile>();
- newResultList = new ArrayList<CMLChemFile>();
- CDKTavernaTestData.reloadTestData();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- resultList = inputList;
- inputMap.put(atomcount.inputNames()[0], new DataThing(inputList));
- resultMap = atomcount.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(atomcount.outputNames()[0]))).getDataObject();
- inputMap.put(xLogP.inputNames()[0], new DataThing(resultList));
- resultMap = xLogP.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(xLogP.outputNames()[0]))).getDataObject();
- inputMap.put(ad.inputNames()[0], new DataThing(resultList));
- resultMap = ad.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ad.outputNames()[0]))).getDataObject();
- inputMap.put(weight.inputNames()[0], new DataThing(resultList));
- resultMap = weight.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(weight.outputNames()[0]))).getDataObject();
- inputMap.put(bondsToAtom.inputNames()[0], new DataThing(resultList));
- resultMap = bondsToAtom.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bondsToAtom.outputNames()[0]))).getDataObject();
- inputMap.put(bcut.inputNames()[0], new DataThing(resultList));
- resultMap = bcut.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bcut.outputNames()[0]))).getDataObject();
- inputMap.put(ptpc.inputNames()[0], new DataThing(resultList));
- resultMap = ptpc.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ptpc.outputNames()[0]))).getDataObject();
- inputMap.put(piE.inputNames()[0], new DataThing(resultList));
- resultMap = piE.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(piE.outputNames()[0]))).getDataObject();
- inputMap.put(aVa.inputNames()[0], new DataThing(resultList));
- resultMap = aVa.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(aVa.outputNames()[0]))).getDataObject();
- inputMap.put(coRadius.inputNames()[0], new DataThing(resultList));
- resultMap = coRadius.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(coRadius.outputNames()[0]))).getDataObject();
- inputMap.put(selection.inputNames()[0], new DataThing(resultList));
- for (int i = 0; i < resultList.size(); i++) {
- if (i%2 == 0) newResultList.add(resultList.get(i));
- }
- inputMap.put(selection.inputNames()[1], new DataThing(newResultList));
- resultMap = selection.execute(inputMap);
- resultMap = standardise.execute(resultMap);
- return gdbcm.execute(resultMap);
- }
-}
Deleted: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMClusterTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMClusterTest.java 2009-03-02 20:32:21 UTC (rev 14321)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMClusterTest.java 2009-03-02 20:33:24 UTC (rev 14322)
@@ -1,239 +0,0 @@
-/*
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2006 by Mario Baseda <mar...@us...>
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-package org.openscience.cdk.applications.taverna.qsar.model.weka;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegree;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomValence;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.BondsToAtom;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.CovalentRadius;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.PiElectronegativity;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.ProtonTotalPartialCharge;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AtomCount;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.BCUT;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.Weight;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.XLogP;
-
-/**
- * TestSuite that runs a test for the GenerateEMCluster
- *
- * @author Mario Baseda
- * @cdk.module taverna test-qsar
- */
-public class GenerateEMClusterTest extends CDKTavernaTestCases{
-// CMLChemFile which contains the original data for the calculation of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List<CMLChemFile> inputList = null;
- // map for the local worker input
- private Map<String, DataThing> inputMap = null;
- // map for the local worker result
- private Map<String, DataThing> resultMap = null;
- // List which contains the calculated results of the local worker
- private List<CMLChemFile> resultList = null;
- private List<CMLChemFile> newResultList = null;
- // String[] contains the descriptor titles of which the descriptor values should be select
- private String[] attributs = {"org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor",
- "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.BCUT",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor"};
- // String[] contains the dependent values in the same order like the CML Chemfiles
- private String[] y = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Aromat", "Amin", "Alkan", "Alkohol", "Amin"};
- // String[] contains the possible class attributes
- private String[] classAttribs = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Amin"};
-
- /**
- * Constructor of the GenerateEMClusterTest object
- *
- */
- public GenerateEMClusterTest(){}
-
- /**
- * A unit test suite for JUnit
- *
- * @return The test suite
- */
- public static Test suite() {
- return new TestSuite(GenerateEMClusterTest.class);
- }
-
- /** Generate a cluster of the given CMLChemfiles
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public void test_LocalWorkerGenerateEMCluster()throws Exception {
- boolean hasAnError = false;
- GenerateEMCluster gemc = new GenerateEMCluster();
- gemc.setClassAttributs(classAttribs);
- gemc.setY(y);
- gemc.setOptions(new String[]{"M", "0.0001"});
- Map<String, DataThing> resultMap = generate(gemc);
-
- if ((resultMap.get(gemc.outputNames()[2]) == null) || ((Double)((List)((DataThing)(resultMap.get(gemc.outputNames()[2]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if ((resultMap.get(gemc.outputNames()[5]) == null) || ((Double)((List)((DataThing)(resultMap.get(gemc.outputNames()[5]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if ((resultMap.get(gemc.outputNames()[6]) == null) || ((Double)((List)((DataThing)(resultMap.get(gemc.outputNames()[6]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if ((resultMap.get(gemc.outputNames()[7]) == null) || ((Double)((List)((DataThing)(resultMap.get(gemc.outputNames()[7]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if ((resultMap.get(gemc.outputNames()[8]) == null) || ((Double)((List)((DataThing)(resultMap.get(gemc.outputNames()[8]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if (resultMap.get(gemc.outputNames()[3]) != null){
- List<Double> clusterSizes = (List<Double>) ((DataThing)(resultMap.get(gemc.outputNames()[3]))).getDataObject();
- for (Double element : clusterSizes) {
- if (element.isNaN()) hasAnError = true;
- }
- } else hasAnError = true;
- if (resultMap.get(gemc.outputNames()[4]) != null){
- List<Double> clusterSizes = (List<Double>) ((DataThing)(resultMap.get(gemc.outputNames()[4]))).getDataObject();
- for (Double element : clusterSizes) {
- if (element.isNaN()) hasAnError = true;
- }
- } else hasAnError = true;
- if (resultMap.get(gemc.outputNames()[0]) != null){
- List<List<List<Double>>> list = (List<List<List<Double>>>)((DataThing)(resultMap.get(gemc.outputNames()[0]))).getDataObject();
- for (List<List<Double>> list2 : list) {
- for (List<Double> list3 : list2) {
- for (Double elem : list3) {
- if (elem.isNaN()) hasAnError = true;
- }
- }
- }
- } else hasAnError = true;
- if (resultMap.get(gemc.outputNames()[1]) != null){
- List<List<Double>> Stds = (List<List<Double>>)((DataThing)(resultMap.get(gemc.outputNames()[1]))).getDataObject();
- for (List<Double> list : Stds) {
- for (Double elem : list) {
- if (elem.isNaN()) hasAnError = true;
- }
- }
- } else hasAnError = true;
- assertEquals(hasAnError, false);
-
- }
- /** This method lets calculate the descriptor values of the molecules
- * @param gemc The cluster which should be built
- * @return Map A Map with specific parameters for the built model
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public Map<String, DataThing> generate(GenerateEMCluster gemc) throws Exception{
- resultMap = new HashMap<String, DataThing>();
- inputMap = new HashMap<String, DataThing>();
- AtomCount atomcount = new AtomCount();
- XLogP xLogP = new XLogP();
- AtomDegree ad = new AtomDegree();
- Weight weight = new Weight();
- BondsToAtom bondsToAtom = new BondsToAtom();
- BCUT bcut = new BCUT();
- ProtonTotalPartialCharge ptpc = new ProtonTotalPartialCharge();
- PiElectronegativity piE = new PiElectronegativity();
-// PartialTChargePEOE pTC = new PartialTChargePEOE();
- AtomValence aVa = new AtomValence();
- CovalentRadius coRadius = new CovalentRadius();
- Selection selection = new Selection();
- Standardise standardise = new Standardise();
- standardise.setMinMax(0.1, 0.9);
- selection.setDescriptor(attributs);
- Map<String, Integer> cases = new HashMap<String, Integer>();
- for (int i = 0; i < attributs.length; i++){
- switch (i)
- {
- case 3: cases.put(attributs[i], 1);
- break;
- case 4: cases.put(attributs[i], 2);
- break;
- case 5: cases.put(attributs[i], 3);
- break;
- case 6: cases.put(attributs[i], 4);
- break;
- case 7: cases.put(attributs[i], 5);
- break;
- case 8: cases.put(attributs[i], 6);
- break;
- default:
- break;
- }
- }
- standardise.setCases(cases);
- inputList = new ArrayList<CMLChemFile>();
- newResultList = new ArrayList<CMLChemFile>();
- resultList = new ArrayList<CMLChemFile>();
- CDKTavernaTestData.reloadTestData();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- resultList = inputList;
- inputMap.put(atomcount.inputNames()[0], new DataThing(inputList));
- resultMap = atomcount.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(atomcount.outputNames()[0]))).getDataObject();
- inputMap.put(xLogP.inputNames()[0], new DataThing(resultList));
- resultMap = xLogP.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(xLogP.outputNames()[0]))).getDataObject();
- inputMap.put(ad.inputNames()[0], new DataThing(resultList));
- resultMap = ad.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ad.outputNames()[0]))).getDataObject();
- inputMap.put(weight.inputNames()[0], new DataThing(resultList));
- resultMap = weight.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(weight.outputNames()[0]))).getDataObject();
- inputMap.put(bondsToAtom.inputNames()[0], new DataThing(resultList));
- resultMap = bondsToAtom.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bondsToAtom.outputNames()[0]))).getDataObject();
- inputMap.put(bcut.inputNames()[0], new DataThing(resultList));
- resultMap = bcut.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bcut.outputNames()[0]))).getDataObject();
- inputMap.put(ptpc.inputNames()[0], new DataThing(resultList));
- resultMap = ptpc.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ptpc.outputNames()[0]))).getDataObject();
- inputMap.put(piE.inputNames()[0], new DataThing(resultList));
- resultMap = piE.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(piE.outputNames()[0]))).getDataObject();
- inputMap.put(aVa.inputNames()[0], new DataThing(resultList));
- resultMap = aVa.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(aVa.outputNames()[0]))).getDataObject();
- inputMap.put(coRadius.inputNames()[0], new DataThing(resultList));
- resultMap = coRadius.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(coRadius.outputNames()[0]))).getDataObject();
- //////////////////////////////////////////////////////////////////////
- inputMap.put(selection.inputNames()[0], new DataThing(resultList));
- for (int i = 0; i < resultList.size(); i++) {
- if (i%2 == 0) newResultList.add(resultList.get(i));
- }
- inputMap.put(selection.inputNames()[1], new DataThing(newResultList));
- resultMap = selection.execute(inputMap);
- resultMap = standardise.execute(resultMap);
- return gemc.execute(resultMap);
- }
-}
Deleted: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModelTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModelTest.java 2009-03-02 20:32:21 UTC (rev 14321)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModelTest.java 2009-03-02 20:33:24 UTC (rev 14322)
@@ -1,231 +0,0 @@
-/*
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2006 by Mario Baseda <mar...@us...>
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-package org.openscience.cdk.applications.taverna.qsar.model.weka;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegree;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomValence;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.BondsToAtom;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.CovalentRadius;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.PiElectronegativity;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.ProtonTotalPartialCharge;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AtomCount;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.BCUT;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.Weight;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.XLogP;
-
-/**
- * TestSuite that runs a test for the GenerateJ48WModel
- *
- * @author Mario Baseda
- * @cdk.module taverna test-qsar
- */
-public class GenerateJ48WModelTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculation of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List<CMLChemFile> inputList = null;
- // map for the local worker input
- private Map<String, DataThing> inputMap = null;
- // map for the local worker result
- private Map<String, DataThing> resultMap = null;
- // Lists which contains the calculated results of the local worker
- private List<CMLChemFile> resultList = null;
- private List<CMLChemFile> newResultList = null;
- // String[] contains the descriptor titles of which the descriptor values should be select
- private String[] attributs = {"org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor",
- "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.BCUT",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor"};
- // String[] contains the dependent values in the same order like the CML Chemfiles
- private String[] y = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Aromat", "Amin", "Alkan", "Alkohol", "Amin"};
- // String[] contains the possible class attributes
- private String[] classAttribs = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Amin"};
- /**
- * Constructor of the GenerateJ48WModelTest
- */
- public GenerateJ48WModelTest() {}
-
- /**
- * A unit test suite for JUnit
- *
- * @return The test suite
- */
- public static Test suite() {
- return new TestSuite(GenerateJ48WModelTest.class);
- }
-
- /** Generate a model of the given CML Chemfiles
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public void test_LocalWorkerGenerateJ48WModel_Default()throws Exception {
- boolean hasAnError = false;
- GenerateJ48WModel j48w = new GenerateJ48WModel();
- j48w.setY(y);
- j48w.setClassAttributs(classAttribs);
- j48w.setOptions(new String[] {"-U", "-A", "-M", "2","B","-L","-Q","2"});
- Map<String, DataThing> resultMap_D = generate(j48w);
-
- if (resultMap_D.get(j48w.outputNames()[0])!= null){
- List<String> tmp = (List<String>) ((DataThing)resultMap_D.get(j48w.outputNames()[0])).getDataObject();
- for (int i = 0; i < tmp.size(); i++) {
- switch (i)
- {
- case 0: if ((String)tmp.get(i) != "Alkan") hasAnError = true;
- break;
- case 1: if ((String)tmp.get(i) != "Alkohol") hasAnError = true;
- break;
-// case 2: if ((String)tmp.get(i) != "Ether") hasAnError = true;
-// break;
- case 3: if ((String)tmp.get(i) != "Aromat") hasAnError = true;
- break;
-// case 4: if ((String)tmp.get(i) != "Alken") hasAnError = true;
-// break;
- case 5: if ((String)tmp.get(i) != "Aromat") hasAnError = true;
- break;
- case 6: if ((String)tmp.get(i) != "Amin") hasAnError = true;
- break;
- case 7: if ((String)tmp.get(i) != "Alkan") hasAnError = true;
- break;
- case 8: if ((String)tmp.get(i) != "Alkohol") hasAnError = true;
- break;
- case 9: if ((String)tmp.get(i) != "Amin") hasAnError = true;
- break;
- default:
- break;
- }
- }
- }
- assertEquals(hasAnError, false);
- }
- /** This method lets calculate the descriptor values for the molecules
- * @param j48w The model which should be built
- * @return Map A Map with predicted dependent values
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public Map<String, DataThing> generate(GenerateJ48WModel j48w) throws Exception{
- resultMap = new HashMap<String, DataThing>();
- inputMap = new HashMap<String, DataThing>();
- AtomCount atomcount = new AtomCount();
- XLogP xLogP = new XLogP();
- AtomDegree ad = new AtomDegree();
- Weight weight = new Weight();
- BondsToAtom bondsToAtom = new BondsToAtom();
- BCUT bcut = new BCUT();
- ProtonTotalPartialCharge ptpc = new ProtonTotalPartialCharge();
- PiElectronegativity piE = new PiElectronegativity();
- AtomValence aVa = new AtomValence();
- CovalentRadius coRadius = new CovalentRadius();
- Selection selection = new Selection();
- Standardise standardise = new Standardise();
- standardise.setMinMax(0.1, 0.9);
- selection.setDescriptor(attributs);
- Map<String, Integer> cases = new HashMap<String, Integer>();
- for (int i = 0; i < attributs.length; i++){
- switch (i)
- {
- case 3: cases.put(attributs[i], 1);
- break;
- case 4: cases.put(attributs[i], 2);
- break;
- case 5: cases.put(attributs[i], 3);
- break;
- case 6: cases.put(attributs[i], 4);
- break;
- case 7: cases.put(attributs[i], 5);
- break;
- case 8: cases.put(attributs[i], 6);
- break;
- default:
- break;
- }
- }
- standardise.setCases(cases);
- inputList = new ArrayList<CMLChemFile>();
- resultList = new ArrayList<CMLChemFile>();
- newResultList = new ArrayList<CMLChemFile>();
- CDKTavernaTestData.reloadTestData();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- resultList = inputList;
- inputMap.put(atomcount.inputNames()[0], new DataThing(inputList));
- resultMap = atomcount.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(atomcount.outputNames()[0]))).getDataObject();
- inputMap.put(xLogP.inputNames()[0], new DataThing(resultList));
- resultMap = xLogP.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(xLogP.outputNames()[0]))).getDataObject();
- inputMap.put(ad.inputNames()[0], new DataThing(resultList));
- resultMap = ad.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ad.outputNames()[0]))).getDataObject();
- inputMap.put(weight.inputNames()[0], new DataThing(resultList));
- resultMap = weight.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(weight.outputNames()[0]))).getDataObject();
- inputMap.put(bondsToAtom.inputNames()[0], new DataThing(resultList));
- resultMap = bondsToAtom.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bondsToAtom.outputNames()[0]))).getDataObject();
- inputMap.put(bcut.inputNames()[0], new DataThing(resultList));
- resultMap = bcut.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bcut.outputNames()[0]))).getDataObject();
- inputMap.put(ptpc.inputNames()[0], new DataThing(resultList));
- resultMap = ptpc.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ptpc.outputNames()[0]))).getDataObject();
- inputMap.put(piE.inputNames()[0], new DataThing(resultList));
- resultMap = piE.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(piE.outputNames()[0]))).getDataObject();
- inputMap.put(aVa.inputNames()[0], new DataThing(resultList));
- resultMap = aVa.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(aVa.outputNames()[0]))).getDataObject();
- inputMap.put(coRadius.inputNames()[0], new DataThing(resultList));
- resultMap = coRadius.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(coRadius.outputNames()[0]))).getDataObject();
- //////////////////////////////////////////////////////////////////////////////////
- inputMap.put(selection.inputNames()[0], new DataThing(resultList));
-// for (int i = 0; i < resultList.size(); i++) {
-// if (i%2 == 0) newResultList.add(resultList.get(i));
-// }
- newResultList.addAll(resultList);
- inputMap.put(selection.inputNames()[1], new DataThing(newResultList));
- resultMap = selection.execute(inputMap);
- resultMap = standardise.execute(resultMap);
- return j48w.execute(resultMap);
- }
-}
Deleted: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanClusterTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanClusterTest.java 2009-03-02 20:32:21 UTC (rev 14321)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanClusterTest.java 2009-03-02 20:33:24 UTC (rev 14322)
@@ -1,325 +0,0 @@
-/*
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2006 by Mario Baseda <mar...@us...>
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-
-package org.openscience.cdk.applications.taverna.qsar.model.weka;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomDegree;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.AtomValence;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.BondsToAtom;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.CovalentRadius;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.PiElectronegativity;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.atomic.ProtonTotalPartialCharge;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AtomCount;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.BCUT;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.Weight;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.XLogP;
-
-
-/**
- * TestSuite that runs a test for the GenerateKmeanCluster
- *
- * @author Mario Baseda
- * @cdk.module taverna test-qsar
- */
-@SuppressWarnings("unchecked")
-public class GenerateKMeanClusterTest extends CDKTavernaTestCases {
-// CMLChemFile which contains the original data for the calculation of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List<CMLChemFile> inputList = null;
- // map for the local worker input
- private Map<String, DataThing> inputMap = null;
- // map for the local worker result
- private Map<String, DataThing> resultMap = null;
- // List which contains the calculated results of the local worker
- private List<CMLChemFile> resultList = null;
- private List<CMLChemFile> newResultList = null;
-// String[] contains the descriptor titles of which the descriptor values should be select
- private String[] attributs = {"org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor",
- "org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor", "org.openscience.cdk.qsar.descriptors.molecular.BCUT",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomDegreeDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.PiElectronegativityDescriptor",
- "org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor", "org.openscience.cdk.qsar.descriptors.atomic.CovalentRadiusDescriptor"};
-// String[] contains the dependent values in the same order like the CML Chemfiles
- private String[] y = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Aromat", "Amin", "Alkan", "Alkohol", "Amin"};
- // String[] contains the possible class attributes
- private String[] classAttribs = {"Alkan", "Alkohol", "Ether", "Aromat", "Alken", "Amin"};
-
- /**
- * Constructor of the GenerateKmeanClusterTest
- */
- public GenerateKMeanClusterTest() {}
-
- /**
- * A unit test suite for JUnit
- *
- * @return The test suite
- */
- public static Test suite() {
- return new TestSuite(GenerateKMeanClusterTest.class);
- }
-
- /** Generate a k mean cluster without set the options and so as default
- * @throws Exception
- */
- public void test_LocalWorkerGenerateKMeanCluster_Default()throws Exception {
- boolean hasAnError = false;
- GenerateKMeanCluster kMean_D = new GenerateKMeanCluster();
- kMean_D.setClassAttributs(classAttribs);
- kMean_D.setY(y);
- Map<String, DataThing> resultMap_D = generate(kMean_D);
- if ((resultMap_D.get(kMean_D.outputNames()[0]) == null) || ((Integer)((List<Integer>)((DataThing)(resultMap_D.get(kMean_D.outputNames()[0]))).getDataObject()).get(0))== 0) hasAnError = true;
- if ((resultMap_D.get(kMean_D.outputNames()[1]) == null) || ((Double) ((List<Double>)((DataThing)(resultMap_D.get(kMean_D.outputNames()[1]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if (resultMap_D.get(kMean_D.outputNames()[2]) != null){
- List<Double> clusterSizes = (List<Double>) ((DataThing)(resultMap_D.get(kMean_D.outputNames()[2]))).getDataObject();
- for (Double element : clusterSizes) {
- if (element.isNaN()) hasAnError = true;
- }
- } else hasAnError = true;
- if (resultMap_D.get(kMean_D.outputNames()[3]) != null){
- List<List<Double>> centroids = (List<List<Double>>)((DataThing)(resultMap_D.get(kMean_D.outputNames()[3]))).getDataObject();
- for (List<Double> list : centroids) {
- for (Double elem : list) {
- if (elem.isNaN()) hasAnError = true;
- }
- }
- } else hasAnError = true;
- if (resultMap_D.get(kMean_D.outputNames()[4]) != null){
- List<List<Double>> Stds = (List<List<Double>>)((DataThing)(resultMap_D.get(kMean_D.outputNames()[4]))).getDataObject();
- for (List<Double> list2 : Stds) {
- int i = 0;
- for (Double elem : list2) {
- if (i < 9){ if (elem.isNaN()) hasAnError = true;
- i++;
- }
- }
- }
- } else hasAnError = true;
- if (resultMap_D.get(kMean_D.outputNames()[5]) != null){
- List<Double> list = (List<Double>) ((DataThing)(resultMap_D.get(kMean_D.outputNames()[5]))).getDataObject();
- for (Double element : list) {
- if (element.isNaN()) hasAnError = true;
- }
- } else hasAnError = true;
- assertEquals(hasAnError, false);
- }
-
- /** Generate a k mean cluster with the set of the options to build 3 clusters
- * @throws Exception
- */
- public void test_LocalWorkerGenerateKMeanCluster_N()throws Exception {
- boolean hasAnError = false;
- GenerateKMeanCluster kMean_N = new GenerateKMeanCluster();
- kMean_N.setClassAttributs(classAttribs);
- kMean_N.setY(y);
- kMean_N.setOptions(new String[]{"-N", "3"});
- Map<String, DataThing> resultMap_N = generate(kMean_N);
- if ((resultMap_N.get(kMean_N.outputNames()[0]) == null) || ((Integer)((List<Integer>)((DataThing)(resultMap_N.get(kMean_N.outputNames()[0]))).getDataObject()).get(0)!= 3)) hasAnError = true;
- if ((resultMap_N.get(kMean_N.outputNames()[1]) == null) || ((Double) ((List<Double>)((DataThing)(resultMap_N.get(kMean_N.outputNames()[1]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if (resultMap_N.get(kMean_N.outputNames()[2]) != null){
- List<Double> clusterSizes = (List<Double>) ((DataThing)(resultMap_N.get(kMean_N.outputNames()[2]))).getDataObject();
- for (Double element : clusterSizes) {
- if (element == 0) hasAnError = true;
- }
- } else hasAnError = true;
- if (resultMap_N.get(kMean_N.outputNames()[3]) != null){
- List<List<Double>> centroids = (List<List<Double>>)((DataThing)(resultMap_N.get(kMean_N.outputNames()[3]))).getDataObject();
- for (List<Double> list : centroids) {
- for (Double elem : list) {
- if (elem.isNaN()) hasAnError = true;
- }
- }
- } else hasAnError = true;
- if (resultMap_N.get(kMean_N.outputNames()[4]) != null){
- List<List<Double>> Stds = (List<List<Double>>)((DataThing)(resultMap_N.get(kMean_N.outputNames()[4]))).getDataObject();
- for (List<Double> list2 : Stds) {
- int i = 0;
- for (Double elem : list2) {
- if (i < 9){ if (elem.isNaN()) hasAnError = true;
- i++;
- }
- }
- }
- } else hasAnError = true;
- if (resultMap_N.get(kMean_N.outputNames()[5]) != null){
- List<Double> list = (List<Double>) ((DataThing)(resultMap_N.get(kMean_N.outputNames()[5]))).getDataObject();
- for (Double element : list) {
- if (element.isNaN()) hasAnError = true;
- }
- } else hasAnError = true;
- assertEquals(hasAnError, false);
- }
-
- /** Generate a k mean cluster with the set of the options to S
- * @throws Exception
- */
- public void test_LocalWorkerGenerateKMeanCluster_S()throws Exception {
- boolean hasAnError = false;
- GenerateKMeanCluster kMean_S = new GenerateKMeanCluster();
- kMean_S.setClassAttributs(classAttribs);
- kMean_S.setY(y);
- kMean_S.setOptions(new String[]{"-S", "10"});
- Map<String, DataThing> resultMap_S = generate(kMean_S);
- if ((resultMap_S.get(kMean_S.outputNames()[0]) == null) || ((Integer)((List)((DataThing)(resultMap_S.get(kMean_S.outputNames()[0]))).getDataObject()).get(0)== 0)) hasAnError = true;
- if ((resultMap_S.get(kMean_S.outputNames()[1]) == null) || ((Double) ((List)((DataThing)(resultMap_S.get(kMean_S.outputNames()[1]))).getDataObject()).get(0)).isNaN()) hasAnError = true;
- if (resultMap_S.get(kMean_S.outputNames()[2]) != null){
- List<Double> clusterSizes = (List<Double>) ((DataThing)(resultMap_S.get(kMean_S.outputNames()[2]))).getDataObject();
- for (Double element : clusterSizes) {
- if (element == 0) hasAnError = true;
- }
- } else hasAnError = true;
- if (resultMap_S.get(kMean_S.outputNames()[3]) != null){
- List<List<Double>> centroids = (List<List<Double>>)((DataThing)(resultMap_S.get(kMean_S.outputNames()[3]))).getDataObject();
- for (List<Double> list : centroids) {
- for (Double elem : list) {
- if (elem.isNaN()) hasAnError = true;
- }
- }
- } else hasAnError = true;
- if (resultMap_S.get(kMean_S.outputNames()[4]) != null){
- List<List<Double>> Stds = (List<List<Double>>)((DataThing)(resultMap_S.get(kMean_S.outputNames()[4]))).getDataObject();
- for (List<Double> list2 : Stds) {
- int i = 0;
- for (Double elem : list2) {
- if (i < 9){ if (elem.isNaN()) hasAnError = true;
- i++;
- }
- }
- }
- } else hasAnError = true;
- if (resultMap_S.get(kMean_S.outputNames()[5]) != null){
- List<Double> list = (List<Double>) ((DataThing)(resultMap_S.get(kMean_S.outputNames()[5]))).getDataObject();
- for (Double element : list) {
- if (element.isNaN()) hasAnError = true;
- }
- } else hasAnError = true;
- assertEquals(hasAnError, false);
- }
-
- /** This method lets calculate the descriptor values for the molecules
- * @param kMean The k mean cluster which should be build
- * @return A Map with molecules, each of them has calculated descriptor values
- * @throws Exception
- */
- public Map<String, DataThing> generate(GenerateKMeanCluster kMean) throws Exception{
- resultMap = new HashMap<String, DataThing>();
- inputMap = new HashMap<String, DataThing>();
- AtomCount atomcount = new AtomCount();
- XLogP xLogP = new XLogP();
- AtomDegree ad = new AtomDegree();
- Weight weight = new Weight();
- BondsToAtom bondsToAtom = new BondsToAtom();
- BCUT bcut = new BCUT();
- ProtonTotalPartialCharge ptpc = new ProtonTotalPartialCharge();
- PiElectronegativity piE = new PiElectronegativity();
- AtomValence aVa = new AtomValence();
- CovalentRadius coRadius = new CovalentRadius();
- Selection selection = new Selection();
- Standardise standardise = new Standardise();
- standardise.setMinMax(0.1, 0.9);
- selection.setDescriptor(attributs);
- Map<String, Integer> cases = new HashMap<String, Integer>();
- for (int i = 0; i < attributs.length; i++){
- switch (i)
- {
- case 3: cases.put(attributs[i], 1);
- break;
- case 4: cases.put(attributs[i], 2);
- break;
- case 5: cases.put(attributs[i], 3);
- break;
- case 6: cases.put(attributs[i], 4);
- break;
- case 7: cases.put(attributs[i], 5);
- break;
- case 8: cases.put(attributs[i], 6);
- break;
- default:
- break;
- }
- }
- standardise.setCases(cases);
- inputList = new ArrayList<CMLChemFile>();
- resultList = new ArrayList<CMLChemFile>();
- newResultList = new ArrayList<CMLChemFile>();
- CDKTavernaTestData.reloadTestData();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- resultList = inputList;
- inputMap.put(atomcount.inputNames()[0], new DataThing(inputList));
- resultMap = atomcount.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(atomcount.outputNames()[0]))).getDataObject();
- inputMap.put(xLogP.inputNames()[0], new DataThing(resultList));
- resultMap = xLogP.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(xLogP.outputNames()[0]))).getDataObject();
- inputMap.put(ad.inputNames()[0], new DataThing(resultList));
- resultMap = ad.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ad.outputNames()[0]))).getDataObject();
- inputMap.put(weight.inputNames()[0], new DataThing(resultList));
- resultMap = weight.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(weight.outputNames()[0]))).getDataObject();
- inputMap.put(bondsToAtom.inputNames()[0], new DataThing(resultList));
- resultMap = bondsToAtom.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bondsToAtom.outputNames()[0]))).getDataObject();
- inputMap.put(bcut.inputNames()[0], new DataThing(resultList));
- resultMap = bcut.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bcut.outputNames()[0]))).getDataObject();
- inputMap.put(ptpc.inputNames()[0], new DataThing(resultList));
- resultMap = ptpc.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(ptpc.outputNames()[0]))).getDataObject();
- inputMap.put(piE.inputNames()[0], new DataThing(resultList));
- resultMap = piE.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(piE.outputNames()[0]))).getDataObject();
- inputMap.put(aVa.inputNames()[0], new DataThing(resultList));
- resultMap = aVa.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(aVa.outputNames()[0]))).getDataObject();
- inputMap.put(coRadius.inputNames()[0], new DataThing(resultList));
- resultMap = coRadius.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(coRadius.outputNames()[0]))).getDataObject();
- inputMap.put(selection.inputNames()[0], new DataThing(resultList));
- for (int i = 0; i < resultList.size(); i++) {
- if (i%2 == 0) newResultList.add(resultList.get(i));
- }
- inputMap.put(selection.inputNames()[1], new DataThing(newResultList));
- resultMap = selection.execute(inputMap);
- resultMap = standardise.execute(resultMap);
- return kMean.execute(resultMap);
- }
-}
Deleted: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateLinearRegressionWModelTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateLinearRegressionWModelTest.java 2009-03-02 20:32:21 UTC (rev 14321)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateLinearRegressionWModelTest.java 2009-03-02 20:33:24 UTC (rev 14322)
@@ -1,147 +0,0 @@
-/*
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2006 by Mario Baseda <mar...@us...>
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All we ask is that proper credit is given for our work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- */
-package org.openscience.cdk.applications.taverna.qsar.model.weka;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import junit.framework.Test;
-import junit.framework.TestSuite;
-
-import org.embl.ebi.escience.baclava.DataThing;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestCases;
-import org.openscience.cdk.applications.taverna.CDKTavernaTestData;
-import org.openscience.cdk.applications.taverna.CMLChemFile;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.AtomCount;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.BCUT;
-import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.Weight;
-
-/**
- * TestSuite that runs a test for the GenerateLinearRegressionWModel
- *
- * @author Mario Baseda
- * @cdk.module taverna test-qsar
- */
-public class GenerateLinearRegressionWModelTest extends CDKTavernaTestCases {
- // CMLChemFile which contains the original data for the calculation of the descriptors
- private CMLChemFile[] originalData = null;
- // inputList which contains a list of the input data for the local workers
- private List<CMLChemFile> inputList = null;
- // map for the local worker input
- private Map<String, DataThing> inputMap = null;
- // map for the local worker result
- private Map<String, DataThing> resultMap = null;
- // Lists which contains the calculated results of the local worker
- private List<CMLChemFile> resultList = null;
- private List<CMLChemFile> newResultList = null;
- // String[] contains the descriptor titles of which the descriptor values should be select
- private String[] attributs = {"org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptor","org.openscience.cdk.qsar.descriptors.molecular.BCUT",
- "org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor"};
- private String[] yAttributs = {"org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor"};
-
- /**
- * Constructor of the GenerateLinearRegressionWModelTest object
- *
- */
- public GenerateLinearRegressionWModelTest(){}
-
- /**
- * A unit test suite for JUnit
- *
- * @return The test suite
- */
- public static Test suite() {
- return new TestSuite(GenerateLinearRegressionWModelTest.class);
- }
-
- /** Generate a model of the given CML Chemfiles
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public void test_LocalWorkerGenerateLinearRegressionWModel()throws Exception {
- boolean hasAnError = false;
- GenerateLinearRegressionWModel glrwm = new GenerateLinearRegressionWModel();
-// glrwm.setOptions(new String[] {"-R", "1.0e-8"});
- Map<String, DataThing> resultMap_D = generate(glrwm);
- if (resultMap_D.get(glrwm.outputNames()[0])!= null){
- List<Double> tmp = (List<Double>) ((DataThing)resultMap_D.get(glrwm.outputNames()[0])).getDataObject();
- if (tmp.size() != 5) hasAnError = true;
- } else hasAnError = true;
- assertEquals(hasAnError, false);
- }
-
- /** This method lets calculate the descriptor values for the molecules
- * @param glrwm The model which should be built
- * @return Map A Map with predicted dependent values
- * @throws Exception
- */
- @SuppressWarnings("unchecked")
- public Map<String, DataThing> generate(GenerateLinearRegressionWModel glrwm) throws Exception{
- resultMap = new HashMap<String, DataThing>();
- inputMap = new HashMap<String, DataThing>();
- AtomCount atomcount = new AtomCount();
- Weight weight = new Weight();
- BCUT bcut = new BCUT();
- Selection selection = new Selection();
- Standardise standardise = new Standardise();
- selection.setDescriptor(attributs);
- selection.setDependent(yAttributs);
- Map<String, Integer> cases = new HashMap<String, Integer>();
- cases.put(attributs[1], 5);
- standardise.setCases(cases);
- inputList = new ArrayList<CMLChemFile>();
- resultList = new ArrayList<CMLChemFile>();
- newResultList = new ArrayList<CMLChemFile>();
- CDKTavernaTestData.reloadTestData();
- originalData = CDKTavernaTestData.getCMLChemFile();
- for (int i = 0; i < originalData.length; i++) {
- inputList.add(originalData[i]);
- }
- resultList = inputList;
- inputMap.put(atomcount.inputNames()[0], new DataThing(inputList));
- resultMap = atomcount.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(atomcount.outputNames()[0]))).getDataObject();
- inputMap.put(weight.inputNames()[0], new DataThing(resultList));
- resultMap = weight.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(weight.outputNames()[0]))).getDataObject();
- inputMap.put(bcut.inputNames()[0], new DataThing (resultList));
- resultMap = bcut.execute(inputMap);
- resultList = (List<CMLChemFile>)((DataThing)(resultMap.get(bcut.outputNames()[0]))).getDataObject();
- inputMap.put(selection.inputNames()[0], new DataThing(resultList));
- for (int i = 0; i < resultList.size(); i++) {
- if (i%2 == 0) newResultList.add(resultList.get(i));
- }
- inputMap.put(selection.inputNames()[1], new DataThing(newResultList));
-// List list = new ArrayList();
-// list.add("org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor");
-// inputMap.put(glrwm.inputNames()[2], new DataThing(list));
- resultMap = selection.execute(inputMap);
- resultMap = standardise.execute(resultMap);
- return glrwm.execute(resultMap);
- }
-}
Deleted: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateMultilayerPerceptronModelTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/open...
[truncated message content] |