Package edu.msu.cme.rdp.classifier

Examples of edu.msu.cme.rdp.classifier.TrainingInfo

98
99
100
101
102
103
104
105
106
107
108
    public synchronized static ClassifierFactory getFactory(String gene) throws IOException, TrainingDataException {
        if (!classifierFactoryMap.containsKey(gene)) {

            if (relativePath) {
                ClassifierFactory factory = new ClassifierFactory(gene);
                factory.trainingInfo = new TrainingInfo();

                InputStreamReader in = new InputStreamReader(ClassifierFactory.class.getResourceAsStream(dataDir + gene + "/" + convert("probabilityList")));
    try {
        factory.trainingInfo.createGenusWordProbList(in);
    } finally {
View Full Code Here
147
148
149
150
151
152
153
154
155
156
157
     * Returns a factory with the training information for the non-default training data files.
     */
    private static ClassifierFactory getNonDefaultFactory(String gene) throws IOException, TrainingDataException {
        if (classifierFactoryMap.get(gene) == null) {
            ClassifierFactory factory = new ClassifierFactory(gene);
            factory.trainingInfo = new TrainingInfo();
            String filename = parentPath + File.separatorChar + convert("probabilityList");

            FileReader in = new FileReader(filename);
            factory.trainingInfo.createGenusWordProbList(in);
            // the tree information has to be read after at least one of the other
View Full Code Here
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
    public void testCreateLogWordPriorArr() throws Exception{
        System.out.println("testCreateLogWordPriorArr");
        InputStream dstream = System.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt");
        Reader in =  new InputStreamReader( dstream );
       
        TrainingInfo train = new TrainingInfo();
        train.createLogWordPriorArr(in);
        float wordPrior = train.getLogWordPrior(10);
        assertEquals(wordPrior, -2.77, 0.1);
        wordPrior = train.getLogWordPrior(55);
        assertEquals(wordPrior, -1.67, 0.1);
       
        // test getWordPairPriorDiff()
        wordPrior = train.getLogWordPrior(24573);
        assertEquals(wordPrior, -2.77, 0.01);
        float revWordPrior = train.getLogWordPrior(10912);
        assertEquals(revWordPrior, -1.67, 0.01);       
       
        float wordPriorDiff = train.getWordPairPriorDiff(24573);
        assertEquals(wordPriorDiff, (wordPrior - revWordPrior), 0.01);
        float revWordPriorDiff = train.getWordPairPriorDiff(10912);
        assertEquals(revWordPriorDiff, (revWordPrior - wordPrior), 0.01);
        assertEquals( (wordPriorDiff + revWordPriorDiff), 0, 0.01);
       
    }
View Full Code Here
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
    /** Test of createGenusWordProbLis method, of class classification.TrainingInfo. */
    public void testCreateGenusWordProbList() throws Exception{
        System.out.println("testCreateGenusWordConditionalProbList");
        InputStream dstream = System.class.getResourceAsStream("/test/classifier/testGenus_probList.txt");
        Reader in =  new InputStreamReader( dstream );
        TrainingInfo train = new TrainingInfo();
        train.createGenusWordProbList(in);
        GenusWordConditionalProb gProb = train.getWordConditionalProbObject(8);
        int genusIndex = gProb.getGenusIndex();
        float prob = gProb.getProbability();
        assertEquals(genusIndex, 4);
        assertEquals(prob, -0.15, 0.1);
       
        gProb = train.getWordConditionalProbObject(1865);
        genusIndex = gProb.getGenusIndex();
        prob = gProb.getProbability();
        assertEquals(genusIndex, 0);
        assertEquals(prob, -0.5, 0.1);
       
View Full Code Here
104
105
106
107
108
109
110
111
112
113
114
115
116
    /** Test of makeProbIndexArr method, of class classification.TrainingInfo. */
    public void testCreateProbIndexArr() throws Exception {
        System.out.println("testCreateProbIndexArr");
        InputStream dstream = System.class.getResourceAsStream("/test/classifier/testProbIndex.txt");
        Reader in =  new InputStreamReader( dstream );
        TrainingInfo train = new TrainingInfo();
        train.createProbIndexArr(in);
        int start = train.getStartIndex(100);
        int stop = train.getStopIndex(65535);
        assertEquals(start, 1);
        assertEquals(stop, 1866);
       
    }
View Full Code Here
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
    }
   
    /** Test of getRootTree method, of class classification.TrainingInfo. */
    public void testCreateClassifier() throws Exception{
        System.out.println("testCreateClassifier");
        TrainingInfo train = new TrainingInfo();
       
        InputStream dstream = System.class.getResourceAsStream("/test/classifier/testGenus_probList.txt");
        Reader in =  new InputStreamReader( dstream );
        train.createGenusWordProbList(in);
       
        dstream = System.class.getResourceAsStream("/test/classifier/test_bergeyTrainingTree.xml");
        in =  new InputStreamReader( dstream );
        train.createTree(in);
       
        dstream = System.class.getResourceAsStream("/test/classifier/testProbIndex.txt");
        in =  new InputStreamReader( dstream );
        train.createProbIndexArr(in);
       
        dstream = System.class.getResourceAsStream("/test/classifier/testLogWordPrior.txt");
        in =  new InputStreamReader( dstream );
        train.createLogWordPriorArr(in);
       
        int genusNodeListSize = train.getGenusNodeListSize();
        assertEquals(genusNodeListSize, 6);
       
        HierarchyTree genusNode = train.getGenusNodebyIndex(3);
        assertEquals(genusNode.getGenusIndex(), 3);
        assertEquals(genusNode.getName(), "Pseudomonas");
        int leaveCount = genusNode.getLeaveCount();
        float logLeaveCount = train.getLogLeaveCount(1);
        assertEquals((double)leaveCount, Math.exp(logLeaveCount) -1, 0.1);
       
        HierarchyTree rootTree = train.getRootTree();
        assertEquals(rootTree.getName(), "Bacteria");
        assertNotNull( rootTree.getSubclasses());
       
        Classifier aClassifier = train.createClassifier();
       
        //test addConfidence()
       
        HashMap<HierarchyTree, RankAssignment> determinedMap = new HashMap <HierarchyTree, RankAssignment>();
    HierarchyTree determinedGenusNode = train.getGenusNodebyIndex(4);
    HierarchyTree Enterobacteriales = determinedGenusNode.getParent().getParent();
    HierarchyTree Gammaproteobacteria = Enterobacteriales.getParent();
   
    HierarchyTree aNode = determinedGenusNode;
    while (aNode != null){     
      determinedMap.put(aNode, new RankAssignment(aNode, 0));
      aNode = aNode.getParent();
    }
   
    HierarchyTree bestNode = train.getGenusNodebyIndex(1);  // Vibrio
    aClassifier.addConfidence(bestNode, determinedMap);
    assertEquals( determinedMap.get(determinedGenusNode).getConfidence(), 0.0f, 0.0001);  //Enterobacter
    assertEquals( determinedMap.get(Enterobacteriales).getConfidence(), 0.0f, 0.0001);  //Enterobacteriales
    assertEquals( determinedMap.get(Gammaproteobacteria).getConfidence(), 1.0f, 0.0001);  //Gammaproteobacteria
       
    bestNode = train.getGenusNodebyIndex(4);   //Enterobacter
    aClassifier.addConfidence(bestNode, determinedMap);
    assertEquals( determinedMap.get(determinedGenusNode).getConfidence(), 1.0f, 0.0001);  //Enterobacter
    assertEquals( determinedMap.get(Enterobacteriales).getConfidence(), 1.0f, 0.0001);  //Enterobacteriales
    assertEquals( determinedMap.get(Gammaproteobacteria).getConfidence(), 2.0f, 0.0001);  //Gammaproteobacteria
   
    aClassifier.addConfidence(train.getGenusNodebyIndex(4), determinedMap);  //Enterobacter
    aClassifier.addConfidence(train.getGenusNodebyIndex(0), determinedMap);  //Clostridium
    assertEquals( determinedMap.get(determinedGenusNode).getConfidence(), 2.0f, 0.0001);  //Enterobacter
    assertEquals( determinedMap.get(Enterobacteriales).getConfidence(), 2.0f, 0.0001);  //Enterobacteriales
    assertEquals( determinedMap.get(Gammaproteobacteria).getConfidence(), 3.0f, 0.0001);  //Gammaproteobacteria
    assertEquals( determinedMap.get(rootTree).getConfidence(), 4.0f, 0.0001);  //Bacteria
        // end test addConfidence()
View Full Code Here
TOP

Related Classes of edu.msu.cme.rdp.classifier.TrainingInfo

  • edu.msu.cme.rdp.classifier.io.TreeFileParser
  • edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
  • edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  • java.util.ArrayList
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.