import jalview.datamodel.HiddenMarkovModel;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
public class HMMFileTest {
- HMMFile fn3 = new HMMFile("H:/fn3.hmm");
- HMMFile emptyFile = new HMMFile("H:/EmptyFile.hmm");
- HMMFile pKinase = new HMMFile("H:/Pkinase.hmm");
+ HMMFile fn3 = new HMMFile(
+ new FileParse("H:/fn3.hmm", DataSourceType.FILE));
+
+ HMMFile pKinase = new HMMFile(
+ new FileParse("H:/Pkinase.hmm", DataSourceType.FILE));
+
+ HMMFile made1 = new HMMFile(
+ new FileParse("H:/MADE1.hmm", DataSourceType.FILE));
+
+ HMMFileTest() throws IOException
+ {
+
+ }
+
+
- HMMFile made1 = new HMMFile("H:/MADE1.hmm");
@Test
public void testParse() throws IOException
{
-
+
pKinase.parse();
-
- assertEquals(pKinase.hmm.getName(), "Pkinase");
- assertEquals(pKinase.hmm.getAccessionNumber(), "PF00069.17");
- assertEquals(pKinase.hmm.getDescription(), "Protein kinase domain");
- assertEquals(pKinase.hmm.getLength().intValue(), 260);
- assertNull(pKinase.hmm.getMaxInstanceLength());
- assertEquals(pKinase.hmm.getAlphabetType(), "amino");
- assertEquals(pKinase.hmm.referenceAnnotationIsActive(), false);
- assertEquals(pKinase.hmm.maskValueIsActive(), false);
- assertEquals(pKinase.hmm.consensusResidueIsActive(), true);
- assertEquals(pKinase.hmm.consensusStructureIsActive(),
+ HiddenMarkovModel hmm = pKinase.getHMM();
+ assertEquals(hmm.getName(), "Pkinase");
+ assertEquals(hmm.getAccessionNumber(), "PF00069.17");
+ assertEquals(hmm.getDescription(), "Protein kinase domain");
+ assertEquals(hmm.getLength().intValue(), 260);
+ assertNull(hmm.getMaxInstanceLength());
+ assertEquals(hmm.getAlphabetType(), "amino");
+ assertEquals(hmm.referenceAnnotationIsActive(), false);
+ assertEquals(hmm.maskValueIsActive(), false);
+ assertEquals(hmm.consensusResidueIsActive(), true);
+ assertEquals(hmm.consensusStructureIsActive(),
true);
- assertEquals(pKinase.hmm.mapIsActive(), true);
- assertEquals(pKinase.hmm.getDate(), "Thu Jun 16 11:44:06 2011");
- assertNull(pKinase.hmm.getCommandLineLog());
- assertEquals(pKinase.hmm.getNumberOfSequences().intValue(), 54);
- assertEquals(pKinase.hmm.getEffectiveNumberOfSequences(), 3.358521, 4d);
- assertEquals(pKinase.hmm.getCheckSum().longValue(), 3106786190l);
- assertEquals(pKinase.hmm.getGatheringThreshold(), "70.30 70.30");
- assertEquals(pKinase.hmm.getTrustedCutoff(), "70.30 70.30");
- assertEquals(pKinase.hmm.getNoiseCutoff(), "70.20 70.20");
-
+ assertEquals(hmm.mapIsActive(), true);
+ assertEquals(hmm.getDate(), "Thu Jun 16 11:44:06 2011");
+ assertNull(hmm.getCommandLineLog());
+ assertEquals(hmm.getNumberOfSequences().intValue(), 54);
+ assertEquals(hmm.getEffectiveNumberOfSequences(), 3.358521, 4d);
+ assertEquals(hmm.getCheckSum().longValue(), 3106786190l);
+ assertEquals(hmm.getGatheringThreshold(), "70.30 70.30");
+ assertEquals(hmm.getTrustedCutoff(), "70.30 70.30");
+ assertEquals(hmm.getNoiseCutoff(), "70.20 70.20");
+
List<Character> symbols = new ArrayList<>();
symbols.add('A');
symbols.add('C');
symbols.add('V');
symbols.add('W');
symbols.add('Y');
-
- assertEquals(pKinase.hmm.getSymbols(), symbols);
-
- assertEquals(pKinase.hmm.getMatchEmission(0, 19), 3.43274);
- assertEquals(pKinase.hmm.getMatchEmission(12, 12), 4.33979);
- assertEquals(pKinase.hmm.getMatchEmission(23, 7), 3.65600);
- assertEquals(pKinase.hmm.getMatchEmission(54, 1), 4.76187);
- assertEquals(pKinase.hmm.getMatchEmission(79, 0), 2.81579);
- assertEquals(pKinase.hmm.getMatchEmission(100, 0), 1.86496);
- assertEquals(pKinase.hmm.getMatchEmission(112, 14), 2.77179);
- assertEquals(pKinase.hmm.getMatchEmission(143, 17), 5.10478);
- assertEquals(pKinase.hmm.getMatchEmission(156, 4), 4.69372);
- assertEquals(pKinase.hmm.getMatchEmission(178, 3), 2.52594);
- assertEquals(pKinase.hmm.getMatchEmission(210, 2), 4.23598);
- assertEquals(pKinase.hmm.getMatchEmission(260, 19), 3.81122);
-
- assertEquals(pKinase.hmm.getInsertEmission(2, 1), 4.42225);
- assertEquals(pKinase.hmm.getInsertEmission(15, 6), 3.72501);
- assertEquals(pKinase.hmm.getInsertEmission(22, 9), 2.69355);
- assertEquals(pKinase.hmm.getInsertEmission(57, 2), 2.77519);
- assertEquals(pKinase.hmm.getInsertEmission(62, 14), 2.89801);
- assertEquals(pKinase.hmm.getInsertEmission(95, 17), 2.98532);
- assertEquals(pKinase.hmm.getInsertEmission(105, 4), 3.46354);
- assertEquals(pKinase.hmm.getInsertEmission(134, 1), 4.42225);
- assertEquals(pKinase.hmm.getInsertEmission(143, 0), 2.68618);
- assertEquals(pKinase.hmm.getInsertEmission(152, 16), 2.77519);
- assertEquals(pKinase.hmm.getInsertEmission(203, 16), 2.77519);
- assertEquals(pKinase.hmm.getInsertEmission(255, 12), 2.73739);
-
- assertEquals(pKinase.hmm.getStateTransition(0, 6),
+
+ assertEquals(hmm.getSymbols(), symbols);
+
+ assertEquals(getMatchEmission(0, 19, hmm), 3.43274);
+ assertEquals(getMatchEmission(12, 12, hmm), 4.33979);
+ assertEquals(getMatchEmission(23, 7, hmm), 3.65600);
+ assertEquals(getMatchEmission(54, 1, hmm), 4.76187);
+ assertEquals(getMatchEmission(79, 0, hmm), 2.81579);
+ assertEquals(getMatchEmission(100, 0, hmm), 1.86496);
+ assertEquals(getMatchEmission(112, 14, hmm), 2.77179);
+ assertEquals(getMatchEmission(143, 17, hmm), 5.10478);
+ assertEquals(getMatchEmission(156, 4, hmm), 4.69372);
+ assertEquals(getMatchEmission(178, 3, hmm), 2.52594);
+ assertEquals(getMatchEmission(210, 2, hmm), 4.23598);
+ assertEquals(getMatchEmission(260, 19, hmm), 3.81122);
+
+ assertEquals(getInsertEmission(2, 1, hmm), 4.42225);
+ assertEquals(getInsertEmission(15, 6, hmm), 3.72501);
+ assertEquals(getInsertEmission(22, 9, hmm), 2.69355);
+ assertEquals(getInsertEmission(57, 2, hmm), 2.77519);
+ assertEquals(getInsertEmission(62, 14, hmm), 2.89801);
+ assertEquals(getInsertEmission(95, 17, hmm), 2.98532);
+ assertEquals(getInsertEmission(105, 4, hmm), 3.46354);
+ assertEquals(getInsertEmission(134, 1, hmm), 4.42225);
+ assertEquals(getInsertEmission(143, 0, hmm), 2.68618);
+ assertEquals(getInsertEmission(152, 16, hmm), 2.77519);
+ assertEquals(getInsertEmission(203, 16, hmm), 2.77519);
+ assertEquals(getInsertEmission(255, 12, hmm), 2.73739);
+
+ assertEquals(getStateTransition(0, 6, hmm),
Double.NEGATIVE_INFINITY);
- assertEquals(pKinase.hmm.getStateTransition(3, 6), 0.95510);
- assertEquals(pKinase.hmm.getStateTransition(29, 3), 0.61958);
- assertEquals(pKinase.hmm.getStateTransition(46, 4), 0.77255);
- assertEquals(pKinase.hmm.getStateTransition(53, 1), 5.01631);
- assertEquals(pKinase.hmm.getStateTransition(79, 2), 5.73865);
- assertEquals(pKinase.hmm.getStateTransition(101, 2), 5.73865);
- assertEquals(pKinase.hmm.getStateTransition(120, 5), 0.48576);
- assertEquals(pKinase.hmm.getStateTransition(146, 5), 0.70219);
- assertEquals(pKinase.hmm.getStateTransition(169, 3), 1.23224);
- assertEquals(pKinase.hmm.getStateTransition(209, 0), 0.01003);
- assertEquals(pKinase.hmm.getStateTransition(243, 1), 5.01631);
-
- assertEquals(pKinase.hmm.getNodeAlignmentColumn(3).intValue(), 3);
- assertEquals(pKinase.hmm.getReferenceAnnotation(7), '-');
- assertEquals(pKinase.hmm.getConsensusResidue(23), 't');
- assertEquals(pKinase.hmm.getMaskedValue(30), '-');
- assertEquals(pKinase.hmm.getConsensusStructure(56), 'S');
-
- assertEquals(pKinase.hmm.getNodeAlignmentColumn(78).intValue(), 136);
- assertEquals(pKinase.hmm.getReferenceAnnotation(93), '-');
- assertEquals(pKinase.hmm.getConsensusResidue(145), 'a');
- assertEquals(pKinase.hmm.getMaskedValue(183), '-');
- assertEquals(pKinase.hmm.getConsensusStructure(240), 'H');
-
+ assertEquals(getStateTransition(3, 6, hmm), 0.95510);
+ assertEquals(getStateTransition(29, 3, hmm), 0.61958);
+ assertEquals(getStateTransition(46, 4, hmm), 0.77255);
+ assertEquals(getStateTransition(53, 1, hmm), 5.01631);
+ assertEquals(getStateTransition(79, 2, hmm), 5.73865);
+ assertEquals(getStateTransition(101, 2, hmm), 5.73865);
+ assertEquals(getStateTransition(120, 5, hmm), 0.48576);
+ assertEquals(getStateTransition(146, 5, hmm), 0.70219);
+ assertEquals(getStateTransition(169, 3, hmm), 1.23224);
+ assertEquals(getStateTransition(209, 0, hmm), 0.01003);
+ assertEquals(getStateTransition(243, 1, hmm), 5.01631);
+
+ assertEquals(hmm.getNodeAlignmentColumn(3).intValue(), 3);
+ assertEquals(hmm.getReferenceAnnotation(7), '-');
+ assertEquals(hmm.getConsensusResidue(23), 't');
+ assertEquals(hmm.getMaskedValue(30), '-');
+ assertEquals(hmm.getConsensusStructure(56), 'S');
+
+ assertEquals(hmm.getNodeAlignmentColumn(78).intValue(), 136);
+ assertEquals(hmm.getReferenceAnnotation(93), '-');
+ assertEquals(hmm.getConsensusResidue(145), 'a');
+ assertEquals(hmm.getMaskedValue(183), '-');
+ assertEquals(hmm.getConsensusStructure(240), 'H');
+
}
-
+
@Test
public void testParseFileProperties() throws IOException
{
- FileReader fr = new FileReader(fn3.getDataObject());
+ FileReader fr = new FileReader(new File("H:/fn3.hmm"));
BufferedReader br = new BufferedReader(fr);
fn3.parseFileProperties(br);
fn3.parseModel(br); // this is for a later test
HiddenMarkovModel testHMM = new HiddenMarkovModel();
- testHMM = fn3.getHmm();
+ testHMM = fn3.getHMM();
br.close();
fr.close();
-
+
assertEquals(testHMM.getName(), "fn3");
assertEquals(testHMM.getAccessionNumber(), "PF00041.13");
assertEquals(testHMM.getDescription(),
assertEquals(testHMM.getViterbi(), "-9.7737 0.71847");
assertEquals(testHMM.getMSV(), "-9.4043 0.71847");
assertEquals(testHMM.getForward(), "-3.8341 0.71847");
-
- FileReader fr2 = new FileReader(emptyFile.getDataObject());
- BufferedReader br2 = new BufferedReader(fr2);
- emptyFile.parseFileProperties(br2);
- testHMM = emptyFile.getHmm();
- br2.close();
- fr2.close();
-
- assertNull(testHMM.getName());
- assertNull(testHMM.getAccessionNumber());
- assertNull(testHMM.getDescription());
- assertNull(testHMM.getLength());
- assertNull(testHMM.getMaxInstanceLength());
- assertNull(testHMM.getAlphabetType());
- assertEquals(testHMM.referenceAnnotationIsActive(), false);
- assertEquals(testHMM.maskValueIsActive(), false);
- assertEquals(testHMM.consensusResidueIsActive(), false);
- assertEquals(testHMM.consensusStructureIsActive(),
- false);
- assertEquals(testHMM.mapIsActive(), false);
- assertNull(testHMM.getDate());
- assertNull(testHMM.getCommandLineLog());
- assertNull(testHMM.getNumberOfSequences());
- assertNull(testHMM.getEffectiveNumberOfSequences());
- assertNull(testHMM.getCheckSum());
- assertNull(testHMM.getGatheringThreshold());
- assertNull(testHMM.getGatheringThreshold());
- assertNull(testHMM.getTrustedCutoff());
- assertNull(testHMM.getTrustedCutoff());
- assertNull(testHMM.getNoiseCutoff());
- assertNull(testHMM.getNoiseCutoff());
- assertNull(testHMM.getViterbi());
- assertNull(testHMM.getMSV());
- assertNull(testHMM.getForward());
-
- FileReader fr3 = new FileReader(made1.getDataObject());
+
+
+ FileReader fr3 = new FileReader(new File("H:/MADE1.hmm"));
BufferedReader br3 = new BufferedReader(fr3);
made1.parseFileProperties(br3);
- testHMM = made1.getHmm();
+ testHMM = made1.getHMM();
br3.close();
fr3.close();
-
+
assertEquals(testHMM.getName(), "MADE1");
assertEquals(testHMM.getAccessionNumber(), "DF0000629.2");
assertEquals(testHMM.getDescription(),
assertEquals(testHMM.getViterbi(), "-9.3632 0.71858");
assertEquals(testHMM.getMSV(), "-8.5786 0.71858");
assertEquals(testHMM.getForward(), "-3.4823 0.71858");
-
-
+
+
}
-
+
@Test
public void testGetTransitionType()
{
-
- assertEquals(fn3.getTransitionType("mm").intValue(), 0);
- assertEquals(fn3.getTransitionType("mi").intValue(), 1);
- assertEquals(fn3.getTransitionType("md").intValue(), 2);
- assertEquals(fn3.getTransitionType("im").intValue(), 3);
- assertEquals(fn3.getTransitionType("ii").intValue(), 4);
- assertEquals(fn3.getTransitionType("dm").intValue(), 5);
- assertEquals(fn3.getTransitionType("dd").intValue(), 6);
- assertNull(fn3.getTransitionType("df"));
-
+ HiddenMarkovModel hmm = fn3.getHMM();
+ assertEquals(hmm.getTransitionType("mm").intValue(), 0);
+ assertEquals(hmm.getTransitionType("mi").intValue(), 1);
+ assertEquals(hmm.getTransitionType("md").intValue(), 2);
+ assertEquals(hmm.getTransitionType("im").intValue(), 3);
+ assertEquals(hmm.getTransitionType("ii").intValue(), 4);
+ assertEquals(hmm.getTransitionType("dm").intValue(), 5);
+ assertEquals(hmm.getTransitionType("dd").intValue(), 6);
+ assertNull(hmm.getTransitionType("df"));
+
}
-
+
@Test
public void testFillList()
{
Scanner scanner1 = new Scanner("1.3 2.4 5.3 3.9 9.8 4.7 4.3 2.3 6.9");
ArrayList<Double> filledArray = new ArrayList<>();
-
+
filledArray.add(1.3);
filledArray.add(2.4);
filledArray.add(5.3);
filledArray.add(4.3);
filledArray.add(2.3);
filledArray.add(6.9);
-
+
assertEquals(HMMFile.fillList(scanner1, 9), filledArray);
filledArray.clear();
scanner1.close();
-
+
Scanner scanner2 = new Scanner(
"1.346554 5.58756754 35.3523645 12345.3564 1.4");
filledArray.add(1.346554);
filledArray.add(35.3523645);
filledArray.add(12345.3564);
filledArray.add(1.4);
-
+
assertEquals(HMMFile.fillList(scanner2, 5), filledArray);
scanner2.close();
-
+
}
-
+
@Test
public void testParseModel() throws IOException
{
- FileReader fr = new FileReader(made1.getDataObject());
+ FileReader fr = new FileReader(new File("H:/MADE1.hmm"));
BufferedReader br = new BufferedReader(fr);
HiddenMarkovModel testHMM = new HiddenMarkovModel();
for (int i = 0; i < 24; i++)
br.readLine();
}
made1.parseModel(br);
- testHMM = made1.getHmm();
+ testHMM = made1.getHMM();
br.close();
fr.close();
-
- assertEquals(testHMM.getMatchEmission(0, 2), 1.62906);
- assertEquals(testHMM.getMatchEmission(2, 1), 2.37873);
- assertEquals(testHMM.getMatchEmission(12, 2), 2.61355);
- assertEquals(testHMM.getMatchEmission(26, 0), 1.86925);
- assertEquals(testHMM.getMatchEmission(32, 3), 2.58263);
- assertEquals(testHMM.getMatchEmission(59, 3), 2.20507);
- assertEquals(testHMM.getMatchEmission(63, 0), 0.41244);
- assertEquals(testHMM.getMatchEmission(69, 1), 3.17398);
- assertEquals(testHMM.getMatchEmission(76, 2), 2.65861);
-
- assertEquals(testHMM.getInsertEmission(0, 1), 1.38629);
- assertEquals(testHMM.getInsertEmission(1, 2), 1.38629);
- assertEquals(testHMM.getInsertEmission(31, 3), 1.28150);
- assertEquals(testHMM.getInsertEmission(43, 0), 1.32290);
- assertEquals(testHMM.getInsertEmission(48, 2), 1.52606);
- assertEquals(testHMM.getInsertEmission(52, 1), 1.62259);
- assertEquals(testHMM.getInsertEmission(67, 0), 1.38141);
- assertEquals(testHMM.getInsertEmission(70, 3), 1.38629);
- assertEquals(testHMM.getInsertEmission(80, 3), 1.38629);
-
- assertEquals(testHMM.getStateTransition(2, 0), 0.03725);
- assertEquals(testHMM.getStateTransition(6, 1), 3.89715);
- assertEquals(testHMM.getStateTransition(9, 3), 1.38021);
- assertEquals(testHMM.getStateTransition(20, 4), 0.23815);
- assertEquals(testHMM.getStateTransition(34, 6), 0.33363);
- assertEquals(testHMM.getStateTransition(46, 5), 1.05474);
- assertEquals(testHMM.getStateTransition(57, 6), 0.31164);
- assertEquals(testHMM.getStateTransition(68, 2), 3.99242);
- assertEquals(testHMM.getStateTransition(80, 6),
+
+ assertEquals(getMatchEmission(0, 2, testHMM), 1.62906);
+ assertEquals(getMatchEmission(2, 1, testHMM), 2.37873);
+ assertEquals(getMatchEmission(12, 2, testHMM), 2.61355);
+ assertEquals(getMatchEmission(26, 0, testHMM), 1.86925);
+ assertEquals(getMatchEmission(32, 3, testHMM), 2.58263);
+ assertEquals(getMatchEmission(59, 3, testHMM), 2.20507);
+ assertEquals(getMatchEmission(63, 0, testHMM), 0.41244);
+ assertEquals(getMatchEmission(69, 1, testHMM), 3.17398);
+ assertEquals(getMatchEmission(76, 2, testHMM), 2.65861);
+
+ assertEquals(getInsertEmission(0, 1, testHMM), 1.38629);
+ assertEquals(getInsertEmission(1, 2, testHMM), 1.38629);
+ assertEquals(getInsertEmission(31, 3, testHMM), 1.28150);
+ assertEquals(getInsertEmission(43, 0, testHMM), 1.32290);
+ assertEquals(getInsertEmission(48, 2, testHMM), 1.52606);
+ assertEquals(getInsertEmission(52, 1, testHMM), 1.62259);
+ assertEquals(getInsertEmission(67, 0, testHMM), 1.38141);
+ assertEquals(getInsertEmission(70, 3, testHMM), 1.38629);
+ assertEquals(getInsertEmission(80, 3, testHMM), 1.38629);
+
+ assertEquals(getStateTransition(2, 0, testHMM), 0.03725);
+ assertEquals(getStateTransition(6, 1, testHMM), 3.89715);
+ assertEquals(getStateTransition(9, 3, testHMM), 1.38021);
+ assertEquals(getStateTransition(20, 4, testHMM), 0.23815);
+ assertEquals(getStateTransition(34, 6, testHMM), 0.33363);
+ assertEquals(getStateTransition(46, 5, testHMM), 1.05474);
+ assertEquals(getStateTransition(57, 6, testHMM), 0.31164);
+ assertEquals(getStateTransition(68, 2, testHMM), 3.99242);
+ assertEquals(getStateTransition(80, 6, testHMM),
Double.NEGATIVE_INFINITY);
-
+
}
-
+
@Test
public void testParseAnnotations()
{
- HMMFile testFile = new HMMFile("H:/EmptyFile.hmm");
- testFile.hmm.getNodes().add(new HMMNode());
- testFile.hmm.getNodes().add(new HMMNode());
-
- testFile.hmm.setConsensusResidueStatus(true);
- testFile.hmm.setMAPStatus(true);
- testFile.hmm.setReferenceAnnotationStatus(true);
- testFile.hmm.setConsensusStructureStatus(true);
- testFile.hmm.setMaskedValueStatus(true);
+ HMMFile testFile = new HMMFile();
+ testFile.getHMM().getNodes().add(new HMMNode());
+ testFile.getHMM().getNodes().add(new HMMNode());
+ testFile.getHMM().getNodes().add(new HMMNode());
+
+
+ testFile.getHMM().setConsensusResidueStatus(true);
+ testFile.getHMM().setMAPStatus(true);
+ testFile.getHMM().setReferenceAnnotationStatus(true);
+ testFile.getHMM().setConsensusStructureStatus(true);
+ testFile.getHMM().setMaskedValueStatus(true);
Scanner scanner = new Scanner("1345 t t t t");
- testFile.parseAnnotations(scanner, 0);
- assertEquals(testFile.hmm.getNodeAlignmentColumn(0).intValue(), 1345);
- assertEquals(testFile.hmm.getConsensusResidue(0), 't');
- assertEquals(testFile.hmm.getReferenceAnnotation(0), 't');
- assertEquals(testFile.hmm.getMaskedValue(0), 't');
- assertEquals(testFile.hmm.getConsensusStructure(0), 't');
-
- scanner.close();
-
- testFile.hmm.setConsensusResidueStatus(true);
- testFile.hmm.setMAPStatus(false);
- testFile.hmm.setReferenceAnnotationStatus(true);
- testFile.hmm.setConsensusStructureStatus(false);
- testFile.hmm.setMaskedValueStatus(false);
+ testFile.parseAnnotations(scanner, 1);
+
+ testFile.getHMM().setConsensusResidueStatus(true);
+ testFile.getHMM().setMAPStatus(false);
+ testFile.getHMM().setReferenceAnnotationStatus(true);
+ testFile.getHMM().setConsensusStructureStatus(false);
+ testFile.getHMM().setMaskedValueStatus(false);
Scanner scanner2 = new Scanner("- y x - -");
- testFile.parseAnnotations(scanner2, 1);
- assertNull(testFile.hmm.getNodeAlignmentColumn(1));
- assertEquals(testFile.hmm.getConsensusResidue(1), 'y');
- assertEquals(testFile.hmm.getReferenceAnnotation(1), 'x');
- assertEquals(testFile.hmm.getMaskedValue(1), '-');
- assertEquals(testFile.hmm.getConsensusStructure(1), '-');
-
+ testFile.parseAnnotations(scanner2, 2);
+
+ HiddenMarkovModel hmm = testFile.getHMM();
+
+ assertEquals(hmm.getNodeAlignmentColumn(1).intValue(), 1345);
+ assertEquals(hmm.getConsensusResidue(1), 't');
+ assertEquals(hmm.getReferenceAnnotation(1), 't');
+ assertEquals(hmm.getMaskedValue(1), 't');
+ assertEquals(hmm.getConsensusStructure(1), 't');
+
+ assertEquals(hmm.findNodeIndex(1345).intValue(), 1);
+
+ scanner.close();
+
+ assertNull(hmm.getNodeAlignmentColumn(2));
+ assertEquals(hmm.getConsensusResidue(2), 'y');
+ assertEquals(hmm.getReferenceAnnotation(2), 'x');
+ assertEquals(hmm.getMaskedValue(2), '-');
+ assertEquals(hmm.getConsensusStructure(2), '-');
+
+ assertNull(hmm.findNodeIndex(2));
+
scanner2.close();
}
+
+ /**
+ * tests to see if file produced by the output matches the file from the input
+ *
+ * @throws IOException
+ */
+
@Test(priority = 3)
public void testExportFile() throws IOException
{
-
- fn3.exportFile("H:/WriteFileTest.hmm");
+ fn3.exportFile("H:/WriteFileTest.txt");
+ HMMFile fn3Clone = new HMMFile(
+ new FileParse("H:/WriteFileTest.txt", DataSourceType.FILE));
+ fn3Clone.parse();
+ HiddenMarkovModel fn3HMM = new HiddenMarkovModel();
+ HiddenMarkovModel fn3CloneHMM = new HiddenMarkovModel();
+ fn3HMM = fn3.getHMM();
+ fn3CloneHMM = fn3Clone.getHMM();
+
+ for (int i = 0; i < fn3HMM.getLength(); i++)
+ {
+ List<Double> list1;
+ List<Double> list2;
+ boolean result;
+
+ list1 = fn3HMM.getNode(i).getMatchEmissions();
+ list2 = fn3CloneHMM.getNode(i).getMatchEmissions();
+
+ result = checkIfListsAreIdentical(list1, list2);
+ assertEquals(result, true);
+
+ list1 = fn3HMM.getNode(i).getInsertEmissions();
+ list2 = fn3CloneHMM.getNode(i).getInsertEmissions();
+
+ result = checkIfListsAreIdentical(list1, list2);
+ assertEquals(result, true);
+
+ list1 = fn3HMM.getNode(i).getStateTransitions();
+ list2 = fn3CloneHMM.getNode(i).getStateTransitions();
+
+ result = checkIfListsAreIdentical(list1, list2);
+ assertEquals(result, true);
+
+ if (i > 0)
+ {
+ int alignColumn1;
+ int alignColumn2;
+
+ alignColumn1 = fn3HMM.getNodeAlignmentColumn(i);
+ alignColumn2 = fn3CloneHMM.getNodeAlignmentColumn(i);
+
+ assertEquals(alignColumn1, alignColumn2);
+
+ char annotation1;
+ char annotation2;
+
+ annotation1 = fn3HMM.getReferenceAnnotation(i);
+ annotation2 = fn3CloneHMM.getReferenceAnnotation(i);
+
+ assertEquals(annotation1, annotation2);
+
+ annotation1 = fn3HMM.getConsensusResidue(i);
+ annotation2 = fn3CloneHMM.getConsensusResidue(i);
+
+ assertEquals(annotation1, annotation2);
+ }
+
+ }
+
}
-
+
@Test(priority = 1)
public void testAppendFileProperties()
{
StringBuilder testBuilder = new StringBuilder();
fn3.appendFileProperties(testBuilder);
Scanner testScanner = new Scanner(testBuilder.toString());
-
+
String[] expected = new String[] { "HMMER3/f [3.1b1 | May 2013]",
"NAME fn3", "ACC PF00041.13",
"DESC Fibronectin type III domain", "LENG 86", "ALPH amino",
"NC 7.90 7.90", "STATS LOCAL MSV -9.4043 0.71847",
"STATS LOCAL VITERBI -9.7737 0.71847",
"STATS LOCAL FORWARD -3.8341 0.71847" };
-
+
for (String value : expected)
{
assertEquals(testScanner.nextLine(), value);
}
-
+
testScanner.close();
}
-
+
@Test(priority = 2)
public void testAppendModel()
{
String string = testBuilder.toString();
assertEquals(findValue(2, 2, 2, string), "4.42225");
assertEquals(findValue(12, 14, 1, string), "2.79307");
+ assertEquals(findValue(6, 24, 3, string), "0.48576");
+ assertEquals(findValue(19, 33, 2, string), "4.58477");
+ assertEquals(findValue(20, 64, 2, string), "3.61505");
+ assertEquals(findValue(3, 72, 3, string), "6.81068");
+ assertEquals(findValue(10, 80, 2, string), "2.69355");
+ assertEquals(findValue(16, 65, 1, string), "2.81003");
+ assertEquals(findValue(14, 3, 1, string), "2.69012");
+ assertEquals(findValue(11, 32, 1, string), "4.34805");
+
}
+
+ /**
+ *
+ * @param symbolIndex
+ * index of symbol being searched. First symbol has index 1.
+ * @param nodeIndex
+ * index of node being searched. Begin node has index 0. First node
+ * has index 1.
+ * @param line
+ * index of line being searched in node. First line has index 1.
+ * @param model
+ * string model being searched
+ * @return value at specified position
+ */
public String findValue(int symbolIndex, int nodeIndex, int line,
String model)
{
-
+
String value = "";
Scanner scanner = new Scanner(model);
scanner.nextLine();
scanner.nextLine();
-
+
for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
{
scanner.nextLine();
scanner.nextLine();
scanner.nextLine();
}
-
+
for (int symbol = 0; symbol < symbolIndex; symbol++)
{
value = scanner.next();
{
scanner.next();
}
-
+
+ }
+ return value;
+
+ }
+
+ public boolean checkIfListsAreIdentical(List<Double> list1,
+ List<Double> list2)
+ {
+ boolean isDifferent = false;
+ for (int i = 0; i < list1.size(); i++)
+ {
+ Double entry1;
+ Double entry2;
+ entry1 = list1.get(i);
+ entry2 = list2.get(i);
+ if (!(entry1 == entry2))
+ {
+ isDifferent = true;
+ }
}
+ return isDifferent;
+ }
+
+ /**
+ * gets the match emission at a node for a symbol
+ *
+ * @param nodeIndex
+ * position of node in model
+ * @param symbolIndex
+ * index of symbol being searched
+ * @return negative log probability of a match emission of the given symbol
+ */
+ public double getMatchEmission(int nodeIndex, int symbolIndex,
+ HiddenMarkovModel hmm)
+ {
+ double value = hmm.getNodes().get(nodeIndex).getMatchEmissions()
+ .get(symbolIndex);
+ return value;
+ }
+
+ /**
+ * gets the insert emission at a node for a symbol
+ *
+ * @param nodeIndex
+ * position of node in model
+ * @param symbolIndex
+ * index of symbol being searched
+ * @return negative log probability of an insert emission of the given symbol
+ */
+ public double getInsertEmission(int nodeIndex, int symbolIndex,
+ HiddenMarkovModel hmm)
+ {
+ double value = hmm.getNodes().get(nodeIndex).getInsertEmissions()
+ .get(symbolIndex);
return value;
+ }
+ /**
+ * gets the state transition at a node for a specific transition
+ *
+ * @param nodeIndex
+ * position of node in model
+ * @param transitionIndex
+ * index of stransition being searched
+ * @return negative log probability of a state transition of the given type
+ */
+ public double getStateTransition(int nodeIndex, int transitionIndex,
+ HiddenMarkovModel hmm)
+ {
+ double value = hmm.getNodes().get(nodeIndex).getStateTransitions()
+ .get(transitionIndex);
+ return value;
}
}
git://source.jalview.org / jalview.git / commitdiff