import java.io.BufferedReader;
import java.io.File;
+import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
+import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Scanner;
HMMFile fn3 = new HMMFile(
- new FileParse("H:/fn3.hmm", DataSourceType.FILE));
+ new FileParse("test/jalview/io/test_fn3_hmm.txt",
+ DataSourceType.FILE));
HMMFile pKinase = new HMMFile(
- new FileParse("H:/Pkinase.hmm", DataSourceType.FILE));
+ new FileParse("test/jalview/io/test_PKinase_hmm.txt",
+ DataSourceType.FILE));
HMMFile made1 = new HMMFile(
- new FileParse("H:/MADE1.hmm", DataSourceType.FILE));
+ new FileParse("test/jalview/io/test_MADE1_hmm.txt",
+ DataSourceType.FILE));
HMMFileTest() throws IOException
{
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(getMatchEmission(0, 19, hmm), 0.032298, 0.001d);
+ assertEquals(getMatchEmission(12, 12, hmm), 0.0130, 0.001d);
+ assertEquals(getMatchEmission(23, 7, hmm), 0.02583, 0.001d);
+ assertEquals(getMatchEmission(54, 1, hmm), 0.008549, 0.001d);
+ assertEquals(getMatchEmission(178, 3, hmm), 0.07998, 0.001d);
+ assertEquals(getMatchEmission(210, 2, hmm), 0.014465, 0.001d);
+ assertEquals(getMatchEmission(260, 19, hmm), 0.02213, 0.001d);
+
+ assertEquals(getInsertEmission(2, 1, hmm), 0.012, 0.001d);
+ assertEquals(getInsertEmission(15, 6, hmm), 0.02411, 0.001d);
+ assertEquals(getInsertEmission(22, 9, hmm), 0.06764, 0.001d);
+ assertEquals(getInsertEmission(57, 2, hmm), 0.0623, 0.001d);
+ assertEquals(getInsertEmission(203, 16, hmm), 0.0623, 0.001d);
+ assertEquals(getInsertEmission(255, 12, hmm), 0.0647, 0.001d);
assertEquals(getStateTransition(0, 6, hmm),
Double.NEGATIVE_INFINITY);
- 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(getStateTransition(3, 6, hmm), 0.3848, 0.001d);
+ assertEquals(getStateTransition(29, 3, hmm), 0.5382, 0.001d);
+ assertEquals(getStateTransition(169, 3, hmm), 0.2916, 0.001d);
+ assertEquals(getStateTransition(209, 0, hmm), 0.99, 0.001d);
+ assertEquals(getStateTransition(243, 1, hmm), 0.0066, 0.001d);
+
+ assertEquals(hmm.getNodeAlignmentColumn(3).intValue(), 2);
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.getNodeAlignmentColumn(78).intValue(), 135);
assertEquals(hmm.getReferenceAnnotation(93), '-');
assertEquals(hmm.getConsensusResidue(145), 'a');
assertEquals(hmm.getMaskedValue(183), '-');
@Test
public void testParseFileProperties() throws IOException
{
- FileReader fr = new FileReader(new File("H:/fn3.hmm"));
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_fn3_hmm.txt"));
BufferedReader br = new BufferedReader(fr);
fn3.parseFileProperties(br);
fn3.parseModel(br); // this is for a later test
assertEquals(testHMM.getForward(), "-3.8341 0.71847");
- FileReader fr3 = new FileReader(new File("H:/MADE1.hmm"));
+ FileReader fr3 = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
BufferedReader br3 = new BufferedReader(fr3);
made1.parseFileProperties(br3);
testHMM = made1.getHMM();
}
@Test
- public void testGetTransitionType()
- {
- 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(3.9);
- filledArray.add(9.8);
- filledArray.add(4.7);
- filledArray.add(4.3);
- filledArray.add(2.3);
- filledArray.add(6.9);
-
- assertEquals(HMMFile.fillList(scanner1, 9), filledArray);
+ filledArray.add(0.27253);
+ filledArray.add(0.0907);
+ filledArray.add(0.00499);
+ filledArray.add(0.02024);
+ filledArray.add(0.00005);
+ filledArray.add(0.00909);
+ filledArray.add(0.01357);
+ filledArray.add(0.10026);
+ filledArray.add(0.001);
+
+ List<Double> testList = HMMFile.fillList(scanner1, 9);
+
+ for (int i = 0; i < 9; i++)
+ {
+ assertEquals(testList.get(i), filledArray.get(i), 0.001d);
+
+ }
+
filledArray.clear();
scanner1.close();
Scanner scanner2 = new Scanner(
- "1.346554 5.58756754 35.3523645 12345.3564 1.4");
- filledArray.add(1.346554);
- filledArray.add(5.58756754);
- filledArray.add(35.3523645);
- filledArray.add(12345.3564);
- filledArray.add(1.4);
-
- assertEquals(HMMFile.fillList(scanner2, 5), filledArray);
- scanner2.close();
+ "1.346 5.554 35.345 5.64 1.4");
+ filledArray.add(0.2603);
+ filledArray.add(0.00387);
+ filledArray.add(0d);
+ filledArray.add(0.00355);
+ filledArray.add(0.2466);
+
+ testList = HMMFile.fillList(scanner2, 5);
+
+ for (int i = 0; i < 5; i++)
+ {
+ assertEquals(testList.get(i), filledArray.get(i), 0.001d);
+ }
}
@Test
public void testParseModel() throws IOException
{
- FileReader fr = new FileReader(new File("H:/MADE1.hmm"));
+ FileReader fr = new FileReader(
+ new File("test/jalview/io/test_MADE1_hmm.txt"));
BufferedReader br = new BufferedReader(fr);
HiddenMarkovModel testHMM = new HiddenMarkovModel();
for (int i = 0; i < 24; i++)
br.close();
fr.close();
- 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(getMatchEmission(0, 2, testHMM), 0.1961, 0.001d);
+ assertEquals(getMatchEmission(2, 1, testHMM), 0.09267, 0.001d);
+ assertEquals(getMatchEmission(12, 2, testHMM), 0.07327, 0.001d);
+ assertEquals(getMatchEmission(69, 1, testHMM), 0.04184, 0.001d);
+ assertEquals(getMatchEmission(76, 2, testHMM), 0.07, 0.001d);
+
+ assertEquals(getInsertEmission(0, 1, testHMM), 0.25, 0.001d);
+ assertEquals(getInsertEmission(1, 2, testHMM), 0.25, 0.001d);
+ assertEquals(getInsertEmission(31, 3, testHMM), 0.2776, 0.001d);
+ assertEquals(getInsertEmission(70, 3, testHMM), 0.25, 0.001d);
+ assertEquals(getInsertEmission(80, 3, testHMM), 0.25, 0.001d);
+
+ assertEquals(getStateTransition(2, 0, testHMM), 0.9634, 0.001d);
+ assertEquals(getStateTransition(6, 1, testHMM), 0.0203, 0.001d);
+ assertEquals(getStateTransition(9, 3, testHMM), 0.2515, 0.001d);
+ assertEquals(getStateTransition(20, 4, testHMM), 0.78808, 0.001d);
+ assertEquals(getStateTransition(68, 2, testHMM), 0.01845, 0.001d);
assertEquals(getStateTransition(80, 6, testHMM),
Double.NEGATIVE_INFINITY);
HiddenMarkovModel hmm = testFile.getHMM();
- assertEquals(hmm.getNodeAlignmentColumn(1).intValue(), 1345);
+ assertEquals(hmm.getNodeAlignmentColumn(1).intValue(), 1344);
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);
+ assertEquals(hmm.findNodeIndex(1344).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();
}
/**
@Test(priority = 3)
public void testExportFile() throws IOException
{
- 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++)
+ pKinase.exportFile("test/jalview/io/test_export_hmm.txt");
+ HMMFile pKinaseClone = new HMMFile(
+ new FileParse("test/jalview/io/test_export_hmm.txt",
+ DataSourceType.FILE));
+ pKinaseClone.parse();
+ HiddenMarkovModel pKinaseHMM = new HiddenMarkovModel();
+ HiddenMarkovModel pKinaseCloneHMM = new HiddenMarkovModel();
+ pKinaseHMM = pKinase.getHMM();
+ pKinaseCloneHMM = pKinaseClone.getHMM();
+
+ for (int i = 0; i < pKinaseHMM.getLength(); i++)
{
List<Double> list1;
List<Double> list2;
boolean result;
- list1 = fn3HMM.getNode(i).getMatchEmissions();
- list2 = fn3CloneHMM.getNode(i).getMatchEmissions();
+ list1 = pKinaseHMM.getNode(i).getMatchEmissions();
+ list2 = pKinaseCloneHMM.getNode(i).getMatchEmissions();
result = checkIfListsAreIdentical(list1, list2);
assertEquals(result, true);
- list1 = fn3HMM.getNode(i).getInsertEmissions();
- list2 = fn3CloneHMM.getNode(i).getInsertEmissions();
+ list1 = pKinaseHMM.getNode(i).getInsertEmissions();
+ list2 = pKinaseCloneHMM.getNode(i).getInsertEmissions();
result = checkIfListsAreIdentical(list1, list2);
assertEquals(result, true);
- list1 = fn3HMM.getNode(i).getStateTransitions();
- list2 = fn3CloneHMM.getNode(i).getStateTransitions();
+ list1 = pKinaseHMM.getNode(i).getStateTransitions();
+ list2 = pKinaseCloneHMM.getNode(i).getStateTransitions();
result = checkIfListsAreIdentical(list1, list2);
assertEquals(result, true);
int alignColumn1;
int alignColumn2;
- alignColumn1 = fn3HMM.getNodeAlignmentColumn(i);
- alignColumn2 = fn3CloneHMM.getNodeAlignmentColumn(i);
+ alignColumn1 = pKinaseHMM.getNodeAlignmentColumn(i);
+ alignColumn2 = pKinaseCloneHMM.getNodeAlignmentColumn(i);
assertEquals(alignColumn1, alignColumn2);
char annotation1;
char annotation2;
- annotation1 = fn3HMM.getReferenceAnnotation(i);
- annotation2 = fn3CloneHMM.getReferenceAnnotation(i);
+ annotation1 = pKinaseHMM.getReferenceAnnotation(i);
+ annotation2 = pKinaseCloneHMM.getReferenceAnnotation(i);
assertEquals(annotation1, annotation2);
- annotation1 = fn3HMM.getConsensusResidue(i);
- annotation2 = fn3CloneHMM.getConsensusResidue(i);
+ annotation1 = pKinaseHMM.getConsensusResidue(i);
+ annotation2 = pKinaseCloneHMM.getConsensusResidue(i);
assertEquals(annotation1, annotation2);
}
}
@Test(priority = 1)
- public void testAppendFileProperties()
+ public void testAppendFileProperties() throws FileNotFoundException
{
- StringBuilder testBuilder = new StringBuilder();
- fn3.appendFileProperties(testBuilder);
- Scanner testScanner = new Scanner(testBuilder.toString());
+ PrintWriter writer = new PrintWriter(
+ "test/jalview/io/test_export_hmm.txt");
+ fn3.appendFileProperties(writer);
+ writer.close();
+ String content;
+ File file = new File("test/jalview/io/test_export_hmm.txt");
+
+ Scanner testScanner = new Scanner(file);
+ testScanner.useDelimiter("\\Z");
String[] expected = new String[] { "HMMER3/f [3.1b1 | May 2013]",
"NAME fn3", "ACC PF00041.13",
}
@Test(priority = 2)
- public void testAppendModel()
+ public void testAppendModel() throws FileNotFoundException
{
- StringBuilder testBuilder = new StringBuilder();
- fn3.appendModel(testBuilder);
- String string = testBuilder.toString();
+ PrintWriter writer = new PrintWriter(
+ "test/jalview/io/test_export_hmm.txt");
+ fn3.appendModel(writer);
+ writer.close();
+ String string;
+ File file = new File("test/jalview/io/test_export_hmm.txt");
+ Scanner scanner = new Scanner(file);
+ scanner.useDelimiter("\\Z");
+ string = scanner.next();
+
assertEquals(findValue(2, 2, 2, string), "4.42225");
assertEquals(findValue(12, 14, 1, string), "2.79307");
assertEquals(findValue(6, 24, 3, string), "0.48576");
git://source.jalview.org / jalview.git / blobdiff