package test.beast.util;
import java.io.File;
import java.io.FilenameFilter;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import org.junit.Test;
import beast.util.NexusParser;
import junit.framework.TestCase;
public class NexusParserTest extends TestCase {
@Test
public void testThatNexusExamplesParse() {
try {
String dirName = System.getProperty("user.dir") + "/examples/nexus";
System.out.println("Test Nexus Examples in " + dirName);
File exampleDir = new File(dirName);
String[] exampleFiles = exampleDir.list(new FilenameFilter() {
@Override
public boolean accept(File dir, String name) {
return name.endsWith(".nex") || name.endsWith(".nxs") ;
}
});
List<String> failedFiles = new ArrayList<>();
for (String fileName : exampleFiles) {
System.out.println("Processing " + fileName);
NexusParser parser = new NexusParser();
try {
parser.parseFile(new File(dirName + "/" + fileName));
} catch (Exception e) {
System.out.println("ExampleNexusParsing::Failed for " + fileName
+ ": " + e.getMessage());
failedFiles.add(fileName);
}
System.out.println("Done " + fileName);
}
if (failedFiles.size() > 0) {
System.out.println("\ntest_ThatNexusExamplesParse::Failed for : " + failedFiles.toString());
} else {
System.out.println("\ntest_ThatNexusExamplesParse::Success");
}
assertTrue(failedFiles.toString(), failedFiles.size() == 0);
} catch (Exception e) {
System.out.println("exception thrown ");
System.out.println(e.getMessage());
}
}
@Test
public void testTranslateBlock() {
String nexusTreeWithTranslateBlock = "#NEXUS\n" +
"\n" +
"Begin trees;\n" +
"\tTranslate\n" +
"\t\t1 ID1,\n" +
"\t\t2 ID0,\n" +
"\t\t3 ID4,\n" +
"\t\t4 ID2,\n" +
"\t\t5 ID3,\n" +
"\t\t6 ID5,\n" +
"\t\t7 ID6\n" +
"\t\t;\n" +
"tree TREE1 = [&R] (((1[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.885354014841496E-17,height_range={0.0,8.881784197001252E-16}]:0.3500782084890231,2[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.885336674542856E-17,height_range={0.0,8.881784197001252E-16}]:0.3500782084890231)[&height_95%_HPD={0.07176417767165222,0.32897302210795143},height_median=0.1721780016900536,height=0.18167779468916231,posterior=0.9992003198720512,height_range={0.019500497296338903,0.472878180264112}]:0.9248218821607495,(3[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.9830145767837334E-17,height_range={0.0,4.440892098500626E-16}]:0.9953937953591572,(4[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=4.332577657073782E-17,height_range={0.0,8.881784197001252E-16}]:0.2885313407858645,5[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=4.332594997372422E-17,height_range={0.0,8.881784197001252E-16}]:0.2885313407858645)[&height_95%_HPD={0.03428997737185302,0.29384644242980307},height_median=0.13917660355071027,height=0.15063132242919447,posterior=0.9992003198720512,height_range={0.012135234424637736,0.43470259067266337}]:0.7068624545732927)[&height_95%_HPD={0.4703860181701143,1.2401041356897795},height_median=0.8841915264598103,height=0.8799641568544527,posterior=0.9668132746901239,height_range={0.2376833426394811,1.5008735971013971}]:0.2795062952906153)[&height_95%_HPD={0.871170115451148,1.736574411464855},height_median=1.3388341576137588,height=1.3419155689487607,posterior=0.8912435025989605,height_range={0.609339147487161,2.0082114277758554}]:0.1115505866359714,(6[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.805449918706939E-17,height_range={0.0,4.440892098500626E-16}]:0.1143648180955704,7[&height_95%_HPD={0.0,2.220446049250313E-16},height_median=0.0,height=3.805449918706939E-17,height_range={0.0,4.440892098500626E-16}]:0.1143648180955704)[&height_95%_HPD={0.07189918035503462,0.3145415291508802},height_median=0.1807116511737813,height=0.18641149700061227,posterior=0.9996001599360256,height_range={0.0042543872372436675,0.4254547656747345}]:1.2720858591901736)[&height_95%_HPD={1.2498874674331548,2.2880779508436415},height_median=1.7581890486365315,height=1.7391129102773757,posterior=1.0,height_range={0.003684245207410762,2.42575160443681}];\n" +
"End;\n";
NexusParser parser = new NexusParser();
try {
Set<String> taxa = new TreeSet<>();
taxa.add("ID0");
taxa.add("ID1");
taxa.add("ID2");
taxa.add("ID3");
taxa.add("ID4");
taxa.add("ID5");
taxa.add("ID6");
parser.parseFile("testTranslateBlock", new StringReader(nexusTreeWithTranslateBlock));
assertEquals(1, parser.trees.size());
assertNotNull(parser.trees.get(0));
assertEquals(7, parser.trees.get(0).getTaxaNames().length);
for (String taxaName : parser.trees.get(0).getTaxaNames()) {
assertNotNull(taxaName);
}
assertTrue(taxa.containsAll(Arrays.asList(parser.trees.get(0).getTaxaNames())));
} catch (Exception e) {
e.printStackTrace();
assertTrue(false);
}
}
@Test
public void testTranslateBlock2() {
String nexusTreeWithTranslateBlock = "#NEXUS\n" +
"\n" +
"Begin trees;\n" +
"\tTranslate\n" +
"\t\t1 C,\n" +
"\t\t2 B,\n" +
"\t\t3 A\n" +
"\t\t;\n" +
"tree TREE1 = [&R] (1:10,(3:30,2:20):10);\n" +
"End;\n";
NexusParser parser = new NexusParser();
try {
List<String> taxa = new ArrayList<>();
taxa.add("2");
taxa.add("0");
taxa.add("1");
parser.parseFile("testTranslateBlock", new StringReader(nexusTreeWithTranslateBlock));
assertEquals(1, parser.trees.size());
assertNotNull(parser.trees.get(0));
String t = parser.trees.get(0).getRoot().toNewick();
System.out.println(t);
assertEquals("(C:10.0,(B:20.0,A:30.0):10.0):0.0", t);
} catch (Exception e) {
e.printStackTrace();
assertTrue(false);
}
}
@Test
public void testAssumptionsParse() {
try {
String fileName = System.getProperty("user.dir") + "/examples/nexus/Primates.nex";
NexusParser parser = new NexusParser();
parser.parseFile(new File(fileName));
assertEquals(2, parser.filteredAlignments.size());
} catch (Exception e) {
System.out.println("exception thrown ");
System.out.println(e.getMessage());
}
}
}