Example usage for org.apache.commons.io FileUtils contentEquals

Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils contentEquals.

Prototype

public static boolean contentEquals(File file1, File file2) throws IOException 

Source Link

Document

Compares the contents of two files to determine if they are equal or not.

Usage

From source file:org.corehunter.tests.data.simple.SimpleDefaultGenotypeDataTest.java

@Test
public void homozygousToCsvFileWithUnselectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES_DEFAULT;
    expectedAlleleNames = ALLELE_NAMES_HOMOZYGOUS;

    SimpleDefaultGenotypeData genotypicData = new SimpleDefaultGenotypeData(NAME, HEADERS_UNIQUE_NAMES,
            MARKER_NAMES_DEFAULT, ALLELE_OBS_HOMOZYGOUS);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoHomozygous-UnselectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//w w w  . j  a v  a  2  s .  com
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (homozygous, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, false, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/homozygous_genotypes/out/unsel-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (homozygous, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, false, true, false);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/homozygous_genotypes/out/unsel-no-ids.csv").getPath()),
                    path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleDefaultGenotypeDataTest.java

@Test
public void diploidToCsvFileWithAllIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES_DEFAULT;
    expectedAlleleNames = ALLELE_NAMES_DIPLOID;

    SimpleDefaultGenotypeData genotypicData = new SimpleDefaultGenotypeData(NAME, HEADERS_UNIQUE_NAMES,
            MARKER_NAMES_DEFAULT, ALLELE_OBS_DIPLOID);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoDiploid-AllIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//from www . ja v a2s  . c o  m
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (diploid, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, true);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/diploid_genotypes/out/all-with-ids.csv").getPath()),
                            path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (diploid, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, false);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/diploid_genotypes/out/all-no-ids.csv").getPath()),
                            path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleDefaultGenotypeDataTest.java

@Test
public void diploidToCsvFileWithSelectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES_DEFAULT;
    expectedAlleleNames = ALLELE_NAMES_DIPLOID;

    SimpleDefaultGenotypeData genotypicData = new SimpleDefaultGenotypeData(NAME, HEADERS_UNIQUE_NAMES,
            MARKER_NAMES_DEFAULT, ALLELE_OBS_DIPLOID);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoDiploid-SelectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//ww  w.  j  a  v a 2 s .  com
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (diploid, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, true);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/diploid_genotypes/out/sel-with-ids.csv").getPath()),
                            path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (diploid, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, false);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/diploid_genotypes/out/sel-no-ids.csv").getPath()),
                            path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleDefaultGenotypeDataTest.java

@Test
public void diploidToCsvFileWithUnselectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES_DEFAULT;
    expectedAlleleNames = ALLELE_NAMES_DIPLOID;

    SimpleDefaultGenotypeData genotypicData = new SimpleDefaultGenotypeData(NAME, HEADERS_UNIQUE_NAMES,
            MARKER_NAMES_DEFAULT, ALLELE_OBS_DIPLOID);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoDiploid-UnselectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//w  w w .  ja v a 2 s.  co  m
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (diploid, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, false, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/diploid_genotypes/out/unsel-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write default genotypes file (diploid, with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, false, true, false);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/diploid_genotypes/out/unsel-no-ids.csv").getPath()),
                            path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleDistanceMatrixDataTest.java

@Test
public void toCsvFileWithAllIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    SimpleDistanceMatrixData distanceData = new SimpleDistanceMatrixData(expectedHeaders, DISTANCES);

    Set<Integer> ids = distanceData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "DistanceMatrix-AllIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//  w  w w.j a  va2s . co  m
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, true, true, true);

    assertTrue("Output is not correct!", FileUtils.contentEquals(new File(
            SimpleDistanceMatrixDataTest.class.getResource("/distances/out/all-with-ids.csv").getPath()),
            path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, false, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(new File(
                    SimpleDistanceMatrixDataTest.class.getResource("/distances/out/all-no-ids.csv").getPath()),
                    path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleDistanceMatrixDataTest.java

@Test
public void toCsvFileWithSelectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    SimpleDistanceMatrixData distanceData = new SimpleDistanceMatrixData(expectedHeaders, DISTANCES);

    Set<Integer> ids = distanceData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "DistanceMatrix-SelectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);// www .  ja v  a 2s.  com
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, true, true, false);

    assertTrue("Output is not correct!", FileUtils.contentEquals(new File(
            SimpleDistanceMatrixDataTest.class.getResource("/distances/out/sel-with-ids.csv").getPath()),
            path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, false, true, false);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(new File(
                    SimpleDistanceMatrixDataTest.class.getResource("/distances/out/sel-no-ids.csv").getPath()),
                    path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleDistanceMatrixDataTest.java

@Test
public void toCsvFileWithUnselectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    SimpleDistanceMatrixData distanceData = new SimpleDistanceMatrixData(expectedHeaders, DISTANCES);

    Set<Integer> ids = distanceData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "DistanceMatrix-UnselectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);//from   ww w .  ja v  a2  s .co  m
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, true, false, true);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/distances/out/unsel-with-ids.csv").getPath()),
                            path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write distance matrix file (with solution) " + dataName);

    distanceData.writeData(path, FileType.CSV, solution, false, false, true);

    assertTrue("Output is not correct!", FileUtils.contentEquals(new File(
            SimpleDistanceMatrixDataTest.class.getResource("/distances/out/unsel-no-ids.csv").getPath()),
            path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleFrequencyGenotypeDataTest.java

@Test
public void toCsvFileWithAllIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;//from   w ww  .j  ava 2s. c  om
    expectedAlleleNames = ALLELE_NAMES;

    SimpleFrequencyGenotypeData genotypicData = new SimpleFrequencyGenotypeData(expectedHeaders,
            expectedMarkerNames, expectedAlleleNames, ALLELE_FREQUENCIES);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoFreqs-AllIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/frequency_genotypes/out/all-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, true, false);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/frequency_genotypes/out/all-no-ids.csv").getPath()),
                            path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleFrequencyGenotypeDataTest.java

@Test
public void toCsvFileWithSelectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;//  ww  w  . j  a  v a  2s  .  c  o  m
    expectedAlleleNames = ALLELE_NAMES;

    SimpleFrequencyGenotypeData genotypicData = new SimpleFrequencyGenotypeData(expectedHeaders,
            expectedMarkerNames, expectedAlleleNames, ALLELE_FREQUENCIES);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoFreqs-SelectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/frequency_genotypes/out/sel-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, true, false, false);

    assertTrue("Output is not correct!",
            FileUtils
                    .contentEquals(
                            new File(SimpleDistanceMatrixDataTest.class
                                    .getResource("/frequency_genotypes/out/sel-no-ids.csv").getPath()),
                            path.toFile()));

}

---

From source file:org.corehunter.tests.data.simple.SimpleFrequencyGenotypeDataTest.java

@Test
public void toCsvFileWithUnselectedIds() throws IOException {
    expectedHeaders = HEADERS_UNIQUE_NAMES;
    expectedMarkerNames = MARKER_NAMES;//from  w  w w  .ja v a 2s .  c o m
    expectedAlleleNames = ALLELE_NAMES;

    SimpleFrequencyGenotypeData genotypicData = new SimpleFrequencyGenotypeData(expectedHeaders,
            expectedMarkerNames, expectedAlleleNames, ALLELE_FREQUENCIES);

    Set<Integer> ids = genotypicData.getIDs();

    Path dirPath = Paths.get(TEST_OUTPUT);

    Files.createDirectories(dirPath);

    dirPath = Files.createTempDirectory(dirPath, "GenoFreqs-UnselectedIds");

    // create solution
    SubsetSolution solution = new SubsetSolution(ids);
    for (int sel : SELECTION) {
        solution.select(sel);
    }

    Path path;

    // write with integer ids
    dataName = "with-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, false, true, true);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/frequency_genotypes/out/unsel-with-ids.csv").getPath()),
                    path.toFile()));

    // write without integer ids
    dataName = "no-ids.csv";

    path = Paths.get(dirPath.toString(), dataName);

    System.out.println(" |- Write frequency genotypes file (with solution) " + dataName);

    genotypicData.writeData(path, FileType.CSV, solution, false, true, false);

    assertTrue("Output is not correct!",
            FileUtils.contentEquals(
                    new File(SimpleDistanceMatrixDataTest.class
                            .getResource("/frequency_genotypes/out/unsel-no-ids.csv").getPath()),
                    path.toFile()));

}

---

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