Example usage for org.apache.commons.lang.math IntRange IntRange

Introduction

In this page you can find the example usage for org.apache.commons.lang.math IntRange IntRange.

Prototype

public IntRange(Number number1, Number number2) 

Source Link

Document

Constructs a new IntRange with the specified minimum and maximum numbers (both inclusive).

The arguments may be passed in the order (min,max) or (max,min).

Usage

From source file:au.org.ala.delta.key.AllowImproperSubgroupsTest.java

public void testAllowImproperSubgroups() throws Exception {
    URL directivesFileURL = getClass().getResource("/sample/mykey");
    File directivesFile = new File(directivesFileURL.toURI());

    URL charFileURL = getClass().getResource("/sample/kchars");
    File charFile = new File(charFileURL.toURI());

    URL itemsFileURL = getClass().getResource("/sample/kitems");
    File itemsFile = new File(itemsFileURL.toURI());

    // Use dummy temp file for data directory seeing as we don't have a use
    // for it here
    KeyContext context = new KeyContext(directivesFile);
    context.setABase(1.0);/*from   ww w. ja v a 2s. c  om*/
    context.setVaryWt(1.0);
    context.setRBase(1.0);
    context.setReuse(1.0);
    context.setCharactersFile(charFile);
    context.setItemsFile(itemsFile);

    context.setAllowImproperSubgroups(false);

    KeyUtils.loadDataset(context);

    List<Integer> availableCharacterNumbers = Arrays
            .asList(ArrayUtils.toObject(new IntRange(1, context.getNumberOfCharacters()).toArray()));
    List<Integer> availableTaxaNumbers = Arrays
            .asList(ArrayUtils.toObject(new IntRange(1, context.getMaximumNumberOfItems()).toArray()));

    Map<Character, Double> bestMap = KeyBest.orderBest(context.getDataSet(), context.getCharacterCostsAsArray(),
            context.getCalculatedItemAbundanceValuesAsArray(), availableCharacterNumbers, availableTaxaNumbers,
            context.getRBase(), context.getABase(), context.getReuse(), context.getVaryWt(),
            context.getAllowImproperSubgroups());

    assertFalse(bestMap.containsKey(context.getCharacter(10)));

    context.setAllowImproperSubgroups(true);

    Map<Character, Double> bestMap2 = KeyBest.orderBest(context.getDataSet(),
            context.getCharacterCostsAsArray(), context.getCalculatedItemAbundanceValuesAsArray(),
            availableCharacterNumbers, availableTaxaNumbers, context.getRBase(), context.getABase(),
            context.getReuse(), context.getVaryWt(), context.getAllowImproperSubgroups());

    assertTrue(bestMap2.containsKey(context.getCharacter(10)));
}

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From source file:com.linkedin.pinot.common.config.ColumnPartitionConfig.java

/**
 * Helper method to convert an array of ranges in string form (eg [2 3]) into a list
 * of {@link IntRange}. Expects each string range to be formatted correctly.
 *
 * @param inputs Array of ranges in string form.
 * @return List of IntRange's for the given input.
 *///w ww.  ja  v  a  2s .  c  o m
public static List<IntRange> rangesFromString(String[] inputs) {
    List<IntRange> ranges = new ArrayList<>(inputs.length);
    for (String input : inputs) {

        String trimmed = input.trim();
        String[] split = trimmed.split("\\s+");
        String startString = split[0].substring(1, split[0].length());
        String endString = split[1].substring(0, split[1].length() - 1);
        ranges.add(new IntRange(Integer.parseInt(startString), Integer.parseInt(endString)));
    }
    return ranges;
}

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From source file:com.mobiquitynetworks.statsutilspig.CreateCombinations.java

public Map<Integer, Object> getVectors(Integer fieldsCardinality) {
    Map<Integer, Object> vectors = new HashMap<>();
    for (int i = 0; i < fieldsCardinality; i++) {
        int[] intArray = new IntRange(0, i).toArray();
        vectors.put(i + 1, intArray);/*www  . j  av a  2  s  . c om*/
    }
    return vectors;
}

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From source file:edu.cornell.med.icb.goby.reads.TestQualityEncoding.java

/**
 * Validate score conversion for {@link edu.cornell.med.icb.goby.reads.QualityEncoding#SANGER}.
 *//*w ww  .jav a2  s.c om*/
@Test
public void sanger() {
    final Range qualityRange = new IntRange(0, 40);
    final String qualityChars = encodedQualityCharacters.substring(0, 40);
    final QualityEncoding encoding = QualityEncoding.SANGER;
    for (int i = 0; i < 40; i++) {
        final byte score = (byte) (qualityRange.getMinimumInteger() + i);
        assertEquals("wrong character for score " + score, qualityChars.charAt(i),
                encoding.phredQualityScoreToAsciiEncoding(score));
        assertEquals("wrong score for character " + qualityChars.charAt(i), score,
                encoding.asciiEncodingToPhredQualityScore(qualityChars.charAt(i)));
    }

    final QualityEncoding solexaEncoding = QualityEncoding.ILLUMINA;
    for (byte qPhred = 0; qPhred < 93; qPhred++) {
        final char sanger = solexaEncoding.phredQualityScoreToAsciiEncoding(qPhred);
        final byte roundTrip = solexaEncoding.asciiEncodingToPhredQualityScore(sanger);
        assertEquals(qPhred, roundTrip);

    }
}

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From source file:au.org.ala.delta.directives.AbstractDirective.java

protected IntRange parseRange(String str) {
    Matcher m = RANGE_PATTERN.matcher(str);
    if (m.matches()) {
        int lhs = Integer.parseInt(m.group(1));
        int rhs = Integer.parseInt(m.group(2));
        return new IntRange(lhs, rhs);
    } else {/*  w  ww  .ja  va2 s  .co  m*/
        return new IntRange(Integer.parseInt(str));
    }
}

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From source file:edu.harvard.med.screensaver.io.libraries.rnai.WorkbookLibraryContentsParser.java

public void convert() throws IOException {
    Workbook _workbook = new Workbook("Library Contents Input Stream", getStream());
    File tmpFile = File.createTempFile("workbook", ".csv");
    tmpFile.deleteOnExit();//from  www .ja v  a2s  . c  o m
    log.debug("converting workbook into csv file: " + tmpFile.getAbsolutePath());
    CSVPrintWriter writer = new CSVPrintWriter(new BufferedWriter(new FileWriter(tmpFile)), "\n",
            FIELD_DELIMITER);
    Iterator<Worksheet> worksheetsIterator = _workbook.iterator();
    int prevSheetLastRecord = 0;
    int record = 0;
    _worksheetRecordRanges = Maps.newHashMap();
    while (worksheetsIterator.hasNext()) {
        Worksheet worksheet = worksheetsIterator.next().forOrigin(0, FIRST_DATA_ROW);
        Iterator<Row> rowsIterator = worksheet.iterator();
        while (rowsIterator.hasNext()) {
            for (Cell cell : rowsIterator.next()) {
                writer.print(cell.getAsString());
            }
            writer.println();
            ++record;
        }
        IntRange worksheetRecordRange = new IntRange(prevSheetLastRecord, record);
        _worksheetRecordRanges.put(worksheetRecordRange, worksheet.getName());
        prevSheetLastRecord = record;
    }
    writer.close();
    _reader = new BufferedReader(new FileReader(tmpFile));
    log.debug("done converting workbook into csv file");
}

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From source file:edu.cornell.med.icb.goby.reads.TestQualityEncoding.java

/**
 * Validate score conversion for//ww w. j a  va2  s  . c om
 * {@link edu.cornell.med.icb.goby.reads.QualityEncoding#ILLUMINA}.
 */
@Test
public void illumina() {
    final Range qualityRange = new IntRange(0, 40);
    final String qualityChars = encodedQualityCharacters.substring(31, 71);
    final QualityEncoding encoding = QualityEncoding.ILLUMINA;
    for (int i = 0; i < 40; i++) {
        final byte score = (byte) (qualityRange.getMinimumInteger() + i);
        assertEquals("wrong character for score " + score, qualityChars.charAt(i),
                encoding.phredQualityScoreToAsciiEncoding(score));
        assertEquals("wrong score for character " + qualityChars.charAt(i), score,
                encoding.asciiEncodingToPhredQualityScore(qualityChars.charAt(i)));
    }

    final QualityEncoding solexaEncoding = QualityEncoding.ILLUMINA;
    for (byte qPhred = 0; qPhred < 62; qPhred++) {
        final char illumina13 = solexaEncoding.phredQualityScoreToAsciiEncoding(qPhred);
        final byte roundTrip = solexaEncoding.asciiEncodingToPhredQualityScore(illumina13);
        assertEquals(qPhred, roundTrip);

    }
}

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From source file:au.org.ala.delta.directives.args.DirectiveArgsParser.java

protected IntRange readIds(IntegerValidator validator) throws ParseException {
    int startPos = _position;
    int first = readInteger();
    validateId(first, validator, startPos);
    if (_currentChar == '-') {
        readNext();//from   w  w w  .ja v  a 2s. c o  m
        startPos = _position;
        int last = readInteger();
        validateId(last, validator, startPos);

        if (_validateRangeOrder && first > last) {
            throw DirectiveError.asException(DirectiveError.Error.RANGE_SEQUENCE_ERROR, startPos);
        }

        return new IntRange(first, last);
    }
    return new IntRange(first);
}

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From source file:au.org.ala.delta.intkey.directives.ParsingUtils.java

public static IntRange parseIntRange(String text) {
    try {/*from   w  ww .  ja  va  2s.c o  m*/
        Matcher m = INT_RANGE_PATTERN.matcher(text);
        if (m.matches()) {
            int lhs = Integer.parseInt(m.group(1));
            int rhs = Integer.parseInt(m.group(2));
            return new IntRange(lhs, rhs);
        } else {
            return new IntRange(Integer.parseInt(text));
        }
    } catch (NumberFormatException ex) {
        return null;
    }
}

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From source file:com.linkedin.pinot.core.segment.creator.impl.stats.AbstractColumnStatisticsCollector.java

/**
 * Returns the partition range within which the column values exist.
 *
 * @return List of ranges for the column values.
 *//*from  w  w  w .  j a v  a 2  s . c  o m*/
@Nullable
public List<IntRange> getPartitionRanges() {
    if (partitionRangeStart <= partitionRangeEnd) {
        return Arrays.asList(new IntRange(partitionRangeStart, partitionRangeEnd));
    } else {
        return null;
    }
}

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