Example usage for org.apache.commons.math3.util Pair getValue

Introduction

In this page you can find the example usage for org.apache.commons.math3.util Pair getValue.

Prototype

public V getValue() 

Source Link

Document

Get the value.

Usage

From source file:ldbc.snb.datagen.generator.distribution.utils.Bucket.java

public static ArrayList<Bucket> bucketizeHistogram(ArrayList<Pair<Integer, Integer>> histogram,
        int num_buckets) {

    ArrayList<Bucket> buckets = new ArrayList<Bucket>();
    int population = 0;
    int num_edges = 0;
    for (Pair<Integer, Integer> i : histogram) {
        population += i.getValue();
        num_edges += i.getValue() * i.getKey();
    }/*from  ww w  .  j  av  a 2  s.  c o m*/
    num_edges /= 2;

    int avgDegreeAt1B = 200;
    int avgDegree = num_edges / population;
    double aCoeff = Math.log(avgDegreeAt1B) / Math.log(1000000000);
    double bCoeff = (aCoeff - (Math.log(avgDegree) / Math.log(population))) / Math.log10(population);

    int target_mean = (int) Math.round(
            Math.pow(DatagenParams.numPersons, (aCoeff - bCoeff * Math.log10(DatagenParams.numPersons))));
    System.out.println("Distribution mean degree: " + avgDegree + " Distribution target mean " + target_mean);
    int bucket_size = (int) (Math.ceil(population / (double) (num_buckets)));
    int current_histogram_index = 0;
    int current_histogram_left = histogram.get(current_histogram_index).getValue();
    for (int i = 0; i < num_buckets && (current_histogram_index < histogram.size()); ++i) {
        int current_bucket_count = 0;
        int min = population;
        int max = 0;
        while (current_bucket_count < bucket_size && current_histogram_index < histogram.size()) {
            int degree = histogram.get(current_histogram_index).getKey();
            min = degree < min ? degree : min;
            max = degree > max ? degree : max;
            if ((bucket_size - current_bucket_count) > current_histogram_left) {
                current_bucket_count += current_histogram_left;
                current_histogram_index++;
                if (current_histogram_index < histogram.size()) {
                    current_histogram_left = histogram.get(current_histogram_index).getValue();
                }
            } else {
                current_histogram_left -= (bucket_size - current_bucket_count);
                current_bucket_count = bucket_size;
            }
        }
        min = (int) (min * target_mean / (double) avgDegree);
        max = (int) (max * target_mean / (double) avgDegree);
        buckets.add(new Bucket(min, max));
    }
    return buckets;
}

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From source file:com.insightml.utils.Collections.java

public static <V> LinkedList<V> values(final List<? extends Pair<?, V>> run) {
    final LinkedList<V> values = new LinkedList<>();
    for (final Pair<?, V> entry : run) {
        if (entry.getValue() != null) {
            values.add(entry.getValue());
        }/*from  ww w.  jav a2  s .  c o m*/
    }
    return values;
}

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From source file:database.HashTablesTools.java

public static boolean addAFile(String pathToFile, String fourLetterCode, Connection connexion, String tableName,
        String tableFailureName, AlgoParameters algoParameters) throws IOException, NoSuchAlgorithmException {

    String hash = HashTablesTools.getMD5hash(pathToFile);

    // TODO add check to failure db
    boolean alreadyParsed = false;
    try {//from ww w.j av  a2  s . c  o  m
        alreadyParsed = fileAlreadyParsedDetectedByHash(connexion, tableName, tableFailureName, hash);
    } catch (SQLException e) {
        return false;
    }
    if (alreadyParsed == true) {
        //System.out.println("Already parsed in DB, nothing to do");
        return false;
    }
    Pair<String, MyStructureIfc> pairPathMyStructure = IOTools.getMyStructureIfc(algoParameters, pathToFile);

    if (pairPathMyStructure == null || pairPathMyStructure.getValue() == null) {
        insertIntoFailureTable(connexion, tableFailureName, hash, fourLetterCode);
        return false;
    }
    MyChainIfc[] chainsForShapeBuilding = pairPathMyStructure.getValue().getAllChainsRelevantForShapeBuilding();

    int countEntries = 0;
    Chains: for (MyChainIfc chain : chainsForShapeBuilding) {

        MyMonomerType monomerType = MyMonomerType.getEnumType(chain.getMyMonomers()[0].getType());
        char[] chainType = "  ".toCharArray();
        if (monomerType.equals(MyMonomerType.AMINOACID)) {
            chainType = "AA".toCharArray();
        }
        if (monomerType.equals(MyMonomerType.NUCLEOTIDE)) {
            chainType = "NU".toCharArray();
        }
        if (monomerType.equals(MyMonomerType.HETATM)) {
            continue Chains;
        }
        char[] chainName = chain.getChainId();
        String sequence = SequenceTools.generateSequence(chain);

        if (sequence.length() > HashTablesTools.maxCharInVarchar) {
            String truncatedSequence = sequence.substring(0, HashTablesTools.maxCharInVarchar);
            sequence = truncatedSequence;
        }

        countEntries += enterInPDBfilesHashDB(connexion, hash, fourLetterCode, tableName, chainType, chainName,
                sequence);
    }
    if (countEntries == 0) {
        insertIntoFailureTable(connexion, tableFailureName, hash, fourLetterCode);
    }
    return true;
}

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From source file:io.IOTools.java

public static Pair<String, MyStructureIfc> getMyStructureIfc(AlgoParameters algoParameters, String pathToFile) {

    BiojavaReader reader = new BiojavaReader(algoParameters);
    Pair<String, Structure> pairPathStructure = null;
    try {//from  www.j  ava2 s .  c o  m
        pairPathStructure = reader.read(pathToFile, algoParameters.getPATH_TO_CHEMCOMP_FOLDER());
    } catch (IOException | ExceptionInIOPackage e) {
        return null;
    }
    AdapterBioJavaStructure adapterBioJavaStructure = new AdapterBioJavaStructure(algoParameters);
    MyStructureIfc mystructure = null;
    String pdbFileHash = null;
    try {
        pdbFileHash = HashTablesTools.getMD5hash(pathToFile);
    } catch (NoSuchAlgorithmException | IOException e) {
        e.printStackTrace();
    }
    try {

        mystructure = adapterBioJavaStructure.getMyStructureAndSkipHydrogens(pairPathStructure.getValue(),
                pdbFileHash);
    } catch (ExceptionInMyStructurePackage | ReadingStructurefileException | ExceptionInConvertFormat e) {
        return null;
    }
    Pair<String, MyStructureIfc> pairPathMyStructure = new Pair(pairPathStructure.getKey(), mystructure);
    return pairPathMyStructure;
}

---

From source file:io.IOTools.java

/**
 * @param algoParameters/* ww  w .j a  v a 2 s .c o  m*/
 * @param fourLetterCode that must be lower case
 * @return Can return null
 */
public static Pair<String, MyStructureIfc> getMyStructureIfc(AlgoParameters algoParameters,
        char[] fourLetterCode) {
    BiojavaReader reader = new BiojavaReader(algoParameters);
    Pair<String, Structure> pairPathStructure = null;
    try {
        // TODO change to char[]
        pairPathStructure = reader.readFromPDBFolder(String.valueOf(fourLetterCode),
                algoParameters.getPATH_TO_REMEDIATED_PDB_MMCIF_FOLDER(),
                algoParameters.getPATH_TO_CHEMCOMP_FOLDER());
    } catch (IOException | ExceptionInIOPackage e) {
        return null;
    }
    String pdbFileHash = null;
    try {
        pdbFileHash = HashTablesTools.getMD5hash(pairPathStructure.getKey());
    } catch (NoSuchAlgorithmException | IOException e) {
        e.printStackTrace();
    }
    AdapterBioJavaStructure adapterBioJavaStructure = new AdapterBioJavaStructure(algoParameters);
    MyStructureIfc mystructure = null;
    try {
        mystructure = adapterBioJavaStructure.getMyStructureAndSkipHydrogens(pairPathStructure.getValue(),
                pdbFileHash);
    } catch (ExceptionInMyStructurePackage | ReadingStructurefileException | ExceptionInConvertFormat e) {
        return null;
    }
    Pair<String, MyStructureIfc> pairPathMyStructure = new Pair(pairPathStructure.getKey(), mystructure);
    return pairPathMyStructure;
}

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From source file:genericBuffer.MyStructureBuffer.java

public synchronized MyStructureIfc getStructure(char[] fourLettercode) {

    String fourLettercodeString = String.valueOf(fourLettercode);
    for (Pair<String, MyStructureIfc> storeElement : queue) {
        if (storeElement.getFirst().equals(fourLettercodeString)) {
            return storeElement.getValue();
        }/*from   ww  w.java2  s. c  o  m*/
    }
    return null;
}

---

From source file:io.warp10.script.functions.OPTDTW.java

@Override
public Object apply(WarpScriptStack stack) throws WarpScriptException {
    Object o = stack.pop();/*from  w  ww . j ava 2  s.c o m*/

    if (!(o instanceof Number)) {
        throw new WarpScriptException(
                getName() + " expects a count of best restults to return on top of the stack.");
    }

    int count = ((Number) o).intValue();

    o = stack.pop();

    if (!(o instanceof List)) {
        throw new WarpScriptException(getName() + " expects a numeric list to use as query below the count.");
    }

    double[] query = new double[((List) o).size()];
    int i = 0;
    for (Object oo : (List) o) {
        query[i++] = ((Number) oo).doubleValue();
    }

    // Z-Normalize query
    double[] musigma = DoubleUtils.musigma(query, true);
    for (i = 0; i < query.length; i++) {
        query[i] = (query[i] - musigma[0]) / musigma[1];
    }

    o = stack.pop();

    if (!(o instanceof List)) {
        throw new WarpScriptException(getName()
                + " expects a numeric list as the sequence in which to find best matches below the 'query' list.");
    }

    double[] sequence = new double[((List) o).size()];
    i = 0;
    for (Object oo : (List) o) {
        sequence[i++] = ((Number) oo).doubleValue();
    }

    if (sequence.length <= query.length) {
        throw new WarpScriptException(
                getName() + " expects the query list to be shorter than the sequence list.");
    }

    double mindist = 0.0;

    PriorityQueue<Pair<Integer, Double>> distances = new PriorityQueue<Pair<Integer, Double>>(
            new Comparator<Pair<Integer, Double>>() {
                @Override
                public int compare(Pair<Integer, Double> o1, Pair<Integer, Double> o2) {
                    return o1.getValue().compareTo(o2.getValue());
                }
            });

    double[] subsequence = new double[query.length];

    for (i = 0; i <= sequence.length - query.length; i++) {
        System.arraycopy(sequence, i, subsequence, 0, query.length);
        // Z-Normalize the subsequence
        musigma = DoubleUtils.musigma(subsequence, true);
        for (int j = 0; j < subsequence.length; j++) {
            subsequence[j] = (subsequence[j] - musigma[0]) / musigma[1];
        }
        double dist = dtw.compute(query, 0, query.length, subsequence, 0, query.length, mindist);

        if (dist < 0) {
            continue;
        }

        distances.add(new Pair<Integer, Double>(i, dist));

        //
        // If the priority queue is of 'count' size, retrieve the largest distance and
        // use it as the threshold for the DTW computation
        //

        if (count > 0 && distances.size() >= count) {
            Object adist[] = distances.toArray();
            mindist = ((Pair<Integer, Double>) adist[count - 1]).getValue();
        }
    }

    List<List<Object>> results = new ArrayList<List<Object>>();

    while (!distances.isEmpty()) {

        Pair<Integer, Double> entry = distances.poll();

        List<Object> result = new ArrayList<Object>();
        result.add(entry.getKey());
        result.add(entry.getValue());
        results.add(result);

        if (count > 0 && count == results.size()) {
            break;
        }
    }

    stack.push(results);

    return stack;
}

---

From source file:myjmol.ScriptCommandOnUltiJmolTest.java

@Test
public void computeHydrogensEnergyAfterHydrogenMinimization() throws IOException, ParsingConfigFileException {

    AlgoParameters algoParameters = Tools.generateModifiedAlgoParametersForTestWithTestFoldersWithUltiJmol();
    int initialCount = algoParameters.ultiJMolBuffer.getSize();

    // Prepare input as environment of MSQ in 1di9
    String fourLetterCode = "1di9";
    Pair<String, MyStructureIfc> pathAndMyStructure = IOTools.getMyStructureIfc(algoParameters,
            fourLetterCode.toCharArray());

    MyMonomerIfc msqLigand = pathAndMyStructure.getValue().getHeteroChain("A".toCharArray())
            .getMyMonomerFromResidueId(500);
    MyChainIfc[] neighbors = msqLigand.getNeighboringAminoMyMonomerByRepresentativeAtomDistance();

    Cloner cloner2 = new Cloner(neighbors, algoParameters);
    MyStructureIfc target = cloner2.getClone();

    Protonate protonate = new Protonate(target, algoParameters);
    try {//from ww w  .  j a  v a2 s. com
        protonate.compute();
    } catch (ExceptionInScoringUsingBioJavaJMolGUI
            | ShapeBuildingException exceptionInScoringUsingBioJavaJMolGUI) {
        assertTrue(false);
    }

    MyStructureIfc protonatedTarget = protonate.getProtonatedMyStructure();
    protonatedTarget.setFourLetterCode("1di9".toCharArray());

    String moleculeV3000 = protonatedTarget.toV3000();

    try {
        Thread.sleep(1000L);
    } catch (InterruptedException e) {
        e.printStackTrace();
    }

    String script = MyJmolScripts.getScriptMinimizationOnlyHydrogens();
    ScriptCommandOnUltiJmol scriptCommandOnUltiJmol = new ScriptCommandOnUltiJmol(script, moleculeV3000,
            algoParameters, null);
    try {
        scriptCommandOnUltiJmol.execute();
    } catch (ExceptionInScoringUsingBioJavaJMolGUI exceptionInScoringUsingBioJavaJMolGUI) {
        assertTrue(false); // Should not happen. Only if energy during minimization failed to be obtained
    }
    Map<Results, Object> results = scriptCommandOnUltiJmol.getResults();

    boolean convergenceReached = (boolean) results.get(Results.CONVERGENCE_REACHED);
    Float finalEnergy = (Float) results.get(Results.FINAL_ENERGY);

    assertTrue(convergenceReached);
    // not reproducible
    System.out.println("finalEnergy = " + finalEnergy);
    // also possible finalEnergy = 5460.785
    //assertEquals(finalEnergy, 597.0f, 50.0f);

    int finalCount = algoParameters.ultiJMolBuffer.getSize();
    assertTrue(finalCount == initialCount);
    try {
        for (int i = 0; i < initialCount; i++) {
            algoParameters.ultiJMolBuffer.get().frame.dispose();
        }
    } catch (InterruptedException e) {
        e.printStackTrace();
    }
    assertTrue(algoParameters.ultiJMolBuffer.getSize() == 0);

}

---

From source file:mystructure.ClonerTest.java

@Test
public void testClonerWithMyMonomerAndConvertionToV3000() throws ParsingConfigFileException, IOException,
        ReadingStructurefileException, ExceptionInMyStructurePackage {

    AlgoParameters algoParameters = Tools.generateModifiedAlgoParametersForTestWithTestFoldersWithUltiJmol();

    String fourLetterCode = "1di9";
    Pair<String, MyStructureIfc> pathAndMyStructure = IOTools.getMyStructureIfc(algoParameters,
            fourLetterCode.toCharArray());

    int initialCount = algoParameters.ultiJMolBuffer.getSize();

    MyMonomerIfc msqLigand = pathAndMyStructure.getValue().getHeteroChain("A".toCharArray())
            .getMyMonomerFromResidueId(500);
    Cloner cloner = new Cloner(msqLigand, algoParameters);
    MyStructureIfc myStructureFromAMyMonomer = cloner.getClone();
    String myStructureV3000 = myStructureFromAMyMonomer.toV3000();

    // write to a temp text file
    String pathToTempFolder = folder.getRoot().getAbsolutePath();
    String pathTOWriteV3000Molfile = pathToTempFolder + "//v3000test.mol";
    WriteTextFile.writeTextFile(myStructureV3000, pathTOWriteV3000Molfile);

    // read it with cdk and check atom and bond count

    IAtomContainer mol = CdkTools.readV3000molFile(pathTOWriteV3000Molfile);
    int atomCount = MyStructureTools.getAtomCount(myStructureFromAMyMonomer);
    int bondCount = TestTools.getBondCount(myStructureFromAMyMonomer);
    assertTrue(mol.getAtomCount() == atomCount);
    assertTrue(mol.getBondCount() * 2 == bondCount);

    int finalCount = algoParameters.ultiJMolBuffer.getSize();
    assertTrue(finalCount == initialCount);
    try {/* w  ww  .  jav  a2 s .  c o  m*/
        for (int i = 0; i < initialCount; i++) {
            algoParameters.ultiJMolBuffer.get().frame.dispose();
        }
    } catch (InterruptedException e) {
        e.printStackTrace();
    }
    assertTrue(algoParameters.ultiJMolBuffer.getSize() == 0);

}

---

From source file:database.SequenceToolsTest.java

@Test
public void testGenerateSequenceFromMyStructureWithThreeUMPcovalentToNucleosides()
        throws ParsingConfigFileException, IOException {

    AlgoParameters algoParameters = Tools.generateModifiedAlgoParametersForTestWithTestFolders();

    String fourLetterCode = "229d";
    Pair<String, MyStructureIfc> pathAndMyStructure = IOTools.getMyStructureIfc(algoParameters,
            fourLetterCode.toCharArray());

    String sequence = SequenceTools.generateSequence(pathAndMyStructure.getValue().getAllNucleosidechains()[0]);
    assertTrue(sequence.equals(" DC DC DA DG DA DCUMP DG DA DAMG1 DAUMP5CMUMP DG DG"));
}

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