Example usage for java.util Arrays binarySearch

List of usage examples for java.util Arrays binarySearch

  1. HOME
  2. Java
  3. java
  4. java.util.*
  5. Arrays
  6. binarySearch

Introduction

In this page you can find the example usage for java.util Arrays binarySearch.

Prototype

public static int binarySearch(Object[] a, Object key)

Source Link

Document

Searches the specified array for the specified object using the binary search algorithm.

Usage

From source file:com.cg.mapreduce.fpgrowth.mahout.fpm.fpgrowth.FPGrowth.java

private static FrequentPatternMaxHeap growth(FPTree tree, MutableLong minSupportMutable, int k,
        FPTreeDepthCache treeCache, int level, int currentAttribute, StatusUpdater updater) {

    FrequentPatternMaxHeap frequentPatterns = new FrequentPatternMaxHeap(k, true);

    int i = Arrays.binarySearch(tree.getHeaderTableAttributes(), currentAttribute);
    if (i < 0) {
        return frequentPatterns;
    }/*  w ww. j av a  2 s.  c  o m*/

    int headerTableCount = tree.getHeaderTableCount();

    while (i < headerTableCount) {
        int attribute = tree.getAttributeAtIndex(i);
        long count = tree.getHeaderSupportCount(attribute);
        if (count < minSupportMutable.longValue()) {
            i++;
            continue;
        }
        updater.update("FPGrowth Algorithm for a given feature: " + attribute);
        FPTree conditionalTree = treeCache.getFirstLevelTree(attribute);
        if (conditionalTree.isEmpty()) {
            traverseAndBuildConditionalFPTreeData(tree.getHeaderNext(attribute), minSupportMutable.longValue(),
                    conditionalTree, tree);
            // printTree(conditionalTree);

        }

        FrequentPatternMaxHeap returnedPatterns;
        if (attribute == currentAttribute) {

            returnedPatterns = growthTopDown(conditionalTree, minSupportMutable, k, treeCache, level + 1, true,
                    currentAttribute, updater);

            frequentPatterns = mergeHeap(frequentPatterns, returnedPatterns, attribute, count, true);
        } else {
            returnedPatterns = growthTopDown(conditionalTree, minSupportMutable, k, treeCache, level + 1, false,
                    currentAttribute, updater);
            frequentPatterns = mergeHeap(frequentPatterns, returnedPatterns, attribute, count, false);
        }
        if (frequentPatterns.isFull() && minSupportMutable.longValue() < frequentPatterns.leastSupport()) {
            minSupportMutable.setValue(frequentPatterns.leastSupport());
        }
        i++;
    }

    return frequentPatterns;
}

From source file:com.puppycrawl.tools.checkstyle.checks.coding.MagicNumberCheck.java

/**
 * Decides whether the number of an AST is in the ignore list of this
 * check./*from w  w  w  .  j a  v a  2 s .  co  m*/
 * @param ast the AST to check
 * @return true if the number of ast is in the ignore list of this check.
 */
private boolean isInIgnoreList(DetailAST ast) {
    double value = CheckUtils.parseDouble(ast.getText(), ast.getType());
    final DetailAST parent = ast.getParent();
    if (parent.getType() == TokenTypes.UNARY_MINUS) {
        value = -1 * value;
    }
    return Arrays.binarySearch(ignoreNumbers, value) >= 0;
}

From source file:net.dorokhov.pony.web.server.common.StreamingViewRenderer.java

/**
 * Returns true if the given accept header accepts the given value.
 * @param acceptHeader The accept header.
 * @param toAccept The value to be accepted.
 * @return True if the given accept header accepts the given value.
 *//*from w  ww  .jav a 2s  . c  om*/
private static boolean accepts(String acceptHeader, String toAccept) {
    String[] acceptValues = acceptHeader.split("\\s*(,|;)\\s*");
    Arrays.sort(acceptValues);
    return Arrays.binarySearch(acceptValues, toAccept) > -1
            || Arrays.binarySearch(acceptValues, toAccept.replaceAll("/.*$", "/*")) > -1
            || Arrays.binarySearch(acceptValues, "*/*") > -1;
}

From source file:fastcall.FastCallSNP.java

private String getVCFString(String[] base, int[] depth, int currentChr, int position, byte refBase) {
    TByteArrayList bList;/*from  w  w  w  .  j  a  v  a2 s.  co  m*/
    boolean ifRecordedDeletion = false;
    TIntHashSet insertionLengthSet = new TIntHashSet();
    TIntHashSet deletionLengthSet = new TIntHashSet();
    int[][] pAlleleCount = new int[base.length][this.possibleAllele.length];
    int[] refDepth = new int[base.length];
    for (int i = 0; i < base.length; i++) {
        bList = new TByteArrayList();
        byte[] ba = base[i].getBytes();
        for (int j = 0; j < ba.length; j++) {
            if (ba[j] == '.') {
                bList.add(refBase);
            } else if (ba[j] == ',') {
                bList.add(refBase);
            } else if (ba[j] == 'A') {
                bList.add((byte) 65);
            } else if (ba[j] == 'a') {
                bList.add((byte) 65);
            } else if (ba[j] == 'C') {
                bList.add((byte) 67);
            } else if (ba[j] == 'c') {
                bList.add((byte) 67);
            } else if (ba[j] == 'G') {
                bList.add((byte) 71);
            } else if (ba[j] == 'g') {
                bList.add((byte) 71);
            } else if (ba[j] == 'T') {
                bList.add((byte) 84);
            } else if (ba[j] == 't') {
                bList.add((byte) 84);
            } else if (ba[j] == '+') {
                int endIndex = j + 2;
                for (int k = j + 1; k < ba.length; k++) {
                    if (ba[k] > 57) {
                        endIndex = k;
                        break;
                    }
                }
                StringBuilder sb = new StringBuilder();
                for (int k = j + 1; k < endIndex; k++) {
                    sb.append((char) ba[k]);
                }
                int length = Integer.valueOf(sb.toString());
                insertionLengthSet.add(length);
                j += sb.length();
                j += length;
                if (ba[j - 1] == '.' || ba[j - 1] == ',') {
                    bList.add((byte) 73);
                }
            } else if (ba[j] == '-') {
                int endIndex = j + 2;
                for (int k = j + 1; k < ba.length; k++) {
                    if (ba[k] > 57) {
                        endIndex = k;
                        break;
                    }
                }
                StringBuilder sb = new StringBuilder();
                for (int k = j + 1; k < endIndex; k++) {
                    sb.append((char) ba[k]);
                }
                int length = Integer.valueOf(sb.toString());
                deletionLengthSet.add(length);
                j += sb.length();
                j += length;
                if (ba[j - 1] == '.' || ba[j - 1] == ',') {
                    bList.add((byte) 68);
                }
            } else if (ba[j] == '^') {
                j++;
            } else if (ba[j] == '*') {
                bList.add(refBase);
                ifRecordedDeletion = true;
            }
            //N, n, $, >, <
            else {
                //do nothing
            }
        }
        byte[] taxonBase = bList.toArray();
        for (int j = 0; j < taxonBase.length; j++) {
            int index = Arrays.binarySearch(this.possibleAllele, taxonBase[j]);
            pAlleleCount[i][index]++;
        }
        int altSum = 0;
        for (int j = 0; j < pAlleleCount[i].length; j++) {
            if (this.possibleAllele[j] == refBase)
                continue;
            //                if (this.possibleAllele[j] == 68) continue;
            //                if (this.possibleAllele[j] == 73) continue;
            altSum += pAlleleCount[i][j];
        }
        refDepth[i] = depth[i] - altSum;
    }
    int totalDepth = 0;
    for (int i = 0; i < depth.length; i++) {
        totalDepth += depth[i];
    }

    int[] indelTypeCount = new int[2];
    indelTypeCount[0] = deletionLengthSet.size();
    indelTypeCount[1] = insertionLengthSet.size();

    //****************************Filter1 IndelFilter*****************************************
    //Too many indels usually means mis-alignment
    if (indelTypeCount[0] + indelTypeCount[1] > 1)
        return null;
    //=======================================Filter1=====================================================

    //****************************Filter2 Depth_ratio_test*****************************************
    //In any individual, alt allele show up < 2 times, ignore
    //In any individual, alt allele show up 2 times when 2 < depth < 5. Pick up
    //In any individual, alt allele show up > individualDepthRatioThresh, when depth >= 5. Pick up
    //When depth is low, tend to have assembly errors, LTR

    TByteHashSet altAlleleSet = new TByteHashSet();
    for (int i = 0; i < pAlleleCount[0].length; i++) {
        if (possibleAllele[i] == refBase)
            continue;
        for (int j = 0; j < pAlleleCount.length; j++) {
            if (depth[j] < 2) {
            } else if (depth[j] < 5) {
                if (pAlleleCount[j][i] >= 2) {
                    altAlleleSet.add(this.possibleAllele[i]);
                }
            } else {
                if ((double) pAlleleCount[j][i] / depth[j] > this.individualDepthRatioThresh) {
                    altAlleleSet.add(this.possibleAllele[i]);
                }
            }
        }
    }
    byte[] altAllele = altAlleleSet.toArray();
    if (altAllele.length == 0)
        return null;
    Arrays.sort(altAllele);
    //=======================================Filter2=====================================================  

    int[] altAllele2PAlleleIndex = new int[altAllele.length];
    for (int i = 0; i < this.possibleAllele.length; i++) {
        int index = Arrays.binarySearch(altAllele, this.possibleAllele[i]);
        if (index < 0)
            continue;
        altAllele2PAlleleIndex[index] = i;
    }
    int[] altAlleleTotalDepth = new int[altAllele.length];
    for (int i = 0; i < altAllele.length; i++) {
        for (int j = 0; j < base.length; j++) {
            altAlleleTotalDepth[i] += pAlleleCount[j][altAllele2PAlleleIndex[i]];
        }
    }
    int[] altAlleleDepthDesendingIndex = FArrayUtils.getIndexByDescendingValue(altAlleleTotalDepth);
    int refTotalDepth = 0;
    for (int i = 0; i < refDepth.length; i++)
        refTotalDepth += refDepth[i];

    //****************************Filter3 third_allele_test************************************************
    //individual should not have the third allele
    if (altAllele.length > 1) {
        for (int i = 0; i < base.length; i++) {
            int[] tempCnt = new int[altAllele.length];
            for (int j = 0; j < altAllele.length; j++) {
                tempCnt[j] = pAlleleCount[i][altAllele2PAlleleIndex[j]];
            }
            int sum = refDepth[i];
            double[] v = new double[altAllele.length + 1];
            for (int j = 0; j < tempCnt.length; j++)
                v[j] = (double) tempCnt[j] / sum;
            v[v.length - 1] = (double) refDepth[i] / sum;
            Arrays.sort(v);
            if (v[v.length - 3] > individualThirdAlleleRatioThresh)
                return null;
        }
    }
    //===========================Filter3=========================================================

    //****************************Filter4 Segregation_test*****************************************
    long[] observed = new long[base.length];
    double[] expected = new double[base.length];
    double[] segregationP = new double[altAllele.length];
    ChiSquareTest ct = new ChiSquareTest();
    int cnt = 0;
    for (int i = 0; i < altAllele.length; i++) {
        double r = (double) altAlleleTotalDepth[i] / (refTotalDepth + altAlleleTotalDepth[i]);
        for (int j = 0; j < base.length; j++) {
            observed[j] = pAlleleCount[j][altAllele2PAlleleIndex[i]];
            expected[j] = r;
        }
        segregationP[i] = ct.chiSquareTest(expected, observed);
        if (segregationP[i] > this.segregationPValueThresh)
            cnt++;
    }
    if (cnt == altAllele.length)
        return null;
    //===========================Filter4=========================================================

    int nonMissingCnt = 0;
    int[] refAndAllelePresence = new int[altAllele.length + 1];
    for (int i = 0; i < base.length; i++) {
        if (refDepth[i] != 0) {
            nonMissingCnt++;
            refAndAllelePresence[0]++;
        } else {
            for (int j = 0; j < altAllele.length; j++) {
                if (pAlleleCount[i][altAllele2PAlleleIndex[j]] != 0) {
                    nonMissingCnt++;
                    break;
                }
            }
        }
        for (int j = 0; j < altAllele.length; j++) {
            if (pAlleleCount[i][altAllele2PAlleleIndex[j]] != 0) {
                refAndAllelePresence[j + 1]++;
            }
        }
    }
    StringBuilder sb = new StringBuilder();
    sb.append(currentChr).append("\t").append(position).append("\t").append((char) refBase).append("\t");
    for (int i = 0; i < altAllele.length; i++)
        sb.append(String.valueOf((char) altAllele[altAlleleDepthDesendingIndex[i]])).append(",");
    sb.deleteCharAt(sb.length() - 1);
    sb.append("\t").append("DP=").append(totalDepth).append(";AD=").append(refTotalDepth);
    for (int i = 0; i < altAllele.length; i++)
        sb.append(",").append(altAlleleTotalDepth[altAlleleDepthDesendingIndex[i]]);
    sb.append(";NZ=").append(nonMissingCnt).append(";AP=");
    for (int i = 0; i < refAndAllelePresence.length; i++)
        sb.append(refAndAllelePresence[i]).append(",");
    sb.deleteCharAt(sb.length() - 1);
    sb.append(";PV=");
    for (int i = 0; i < altAllele.length; i++)
        sb.append(segregationP[i]).append(",");
    sb.deleteCharAt(sb.length() - 1);
    sb.append(";DI=");
    for (int i = 0; i < indelTypeCount.length; i++)
        sb.append(indelTypeCount[i]).append(",");
    sb.deleteCharAt(sb.length() - 1);
    sb.append("\t").append("GT:AD:PL");

    for (int i = 0; i < base.length; i++) {
        int[] dep = new int[altAllele.length + 1];
        dep[0] = refDepth[i];
        for (int j = 0; j < altAllele.length; j++) {
            dep[j + 1] = pAlleleCount[i][altAllele2PAlleleIndex[altAlleleDepthDesendingIndex[j]]];
        }
        sb.append("\t").append(this.getGenotype(dep));
    }
    return sb.toString();
}

From source file:net.sourceforge.checkstyle4ada.TreeWalker4Ada.java

/**
 * Register a check for a given configuration.
 * @param aCheck the check to register// ww w  .j  a v  a2  s . c  o  m
 * @throws CheckstyleException if an error occurs
 */
private void registerCheck(Check aCheck) throws CheckstyleException {
    int[] tokens = new int[] {}; //safety initialization
    final Set checkTokens = aCheck.getTokenNames();
    if (!checkTokens.isEmpty()) {
        tokens = aCheck.getRequiredTokens();

        //register configured tokens
        final int acceptableTokens[] = aCheck.getAcceptableTokens();
        Arrays.sort(acceptableTokens);
        final Iterator it = checkTokens.iterator();
        while (it.hasNext()) {
            final String token = (String) it.next();
            try {
                final int tokenId = TokenTypes4Ada.getTokenId(token);
                if (Arrays.binarySearch(acceptableTokens, tokenId) >= 0) {
                    registerCheck(token, aCheck);
                }
                // TODO: else log warning
            } catch (IllegalArgumentException ex) {
                throw new CheckstyleException("illegal token \"" + token + "\" in check " + aCheck, ex);
            }
        }
    } else {
        tokens = aCheck.getDefaultTokens();
    }
    for (int i = 0; i < tokens.length; i++) {
        registerCheck(tokens[i], aCheck);
    }
    mAllChecks.add(aCheck);
}

From source file:ca.phon.app.project.ProjectWindow.java

private void init() {
    /* Layout *///  w w  w .  j  a  va 2  s  .c  o  m
    setLayout(new BorderLayout());

    final ProjectDataTransferHandler transferHandler = new ProjectDataTransferHandler(this);

    /* Create components */
    newCorpusButton = createNewCorpusButton();
    createCorpusButton = createCorpusButton();

    corpusList = new JList<String>();
    corpusModel = new CorpusListModel(getProject());
    corpusList.setModel(corpusModel);
    corpusList.setCellRenderer(new CorpusListCellRenderer());
    corpusList.setVisibleRowCount(20);
    corpusList.addListSelectionListener(e -> {
        if (getSelectedCorpus() != null) {
            String corpus = getSelectedCorpus();
            sessionModel.setCorpus(corpus);
            sessionList.clearSelection();
            corpusDetails.setCorpus(corpus);

            if (getProject().getCorpusSessions(corpus).size() == 0) {
                onSwapNewAndCreateSession(newSessionButton);
            } else {
                onSwapNewAndCreateSession(createSessionButton);
            }
        }
    });
    corpusList.addMouseListener(new MouseInputAdapter() {

        @Override
        public void mousePressed(MouseEvent e) {
            doPopup(e);
        }

        @Override
        public void mouseReleased(MouseEvent e) {
            doPopup(e);
        }

        public void doPopup(MouseEvent e) {
            if (e.isPopupTrigger()) {
                int clickedIdx = corpusList.locationToIndex(e.getPoint());
                if (clickedIdx >= 0 && Arrays.binarySearch(corpusList.getSelectedIndices(), clickedIdx) < 0) {
                    corpusList.setSelectedIndex(clickedIdx);
                }
                showCorpusListContextMenu(e.getPoint());
            }
        }
    });

    final DragSource corpusDragSource = new DragSource();
    corpusDragSource.createDefaultDragGestureRecognizer(corpusList, DnDConstants.ACTION_COPY, (event) -> {
        final List<ProjectPath> paths = new ArrayList<>();
        for (String corpus : getSelectedCorpora()) {
            final ProjectPath corpusPath = new ProjectPath(getProject(), corpus, null);
            paths.add(corpusPath);
        }
        final ProjectPathTransferable transferable = new ProjectPathTransferable(paths);
        event.startDrag(DragSource.DefaultCopyDrop, transferable);
    });

    corpusList.setDragEnabled(true);
    corpusList.setTransferHandler(transferHandler);

    corpusDetails = new CorpusDetailsPane(getProject());
    corpusDetails.setWrapStyleWord(true);
    corpusDetails.setRows(6);
    corpusDetails.setLineWrap(true);
    corpusDetails.setBackground(Color.white);
    corpusDetails.setOpaque(true);
    JScrollPane corpusDetailsScroller = new JScrollPane(corpusDetails);

    sessionList = new JList<String>();
    newSessionButton = createNewSessionButton();
    createSessionButton = createSessionButton();
    sessionModel = new SessionListModel(getProject());
    sessionList.setModel(sessionModel);
    sessionList.setCellRenderer(new SessionListCellRenderer());
    sessionList.setVisibleRowCount(20);
    sessionList.addListSelectionListener(e -> {
        if (sessionList.getSelectedValue() != null && !e.getValueIsAdjusting()) {
            String corpus = getSelectedCorpus();
            String session = getSelectedSessionName();

            sessionDetails.setSession(corpus, session);
        }
    });
    sessionList.addMouseListener(new MouseInputAdapter() {
        @Override
        public void mouseClicked(MouseEvent e) {
            if (e.getClickCount() == 2 && e.getButton() == 1) {
                // get the clicked item
                int clickedItem = sessionList.locationToIndex(e.getPoint());
                if (sessionList.getModel().getElementAt(clickedItem) == null)
                    return;

                final String session = sessionList.getModel().getElementAt(clickedItem).toString();
                final String corpus = ((SessionListModel) sessionList.getModel()).getCorpus();

                msgPanel.reset();
                msgPanel.setMessageLabel("Opening '" + corpus + "." + session + "'");
                msgPanel.setIndeterminate(true);
                msgPanel.repaint();

                SwingUtilities.invokeLater(() -> {
                    final ActionEvent ae = new ActionEvent(sessionList, -1, "openSession");
                    (new OpenSessionAction(ProjectWindow.this, corpus, session)).actionPerformed(ae);

                    msgPanel.setIndeterminate(false);
                });
            }
        }

        @Override
        public void mousePressed(MouseEvent e) {
            doPopup(e);
        }

        @Override
        public void mouseReleased(MouseEvent e) {
            doPopup(e);
        }

        public void doPopup(MouseEvent e) {
            if (e.isPopupTrigger()) {
                int clickedIdx = sessionList.locationToIndex(e.getPoint());
                if (clickedIdx >= 0 && Arrays.binarySearch(sessionList.getSelectedIndices(), clickedIdx) < 0) {
                    sessionList.setSelectedIndex(clickedIdx);
                }
                showSessionListContextMenu(e.getPoint());
            }
        }
    });

    sessionList.setDragEnabled(true);
    sessionList.setTransferHandler(transferHandler);

    final DragSource sessionDragSource = new DragSource();
    sessionDragSource.createDefaultDragGestureRecognizer(sessionList, DnDConstants.ACTION_COPY, (event) -> {
        final List<ProjectPath> paths = new ArrayList<>();
        final String corpus = getSelectedCorpus();
        if (corpus == null)
            return;
        for (String session : getSelectedSessionNames()) {
            final ProjectPath sessionPath = new ProjectPath(getProject(), corpus, session);
            paths.add(sessionPath);
        }
        final ProjectPathTransferable transferable = new ProjectPathTransferable(paths);
        event.startDrag(DragSource.DefaultCopyDrop, transferable);
    });

    sessionDetails = new SessionDetailsPane(getProject());
    sessionDetails.setLineWrap(true);
    sessionDetails.setRows(6);
    sessionDetails.setWrapStyleWord(true);
    sessionDetails.setBackground(Color.white);
    sessionDetails.setOpaque(true);
    JScrollPane sessionDetailsScroller = new JScrollPane(sessionDetails);

    JScrollPane corpusScroller = new JScrollPane(corpusList);
    JScrollPane sessionScroller = new JScrollPane(sessionList);

    blindModeBox = new JCheckBox("Blind transcription");
    blindModeBox.setSelected(false);

    msgPanel = new StatusPanel();

    corpusPanel = new JPanel(new BorderLayout());
    corpusPanel.add(newCorpusButton, BorderLayout.NORTH);
    corpusPanel.add(corpusScroller, BorderLayout.CENTER);
    corpusPanel.add(corpusDetailsScroller, BorderLayout.SOUTH);

    sessionPanel = new JPanel(new BorderLayout());
    sessionPanel.add(newSessionButton, BorderLayout.NORTH);
    sessionPanel.add(sessionScroller, BorderLayout.CENTER);
    sessionPanel.add(sessionDetailsScroller, BorderLayout.SOUTH);

    final JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
    splitPane.setLeftComponent(corpusPanel);
    splitPane.setRightComponent(sessionPanel);
    splitPane.setResizeWeight(0.5);

    // invoke later
    SwingUtilities.invokeLater(() -> {
        splitPane.setDividerLocation(0.5);
    });

    // the frame layout
    String projectName = null;
    projectName = getProject().getName();

    DialogHeader header = new DialogHeader(projectName, StringUtils.abbreviate(projectLoadPath, 80));

    add(header, BorderLayout.NORTH);

    CellConstraints cc = new CellConstraints();
    final JPanel topPanel = new JPanel(new FormLayout("pref, fill:pref:grow, right:pref", "pref"));
    topPanel.add(msgPanel, cc.xy(1, 1));
    topPanel.add(blindModeBox, cc.xy(3, 1));

    add(splitPane, BorderLayout.CENTER);
    add(topPanel, BorderLayout.SOUTH);

    // if no corpora are currently available, 'prompt' the user to create a new one
    if (getProject().getCorpora().size() == 0) {
        SwingUtilities.invokeLater(() -> {
            onSwapNewAndCreateCorpus(newCorpusButton);
        });
    } else {
        SwingUtilities.invokeLater(() -> {
            corpusList.setSelectedIndex(0);
        });
    }
}

From source file:eu.eidas.node.utils.EidasNodeErrorUtil.java

private static String getSamlSubStatusCode(final String errorCode) {
    for (int i = 0; i < EIDAS_SUB_STATUS_CODES.length; i++) {
        if (EIDAS_ERRORS_CODES_WITH_SAML_GENERATION[i] != null
                && EIDAS_ERRORS_CODES_WITH_SAML_GENERATION[i].length > 0
                && Arrays.binarySearch(EIDAS_ERRORS_CODES_WITH_SAML_GENERATION[i], errorCode) >= 0) {
            return EIDAS_SUB_STATUS_CODES[i].toString();
        }//w w w  .ja  v a 2 s  . co m
    }
    return null;
}

From source file:net.maizegenetics.analysis.imputation.FILLINImputationAccuracy.java

private boolean matchChromosomes() {
    Chromosome[] unimpChr = this.unimp.chromosomes();
    Chromosome[] keyChr = this.maskKey.chromosomes();
    ArrayList<Integer> keepSites = new ArrayList<>();
    for (Chromosome chr : unimpChr) { //if any of the chromosomes in input do not exist in key, return false (which then masks proportion)
        if (Arrays.binarySearch(keyChr, chr) < 0)
            return false;
    }//  www . j  a v a  2  s .  c o  m
    for (Chromosome chr : keyChr) { //keep sites on key that are on matching chromosomes
        if (Arrays.binarySearch(unimpChr, chr) > -1) {
            int[] startEnd = this.maskKey.firstLastSiteOfChromosome(chr);
            for (int site = startEnd[0]; site <= startEnd[1]; site++) {
                keepSites.add(site);
            }
        }
    }
    FilterGenotypeTable filter = FilterGenotypeTable.getInstance(this.maskKey,
            ArrayUtils.toPrimitive(keepSites.toArray(new Integer[keepSites.size()])));
    this.maskKey = filter;//GenotypeTableBuilder.getGenotypeCopyInstance(filter);//Change this back when GenotypeCopyInstance fixed
    if (verboseOutput)
        System.out.println(this.maskKey.numberOfSites() + " sites retained after chromsome filter");
    return true;
}

From source file:net.dorokhov.pony.web.server.common.StreamingViewRenderer.java

/**
 * Returns true if the given match header matches the given value.
 * @param matchHeader The match header./*w w  w.  j a v a2 s. c  o  m*/
 * @param toMatch The value to be matched.
 * @return True if the given match header matches the given value.
 */
private static boolean matches(String matchHeader, String toMatch) {
    String[] matchValues = matchHeader.split("\\s*,\\s*");
    Arrays.sort(matchValues);
    return Arrays.binarySearch(matchValues, toMatch) > -1 || Arrays.binarySearch(matchValues, "*") > -1;
}

From source file:org.apache.sysml.runtime.transform.BinAgent.java

@Override
public MatrixBlock apply(FrameBlock in, MatrixBlock out) {
    for (int j = 0; j < _colList.length; j++) {
        int colID = _colList[j];
        for (int i = 0; i < in.getNumRows(); i++) {
            double inVal = UtilFunctions.objectToDouble(in.getSchema()[colID - 1], in.get(i, colID - 1));
            int ix = Arrays.binarySearch(_binMaxs[j], inVal);
            int binID = ((ix < 0) ? Math.abs(ix + 1) : ix) + 1;
            out.quickSetValue(i, colID - 1, binID);
        }/*w ww  .j  a  v  a  2 s .co  m*/
    }
    return out;
}