Example usage for org.apache.commons.lang3.tuple Pair getRight

Introduction

In this page you can find the example usage for org.apache.commons.lang3.tuple Pair getRight.

Prototype

public abstract R getRight();

Source Link

Document

Gets the right element from this pair.

When treated as a key-value pair, this is the value.

Usage

From source file:com.act.lcms.MS2Simple.java

private List<Pair<MS2Collected, Integer>> filterByMS2PeakMatch(List<Double> ms2SearchMZs,
        List<MS2Collected> scans, Integer pickTopN) {
    List<Pair<MS2Collected, Integer>> results = new ArrayList<>();
    for (MS2Collected scan : scans) {
        Integer matchCount = searchForMatchingPeaks(ms2SearchMZs, scan);
        if (matchCount > 0) {
            results.add(Pair.of(scan, matchCount));
        }//from  ww w .j ava 2s. c  o m
    }

    Collections.sort(results, new Comparator<Pair<MS2Collected, Integer>>() {
        @Override
        public int compare(Pair<MS2Collected, Integer> o1, Pair<MS2Collected, Integer> o2) {
            if (!o1.getRight().equals(o2.getRight())) {
                // Sort in descending order of match count first.
                return o2.getRight().compareTo(o1.getRight());
            }

            // Fall back to sorting on trigger time (in ascending order) to enforce output stability/reproducability.
            return o1.getLeft().triggerTime.compareTo(o2.getLeft().triggerTime);
        }
    });

    if (pickTopN != null && pickTopN > 0 && pickTopN < results.size()) {
        return results.subList(0, pickTopN);
    }
    return results;
}

---

From source file:it.polimi.diceH2020.SPACE4CloudWS.solvers.solversImpl.DagSimSolver.DagSimSolver.java

@Override
protected Pair<Double, Boolean> run(Pair<List<File>, List<File>> pFiles, String remoteName,
        String remoteDirectory) throws Exception {
    if (pFiles.getLeft() == null || pFiles.getLeft().size() != 1) {
        throw new Exception("Model file missing");
    }//from   w w  w.  ja v a 2 s .  c  o m

    if (pFiles.getRight() == null || pFiles.getRight().isEmpty()) {
        throw new Exception("Replayer files missing");
    }

    double result = 0.;
    boolean success = false;
    List<String> remoteMsg = null;

    boolean stillNotOk = true;
    for (int i = 0; stillNotOk && i < MAX_ITERATIONS; ++i) {
        logger.info(remoteName + "-> Starting DagSim resolution on the server");

        File modelFile = pFiles.getLeft().get(0);
        String fileName = modelFile.getName();
        String remotePath = remoteDirectory + File.separator + fileName;

        List<File> workingFiles = pFiles.getRight();
        workingFiles.add(modelFile);
        cleanRemoteSubDirectory(remoteDirectory);
        sendFiles(remoteDirectory, workingFiles);
        logger.debug(remoteName + "-> Working files sent");

        logger.debug(remoteName + "-> Starting DagSim model...");
        String command = String.format("%s %s", connSettings.getSolverPath(), remotePath);
        remoteMsg = connector.exec(command, getClass());

        if (remoteMsg.contains("exit-status: 0")) {
            stillNotOk = false;
            logger.info(remoteName + "-> The remote simulation process completed correctly");
        } else {
            logger.debug(remoteName + "-> Remote exit status: " + remoteMsg);
        }
    }

    if (stillNotOk) {
        logger.info(remoteName + "-> Error in remote simulation on DagSim");
        throw new Exception("Error in the DagSim server");
    } else {
        final String stdout = remoteMsg.get(0);
        final String stderr = remoteMsg.get(1);

        try (Scanner scanner = new Scanner(stdout)) {
            while (!success && scanner.hasNextLine()) {
                Matcher matcher = RESULT_LINE.matcher(scanner.nextLine());
                if (matcher.find()) {
                    result = Double.valueOf(matcher.group("avg"));
                    success = true;
                }
            }
        }

        if (!success) {
            logger.error(String.format("%s -> Error in remote DagSim simulation", remoteName));
            logger.error(String.format("%s -> stdout:\n%s", remoteName, stdout));
            logger.error(String.format("%s -> stderr:\n%s", remoteName, stderr));
        }
    }

    return Pair.of(result, !success);
}

---

From source file:name.martingeisse.phunky.runtime.code.expression.array.ArrayElementExpression.java

@Override
public Variable resolveOrCreateVariable(final Environment environment) {
    Pair<Variable, String> variableArrayAndKey = obtainArrayVariableAndKey(environment);
    if (variableArrayAndKey == null) {
        return null;
    } else {/*w  w w.  ja v a  2 s.com*/
        PhpVariableArray variableArray = variableArrayAndKey.getLeft()
                .getVariableArray(environment.getRuntime(), getLocation());
        String key = variableArrayAndKey.getRight();
        return variableArray.getOrCreateVariable(key);
    }
}

---

From source file:com.act.lcms.v2.fullindex.Searcher.java

private List<MZWindow> mzWindowsInRange(Pair<Double, Double> mzRange) {
    List<MZWindow> mzWindowsInRange = new ArrayList<>( // Same here--access by index.
            mzWindows.stream()/* w  ww .j  av  a2  s  .com*/
                    .filter(x -> rangesOverlap(mzRange.getLeft(), mzRange.getRight(), x.getMin(), x.getMax()))
                    .collect(Collectors.toList()));
    if (mzWindowsInRange.size() == 0) {
        LOGGER.warn("Found zero m/z windows in range %.6f - %.6f", mzRange.getLeft(), mzRange.getRight());
    }
    return mzWindowsInRange;
}

---

From source file:com.act.lcms.plotter.WriteAndPlotMS1Results.java

public void plotFeedings(List<Pair<Double, MS1ScanForWellAndMassCharge>> feedings, String ion, String outPrefix,
        String fmt, String gnuplotFile) throws IOException {
    String outSpectraImg = outPrefix + "." + fmt;
    String outSpectraData = outPrefix + ".data";
    String outFeedingImg = outPrefix + ".fed." + fmt;
    String outFeedingData = outPrefix + ".fed.data";
    String feedingGnuplotFile = gnuplotFile + ".fed";

    boolean useMaxPeak = true;

    // maps that hold the values for across different concentrations
    List<Pair<Double, List<XZ>>> concSpectra = new ArrayList<>();
    List<Pair<Double, Double>> concAreaUnderSpectra = new ArrayList<>();
    List<Pair<Double, Double>> concMaxPeak = new ArrayList<>();

    // we will compute a running max of the intensity in the plot, and integral
    Double maxIntensity = 0.0d, maxAreaUnder = 0.0d;

    // now compute the maps { conc -> spectra } and { conc -> area under spectra }
    for (Pair<Double, MS1ScanForWellAndMassCharge> feedExpr : feedings) {
        Double concentration = feedExpr.getLeft();
        MS1ScanForWellAndMassCharge scan = feedExpr.getRight();

        // get the ms1 spectra for the selected ion, and the max for it as well
        List<XZ> ms1 = scan.getIonsToSpectra().get(ion);
        Double maxInThisSpectra = scan.getMaxIntensityForIon(ion);
        Double areaUnderSpectra = scan.getIntegralForIon(ion);

        // update the max intensity over all different spectra
        maxIntensity = Math.max(maxIntensity, maxInThisSpectra);
        maxAreaUnder = Math.max(maxAreaUnder, areaUnderSpectra);

        // install this concentration and spectra in map, to be dumped to file later
        concSpectra.add(Pair.of(concentration, ms1));
        concAreaUnderSpectra.add(Pair.of(concentration, areaUnderSpectra));
        concMaxPeak.add(Pair.of(concentration, maxInThisSpectra));
    }/*from  www.  j  av  a2 s. c  o  m*/

    // Write data output to outfiles
    List<String> plotID = null;
    try (FileOutputStream outSpectra = new FileOutputStream(outSpectraData)) {
        plotID = writeFeedMS1Values(concSpectra, maxIntensity, outSpectra);
    }

    try (FileOutputStream outFeeding = new FileOutputStream(outFeedingData)) {
        writeFeedMS1Values(useMaxPeak ? concMaxPeak : concAreaUnderSpectra, outFeeding);
    }

    // render outDATA to outPDF using gnuplot
    Gnuplotter gp = new Gnuplotter();
    String[] plotNames = plotID.toArray(new String[plotID.size()]);
    gp.plotOverlayed2D(outSpectraData, outSpectraImg, plotNames, "time", maxIntensity, "intensity", fmt,
            gnuplotFile);
    gp.plot2D(outFeedingData, outFeedingImg, new String[] { "feeding ramp" }, "concentration",
            useMaxPeak ? maxIntensity : maxAreaUnder, "integrated area under spectra", fmt, null, null, null,
            feedingGnuplotFile);
}

---

From source file:com.twitter.distributedlog.TestTruncate.java

@Test
public void testTruncation() throws Exception {
    String name = "distrlog-truncation";

    long txid = 1;
    Map<Long, DLSN> txid2DLSN = new HashMap<Long, DLSN>();
    Pair<DistributedLogManager, AsyncLogWriter> pair = populateData(txid2DLSN, conf, name, 4, 10, true);

    Thread.sleep(1000);/*  w w w  . j  a v a2  s .c o m*/

    // delete invalid dlsn
    assertFalse(Await.result(pair.getRight().truncate(DLSN.InvalidDLSN)));
    verifyEntries(name, 1, 1, 5 * 10);

    for (int i = 1; i <= 4; i++) {
        int txn = (i - 1) * 10 + i;
        DLSN dlsn = txid2DLSN.get((long) txn);
        assertTrue(Await.result(pair.getRight().truncate(dlsn)));
        verifyEntries(name, 1, (i - 1) * 10 + 1, (5 - i + 1) * 10);
    }

    // Delete higher dlsn
    int txn = 43;
    DLSN dlsn = txid2DLSN.get((long) txn);
    assertTrue(Await.result(pair.getRight().truncate(dlsn)));
    verifyEntries(name, 1, 31, 20);

    Utils.close(pair.getRight());
    pair.getLeft().close();
}

---

From source file:com.sludev.commons.vfs2.provider.s3.SS3FileObject.java

/**
 * Callback for handling delete on this File Object
 * @throws Exception //from w ww  .  j a v  a  2 s.c  o  m
 */
@Override
protected void doDelete() throws Exception {
    Pair<String, String> path = getContainerAndPath();

    // Purposely use the more restrictive delete() over deleteIfExists()
    fileSystem.getClient().deleteObject(path.getLeft(), path.getRight());
}

---

From source file:com.act.lcms.db.analysis.PathwayProductAnalysis.java

private static Map<Integer, String> extractPathwayStepIonsFromStandardIonAnalysis(
        List<ChemicalAssociatedWithPathway> pathwayChems, File lcmsDir, DB db, List<StandardWell> standardWells,
        String plottingDir, Map<Integer, Pair<Boolean, Boolean>> ionModesAvailable) throws Exception {

    Map<Integer, String> result = new HashMap<>();

    for (ChemicalAssociatedWithPathway pathwayChem : pathwayChems) {

        Map<StandardWell, StandardIonResult> wellToIonRanking = StandardIonAnalysis
                .getBestMetlinIonsForChemical(pathwayChem.getChemical(), lcmsDir, db, standardWells,
                        plottingDir);/*  w  w  w .ja  va  2s  .  co  m*/

        Pair<Boolean, Boolean> modes = ionModesAvailable.get(pathwayChem.getId());

        Map<StandardIonResult, String> chemicalToCuratedMetlinIon = new HashMap<>();
        List<StandardIonResult> standardIonResults = new ArrayList<>(wellToIonRanking.values());

        for (StandardIonResult standardIonResult : standardIonResults) {
            Integer manualOverrideId = standardIonResult.getManualOverrideId();
            if (manualOverrideId != null) {
                chemicalToCuratedMetlinIon.put(standardIonResult,
                        CuratedStandardMetlinIon.getBestMetlinIon(db, manualOverrideId).getBestMetlinIon());
            }
        }

        String bestMetlinIon = AnalysisHelper.scoreAndReturnBestMetlinIonFromStandardIonResults(
                standardIonResults, chemicalToCuratedMetlinIon, modes.getLeft(), modes.getRight());

        if (bestMetlinIon != null) {
            result.put(pathwayChem.getId(), bestMetlinIon);
        } else {
            result.put(pathwayChem.getId(), DEFAULT_SEARCH_ION);
        }
    }
    return result;
}

---

From source file:com.epam.ngb.cli.manager.command.handler.http.FileRegistrationHandler.java

private RegistrationRequest createRegistrationRequest(Pair<String, String> file,
        BiologicalDataItemFormat format) {
    RegistrationRequest registration = new RegistrationRequest();
    registration.setName(fileName);//from  w w w.  j  av  a  2  s  . c om
    registration.setPrettyName(prettyName);
    registration.setPath(file.getLeft());
    registration.setIndexPath(file.getRight());
    registration.setReferenceId(referenceId);
    registration.setType(BiologicalDataItemResourceType.getTypeFromPath(file.getKey()));

    if (file.getValue() != null) {
        registration.setIndexType(BiologicalDataItemResourceType.getTypeFromPath(file.getValue()));
    }

    if (format == BiologicalDataItemFormat.VCF || format == BiologicalDataItemFormat.GENE) {
        registration.setDoIndex(doIndex);
    }
    return registration;
}

---

From source file:net.malisis.blocks.tileentity.SwapperTileEntity.java

private void applyState(BlockPos pos, Pair<IBlockState, NBTTagCompound> state) {
    if (getWorld().getBlockState(pos).getBlock() == Blocks.bedrock)
        return;/*from   w w  w .j a v a  2 s  .  com*/

    clearWorldState(pos);
    getWorld().setBlockState(pos, state.getLeft() != null ? state.getLeft() : Blocks.air.getDefaultState(), 0);
    TileEntity te = getWorld().getTileEntity(pos);
    if (te != null && state.getRight() != null)
        te.readFromNBT(state.getRight());
}

---

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