Example usage for java.util LinkedHashMap size

List of usage examples for java.util LinkedHashMap size

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Introduction

In this page you can find the example usage for java.util LinkedHashMap size.

Prototype

int size();

Source Link

Document

Returns the number of key-value mappings in this map.

Usage

From source file:org.opencb.opencga.storage.mongodb.variant.load.variants.MongoDBVariantMerger.java

protected LinkedHashMap<String, Integer> getSamplesPosition(Integer fileId) {
    if (!samplesPositionMap.containsKey(fileId)) {
        synchronized (samplesPositionMap) {
            if (!samplesPositionMap.containsKey(fileId)) {
                LinkedHashMap<String, Integer> samplesPosition = new LinkedHashMap<>();
                for (Integer sampleId : studyConfiguration.getSamplesInFiles().get(fileId)) {
                    samplesPosition.put(studyConfiguration.getSampleIds().inverse().get(sampleId),
                            samplesPosition.size());
                }/*from  ww  w  . j a v a 2  s.  c  o  m*/
                samplesPositionMap.put(fileId, samplesPosition);
            }
        }
    }
    return samplesPositionMap.get(fileId);
}

From source file:org.fao.fenix.wds.web.rest.crowdprices.CrowdPricesDataRESTService.java

private String createGeoJsonDisabled(List<List<String>> table) {

    String s = "{ \"type\":\"FeatureCollection\",\"features\":[";
    int i = 0;//from  w  w  w  .  j  a v  a  2s.  c o m
    LinkedHashMap<String, List<List<String>>> markets = getCrowdPricesPoints(table);
    for (String marketname : markets.keySet()) {
        String popupcontent = "<b>" + marketname
                + "</b><br> No available data for that market in the current selection";
        String lat = "";
        String lon = "";
        for (List<String> row : markets.get(marketname)) {
            lon = row.get(1);
            lat = row.get(2);
        }
        //         System.out.println("popup: " + popupcontent);
        s += "{\"type\":\"Feature\",\"properties\":{\"iconurl\":\"images/marker-icon-disabled.png\","
                + "\"name\":\"Countrys\"," + "\"popupContent\":\"" + popupcontent
                + " \"},\"geometry\":{\"type\":\"Point\",\"coordinates\":[" + lon + "," + lat + "]}}";
        if (i < markets.size() - 1) {
            s += ",";
        }
        i++;
    }
    s += "]}";
    return s;
}

From source file:org.apache.axis2.engine.MessageContextSaveCTest.java

/**
 * Compare two mappings containing object graph info.
 * This uses the class name and object ID.
 * <p/>/*  w  w w.j  a  va2s.  c o m*/
 * Strict comparison includes the object hash codes. If
 * you expect the same object to be represented in
 * both maps, you may want to use Strict checking.
 * <p/>
 *
 * @param map1   The first object graph info map
 * @param map2   The second object graph info map
 * @param strict TRUE if strict comparison
 * @return Outcome of the comparison: TRUE if equivalent, FALSE otherwise
 */
private boolean compareObjectGraphInfo(LinkedHashMap map1, LinkedHashMap map2, boolean strict) {
    String title = "MessageContextSaveCTest: compareObjectGraphInfo(): ";

    if ((map1 != null) && (map2 != null)) {
        if (map1.size() != map2.size()) {
            log.debug(title + "Object graph info mappings are different sizes.");
            return false;
        }

        Iterator it = map1.keySet().iterator();

        while (it.hasNext()) {
            // the key is the class name associated with the object
            String key = (String) it.next();

            // skip certain objects, those will always be unique
            if ((key.indexOf("MessageContext") == -1) && (key.indexOf("OperationContext") == -1)
                    && (key.indexOf("ConfigurationContext") == -1)
                    && (key.indexOf("AxisConfiguration") == -1)) {
                // the class names listed above were not found
                // so we're dealing with the other objects
                MetaDataEntry value1 = (MetaDataEntry) map1.get(key);
                MetaDataEntry value2 = (MetaDataEntry) map2.get(key);

                if ((value1 != null) && (value2 != null)) {
                    // check the object identification
                    String name1 = value1.getName();
                    String name2 = value2.getName();

                    if ((name1 != null) && (name2 != null)) {
                        if (name1.equals(name2) == false) {
                            log.debug(title + "name1 [" + name1 + "]  !=   name2 [" + name2 + "]");
                            return false;
                        }
                    } else if ((name1 == null) && (name2 == null)) {
                        // ok
                    } else {
                        // mismatch
                        log.debug(title + "name1 [" + name1 + "]  !=   name2 [" + name2 + "]");
                        return false;
                    }

                    // Strict testing means checking the object hashcodes.
                    // Use this option when you expect the same
                    // objects in the map.
                    if (strict) {
                        String code1 = value1.getExtraName();
                        String code2 = value2.getExtraName();

                        if ((code1 != null) && (code2 != null)) {
                            if (code1.equals(code2) == false) {
                                log.debug(title + "name [" + name1 + "]  code1 [" + code1 + "]  !=   code2 ["
                                        + code2 + "]");
                                return false;
                            }
                        } else if ((code1 == null) && (code2 == null)) {
                            // ok
                        } else {
                            // mismatch
                            log.debug(title + "name [" + name1 + "]code1 [" + code1 + "]  !=   code2 [" + code2
                                    + "]");
                            return false;
                        }
                    }
                } else if ((value1 == null) && (value2 == null)) {
                    // ok
                } else {
                    // mismatch
                    log.debug(title + "value1 [" + value1 + "]  !=   value2 [" + value2 + "]");
                    return false;
                }
            }
        }

        return true;

    } else if ((map1 == null) && (map2 == null)) {
        return true;
    } else {
        log.debug(title + "mismatch: one or more of the maps are null.  ");
        return false;
    }

}

From source file:org.eclipse.scanning.test.scan.nexus.MandelbrotRemoteTest.java

private void checkNexusFile(IRunnableDevice<ScanModel> scanner, int... sizes)
        throws NexusException, ScanningException, DatasetException {

    final ScanModel mod = ((AbstractRunnableDevice<ScanModel>) scanner).getModel();
    assertEquals(DeviceState.READY, scanner.getDeviceState());

    String filePath = ((AbstractRunnableDevice<ScanModel>) scanner).getModel().getFilePath();
    NexusFile nf = fileFactory.newNexusFile(filePath);
    nf.openToRead();//  ww  w  . j  av a 2  s  .co m

    TreeFile nexusTree = NexusUtils.loadNexusTree(nf);
    NXroot rootNode = (NXroot) nexusTree.getGroupNode();
    NXentry entry = rootNode.getEntry();
    NXinstrument instrument = entry.getInstrument();

    // check that the scan points have been written correctly
    assertSolsticeScanGroup(entry, false, false, sizes);

    LinkedHashMap<String, List<String>> detectorDataFields = new LinkedHashMap<>();
    // axis for additional dimensions of a datafield, e.g. image
    detectorDataFields.put(NXdetector.NX_DATA, Arrays.asList("real", "imaginary"));
    detectorDataFields.put("spectrum", Arrays.asList("spectrum_axis"));
    detectorDataFields.put("value", Collections.emptyList());

    String detectorName = mod.getDetectors().get(0).getName();
    NXdetector detector = instrument.getDetector(detectorName);
    // map of detector data field to name of nxData group where that field is the @signal field
    Map<String, String> expectedDataGroupNames = detectorDataFields.keySet().stream().collect(Collectors
            .toMap(Function.identity(), x -> detectorName + (x.equals(NXdetector.NX_DATA) ? "" : "_" + x)));

    // validate the NXdata generated by the NexusDataBuilder
    Map<String, NXdata> nxDataGroups = entry.getChildren(NXdata.class);
    assertEquals(detectorDataFields.size(), nxDataGroups.size());
    assertTrue(nxDataGroups.keySet().containsAll(expectedDataGroupNames.values()));

    for (String nxDataGroupName : nxDataGroups.keySet()) {
        NXdata nxData = entry.getData(nxDataGroupName);
        String sourceFieldName = nxDataGroupName.equals(detectorName) ? NXdetector.NX_DATA
                : nxDataGroupName.substring(nxDataGroupName.indexOf('_') + 1);
        assertSignal(nxData, sourceFieldName);
        // check the nxData's signal field is a link to the data node of the detector
        DataNode dataNode = detector.getDataNode(sourceFieldName);
        IDataset dataset = dataNode.getDataset().getSlice();
        assertSame(dataNode, nxData.getDataNode(sourceFieldName));

        int[] shape = dataset.getShape();

        for (int i = 0; i < sizes.length; i++)
            assertEquals(sizes[i], shape[i]);

        // Make sure none of the numbers are NaNs. The detector
        // is expected to fill this scan with non-nulls.
        final PositionIterator it = new PositionIterator(shape);
        while (it.hasNext()) {
            int[] next = it.getPos();
            assertFalse(Double.isNaN(dataset.getDouble(next)));
        }

        // Check axes
        final IPosition pos = mod.getPositionIterable().iterator().next();
        final Collection<String> names = pos.getNames();

        // Append _value_demand to each name in list, then add detector axis fields to result
        List<String> expectedAxesNames = Stream.concat(names.stream().map(x -> x + "_value_set"),
                detectorDataFields.get(sourceFieldName).stream()).collect(Collectors.toList());
        assertAxes(nxData, expectedAxesNames.toArray(new String[expectedAxesNames.size()]));

        int[] defaultDimensionMappings = IntStream.range(0, sizes.length).toArray();
        int i = -1;
        for (String positionerName : names) {

            i++;
            NXpositioner positioner = instrument.getPositioner(positionerName);
            assertNotNull(positioner);
            dataNode = positioner.getDataNode("value_set");

            dataset = dataNode.getDataset().getSlice();
            shape = dataset.getShape();
            assertEquals(1, shape.length);
            assertEquals(sizes[i], shape[0]);

            String nxDataFieldName = positionerName + "_value_set";
            assertSame(dataNode, nxData.getDataNode(nxDataFieldName));
            assertIndices(nxData, nxDataFieldName, i);
            assertTarget(nxData, nxDataFieldName, rootNode,
                    "/entry/instrument/" + positionerName + "/value_set");

            // Actual values should be scanD
            dataNode = positioner.getDataNode(NXpositioner.NX_VALUE);
            dataset = dataNode.getDataset().getSlice();
            shape = dataset.getShape();
            assertArrayEquals(sizes, shape);

            nxDataFieldName = positionerName + "_" + NXpositioner.NX_VALUE;
            assertSame(dataNode, nxData.getDataNode(nxDataFieldName));
            assertIndices(nxData, nxDataFieldName, defaultDimensionMappings);
            assertTarget(nxData, nxDataFieldName, rootNode,
                    "/entry/instrument/" + positionerName + "/" + NXpositioner.NX_VALUE);
        }
    }
}

From source file:com.grarak.kerneladiutor.FileBrowserActivity.java

@Override
protected void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);
    fileBrowserActivity = this;
    boolean dark = Utils.getBoolean("darktheme", false, this);
    if (dark)//from w w  w  . j  ava 2 s . co  m
        super.setTheme(R.style.AppThemeDark);
    setContentView(R.layout.activity_filebrowser);

    setSupportActionBar((Toolbar) findViewById(R.id.toolbar));
    ActionBar actionBar;
    if ((actionBar = getSupportActionBar()) != null)
        actionBar.setDisplayHomeAsUpEnabled(true);

    String fileType = getIntent().getExtras().getString(FILE_TYPE_ARG);
    String externalStorage = Utils.getExternalStorage();

    LinkedHashMap<String, Fragment> fragments = new LinkedHashMap<>();
    internalStorage = StorageFragment.newInstance(Environment.getExternalStorageDirectory().getPath(),
            fileType);
    fragments.put(getString(R.string.internal_storage), internalStorage);
    if (externalStorage != null) {
        this.externalStorage = StorageFragment.newInstance(externalStorage, fileType);
        fragments.put(getString(R.string.external_storage), this.externalStorage);
    }

    mViewPager = (ViewPager) findViewById(R.id.view_pager);
    mViewPager.setAdapter(new Adapter(getSupportFragmentManager(), fragments));
    if (dark)
        mViewPager.setBackgroundColor(getResources().getColor(R.color.card_background_dark));

    final SlidingTabLayout mSlidingTabLayout = (SlidingTabLayout) findViewById(R.id.sliding_tabs);
    mSlidingTabLayout.setCustomTabView(R.layout.tab_indicator, android.R.id.text1);
    for (int i = 0; i < fragments.keySet().toArray().length; i++)
        mSlidingTabLayout.setContentDescription(i, (String) fragments.keySet().toArray()[i]);
    mSlidingTabLayout.setSelectedIndicatorColors(
            getResources().getColor(fragments.size() > 1 ? R.color.white : R.color.color_primary));
    mSlidingTabLayout.setDistributeEvenly(true);
    mSlidingTabLayout.setViewPager(mViewPager);

    if (Build.VERSION.SDK_INT >= Build.VERSION_CODES.LOLLIPOP) {
        Window window = getWindow();
        window.addFlags(WindowManager.LayoutParams.FLAG_DRAWS_SYSTEM_BAR_BACKGROUNDS);
        window.clearFlags(WindowManager.LayoutParams.FLAG_TRANSLUCENT_STATUS);
        window.setStatusBarColor(getResources().getColor(R.color.color_primary_dark));
    }
}

From source file:org.opencms.ui.dialogs.CmsNewDialog.java

/**
 * Initializes the view selector, using the given view id as an initial value.<p>
 *
 * @param startId the start view/*w  w  w .  j a  v a  2 s. com*/
 *
 * @return the start view
 */
private CmsElementView initViews(CmsUUID startId) {

    Map<CmsUUID, CmsElementView> viewMap = OpenCms.getADEManager().getElementViews(A_CmsUI.getCmsObject());
    List<CmsElementView> viewList = new ArrayList<CmsElementView>(viewMap.values());
    Collections.sort(viewList, new Comparator<CmsElementView>() {

        public int compare(CmsElementView arg0, CmsElementView arg1) {

            return ComparisonChain.start().compare(arg0.getOrder(), arg1.getOrder()).result();
        }

    });
    m_viewSelector.setItemCaptionMode(ItemCaptionMode.EXPLICIT);
    m_typeHelper = createTypeHelper();
    m_typeHelper.precomputeTypeLists(A_CmsUI.getCmsObject(), m_folderResource.getRootPath(),
            A_CmsUI.getCmsObject().getRequestContext().removeSiteRoot(m_folderResource.getRootPath()), viewList,
            null);

    // also collect types in LinkedHashMap to preserve order and ensure uniqueness
    LinkedHashMap<String, CmsResourceTypeBean> allTypes = Maps.newLinkedHashMap();

    for (CmsElementView view : viewList) {

        if (view.hasPermission(A_CmsUI.getCmsObject(), m_folderResource)) {

            List<CmsResourceTypeBean> typeBeans = m_typeHelper.getPrecomputedTypes(view);

            if (typeBeans.isEmpty()) {
                continue;
            }
            for (CmsResourceTypeBean typeBean : typeBeans) {
                allTypes.put(typeBean.getType(), typeBean);
            }
            m_viewSelector.addItem(view.getId());
            m_viewSelector.setItemCaption(view.getId(),
                    view.getTitle(A_CmsUI.getCmsObject(), A_CmsUI.get().getLocale()));
        }
    }
    m_viewSelector.addItem(VIEW_ALL.getId());
    m_viewSelector.setItemCaption(VIEW_ALL.getId(), CmsVaadinUtils.getMessageText(Messages.GUI_VIEW_ALL_0));
    m_allTypes = Lists.newArrayList(allTypes.values());
    if (allTypes.size() <= 8) {
        startId = ID_VIEW_ALL;
    }
    if (m_viewSelector.getItem(startId) == null) {
        startId = (CmsUUID) (m_viewSelector.getItemIds().iterator().next());
    }

    m_viewSelector.addValueChangeListener(new ValueChangeListener() {

        private static final long serialVersionUID = 1L;

        public void valueChange(ValueChangeEvent event) {

            CmsUUID viewId = (CmsUUID) (event.getProperty().getValue());
            CmsElementView selectedView;
            if (viewId.equals(ID_VIEW_ALL)) {
                selectedView = VIEW_ALL;
            } else {
                selectedView = OpenCms.getADEManager().getElementViews(A_CmsUI.getCmsObject())
                        .get(event.getProperty().getValue());
            }
            init(selectedView, m_defaultLocationCheckbox.getValue().booleanValue());
            if (selectedView != VIEW_ALL) {
                VaadinService.getCurrentRequest().getWrappedSession().setAttribute(SETTING_STANDARD_VIEW,
                        (event.getProperty().getValue()));
            }
        }
    });
    if (startId.equals(ID_VIEW_ALL)) {
        return VIEW_ALL;
    } else {
        return OpenCms.getADEManager().getElementViews(A_CmsUI.getCmsObject()).get(startId);
    }
}

From source file:hydrograph.ui.tooltip.tooltips.ComponentTooltip.java

/**
 * Show errors balloon in case property is having errors.
 * /*from w w  w. j  a  va2  s.com*/
 * @param propertyInfo
 * @param lblLinkProperty
 */
private void showErrors(PropertyToolTipInformation propertyInfo, Control lblLinkProperty) {
    if (propertyInfo.getErrorMessage() != null) {
        logger.debug("ComponentTooltip.showErrors() - Showing error balloon on property "
                + propertyInfo.getPropertyName() + ", Error: " + propertyInfo.getErrorMessage());
        ControlDecoration lblDecorator = WidgetUtility.addDecorator(lblLinkProperty,
                propertyInfo.getErrorMessage());
        if (LIST.equalsIgnoreCase(propertyInfo.getTooltipDataType())) {
            ArrayList<String> keyFieldList;
            LinkedHashMap<String, Object> secondaryKeysList;
            if (KEY_FIELDS.equalsIgnoreCase(propertyInfo.getPropertyName())
                    || OPERATION_FIELDS.equalsIgnoreCase(propertyInfo.getPropertyName())) {
                keyFieldList = (ArrayList<String>) propertyInfo.getPropertyValue();
                if (keyFieldList.size() == 0) {
                    lblDecorator.show();
                } else {
                    lblDecorator.hide();
                }
            }
            if (SECONDARY_KEYS.equalsIgnoreCase(propertyInfo.getPropertyName())
                    || KEY_FIELDS_SORT_COMPONENT.equalsIgnoreCase(propertyInfo.getPropertyName())) {
                secondaryKeysList = (LinkedHashMap<String, Object>) propertyInfo.getPropertyValue();
                if (secondaryKeysList.size() == 0) {
                    lblDecorator.show();
                } else {
                    lblDecorator.hide();
                }
            }

        } else if (propertyInfo.getPropertyValue() != null
                && StringUtils.equalsIgnoreCase(propertyInfo.getPropertyName().toString(), "PORT")) {
            if (propertyInfo.getPropertyValue().toString().matches(Constants.PORT_VALIDATION_REGEX)
                    || ParameterUtil.isParameter(propertyInfo.getPropertyValue().toString())) {
                lblDecorator.hide();
            } else {
                lblDecorator.show();
            }
        } else {
            if (propertyInfo.getPropertyValue() != null && (!propertyInfo.getPropertyValue().equals(""))) {
                lblDecorator.hide();
            } else {
                lblDecorator.show();
            }
        }
    }
}

From source file:org.opencb.opencga.storage.hadoop.variant.converters.HBaseToVariantConverter.java

protected Variant convert(Variant variant, List<VariantTableStudyRow> rows,
        Map<Integer, Map<Integer, VariantStats>> stats, VariantAnnotation annotation) {
    if (annotation == null) {
        annotation = new VariantAnnotation();
        annotation.setConsequenceTypes(Collections.emptyList());
    }//from  w w w . j a  v  a2 s.  co m
    if (failOnEmptyVariants && rows.isEmpty()) {
        throw new IllegalStateException("No Row columns supplied for row " + variant);
    }
    for (VariantTableStudyRow row : rows) {
        Map<String, String> attributesMap = new HashMap<>();
        Integer studyId = row.getStudyId();
        QueryResult<StudyConfiguration> queryResult = scm.getStudyConfiguration(studyId, scmOptions);
        if (queryResult.getResult().isEmpty()) {
            throw new IllegalStateException("No study found for study ID: " + studyId);
        }
        StudyConfiguration studyConfiguration = queryResult.first();

        LinkedHashMap<String, Integer> returnedSamplesPosition = getReturnedSamplesPosition(studyConfiguration);
        if (mutableSamplesPosition) {
            returnedSamplesPosition = new LinkedHashMap<>(returnedSamplesPosition);
        }
        //            Do not throw any exception. It may happen that the study is not loaded yet or no samples are required!
        //            if (returnedSamplesPosition.isEmpty()) {
        //                throw new IllegalStateException("No samples found for study!!!");
        //            }

        BiMap<String, Integer> loadedSamples = StudyConfiguration.getIndexedSamples(studyConfiguration);

        List<String> format = Arrays.asList(VariantMerger.GT_KEY, VariantMerger.GENOTYPE_FILTER_KEY);
        int gtIdx = format.indexOf(VariantMerger.GT_KEY);
        int ftIdx = format.indexOf(VariantMerger.GENOTYPE_FILTER_KEY);

        int loadedSamplesSize = loadedSamples.size();
        calculatePassCallRates(row, attributesMap, loadedSamplesSize);

        Integer nSamples = returnedSamplesPosition.size();

        @SuppressWarnings("unchecked")
        List<String>[] samplesDataArray = new List[nSamples];

        Set<Integer> sampleWithVariant = new HashSet<>();
        BiMap<Integer, String> mapSampleIds = studyConfiguration.getSampleIds().inverse();
        for (String genotype : row.getGenotypes()) {
            sampleWithVariant.addAll(row.getSampleIds(genotype));
            if (genotype.equals(VariantTableStudyRow.OTHER)) {
                continue; // skip OTHER -> see Complex type
            }
            for (Integer sampleId : row.getSampleIds(genotype)) {
                String sampleName = mapSampleIds.get(sampleId);
                Integer sampleIdx = returnedSamplesPosition.get(sampleName);
                if (sampleIdx == null) {
                    continue; //Sample may not be required. Ignore this sample.
                }
                List<String> lst = Arrays.asList(genotype, VariantMerger.PASS_VALUE);
                samplesDataArray[sampleIdx] = lst;
            }
        }

        // Load Secondary Index
        List<VariantProto.AlternateCoordinate> s2cgt = row.getComplexVariant().getSecondaryAlternatesList();
        int secondaryAlternatesCount = row.getComplexVariant().getSecondaryAlternatesCount();
        List<AlternateCoordinate> secAltArr = new ArrayList<AlternateCoordinate>(secondaryAlternatesCount);
        if (secondaryAlternatesCount > 0) {
            for (VariantProto.AlternateCoordinate altcoord : s2cgt) {
                VariantType vart = VariantType.valueOf(altcoord.getType().name());
                String chr = StringUtils.isEmpty(altcoord.getChromosome()) ? variant.getChromosome()
                        : altcoord.getChromosome();
                Integer start = altcoord.getStart() == 0 ? variant.getStart() : altcoord.getStart();
                Integer end = altcoord.getEnd() == 0 ? variant.getEnd() : altcoord.getEnd();
                String reference = StringUtils.isEmpty(altcoord.getReference()) ? "" : altcoord.getReference();
                String alternate = StringUtils.isEmpty(altcoord.getAlternate()) ? "" : altcoord.getAlternate();
                AlternateCoordinate alt = new AlternateCoordinate(chr, start, end, reference, alternate, vart);
                secAltArr.add(alt);
            }
        }
        // Load complex genotypes
        for (Entry<Integer, String> entry : row.getComplexVariant().getSampleToGenotype().entrySet()) {
            sampleWithVariant.add(entry.getKey());
            Integer samplePosition = getSamplePosition(returnedSamplesPosition, mapSampleIds, entry.getKey());
            if (samplePosition == null) {
                continue; //Sample may not be required. Ignore this sample.
            }
            String genotype = entry.getValue();
            String returnedGenotype;
            // FIXME: Decide what to do with lists of genotypes
            if (simpleGenotypes) {
                returnedGenotype = getSimpleGenotype(genotype);
                logger.debug("Return simplified genotype: {} -> {}", genotype, returnedGenotype);
            } else {
                returnedGenotype = genotype;
            }
            samplesDataArray[samplePosition] = Arrays.asList(returnedGenotype, VariantMerger.PASS_VALUE);
        }

        // Fill gaps (with HOM_REF)
        int gapCounter = 0;
        for (int i = 0; i < samplesDataArray.length; i++) {
            if (samplesDataArray[i] == null) {
                ++gapCounter;
                samplesDataArray[i] = Arrays.asList(VariantTableStudyRow.HOM_REF, VariantMerger.PASS_VALUE);
            }
        }

        // Set pass field
        int passCount = loadedSamplesSize;
        for (Entry<String, SampleList> entry : row.getComplexFilter().getFilterNonPass().entrySet()) {
            String filterString = entry.getKey();
            passCount -= entry.getValue().getSampleIdsCount();
            for (Integer id : entry.getValue().getSampleIdsList()) {
                Integer samplePosition = getSamplePosition(returnedSamplesPosition, mapSampleIds, id);
                if (samplePosition == null) {
                    continue; // Sample may not be required. Ignore this sample.
                }
                samplesDataArray[samplePosition].set(ftIdx, filterString);
            }
        }

        // Check pass count
        if (passCount != row.getPassCount()) {
            String message = String.format(
                    "Error parsing variant %s. Pass count %s does not match filter fill count: %s using %s loaded samples.",
                    row.toString(), row.getPassCount(), passCount, loadedSamplesSize);
            wrongVariant(message);
        }

        // Check homRef count
        int homRefCount = loadedSamplesSize;
        homRefCount -= sampleWithVariant.size();
        if (homRefCount != row.getHomRefCount()) {
            String message = "Wrong number of HomRef samples for variant " + variant + ". Got " + homRefCount
                    + ", expect " + row.getHomRefCount() + ". Samples number: " + samplesDataArray.length
                    + " , ";
            message += "'" + VariantTableStudyRow.HOM_REF + "':" + row.getHomRefCount() + " , ";
            for (String studyColumn : VariantTableStudyRow.GENOTYPE_COLUMNS) {
                message += "'" + studyColumn + "':" + row.getSampleIds(studyColumn) + " , ";
            }
            wrongVariant(message);
        }

        List<List<String>> samplesData = Arrays.asList(samplesDataArray);

        StudyEntry studyEntry;
        if (studyNameAsStudyId) {
            studyEntry = new StudyEntry(studyConfiguration.getStudyName());
        } else {
            studyEntry = new StudyEntry(Integer.toString(studyConfiguration.getStudyId()));
        }
        studyEntry.setSortedSamplesPosition(returnedSamplesPosition);
        studyEntry.setSamplesData(samplesData);
        studyEntry.setFormat(format);
        studyEntry.setFiles(Collections.singletonList(new FileEntry("", "", attributesMap)));
        studyEntry.setSecondaryAlternates(secAltArr);

        Map<Integer, VariantStats> convertedStatsMap = stats.get(studyConfiguration.getStudyId());
        if (convertedStatsMap != null) {
            Map<String, VariantStats> statsMap = new HashMap<>(convertedStatsMap.size());
            for (Entry<Integer, VariantStats> entry : convertedStatsMap.entrySet()) {
                String cohortName = studyConfiguration.getCohortIds().inverse().get(entry.getKey());
                statsMap.put(cohortName, entry.getValue());
            }
            studyEntry.setStats(statsMap);
        }

        variant.addStudyEntry(studyEntry);
    }
    variant.setAnnotation(annotation);
    if (StringUtils.isNotEmpty(annotation.getId())) {
        variant.setId(annotation.getId());
    } else {
        variant.setId(variant.toString());
    }
    if (failOnEmptyVariants && variant.getStudies().isEmpty()) {
        throw new IllegalStateException("No Studies registered for variant!!! " + variant);
    }
    return variant;
}

From source file:ubic.gemma.core.datastructure.matrix.ExpressionDataMatrixColumnSort.java

/**
 * Divide the biomaterials up into chunks based on the experimental factor given, keeping everybody in order. If the
 * factor is continuous, there is just one chunk.
 *
 * @return ordered map of fv->bm where fv is of ef, or null if it couldn't be done properly.
 *//*from  w ww  .  j  a v  a  2s.  c o m*/
private static LinkedHashMap<FactorValue, List<BioMaterial>> chunkOnFactor(ExperimentalFactor ef,
        List<BioMaterial> bms) {

    if (bms == null) {
        return null;
    }

    LinkedHashMap<FactorValue, List<BioMaterial>> chunks = new LinkedHashMap<>();

    /*
     * Get the factor values in the order we have things right now
     */
    for (BioMaterial bm : bms) {
        for (FactorValue fv : bm.getFactorValues()) {
            if (!ef.getFactorValues().contains(fv)) {
                continue;
            }
            if (chunks.keySet().contains(fv)) {
                continue;
            }
            chunks.put(fv, new ArrayList<BioMaterial>());
        }
    }

    /*
     * What if bm doesn't have a value for the factorvalue. Need a dummy value.
     */
    FactorValue dummy = FactorValue.Factory.newInstance(ef);
    dummy.setValue("");
    dummy.setId(-1L);
    chunks.put(dummy, new ArrayList<BioMaterial>());

    for (BioMaterial bm : bms) {
        boolean found = false;
        for (FactorValue fv : bm.getFactorValues()) {
            if (ef.getFactorValues().contains(fv)) {
                found = true;
                assert chunks.containsKey(fv);
                chunks.get(fv).add(bm);
            }
        }

        if (!found) {
            if (ExpressionDataMatrixColumnSort.log.isDebugEnabled())
                ExpressionDataMatrixColumnSort.log
                        .debug(bm + " has no value for factor=" + ef + "; using dummy value");
            chunks.get(dummy).add(bm);
        }

    }

    if (chunks.get(dummy).size() == 0) {
        if (ExpressionDataMatrixColumnSort.log.isDebugEnabled())
            ExpressionDataMatrixColumnSort.log.debug("removing dummy");
        chunks.remove(dummy);
    }

    ExpressionDataMatrixColumnSort.log
            .debug(chunks.size() + " chunks for " + ef + ", from current chunk of size " + bms.size());

    /*
     * Sanity check
     */
    int total = 0;
    for (FactorValue fv : chunks.keySet()) {
        List<BioMaterial> chunk = chunks.get(fv);
        total += chunk.size();
    }

    assert total == bms.size() : "expected " + bms.size() + ", got " + total;

    return chunks;
}

From source file:lob.VisualisationGUI.java

public void updatePriceTable(LinkedHashMap<Float, Long> askTree, LinkedHashMap<Float, Long> bidTree) {
    //Clear old entries
    clearTable(jTable2);//from  w  w w  .ja  v a 2 s. co m

    //Get the number of points on each side
    int numberAskPoints = askTree.size();
    int numberBidPoints = bidTree.size();

    int currentTableRow = 7;

    //Fill ask entries
    for (Map.Entry<Float, Long> entry : askTree.entrySet()) {

        float key = entry.getKey();
        long value = entry.getValue();
        jTable2.getModel().setValueAt(key, currentTableRow, 2);
        jTable2.getModel().setValueAt(value, currentTableRow, 1);
        currentTableRow--;
        if (currentTableRow < 1)
            break;
    }

    //Fill bid entries
    currentTableRow = 8 + numberBidPoints;
    for (Map.Entry<Float, Long> entry : bidTree.entrySet()) {

        float key = entry.getKey();
        long value = entry.getValue();
        jTable2.getModel().setValueAt(key, currentTableRow, 0);
        jTable2.getModel().setValueAt(value, currentTableRow, 1);
        currentTableRow--;
        if (currentTableRow < 9)
            break;
    }

}