Example usage for java.util LinkedHashMap containsKey

Introduction

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

Prototype

boolean containsKey(Object key);

Source Link

Document

Returns true if this map contains a mapping for the specified key.

Usage

From source file:nl.systemsgenetics.eqtlannotation.EncodeMultipleTfbsOverlap.java

private static LinkedHashMap<String, HashMap<String, ArrayList<EncodeNarrowPeak>>> readMultipleTfbsInformation(
        String inputFolderTfbsData) throws IOException {
    LinkedHashMap<String, HashMap<String, ArrayList<EncodeNarrowPeak>>> data = new LinkedHashMap<>();
    File file = new File(inputFolderTfbsData);
    File[] files = file.listFiles();
    ArrayList<String> vecFiles = new ArrayList<>();
    for (File f : files) {
        //            System.out.println(f.getAbsolutePath());
        vecFiles.add(f.getAbsolutePath());
    }/*from  w  w w .  j av a2s.co m*/

    for (String fileToRead : vecFiles) {
        TextFile reader = new TextFile(fileToRead, TextFile.R);

        String[] storingInformation = fileToRead.split("_");
        //            String cellLine = storingInformation[1].replace("TFBS\\","");
        String transcriptionFactor = storingInformation[2].replace(".narrowPeak", "");
        if (storingInformation.length > 4) {
            for (int i = 3; i < (storingInformation.length - 1); ++i) {
                transcriptionFactor = transcriptionFactor + "_"
                        + storingInformation[i].replace(".narrowPeak", "");
            }
        }

        String row;
        while ((row = reader.readLine()) != null) {

            String[] parts = StringUtils.split(row, '\t');
            if (!data.containsKey(transcriptionFactor)) {
                data.put(transcriptionFactor, new HashMap<String, ArrayList<EncodeNarrowPeak>>());
            }
            if (!data.get(transcriptionFactor).containsKey(parts[0])) {
                data.get(transcriptionFactor).put(parts[0], new ArrayList<EncodeNarrowPeak>());
            }
            data.get(transcriptionFactor).get(parts[0]).add(new EncodeNarrowPeak(parts, fileToRead));
        }

        reader.close();

    }
    ArrayList<String> cleanList = new ArrayList<>();
    for (Entry<String, HashMap<String, ArrayList<EncodeNarrowPeak>>> tfInformation : data.entrySet()) {
        System.out.println("Transcription factor: " + tfInformation.getKey());
        int counter = 0;
        for (Entry<String, ArrayList<EncodeNarrowPeak>> tfEntry : tfInformation.getValue().entrySet()) {
            Collections.sort(tfEntry.getValue());
            counter += tfEntry.getValue().size();
        }
        System.out.println("\tcontacts: " + counter);

        //remove all with less than 750 contacts
        //            if(counter<750){
        //                cleanList.add(tfInformation.getKey());
        //            }
    }

    for (String k : cleanList) {
        data.remove(k);
    }

    return data;
}

---

From source file:ca.sfu.federation.model.ParametricModel.java

/**
 * Remove a NamedObject from the Context.
 *
 * @param Named The NamedObject to be removed.
 * @throws IllegalArgumentException The NamedObject does not exist in the
 * Context./*from  w w  w . j av  a 2 s . c om*/
 */
public void remove(INamed Named) throws IllegalArgumentException {
    String itemName = Named.getName();
    LinkedHashMap elementsByName = (LinkedHashMap) this.getElementMap();
    if (elementsByName.containsKey(itemName)) {
        // stop listening on the NamedObject
        if (Named instanceof Observable) {
            Observable o = (Observable) Named;
            o.deleteObserver(this);
        }
        // remove the NamedObject from the collection
        this.elements.remove(Named);
        // notify observers
        this.setChanged();
        this.notifyObservers(Integer.valueOf(ApplicationContext.EVENT_ELEMENT_DELETED));
    } else {
        throw new IllegalArgumentException(
                "The object '" + itemName + "' does not exist in the current Context.");
    }
}

---

From source file:net.sf.maltcms.chromaui.normalization.spi.charts.PeakGroupRtBoxPlot.java

protected String getPeakName(IPeakGroupDescriptor pgd) {
    String rt = "mean rt: " + String.format("%.2f", pgd.getMeanApexTime()) + "+/-"
            + String.format("%.2f", pgd.getApexTimeStdDev()) + "; median rt: "
            + String.format("%.2f", pgd.getMedianApexTime()) + ": ";
    LinkedHashMap<String, Integer> names = new LinkedHashMap<>();
    if (!pgd.getDisplayName().equals(pgd.getName())) {
        return rt + pgd.getDisplayName();
    }/*from   w ww .  ja  v  a  2  s  .  c om*/
    for (IPeakAnnotationDescriptor ipad : pgd.getPeakAnnotationDescriptors()) {
        if (names.containsKey(ipad.getName())) {
            names.put(ipad.getName(), names.get(ipad.getName()) + 1);
        } else {
            names.put(ipad.getName(), 1);
        }
    }
    if (names.isEmpty()) {
        return rt + "<NA>";
    }
    if (names.size() > 1) {
        StringBuilder sb = new StringBuilder();
        for (String key : names.keySet()) {
            sb.append(key);
            sb.append(" (" + names.get(key) + ")");
            sb.append(" | ");
        }
        return rt + sb.replace(sb.length() - 1, sb.length() - 1, "").toString();
    } else {
        return rt + names.keySet().toArray(new String[0])[0];
    }
}

---

From source file:net.sf.maltcms.chromaui.normalization.spi.charts.PeakGroupBoxPlot.java

protected String getPeakName(IPeakGroupDescriptor pgd) {
    String rt = "mean area: " + String.format("%.2f", pgd.getMeanArea(normalizer)) + "+/-"
            + String.format("%.2f", pgd.getAreaStdDev(normalizer)) + "; median area: "
            + String.format("%.2f", pgd.getMedianArea(normalizer)) + ": ";
    LinkedHashMap<String, Integer> names = new LinkedHashMap<>();
    if (!pgd.getDisplayName().equals(pgd.getName())) {
        return rt + pgd.getDisplayName();
    }// w  ww.  j  a v  a2 s .  co m
    for (IPeakAnnotationDescriptor ipad : pgd.getPeakAnnotationDescriptors()) {
        if (names.containsKey(ipad.getName())) {
            names.put(ipad.getName(), names.get(ipad.getName()) + 1);
        } else {
            names.put(ipad.getName(), 1);
        }
    }
    if (names.isEmpty()) {
        return rt + "<NA>";
    }
    if (names.size() > 1) {
        StringBuilder sb = new StringBuilder();
        for (String key : names.keySet()) {
            sb.append(key);
            sb.append(" (" + names.get(key) + ")");
            sb.append(" | ");
        }
        return rt + sb.replace(sb.length() - 1, sb.length() - 1, "").toString();
    } else {
        return rt + names.keySet().toArray(new String[0])[0];
    }
}

---

From source file:org.eclipse.php.composer.api.entities.AbstractJsonObject.java

@Override
protected Object buildJson() {
    LinkedList<String> propsOrder = new LinkedList<String>(sortOrder);

    // First: create an index to search for field names and add them to the
    // props order
    HashMap<String, Field> namedFields = new HashMap<String, Field>();
    for (Field field : getFields(this.getClass())) {
        field.setAccessible(true);//  w w w.  jav a2 s . c o  m
        String fieldName = getFieldName(field);
        namedFields.put(fieldName, field);
        propsOrder.add(fieldName);
    }

    // add properties that aren't in the hashmap yet
    for (Entry<String, V> entry : properties.entrySet()) {
        propsOrder.add(entry.getKey());
    }

    // Second: find property contents (either field or property key)
    LinkedHashMap<String, Object> out = new LinkedHashMap<String, Object>();
    for (String entry : propsOrder) {
        if (out.containsKey(entry)) {
            continue;
        }
        Object value = null;

        // search class fields first
        if (namedFields.containsKey(entry)) {
            try {
                value = namedFields.get(entry).get(this);
            } catch (Exception e) {
                log.error(e);
            }
        }

        // check properties
        else if (properties.containsKey(entry)) {
            value = properties.get(entry);
        }

        value = getJsonValue(value);

        if (value == null || value.equals("")) { //$NON-NLS-1$
            continue;
        }

        // add to output
        out.put(entry, value);
    }

    return out;
}

---

From source file:com.intellij.plugins.haxe.haxelib.HaxeLibrary.java

private void collectDependentsInternal(
        /*modifies*/ final @NotNull LinkedHashMap<String, HaxeLibraryDependency> collection) {
    List<HaxeLibraryDependency> dependencies = getDirectDependents();

    for (HaxeLibraryDependency dependency : dependencies) {
        if (!collection.containsKey(dependency.getKey())) { // Don't go down the same path again...
            // TODO: Deal with version mismatches here.  Add multiple versions, but don't add a specific version if the latest version is equal to it.
            collection.put(dependency.getKey(), dependency);
            HaxeLibrary depLib = dependency.getLibrary();
            if (null != depLib) {
                depLib.collectDependentsInternal(collection);
            } // TODO: Else mark dependency unfulfilled somehow??
        } else {//from  w w w. j  a v a2  s .  c o m
            HaxeLibraryDependency contained = collection.get(dependency.getKey());
            LOG.assertLog(contained != null, "Couldn't get a contained object.");
            if (contained != null) {
                contained.addReliant(dependency);
            }
        }
    }
}

---

From source file:org.openmrs.module.muzima.handler.JsonEncounterQueueDataHandler.java

private void createObs(final Encounter encounter, final Obs parentObs, final Concept concept, final Object o) {
    String value = null;/*from   ww  w. ja  v  a2  s . c o  m*/
    Obs obs = new Obs();
    obs.setConcept(concept);

    //check and parse if obs_value / obs_datetime object
    if (o instanceof LinkedHashMap) {
        LinkedHashMap obj = (LinkedHashMap) o;
        if (obj.containsKey("obs_value")) {
            value = (String) obj.get("obs_value");
        }
        if (obj.containsKey("obs_datetime")) {
            String dateString = (String) obj.get("obs_datetime");
            Date obsDateTime = parseDate(dateString);
            obs.setObsDatetime(obsDateTime);
        }
    } else {
        value = o.toString();
    }
    // find the obs value :)
    if (concept.getDatatype().isNumeric()) {
        obs.setValueNumeric(Double.parseDouble(value));
    } else if (concept.getDatatype().isDate() || concept.getDatatype().isTime()
            || concept.getDatatype().isDateTime()) {
        obs.setValueDatetime(parseDate(value));
    } else if (concept.getDatatype().isCoded()) {
        String[] valueCodedElements = StringUtils.split(value, "\\^");
        int valueCodedId = Integer.parseInt(valueCodedElements[0]);
        Concept valueCoded = Context.getConceptService().getConcept(valueCodedId);
        if (valueCoded == null) {
            queueProcessorException.addException(
                    new Exception("Unable to find concept for value coded with id: " + valueCodedId));
        } else {
            obs.setValueCoded(valueCoded);
        }
    } else if (concept.getDatatype().isText()) {
        obs.setValueText(value);
    }
    // only add if the value is not empty :)
    encounter.addObs(obs);
    if (parentObs != null) {
        parentObs.addGroupMember(obs);
    }
}

---

From source file:ca.sfu.federation.model.Assembly.java

/**
 * Add a NamedObject./*from   ww  w  .j  a  v a 2  s  .  c  om*/
 * @param Named NamedObject to be added.
 * @throws IllegalArgumentException An object identified by the same name already exists in the Context.
 */
@Override
public void add(INamed Named) throws IllegalArgumentException {
    LinkedHashMap elementsByName = (LinkedHashMap) this.getElementMap();
    if (!elementsByName.containsKey(Named.getName())) {
        // add object
        this.elements.add(Named);
        // observe element for changes
        if (Named instanceof Observable) {
            Observable o = (Observable) Named;
            o.addObserver(this);
        }
        // notify observers of change
        this.setChanged();
        this.notifyObservers(Integer.valueOf(ApplicationContext.EVENT_ELEMENT_ADD));
    } else {
        throw new IllegalArgumentException(
                "An object identified by the same name already exists in the Context.");
    }
}

---

From source file:ca.sfu.federation.model.Assembly.java

/**
 * Remove a NamedObject from the Context.
 * @param Named The NamedObject to be removed.
 * @throws IllegalArgumentException The NamedObject does not exist in the Context.
 *///www.jav  a2s .  c o  m
@Override
public void remove(INamed Named) throws IllegalArgumentException {
    String childname = Named.getName();
    LinkedHashMap elementsByName = (LinkedHashMap) this.getElementMap();
    if (elementsByName.containsKey(childname)) {
        // stop listening on the NamedObject
        if (Named instanceof Observable) {
            Observable o = (Observable) Named;
            o.deleteObserver(this);
        }
        // remove the NamedObject from the collection
        this.elements.remove(Named);
        // notify observers
        this.setChanged();
        this.notifyObservers(Integer.valueOf(ApplicationContext.EVENT_ELEMENT_DELETED));
    } else {
        throw new IllegalArgumentException(
                "The object '" + childname + "' does not exist in the current Context.");
    }
}

---

From source file:com.redhat.topicindex.security.FedoraAccountSystem.java

@SuppressWarnings("unchecked")
private boolean authenticate() throws LoginException {
    if (password == null || username == null)
        throw new LoginException("No Username/Password found");
    if (password.equals("") || username.equals(""))
        throw new LoginException("No Username/Password found");

    HttpClient client = new HttpClient();
    PostMethod method = new PostMethod(FEDORA_JSON_URL);

    try {//from  www  .j  av  a  2 s.c  om
        // Generate the data to send
        List<NameValuePair> formparams = new ArrayList<NameValuePair>();
        formparams.add(new NameValuePair("username", username));
        formparams.add(new NameValuePair("user_name", username));
        formparams.add(new NameValuePair("password", String.valueOf(password)));
        formparams.add(new NameValuePair("login", "Login"));

        method.addParameters(formparams.toArray(new NameValuePair[formparams.size()]));

        // Send the data and get the response
        client.executeMethod(method);

        // Handle the response
        BufferedReader br = new BufferedReader(
                new InputStreamReader(new ByteArrayInputStream(method.getResponseBody())));

        JSONParser parser = new JSONParser();
        ContainerFactory containerFactory = new ContainerFactory() {
            public List creatArrayContainer() {
                return new LinkedList();
            }

            public Map createObjectContainer() {
                return new LinkedHashMap();
            }
        };

        // Parse the response to check authentication success and valid groups
        String line;
        while ((line = br.readLine()) != null) {
            Map json = (Map) parser.parse(line, containerFactory);
            if (json.containsKey("success") && json.containsKey("person")) {
                if (json.get("person") instanceof LinkedHashMap) {
                    LinkedHashMap person = (LinkedHashMap) json.get("person");
                    if (person.get("status").equals("active")) {
                        if (person.containsKey("approved_memberships")) {
                            if (person.get("approved_memberships") instanceof LinkedList) {
                                if (!checkCLAAgreement(((LinkedList) person.get("approved_memberships")))) {
                                    throw new LoginException("FAS authentication failed for " + username
                                            + ". Contributor License Agreement not yet signed");
                                }
                            } else if (person.get("approved_memberships") instanceof LinkedHashMap) {
                                if (!checkCLAAgreement(((LinkedHashMap) person.get("approved_memberships")))) {
                                    throw new LoginException("FAS authentication failed for " + username
                                            + ". Contributor License Agreement not yet signed");
                                }
                            }
                        } else {
                            throw new LoginException("FAS authentication failed for " + username
                                    + ". Contributor License Agreement not yet signed");
                        }
                    } else {
                        throw new LoginException(
                                "FAS authentication failed for " + username + ". Account is not active");
                    }
                }
            } else {
                throw new LoginException("Error: FAS authentication failed for " + username);
            }
        }
    } catch (LoginException e) {
        throw e;
    } catch (Exception e) {
        log.error(e.getMessage());
        e.printStackTrace();
    } finally {
        method.releaseConnection();
    }
    return true;
}

---

• «
• 1
• 2
• 3
• 4
• 5
• 6
• 7
• 8
• 9
• 10
• 11
• 12
• 13
• 14
• 15
• 16
• 17
• 18
• 19
• 20
• 21
• »