Example usage for java.util LinkedHashMap get

List of usage examples for java.util LinkedHashMap get

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Introduction

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

Prototype

public V get(Object key)

Source Link

Document

Returns the value to which the specified key is mapped, or null if this map contains no mapping for the key.

Usage

From source file:com.smartitengineering.dao.impl.hbase.CommonDao.java

protected void put(Template[] states, final boolean merge) throws IllegalStateException {
    LinkedHashMap<String, List<Put>> allPuts = new LinkedHashMap<String, List<Put>>();
    for (Template state : states) {
        if (!state.isValid()) {
            throw new IllegalStateException("Entity not in valid state!");
        }/* w w  w.  j  ava 2  s  .c  o m*/
        final LinkedHashMap<String, Put> puts;
        puts = getConverter().objectToRows(state, executorService, getLockType().equals(LockType.PESSIMISTIC));
        for (Map.Entry<String, Put> put : puts.entrySet()) {
            final List<Put> putList;
            if (allPuts.containsKey(put.getKey())) {
                putList = allPuts.get(put.getKey());
            } else {
                putList = new ArrayList<Put>();
                allPuts.put(put.getKey(), putList);
            }
            putList.add(put.getValue());
        }
    }
    for (Map.Entry<String, List<Put>> puts : allPuts.entrySet()) {
        if (LockType.OPTIMISTIC.equals(getLockType()) && infoProvider.getVersionColumnFamily() != null
                && infoProvider.getVersionColumnQualifier() != null) {
            putOptimistically(puts, merge, states);
        } else {
            putNonOptimistically(puts, merge, states);
        }
    }
}

From source file:aldenjava.opticalmapping.data.mappingresult.OptMapResultNode.java

public List<OptMapResultNode> getBreakResult(LinkedHashMap<String, DataNode> optrefmap,
        GenomicPosNode unwantedRegion) {
    if (parentFrag == null || optrefmap == null)
        return null;
    List<OptMapResultNode> resultList = new ArrayList<OptMapResultNode>();
    if (!isUsed()) {
        resultList.add(new OptMapResultNode(this));
        return resultList;
    }//from  www  . jav  a  2s  .co  m

    DataNode ref = optrefmap.get(mappedRegion.ref);
    String precigar = this.cigar.getPrecigar();
    int lastrefpos = -1;
    int lastfragpos = -1;
    int currentrefpos = subrefstart;
    int currentfragpos = subfragstart;
    int lastrefstart = -1;
    int lastfragstart = -1;
    for (char c : precigar.toCharArray()) {
        switch (c) {
        case 'M':
            if (lastrefpos != -1) {
                if (lastrefstart == -1) {
                    lastrefstart = lastrefpos;
                    lastfragstart = lastfragpos;
                }
                GenomicPosNode currentRegion = new GenomicPosNode(ref.name, ref.refp[lastrefstart - 1],
                        ref.refp[currentrefpos - 1]);

                boolean pass = !(unwantedRegion.overlapSize(currentRegion) > 0);
                if (!pass) {
                    if (lastfragstart != lastfragpos)
                        resultList.add(this.getSubResult(ref, lastfragstart, lastfragpos - mappedstrand));

                    lastrefstart = -1;
                    lastfragstart = -1;
                } else {
                    if (pass && currentrefpos == subrefstop + 1) {
                        resultList.add(this.getSubResult(ref, lastfragstart, subfragstop));
                        lastrefstart = -1;
                        lastfragstart = -1;
                    }
                }
            }
            lastrefpos = currentrefpos;
            lastfragpos = currentfragpos;
            currentfragpos += mappedstrand;
            currentrefpos += 1;
            break;
        case 'I':
            currentfragpos += mappedstrand;
            break;
        case 'D':
            currentrefpos += 1;
            break;
        default:
            ;
        }
    }
    return resultList;

}

From source file:com.DGSD.Teexter.UI.Recipient.BaseRecipientAdapter.java

private void putOneEntry(TemporaryEntry entry, boolean isAggregatedEntry,
        LinkedHashMap<Long, List<RecipientEntry>> entryMap, List<RecipientEntry> nonAggregatedEntries,
        Set<String> existingDestinations) {
    if (existingDestinations.contains(entry.destination)) {
        return;//from  w w w  .j  a  va2  s  .  co m
    }

    existingDestinations.add(entry.destination);

    if (!isAggregatedEntry) {
        nonAggregatedEntries.add(RecipientEntry.constructTopLevelEntry(entry.displayName, entry.destination,
                entry.destinationType, entry.destinationLabel, entry.contactId, entry.dataId,
                entry.thumbnailUriString));
    } else if (entryMap.containsKey(entry.contactId)) {
        // We already have a section for the person.
        final List<RecipientEntry> entryList = entryMap.get(entry.contactId);
        entryList.add(RecipientEntry.constructSecondLevelEntry(entry.displayName, entry.destination,
                entry.destinationType, entry.destinationLabel, entry.contactId, entry.dataId,
                entry.thumbnailUriString));
    } else {
        final List<RecipientEntry> entryList = new ArrayList<RecipientEntry>();
        entryList.add(RecipientEntry.constructTopLevelEntry(entry.displayName, entry.destination,
                entry.destinationType, entry.destinationLabel, entry.contactId, entry.dataId,
                entry.thumbnailUriString));
        entryMap.put(entry.contactId, entryList);
    }
}

From source file:org.openmeetings.app.remote.UserService.java

/**
 * /*ww  w .  j ava 2 s . c  o  m*/
 * @param SID
 * @param regObjectObj
 * @return
 */
@SuppressWarnings({ "rawtypes" })
public Long saveOrUpdateUser(String SID, Object regObjectObj) {
    try {
        LinkedHashMap argObjectMap = (LinkedHashMap) regObjectObj;
        Long user_idClient = null;
        if (argObjectMap.get("user_idClient") != null) {
            user_idClient = Long.valueOf(argObjectMap.get("user_idClient").toString()).longValue();
        }
        Long users_id = sessionManagement.checkSession(SID);
        Long user_level = userManagement.getUserLevelByID(users_id);

        List<?> orgO = (List<?>) argObjectMap.get("organisations");
        List<Long> orgIds = new ArrayList<Long>(orgO.size());
        for (Object o : orgO) {
            orgIds.add(Long.valueOf((Integer) o));
        }
        Date age = null;
        if (argObjectMap.get("userage") instanceof Date) {
            age = (Date) argObjectMap.get("userage");
        }

        log.debug("Mail : " + argObjectMap.get("email").toString());
        log.debug("Phone : " + argObjectMap.get("phone").toString());

        if (user_idClient == null || user_idClient == 0) {
            return userManagement.registerUserInit(user_level,
                    Long.valueOf(argObjectMap.get("level_id").toString()).longValue(),
                    Integer.valueOf(argObjectMap.get("availible").toString()).intValue(),
                    Integer.valueOf(argObjectMap.get("status").toString()).intValue(),
                    argObjectMap.get("login").toString(), argObjectMap.get("password").toString(),
                    argObjectMap.get("lastname").toString(), argObjectMap.get("firstname").toString(),
                    argObjectMap.get("email").toString(), age, argObjectMap.get("street").toString(),
                    argObjectMap.get("additionalname").toString(), argObjectMap.get("fax").toString(),
                    argObjectMap.get("zip").toString(),
                    Long.valueOf(argObjectMap.get("states_id").toString()).longValue(),
                    argObjectMap.get("town").toString(), new Long(argObjectMap.get("language_id").toString()),
                    true, orgIds, argObjectMap.get("phone").toString(), "", false,
                    argObjectMap.get("sip_user").toString(), argObjectMap.get("sip_pass").toString(),
                    argObjectMap.get("sip_auth").toString(),
                    Boolean.valueOf(argObjectMap.get("generateSipUserData").toString()).booleanValue(),
                    argObjectMap.get("jNameTimeZone").toString(),
                    Boolean.valueOf(argObjectMap.get("forceTimeZoneCheck").toString()).booleanValue(),
                    argObjectMap.get("userOffers").toString(), argObjectMap.get("userSearchs").toString(),
                    Boolean.valueOf(argObjectMap.get("showContactData").toString()).booleanValue(),
                    Boolean.valueOf(argObjectMap.get("showContactDataToContacts").toString()).booleanValue());
        } else {
            return userManagement.updateUser(user_level, user_idClient,
                    Long.valueOf(argObjectMap.get("level_id").toString()).longValue(),
                    argObjectMap.get("login").toString(), argObjectMap.get("password").toString(),
                    argObjectMap.get("lastname").toString(), argObjectMap.get("firstname").toString(), age,
                    argObjectMap.get("street").toString(), argObjectMap.get("additionalname").toString(),
                    argObjectMap.get("zip").toString(),
                    Long.valueOf(argObjectMap.get("states_id").toString()).longValue(),
                    argObjectMap.get("town").toString(), new Long(argObjectMap.get("language_id").toString()),
                    Integer.valueOf(argObjectMap.get("availible").toString()).intValue(),
                    argObjectMap.get("telefon").toString(), argObjectMap.get("fax").toString(),
                    argObjectMap.get("mobil").toString(), argObjectMap.get("email").toString(),
                    argObjectMap.get("comment").toString(),
                    Integer.valueOf(argObjectMap.get("status").toString()).intValue(), orgIds,
                    Integer.valueOf(argObjectMap.get("title_id").toString()).intValue(),
                    argObjectMap.get("phone").toString(), argObjectMap.get("sip_user").toString(),
                    argObjectMap.get("sip_pass").toString(), argObjectMap.get("sip_auth").toString(),
                    Boolean.valueOf(argObjectMap.get("generateSipUserData").toString()).booleanValue(),
                    argObjectMap.get("jNameTimeZone").toString(),
                    Boolean.valueOf(argObjectMap.get("forceTimeZoneCheck").toString()).booleanValue(),
                    argObjectMap.get("userOffers").toString(), argObjectMap.get("userSearchs").toString(),
                    Boolean.valueOf(argObjectMap.get("showContactData").toString()).booleanValue(),
                    Boolean.valueOf(argObjectMap.get("showContactDataToContacts").toString()).booleanValue());
        }
    } catch (Exception ex) {
        log.error("[saveOrUpdateUser]: ", ex);
    }
    return null;
}

From source file:com.opengamma.analytics.financial.curve.ParameterUnderlyingSensitivityCalculator.java

/**
 * Computes the sensitivity with respect to the parameters from the point sensitivities to the continuously compounded rate.
 * @param sensitivity The point sensitivity.
 * @param fixedCurves The fixed curves names (for which the parameter sensitivity are not computed even if they are necessary for the instrument pricing).
 * The curve in the list may or may not be in the bundle. Not null.
 * @param bundle The curve bundle with all the curves with respect to which the sensitivity should be computed. Not null.
 * @return The sensitivity (as a DoubleMatrix1D).
 *//*from   w  ww . j a v a 2s. co m*/
@Override
public DoubleMatrix1D pointToParameterSensitivity(final InterestRateCurveSensitivity sensitivity,
        final Set<String> fixedCurves, final YieldCurveBundle bundle) {
    Integer nbCurve = 0;
    LinkedHashMap<String, Integer> curveNum = new LinkedHashMap<String, Integer>();
    for (final String name : bundle.getAllNames()) { // loop over all curves (by name)
        if (!fixedCurves.contains(name)) {
            curveNum.put(name, nbCurve++);
        }
    }
    nbCurve = 0;
    int[] nbNewParameters = new int[curveNum.size()];
    // Implementation note: 
    int[] startCleanParameter = new int[curveNum.size()];
    // Implementation note: 
    int[][] startDirtyParameter = new int[curveNum.size()][];
    int[][] indexOther = new int[curveNum.size()][];
    // Implementation note: the start of the different blocs of parameters. First the other curves, then the new part.
    int nbCleanParameters = 0;
    int currentDirtyStart = 0;
    for (final String name : bundle.getAllNames()) { // loop over all curves (by name)
        if (!fixedCurves.contains(name)) {
            final YieldAndDiscountCurve curve = bundle.getCurve(name);
            List<String> underlyingCurveNames = curve.getUnderlyingCurvesNames();
            startCleanParameter[nbCurve] = nbCleanParameters;
            nbNewParameters[nbCurve] = curve.getNumberOfParameters();
            List<Integer> indexOtherList = new ArrayList<Integer>();
            List<Integer> startDirtyParameterList = new ArrayList<Integer>();
            for (String u : underlyingCurveNames) {
                Integer i = curveNum.get(u);
                if (i != null) {
                    indexOtherList.add(i);
                    nbNewParameters[nbCurve] -= nbNewParameters[i];
                    startDirtyParameterList.add(currentDirtyStart);
                    currentDirtyStart += nbNewParameters[i];
                }
            }
            startDirtyParameterList.add(currentDirtyStart);
            currentDirtyStart += nbNewParameters[nbCurve];
            indexOther[nbCurve] = ArrayUtils.toPrimitive(indexOtherList.toArray(new Integer[0]));
            startDirtyParameter[nbCurve] = ArrayUtils
                    .toPrimitive(startDirtyParameterList.toArray(new Integer[0]));
            nbCleanParameters += nbNewParameters[nbCurve];
            nbCurve++;
        }
    }
    final List<Double> sensiDirtyList = new ArrayList<Double>();
    for (final String name : bundle.getAllNames()) { // loop over all curves (by name)
        if (!fixedCurves.contains(name)) {
            final YieldAndDiscountCurve curve = bundle.getCurve(name);
            List<Double> oneCurveSensitivity = pointToParameterSensitivity(
                    sensitivity.getSensitivities().get(name), curve);
            sensiDirtyList.addAll(oneCurveSensitivity);
        }
    }
    double[] sensiDirty = ArrayUtils.toPrimitive(sensiDirtyList.toArray(new Double[0]));
    double[] sensiClean = new double[nbCleanParameters];
    for (int loopcurve = 0; loopcurve < nbCurve; loopcurve++) {
        for (int loopo = 0; loopo < indexOther[loopcurve].length; loopo++) {
            for (int loops = 0; loops < nbNewParameters[indexOther[loopcurve][loopo]]; loops++) {
                sensiClean[startCleanParameter[indexOther[loopcurve][loopo]]
                        + loops] += sensiDirty[startDirtyParameter[loopcurve][loopo] + loops];
            }
        }
        for (int loops = 0; loops < nbNewParameters[loopcurve]; loops++) {
            sensiClean[startCleanParameter[loopcurve]
                    + loops] += sensiDirty[startDirtyParameter[loopcurve][indexOther[loopcurve].length]
                            + loops];
        }
    }
    return new DoubleMatrix1D(sensiClean);
}

From source file:com.amalto.workbench.utils.XSDAnnotationsStructure.java

/**
 * @author ymli set the formats; fix the bug:0013463
 * @param fomats/*from   w ww  .j  av  a 2 s  .co m*/
 * @return
 */
public boolean setDisplayFormat(LinkedHashMap<String, String> fomats) {
    Iterator<String> isos = Util.iso2lang.keySet().iterator();
    while (isos.hasNext()) {
        String lang = isos.next();
        removeAppInfos("X_Display_Format_" + lang.toUpperCase());//$NON-NLS-1$
    }

    Iterator<String> isoIter = fomats.keySet().iterator();
    while (isoIter.hasNext()) {
        String iso = isoIter.next();
        removeAppInfos("X_Display_Format_" + iso.toUpperCase());//$NON-NLS-1$
        addAppInfo("X_Display_Format_" + iso.toUpperCase(), fomats.get(iso));//$NON-NLS-1$
    }

    hasChanged = true;
    return true;
}

From source file:com.smartitengineering.dao.impl.hbase.CommonDao.java

protected void deleteNonOptimistically(Template[] states) throws IllegalStateException {
    LinkedHashMap<String, List<Delete>> allDels = new LinkedHashMap<String, List<Delete>>();
    for (Template state : states) {
        if (!state.isValid()) {
            throw new IllegalStateException("Entity not in valid state!");
        }/*from   w  ww .  ja  v  a  2s.c om*/
        LinkedHashMap<String, Delete> dels = getConverter().objectToDeleteableRows(state, executorService,
                getLockType().equals(LockType.PESSIMISTIC));
        for (Map.Entry<String, Delete> del : dels.entrySet()) {
            final List<Delete> putList;
            if (allDels.containsKey(del.getKey())) {
                putList = allDels.get(del.getKey());
            } else {
                putList = new ArrayList<Delete>();
                allDels.put(del.getKey(), putList);
            }
            putList.add(del.getValue());
        }
    }
    for (final Map.Entry<String, List<Delete>> dels : allDels.entrySet()) {
        try {
            executorService.execute(dels.getKey(), new Callback<Void>() {

                @Override
                public Void call(HTableInterface tableInterface) throws Exception {
                    final List<Delete> value = dels.getValue();
                    if (logger.isInfoEnabled()) {
                        logger.info("Attempting to DELETE " + value);
                    }
                    final ArrayList<Delete> list = new ArrayList<Delete>(value);
                    tableInterface.delete(list);
                    return null;
                }
            });
        } finally {
            for (Template state : states) {
                lockAttainer.unlockAndEvictFromCache(state);
            }
        }
    }
}

From source file:com.egt.core.db.ddl.MapaClases.java

private void addClaves(LinkedHashMap tablas, String sql) throws SQLException {
    this.resultSet = TLC.getAgenteSql().executeQuery(sql);
    if (this.resultSet.next()) {
        Integer keytype = null;/*w  w w . j a  v a 2  s. c  o  m*/
        String tabname = null;
        String refname = null;
        String keyname = null;
        Integer colid = null;
        String colname = null;
        String deleterule = null;
        String updaterule = null;
        Long property = null;
        String tabla_anterior = null;
        String clave_anterior = null;
        Tabla t = null;
        Clave k = null;
        do {
            keytype = (Integer) this.resultSet.getObject("keytype");
            tabname = this.resultSet.getString("tabname");
            refname = this.resultSet.getString("refname");
            keyname = this.resultSet.getString("keyname");
            colid = (Integer) this.resultSet.getObject("colid");
            colname = this.resultSet.getString("colname");
            deleterule = this.resultSet.getString("deleterule");
            updaterule = this.resultSet.getString("updaterule");
            property = (Long) this.resultSet.getObject("property");
            if (!tabname.equals(tabla_anterior)) {
                tabla_anterior = tabname;
                clave_anterior = null;
                t = (Tabla) tablas.get(tabname);
            }
            if (t != null) {
                if (!keyname.equals(clave_anterior)) {
                    clave_anterior = keyname;
                    k = t.addClave(keyname, keytype);
                    if (refname != null) {
                        Tabla r = (Tabla) tablas.get(refname);
                        if (r == null) {
                            k.setNombreTablaReferenciada(refname);
                        } else {
                            k.setNombreTablaReferenciada(r.getNombre());
                        }
                        k.setReglaDelete(deleterule);
                        k.setReglaUpdate(updaterule);
                    }
                }
                k.addColumna(t.getColumna(colname, property));
            }
        } while (this.resultSet.next());
    }
    this.resultSet.close();
}

From source file:jp.primecloud.auto.ui.mock.service.MockInstanceService.java

@Override
public List<InstanceDto> getInstances(Long farmNo) {
    List<InstanceDto> result = new ArrayList<InstanceDto>();
    List<Instance> instances = XmlDataLoader.getData("instance.xml", Instance.class);
    List<ComponentInstance> componentInstances = XmlDataLoader.getData("componentInstance.xml",
            ComponentInstance.class);
    List<InstanceConfig> instanceConfigs = XmlDataLoader.getData("instanceConfig.xml", InstanceConfig.class);
    List<AwsInstance> awsInstances = XmlDataLoader.getData("awsInstance.xml", AwsInstance.class);
    List<VmwareInstance> vmwareInstances = XmlDataLoader.getData("vmwareInstance.xml", VmwareInstance.class);
    List<NiftyInstance> niftyInstances = XmlDataLoader.getData("niftyInstance.xml", NiftyInstance.class);
    List<Component> components = XmlDataLoader.getData("component.xml", Component.class);
    List<CloudstackInstance> cloudstackInstances = XmlDataLoader.getData("cloudstackInstance.xml",
            CloudstackInstance.class);

    //Platform/*from  ww w .  j  ava 2 s .  c om*/
    LinkedHashMap<Long, Platform> platformMap = getPlatformMap();
    LinkedHashMap<Long, PlatformAws> platformAwsMap = getPlatformAwsMap();
    LinkedHashMap<Long, PlatformVmware> platformVmwareMap = getPlatformVmwareMap();
    LinkedHashMap<Long, PlatformNifty> platformNiftyMap = getPlatformNiftyMap();
    LinkedHashMap<Long, PlatformCloudstack> platformCloudstackMap = getPlatformCloudstackMap();

    //Image
    LinkedHashMap<Long, Image> imageMap = getImageMap();
    LinkedHashMap<Long, ImageAws> imageAwsMap = getImageAwsMap();
    LinkedHashMap<Long, ImageVmware> imageVmwareMap = getImageVmwareMap();
    LinkedHashMap<Long, ImageNifty> imageNiftyMap = getImageNiftyMap();
    LinkedHashMap<Long, ImageCloudstack> imageCloudstackMap = getImageCloudstackMap();

    for (Instance instance : instances) {
        //Platform
        PlatformDto platformDto = new PlatformDto();
        platformDto.setPlatform(platformMap.get(instance.getPlatformNo()));
        platformDto.setPlatformAws(platformAwsMap.get(instance.getPlatformNo()));
        platformDto.setPlatformVmware(platformVmwareMap.get(instance.getPlatformNo()));
        platformDto.setPlatformNifty(platformNiftyMap.get(instance.getPlatformNo()));
        platformDto.setPlatformCloudstack(platformCloudstackMap.get(instance.getPlatformNo()));

        //Image
        ImageDto imageDto = new ImageDto();
        imageDto.setImage(imageMap.get(instance.getImageNo()));
        imageDto.setImageAws(imageAwsMap.get(instance.getImageNo()));
        imageDto.setImageVmware(imageVmwareMap.get(instance.getImageNo()));
        imageDto.setImageNifty(imageNiftyMap.get(instance.getImageNo()));
        imageDto.setImageCloudstack(imageCloudstackMap.get(instance.getImageNo()));

        AwsInstance awsInstance = null;
        for (AwsInstance tmp : awsInstances) {
            if (tmp.getInstanceNo().equals(instance.getInstanceNo())) {
                awsInstance = tmp;
                break;
            }
        }

        AwsAddress awsAddress = null;
        //ElasticIP?
        if (instance.getInstanceNo() == 6L) {
            awsAddress = new AwsAddress();
            awsAddress.setAddressNo(1L);
            awsAddress.setUserNo(1L);
            awsAddress.setPlatformNo(instance.getPlatformNo());
            awsAddress.setPublicIp(instance.getPublicIp());
            awsAddress.setComment(null);
            awsAddress.setInstanceNo(instance.getInstanceNo());
            awsAddress.setInstanceId(awsInstance.getInstanceId());
        }

        List<AwsVolume> awsVolumes = null;

        CloudstackInstance cloudstackInstance = null;
        for (CloudstackInstance tempCsInstance : cloudstackInstances) {
            if (instance.getInstanceNo().equals(tempCsInstance.getInstanceNo())) {
                cloudstackInstance = tempCsInstance;
            }
        }

        CloudstackAddress cloudstackAddress = new CloudstackAddress();
        cloudstackAddress.setAddressId("1");
        cloudstackAddress.setIpaddress("111.222.333.444");

        List<CloudstackVolume> cloudstackVolumes = null;

        VmwareInstance vmwareInstance = null;
        for (VmwareInstance tmp : vmwareInstances) {
            if (tmp.getInstanceNo().equals(instance.getInstanceNo())) {
                vmwareInstance = tmp;
                break;
            }
        }

        VmwareAddress vmwareAddress = new VmwareAddress();
        if (vmwareInstance != null) {
            vmwareAddress.setIpAddress("172.0.0.1");
            vmwareAddress.setEnabled(false);
            vmwareAddress.setDefaultGateway("172.0.0.1");
            vmwareAddress.setSubnetMask("255.255.0.0");
            vmwareAddress.setInstanceNo(instance.getInstanceNo());
        }

        VmwareKeyPair vmwareKeyPair = null;
        if (vmwareInstance != null) {
            vmwareKeyPair = new VmwareKeyPair();
            vmwareKeyPair.setKeyNo(1L);
            vmwareKeyPair.setKeyName("key01");
            vmwareKeyPair.setUserNo(1L);
            vmwareKeyPair.setKeyPublic("keypublic");
        }

        List<VmwareDisk> vmwareDisks = null;

        NiftyInstance niftyInstance = null;
        for (NiftyInstance tmp : niftyInstances) {
            if (tmp.getInstanceNo().equals(instance.getInstanceNo())) {
                niftyInstance = tmp;
                break;
            }
        }

        NiftyKeyPair niftyKeyPair = null;
        if (niftyInstance != null) {
            niftyKeyPair = new NiftyKeyPair();
            niftyKeyPair.setKeyNo(niftyInstance.getKeyPairNo());
            niftyKeyPair.setKeyName("key0" + niftyInstance.getKeyPairNo());
            niftyKeyPair.setUserNo(1L);
        }

        InstanceDto dto = new InstanceDto();
        // 
        if ("STARTING".equals(instance.getStatus())) {
            instance.setProgress((int) (Math.random() * 100));
            if (instance.getProgress() > 90) {
                instance.setProgress(100);
                instance.setStatus("RUNNING");
            }
        }
        instance.setPublicIp(String.valueOf((int) (Math.random() * 100)));

        List<ComponentInstanceDto> componentInstanceDtos = new ArrayList<ComponentInstanceDto>();
        for (ComponentInstance componentInstance : componentInstances) {

            ComponentInstanceDto componentInstanceDto = new ComponentInstanceDto();
            componentInstanceDto.setComponentInstance(componentInstance);

            Component component = null;
            for (Component tmpComponent : components) {
                if (componentInstance.getComponentNo().equals(tmpComponent.getComponentNo())) {
                    component = tmpComponent;
                    break;
                }
            }

            String url = createUrl(instance.getPublicIp(), component.getComponentTypeNo());
            componentInstanceDto.setUrl(url);
            componentInstanceDtos.add(componentInstanceDto);
        }

        AwsCertificate awsCertificate = null;
        if (platformAwsMap.get(instance.getPlatformNo()) != null) {
            awsCertificate = new AwsCertificate();
            awsCertificate.setPlatformNo(instance.getPlatformNo());
            awsCertificate.setDefSubnet("subnet-00000001");
        }

        dto.setInstance(instance);
        dto.setPlatform(platformDto);
        dto.setImage(imageDto);
        dto.setInstanceConfigs(instanceConfigs);
        dto.setComponentInstances(componentInstanceDtos);
        dto.setAwsInstance(awsInstance);
        dto.setAwsAddress(awsAddress);
        dto.setAwsVolumes(awsVolumes);
        dto.setAwsCertificate(awsCertificate);
        dto.setCloudstackInstance(cloudstackInstance);
        dto.setCloudstackAddress(cloudstackAddress);
        dto.setCloudstackVolumes(cloudstackVolumes);
        dto.setVmwareInstance(vmwareInstance);
        dto.setVmwareAddress(vmwareAddress);
        dto.setVmwareKeyPair(vmwareKeyPair);
        dto.setVmwareDisks(vmwareDisks);
        dto.setNiftyInstance(niftyInstance);
        dto.setNiftyKeyPair(niftyKeyPair);
        result.add(dto);
    }
    return result;
}

From source file:es.uvigo.ei.sing.adops.datatypes.ProjectExperiment.java

private String checkFastaFile() throws IllegalArgumentException {
    final Set<Character> aminos = new HashSet<Character>(
            Arrays.asList('a', 'c', 't', 'g', 'A', 'C', 'T', 'G', '-'));
    BufferedReader br = null;/*from  w  w w . ja va 2s  . c  o  m*/

    try {
        final StringBuilder sb = new StringBuilder();
        final LinkedHashMap<String, StringBuilder> replacements = new LinkedHashMap<String, StringBuilder>();

        br = new BufferedReader(new FileReader(this.fastaFile));

        String line = null;
        while ((line = br.readLine()) != null && !line.startsWith(">")) {
            sb.append(line).append('\n');
        }

        String seqId = null;
        String seq = null;
        while (line != null) {
            seqId = line;
            seq = "";
            while ((line = br.readLine()) != null && !line.startsWith(">")) {
                seq += line;
            }

            // Non ACTG characters replacement
            char[] charSequence = seq.toCharArray();
            String data = "";
            for (int i = 0; i < charSequence.length; i++) {
                if (aminos.contains(charSequence[i])) {
                    data += charSequence[i];
                } else {
                    if (replacements.containsKey(seqId)) {
                        replacements.get(seqId).append(String.format(", [%d,%c]", i + 1, charSequence[i]));
                    } else {
                        replacements.put(seqId,
                                new StringBuilder(String.format("[%d,%c]", i + 1, charSequence[i])));
                    }

                    data += '-';
                }
            }

            // Incomplete codons replacement
            charSequence = data.toCharArray();
            data = "";
            String codon = "";
            for (int i = 0; i < charSequence.length; i++) {
                codon += Character.toString(charSequence[i]);
                if ((i + 1) % 3 == 0) {
                    if (codon.contains("-")) {
                        data += "---";
                        if (replacements.containsKey(seqId)) {
                            replacements.get(seqId).append(String.format(", [%s,---]", codon));
                        } else {
                            replacements.put(seqId, new StringBuilder(String.format("[%s,---]", codon)));
                        }
                    } else {
                        data += codon;

                    }

                    codon = "";
                }
            }

            sb.append(seqId).append('\n');
            sb.append(data).append('\n');
        }

        FileUtils.write(this.fastaFile, sb.toString());

        if (replacements.isEmpty()) {
            return "";
        } else {
            final StringBuilder summary = new StringBuilder("Replacements done on input file\n");
            for (Map.Entry<String, StringBuilder> replacement : replacements.entrySet()) {
                summary.append(replacement.getKey()).append('\n');
                summary.append(replacement.getValue()).append('\n');
            }

            summary.append("\n-----\n");

            return summary.toString();
        }
    } catch (Exception e) {
        throw new IllegalArgumentException("Input file is not a valida Fasta file");
    } finally {
        if (br != null) {
            try {
                br.close();
            } catch (IOException ioe) {
            }
        }
    }
}