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247 changes: 247 additions & 0 deletions
247
src/main/java/io/github/msdk/datamodel/datapointstore/NFSDBDataPointStore.java
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| /* | ||
| * (C) Copyright 2015 by MSDK Development Team | ||
| * | ||
| * This software is dual-licensed under either | ||
| * | ||
| * (a) the terms of the GNU Lesser General Public License version 2.1 | ||
| * as published by the Free Software Foundation | ||
| * | ||
| * or (per the licensee's choosing) | ||
| * | ||
| * (b) the terms of the Eclipse Public License v1.0 as published by | ||
| * the Eclipse Foundation. | ||
| */ | ||
|
|
||
| package io.github.msdk.datamodel.datapointstore; | ||
|
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
| import java.util.HashMap; | ||
|
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| import javax.annotation.Nonnull; | ||
|
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| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
|
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| import com.nfsdb.journal.factory.JournalFactory; | ||
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| import io.github.msdk.MSDKException; | ||
| import io.github.msdk.MSDKRuntimeException; | ||
| import io.github.msdk.datamodel.impl.MSDKObjectBuilder; | ||
| import io.github.msdk.datamodel.peaklists.FeatureDataPointList; | ||
| import io.github.msdk.datamodel.rawdata.ChromatogramDataPointList; | ||
| import io.github.msdk.datamodel.rawdata.MsSpectrumDataPointList; | ||
|
|
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| /** | ||
| * A DataPointStore implementation that stores the data points in memory. Use | ||
| * with caution. When DataPointLists are stored or retrieved, they are not | ||
| * referenced but copied, so the original list can be used for other purpose. | ||
| * | ||
| * The methods of this class are synchronized, therefore it can be safely used | ||
| * by multiple threads. | ||
| */ | ||
| class NFSDBDataPointStore implements DataPointStore { | ||
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| private final Logger logger = LoggerFactory.getLogger(this.getClass()); | ||
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| private HashMap<Object, Object> storageMap = new HashMap<>(); | ||
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| private int lastStorageId = 0; | ||
| private final File tmpDataFileName; | ||
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| NFSDBDataPointStore() throws MSDKException { | ||
|
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| try { | ||
| tmpDataFileName = Files.createTempDirectory("msdk_nfsdb").toFile(); | ||
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| logger.debug("Initializing a new NFSDB journal factory in " | ||
| + tmpDataFileName); | ||
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| JournalFactory factory = new JournalFactory(tmpDataFileName); | ||
|
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|
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| } catch (IOException e) { | ||
| throw new MSDKException(e); | ||
| } | ||
|
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| } | ||
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| /** | ||
| * Stores new array of data points. | ||
| * | ||
| * @return Storage ID for the newly stored data. | ||
| */ | ||
| @Override | ||
| public @Nonnull Integer storeDataPoints( | ||
| @Nonnull MsSpectrumDataPointList dataPoints) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| // Clone the given list for storage | ||
| final MsSpectrumDataPointList newList = MSDKObjectBuilder | ||
| .getSpectrumDataPointList(); | ||
| newList.copyFrom(dataPoints); | ||
|
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| // Save the reference to the new list | ||
| synchronized (storageMap) { | ||
| // Increase the storage ID | ||
| lastStorageId++; | ||
| storageMap.put(lastStorageId, newList); | ||
| } | ||
|
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| return lastStorageId; | ||
| } | ||
|
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| /** | ||
| * Stores new array of data points. | ||
| * | ||
| * @return Storage ID for the newly stored data. | ||
| */ | ||
| @Override | ||
| public @Nonnull Integer storeDataPoints( | ||
| @Nonnull ChromatogramDataPointList dataPoints) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| // Clone the given list for storage | ||
| final ChromatogramDataPointList newList = MSDKObjectBuilder | ||
| .getChromatogramDataPointList(); | ||
| newList.copyFrom(dataPoints); | ||
|
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| // Save the reference to the new list | ||
| synchronized (storageMap) { | ||
| // Increase the storage ID | ||
| lastStorageId++; | ||
| storageMap.put(lastStorageId, newList); | ||
| } | ||
|
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| return lastStorageId; | ||
| } | ||
|
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| /** | ||
| * Stores new array of data points. | ||
| * | ||
| * @return Storage ID for the newly stored data. | ||
| */ | ||
| @Override | ||
| public @Nonnull Integer storeDataPoints( | ||
| @Nonnull FeatureDataPointList dataPoints) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| // Clone the given list for storage | ||
| final FeatureDataPointList newList = MSDKObjectBuilder | ||
| .getFeatureDataPointList(); | ||
| newList.copyFrom(dataPoints); | ||
|
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| // Save the reference to the new list | ||
| synchronized (storageMap) { | ||
| // Increase the storage ID | ||
| lastStorageId++; | ||
| storageMap.put(lastStorageId, newList); | ||
| } | ||
|
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| return lastStorageId; | ||
| } | ||
|
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| /** | ||
| * Reads the data points associated with given ID. | ||
| */ | ||
| @Override | ||
| synchronized public void readDataPoints(@Nonnull Object ID, | ||
| @Nonnull MsSpectrumDataPointList list) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| if (!storageMap.containsKey(ID)) | ||
| throw new IllegalArgumentException( | ||
| "ID " + ID + " not found in storage"); | ||
|
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| // Get the stored DataPointList | ||
| final Object storedObject = storageMap.get(ID); | ||
| if (!(storedObject instanceof MsSpectrumDataPointList)) | ||
| throw new MSDKRuntimeException( | ||
| "Object stored under ID " + ID + " is not of correct type"); | ||
| final MsSpectrumDataPointList storedList = (MsSpectrumDataPointList) storedObject; | ||
|
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| // Copy data | ||
| list.copyFrom(storedList); | ||
|
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| } | ||
|
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| /** | ||
| * Reads the data points associated with given ID. | ||
| */ | ||
| @Override | ||
| synchronized public void readDataPoints(@Nonnull Object ID, | ||
| @Nonnull ChromatogramDataPointList list) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| if (!storageMap.containsKey(ID)) | ||
| throw new IllegalArgumentException( | ||
| "ID " + ID + " not found in storage"); | ||
|
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| // Get the stored DataPointList | ||
| final Object storedObject = storageMap.get(ID); | ||
| if (!(storedObject instanceof ChromatogramDataPointList)) | ||
| throw new MSDKRuntimeException( | ||
| "Object stored under ID " + ID + " is not of correct type"); | ||
| final ChromatogramDataPointList storedList = (ChromatogramDataPointList) storedObject; | ||
|
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| // Copy data | ||
| list.copyFrom(storedList); | ||
|
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| } | ||
|
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| /** | ||
| * Reads the data points associated with given ID. | ||
| */ | ||
| @Override | ||
| synchronized public void readDataPoints(@Nonnull Object ID, | ||
| @Nonnull FeatureDataPointList list) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| if (!storageMap.containsKey(ID)) | ||
| throw new IllegalArgumentException( | ||
| "ID " + ID + " not found in storage"); | ||
|
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| // Get the stored DataPointList | ||
| final Object storedObject = storageMap.get(ID); | ||
| if (!(storedObject instanceof FeatureDataPointList)) | ||
| throw new MSDKRuntimeException( | ||
| "Object stored under ID " + ID + " is not of correct type"); | ||
| final FeatureDataPointList storedList = (FeatureDataPointList) storedObject; | ||
|
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| // Copy data | ||
| list.copyFrom(storedList); | ||
|
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| } | ||
|
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| /** | ||
| * Remove data associated with given storage ID. | ||
| */ | ||
| @Override | ||
| synchronized public void removeDataPoints(@Nonnull Object ID) { | ||
|
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| if (storageMap == null) | ||
| throw new IllegalStateException("This object has been disposed"); | ||
|
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| storageMap.remove(ID); | ||
| } | ||
|
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| @Override | ||
| synchronized public void dispose() { | ||
| storageMap = null; | ||
| } | ||
|
|
||
| } |
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