Java tutorial
/* * The MIT License (MIT) * * Copyright (c) 2007-2015 Broad Institute * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to deal * in the Software without restriction, including without limitation the rights * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the Software is * furnished to do so, subject to the following conditions: * * The above copyright notice and this permission notice shall be included in * all copies or substantial portions of the Software. * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN * THE SOFTWARE. */ package org.broad.igv.plugin.mongocollab; import com.mongodb.BasicDBObject; import com.mongodb.DBCollection; import com.mongodb.DBCursor; import com.mongodb.DBObject; import org.apache.log4j.Logger; import org.broad.igv.dev.api.NamedFeatureSearcher; import org.broad.igv.feature.FeatureUtils; import org.broad.igv.feature.LocusScore; import org.broad.igv.feature.NamedFeature; import org.broad.igv.track.FeatureSource; import org.broad.igv.track.FeatureTrack; import org.broad.igv.track.Track; import org.broad.igv.ui.action.SearchCommand; import java.io.IOException; import java.util.ArrayList; import java.util.Collection; import java.util.Iterator; import java.util.List; /** * User: jacob * Date: 2012-Dec-14 */ public class MongoFeatureSource implements FeatureSource<DBFeature.IGVFeat>, NamedFeatureSearcher { private int featureWindowSize = 1000000; private DBCollection collection; private boolean hasLocusIndex = false; private static Logger log = Logger.getLogger(MongoCollabPlugin.class); public MongoFeatureSource(DBCollection collection, boolean buildLocusIndex) { this.collection = collection; this.collection.setObjectClass(DBFeature.class); checkForLocusIndex(buildLocusIndex); } boolean hasLocusIndex() { return this.hasLocusIndex; } /** * Check to see if we have an index useful for queries * @param buildIndex Whether to build locus index if not found */ private void checkForLocusIndex(boolean buildIndex) { if (buildIndex) { ensureLocusIndex(collection); } //Check to see if we have the index we want List<DBObject> indexes = collection.getIndexInfo(); DBObject neededFields = getLocusIndexKeys(); for (DBObject index : indexes) { boolean isMatchingIndex = true; DBObject indexKey = (DBObject) index.get("key"); for (String key : neededFields.keySet()) { boolean hasKey = indexKey.containsField(key); if (!hasKey) { isMatchingIndex = false; break; } Object value = indexKey.get(key); boolean equals = neededFields.get(key).equals(value); isMatchingIndex &= equals; } if (isMatchingIndex) { this.hasLocusIndex = true; break; } } } private DBObject createQueryObject(String chr, int start, int end) { BasicDBObject query = new BasicDBObject("Chr", chr); //Only query over given interval //See http://docs.mongodb.org/manual/tutorial/query-documents/ query.append("Start", new BasicDBObject("$lte", end)); query.append("End", new BasicDBObject("$gte", start)); return query; } /** * Return the key/value pairs for indexing * Store these as doubles for easier comparison, MongoDB stores everything * as a double in the DB * @return */ private DBObject getLocusIndexKeys() { BasicDBObject indexKeys = new BasicDBObject("Chr", 1.0d); indexKeys.append("Start", 1.0d); indexKeys.append("End", 1.0d); return indexKeys; } /** * Ensures there is an index on Chr, Start, and End * To speed queries * See http://docs.mongodb.org/manual/reference/method/db.collection.ensureIndex/#db.collection.ensureIndex * @param collection */ private void ensureLocusIndex(DBCollection collection) { collection.ensureIndex(getLocusIndexKeys()); } @Override public Iterator<DBFeature.IGVFeat> getFeatures(String chr, int start, int end) throws IOException { return getFeatures(createQueryObject(chr, start, end), 0).iterator(); } @Override public Collection<? extends NamedFeature> search(String name, int limit) { BasicDBObject dbObj = new BasicDBObject("UpperName", name.toUpperCase()); try { return getFeatures(dbObj, limit); } catch (IOException e) { log.error(e.getMessage(), e); return null; } } /** * * @param queryObject * @param limit Limitation on the number of results returned. Setting to 0 is equivalent to unlimited * @return * @throws IOException */ private Collection<DBFeature.IGVFeat> getFeatures(DBObject queryObject, int limit) throws IOException { DBCursor cursor = this.collection.find(queryObject); cursor.limit(limit >= 0 ? limit : 0); //Sort by increasing start value //Only do this if we have an index, otherwise might be too memory intensive if (hasLocusIndex) { cursor.sort(new BasicDBObject("Start", 1)); } boolean isSorted = true; int lastStart = -1; List<DBFeature.IGVFeat> features = new ArrayList<DBFeature.IGVFeat>(); while (cursor.hasNext()) { DBObject obj = cursor.next(); DBFeature feat = (DBFeature) obj; features.add(feat.createIGVFeature()); isSorted &= feat.getStart() >= lastStart; lastStart = feat.getStart(); } if (!isSorted) { FeatureUtils.sortFeatureList(features); } return features; } @Override public List<LocusScore> getCoverageScores(String chr, int start, int end, int zoom) { return null; } @Override public int getFeatureWindowSize() { return featureWindowSize; } @Override public void setFeatureWindowSize(int size) { this.featureWindowSize = size; } DBCollection getCollection() { return this.collection; } public static FeatureTrack loadFeatureTrack(MongoCollabPlugin.Locator locator, List<Track> newTracks) { DBCollection collection = MongoCollabPlugin.getCollection(locator); //TODO Make this more flexible collection.setObjectClass(DBFeature.class); MongoFeatureSource source = new MongoFeatureSource(collection, locator.buildLocusIndex); FeatureTrack track = new MongoFeatureTrack(collection.getFullName(), collection.getName(), source); SearchCommand.registerNamedFeatureSearcher(source); newTracks.add(track); track.setMargin(0); return track; } }