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.google; import com.google.gson.JsonObject; import com.google.gson.JsonParser; import htsjdk.samtools.SAMFileHeader; import htsjdk.samtools.util.CloseableIterator; import org.apache.log4j.Logger; import org.broad.igv.sam.Alignment; import org.broad.igv.sam.reader.AlignmentReader; import org.broad.igv.util.HttpUtils; import java.io.IOException; import java.net.URL; import java.util.*; /** * Class for testing GlobalAlliance API. Loads json from a text file, for development only * <p/> * Created by jrobinso on 7/18/14. */ public class Ga4ghAlignmentReader implements AlignmentReader<Alignment> { private static Logger log = Logger.getLogger(Ga4ghAlignmentReader.class); String readsetId; List<String> sequenceNames; Ga4ghProvider provider; Map<String, String> chromosomeMappings; public Ga4ghAlignmentReader(Ga4ghProvider provider, String readsetId) { this.provider = provider == null ? Ga4ghAPIHelper.GA4GH_GOOGLE_PROVIDER : provider; this.readsetId = readsetId; this.chromosomeMappings = new HashMap<String, String>(); } @Override public void close() throws IOException { } @Override public List<String> getSequenceNames() throws IOException { if (sequenceNames == null) { try { loadMetadata(); } catch (IOException e) { throw e; } catch (Exception e) { log.error("Error fetching metadata", e); } } return sequenceNames; } @Override public SAMFileHeader getFileHeader() { return null; } @Override public Set<String> getPlatforms() { return null; } @Override public CloseableIterator<Alignment> iterator() { throw new RuntimeException("Iterating over google datasets is not supported"); } /** * Return an iterator over alignments overlapping the given region. We first try the sequence name as given, * then try an alias if we have one. This is to handle the common 1 vs chr1 naming problem stemming from * competing conventions. * * @param sequence * @param start 0-based start location * @param end 0-based, exclusive-end coordinate * @param contained * @return * @throws IOException */ @Override public CloseableIterator<Alignment> query(String sequence, int start, int end, boolean contained) throws IOException { boolean sequenceNameConfirmed = false; if (chromosomeMappings.containsKey(sequence)) { sequence = chromosomeMappings.get(sequence); sequenceNameConfirmed = true; } boolean handleError = sequenceNameConfirmed; List<Alignment> alignmentList = Ga4ghAPIHelper.searchReads(provider, readsetId, sequence, start, end, handleError); if (alignmentList != null) { chromosomeMappings.put(sequence, sequence); return new MIterator(alignmentList); } else if (sequenceNameConfirmed == false && COMMON_ALIASES.containsKey(sequence)) { String altSequence = COMMON_ALIASES.get(sequence); log.info("Sequence \"" + sequence + "\" failed. Trying \"" + altSequence + "\""); alignmentList = Ga4ghAPIHelper.searchReads(provider, readsetId, altSequence, start, end, true); if (alignmentList != null) { chromosomeMappings.put(sequence, altSequence); } return alignmentList == null ? null : new MIterator(alignmentList); } else { return null; } } @Override public boolean hasIndex() { return true; } private void loadMetadata() throws IOException { String authKey = provider.apiKey; String baseURL = provider.baseURL; URL url = HttpUtils .createURL(baseURL + "/readgroupsets/" + readsetId + (authKey == null ? "" : "?key=" + authKey)); // TODO -- field selection? Map<String, String> headers = new HashMap<String, String>(); String token = OAuthUtils.getInstance().getAccessToken(); if (token != null) { headers.put("Authorization", "Bearer " + token); } String result = HttpUtils.getInstance().getContentsAsString(url, headers); JsonParser parser = new JsonParser(); JsonObject root = parser.parse(result).getAsJsonObject(); if (root.has("referenceSetId")) { String referenceSetId = root.getAsJsonPrimitive("referenceSetId").getAsString(); List<JsonObject> refererences = Ga4ghAPIHelper.searchReferences(provider, referenceSetId, 1000); sequenceNames = new ArrayList(); for (JsonObject refObject : refererences) { sequenceNames.add(refObject.getAsJsonPrimitive("name").getAsString()); } } } public static boolean supportsFileType(String type) { return Ga4ghAPIHelper.RESOURCE_TYPE.equals(type); } class MIterator implements CloseableIterator<Alignment> { Iterator<Alignment> iter; MIterator(List<Alignment> alignmentList) { iter = alignmentList.iterator(); } @Override public void close() { } @Override public boolean hasNext() { return iter.hasNext(); } @Override public Alignment next() { return iter.next(); } @Override public void remove() { iter.remove(); } } static Map<String, String> COMMON_ALIASES = new HashMap<String, String>(); static { for (int i = 1; i <= 23; i++) { COMMON_ALIASES.put(("" + i), ("chr" + i)); COMMON_ALIASES.put(("chr" + i), ("" + i)); } COMMON_ALIASES.put("chrX", "X"); COMMON_ALIASES.put("X", "chrX"); COMMON_ALIASES.put("chrY", "Y"); COMMON_ALIASES.put("Y", "chrY"); COMMON_ALIASES.put("chrM", "MT"); COMMON_ALIASES.put("MT", "chrM"); } }