List of usage examples for org.apache.hadoop.io LongWritable set
public void set(long value)
From source file:org.broadinstitute.sting.gatk.walkers.indels.ConstrainedMateFixingManager.java
License:Open Source License
private void writeRead(GATKSAMRecord read) { try {//w w w . ja va2 s . co m if (!CommandLineGATK.runningOnHadoop) { writer.addAlignment(read); } else { if (read.getIncludeRead()) { LongWritable key = new LongWritable(); SAMRecordWritable record = new SAMRecordWritable(); if (read.getReferenceName().equals("*")) key.set(Long.MAX_VALUE); else key.set((long) read.getReferenceIndex() << 32 | read.getAlignmentStart() - 1); record.set(((SAMRecord) read)); IndelMapReduce.IMContext.write(key, record); } } } catch (IllegalArgumentException e) { throw new UserException( "If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details. " + e.getMessage(), e); } catch (Exception e) { } }
From source file:org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker.java
License:Open Source License
/** * Output each read to disk/*from ww w. j av a2 s . c o m*/ * * @param read The read to output * @param output The FileWriter to write the read to * @return The FileWriter */ public SAMFileWriter reduce(SAMRecord read, SAMFileWriter output) { if (output != null) { if (!CommandLineGATK.runningOnHadoop) { output.addAlignment(read); } else { if (((GATKSAMRecord) read).getIncludeRead()) { if (!RecalMapReduce.isVariant) { try { LongWritable key = new LongWritable(); SAMRecordWritable record = new SAMRecordWritable(); if (read.getReferenceName().equals("*")) key.set(Long.MAX_VALUE); else key.set((long) read.getReferenceIndex() << 32 | read.getAlignmentStart() - 1); record.set(read); RecalMapReduce.RMContext.write(key, record); } catch (Exception e) { } } else { output.addAlignment(read); } } } } return output; }
From source file:org.data2semantics.giraph.SimpleInDegreeCountComputation.java
License:Apache License
@Override public void compute(Vertex<Text, LongWritable, NullWritable> vertex, Iterable<DoubleWritable> messages) throws IOException { if (getSuperstep() == 0) { Iterable<Edge<Text, NullWritable>> edges = vertex.getEdges(); for (Edge<Text, NullWritable> edge : edges) { sendMessage(edge.getTargetVertexId(), new DoubleWritable(1.0)); }//from ww w . java2s.co m } else { long sum = 0; for (@SuppressWarnings("unused") DoubleWritable message : messages) { sum++; } LongWritable vertexValue = vertex.getValue(); vertexValue.set(sum); vertex.setValue(vertexValue); vertex.voteToHalt(); } }
From source file:org.data2semantics.giraph.SimpleOutDegreeCountComputation.java
License:Apache License
@Override public void compute(Vertex<Text, LongWritable, NullWritable> vertex, Iterable<DoubleWritable> messages) throws IOException { if (getSuperstep() == 0) { LongWritable vertexValue = vertex.getValue(); vertexValue.set(vertex.getNumEdges()); vertex.setValue(vertexValue);/* w ww . j av a2s. c o m*/ //we want to send a message to our target vertices as well. otherwise, our output only contains the vertices with an outdegree > 0 Iterable<Edge<Text, NullWritable>> edges = vertex.getEdges(); for (Edge<Text, NullWritable> edge : edges) { sendMessage(edge.getTargetVertexId(), new DoubleWritable(1.0)); } } else { if (vertex.getNumEdges() == 0) { LongWritable vertexValue = vertex.getValue(); vertexValue.set(0); vertex.setValue(vertexValue); } else { //if it has a number of outgoing edges, the proper value is already set in the first step } vertex.voteToHalt(); } }
From source file:org.gradoop.flink.io.impl.tlf.inputformats.TLFRecordReader.java
License:Apache License
/** * Reads the next key/value pair from the input for processing. * * @param key the new key//from ww w.ja v a2 s .c o m * @param value the new value * @return true if a key/value pair was found * @throws IOException */ private boolean next(LongWritable key, Text value) throws IOException { if (fsin.getPos() < end && readUntilMatch(TLFConstants.START_TAG.getBytes(Charsets.UTF_8), false)) { try { buffer.write(TLFConstants.START_TAG.getBytes(Charsets.UTF_8)); if (readUntilMatch(TLFConstants.END_TAG.getBytes(Charsets.UTF_8), true)) { key.set(fsin.getPos()); if (fsin.getPos() != end) { //- end tag because it is the new start tag and shall not be added valueLength = buffer.getLength() - TLFConstants.END_TAG.getBytes(Charsets.UTF_8).length; } else { // in this case there is no new start tag valueLength = buffer.getLength(); } //- end tag because it is the new start tag and shall not be added value.set(buffer.getData(), 0, valueLength); //set the buffer to position before end tag of old graph which is // start tag of the new one fsin.seek(fsin.getPos() - TLFConstants.END_TAG.getBytes(Charsets.UTF_8).length); return true; } } finally { buffer.reset(); } } return false; }
From source file:org.gradoop.io.impl.tlf.inputformats.TLFRecordReader.java
License:Open Source License
/** * Reads the next key/value pair from the input for processing. * * @param key the new key//w w w . j a va 2 s .co m * @param value the new value * @return true if a key/value pair was found * @throws IOException */ private boolean next(LongWritable key, Text value) throws IOException { if (fsin.getPos() < end && readUntilMatch(START_TAG_BYTE, false)) { try { buffer.write(START_TAG_BYTE); if (readUntilMatch(END_TAG_BYTE, true)) { key.set(fsin.getPos()); if (fsin.getPos() != end) { //- end tag because it is the new start tag and shall not be added valueLength = buffer.getLength() - END_TAG_BYTE.length; } else { // in this case there is no new start tag valueLength = buffer.getLength(); } //- end tag because it is the new start tag and shall not be added value.set(buffer.getData(), 0, valueLength); //set the buffer to position before end tag of old graph which is // start tag of the new one fsin.seek(fsin.getPos() - END_TAG_BYTE.length); return true; } } finally { buffer.reset(); } } return false; }
From source file:org.hadoop.tdg.TestPseudoHadoop.java
License:Apache License
/** * sorted sequence file/* w ww. j a v a 2s . c o m*/ * * @throws IOException */ @Test public void mapFileIO() throws IOException { LongWritable key = new LongWritable(); Text value = new Text(); MapFile.Writer writer = null; try { writer = new MapFile.Writer(fs.getConf(), fs, DST, key.getClass(), value.getClass()); for (int i = 0; i < 100; i++) { key.set(i); value.set(DATA[i % DATA.length]); writer.append(key, value); } } finally { IOUtils.closeStream(writer); } MapFile.Reader reader = null; try { reader = new MapFile.Reader(fs, DST, fs.getConf()); LongWritable readerKey = (LongWritable) ReflectionUtils.newInstance(reader.getKeyClass(), fs.getConf()); Text readerValue = (Text) ReflectionUtils.newInstance(reader.getValueClass(), fs.getConf()); while (reader.next(readerKey, readerValue)) { System.out.printf("%s\t%s\n", readerKey, readerValue); } } finally { IOUtils.closeStream(writer); } }
From source file:org.mitre.bio.mapred.io.FastaRecordReader.java
License:Open Source License
/** * Reads the next key/value pair from the input for processing. * * @param key the key to read data into//from ww w . j a va2 s . co m * @param value the value to read data into * @return true iff a key/value was read, false if at EOF */ @Override public synchronized boolean next(LongWritable key, Text value) throws IOException { this.buffer.reset(); if (this.pos < this.end) { try { // Find the being of a new record block if (readLinesUntilStartsWithMatch(startTag, false)) { // Read until we find the endTag or EOF readLinesBeforeStartsWithMatch(startTag, true); if (buffer.size() > 0) { key.set(this.pos); value.set(buffer.getData(), 0, buffer.getLength()); return true; } } } finally { LOG.debug("Uncaught exception!"); this.buffer.reset(); } } return false; }
From source file:org.msgpack.hadoop.mapred.MessagePackRecordReader.java
License:Apache License
public boolean next(LongWritable key, MessagePackWritable val) throws IOException { if (unpacker_.hasNext()) { key.set(fileIn_.getPos()); ImmutableValue obj = unpacker_.unpackValue(); val.set(obj); return true; }/*www . java 2 s . co m*/ return false; }
From source file:org.pentaho.hadoop.mapreduce.converter.converters.KettleTypeToLongWritableConverter.java
License:Apache License
@Override public LongWritable convert(ValueMetaInterface meta, Object obj) throws TypeConversionException { try {//from www. j a v a 2 s . c o m LongWritable result = new LongWritable(); result.set(meta.getInteger(obj)); return result; } catch (KettleValueException ex) { throw new TypeConversionException(BaseMessages.getString(TypeConverterFactory.class, "ErrorConverting", LongWritable.class.getSimpleName(), obj), ex); } }