private void writeIndexPosition(String file, long indexPosition, int nbytes) { try { RandomAccessFile raf = new RandomAccessFile(file, "rw"); raf.getChannel().position(indexPositionPosition); // Write as little endian BufferedByteWriter buffer = new BufferedByteWriter(); buffer.putLong(indexPosition); buffer.putInt(nbytes); raf.write(buffer.getBytes()); raf.close(); } catch (IOException ex) { ex.printStackTrace(); } }
private void writeIndexPosition(long indexPosition, int nbytes) { try { RandomAccessFile raf = new RandomAccessFile(file, "rw"); raf.getChannel().position(indexPositionPosition); // Write as little endian BufferedByteWriter buffer = new BufferedByteWriter(); buffer.putLong(indexPosition); buffer.putInt(nbytes); raf.write(buffer.getBytes()); raf.close(); } catch (IOException ex) { ex.printStackTrace(); } }
private void writeIndexPosition(long indexPosition, int nbytes) { try { RandomAccessFile raf = new RandomAccessFile(file, "rw"); raf.getChannel().position(indexPositionPosition); // Write as little endian BufferedByteWriter buffer = new BufferedByteWriter(); buffer.putLong(indexPosition); buffer.putInt(nbytes); raf.write(buffer.getBytes()); raf.close(); } catch (IOException ex) { ex.printStackTrace(); } }
private void writeDatasets() throws IOException { for (TDFDataset dataset : datasetCache.values()) { long position = bytesWritten; BufferedByteWriter buffer = new BufferedByteWriter(); dataset.write(buffer); write(buffer.getBytes()); int nBytes = (int) (bytesWritten - position); datasetIndex.put(dataset.getName(), new IndexEntry(position, nBytes)); } }
private void writeGroups() throws IOException { for (TDFGroup group : groupCache.values()) { long position = bytesWritten; BufferedByteWriter buffer = new BufferedByteWriter(); group.write(buffer); write(buffer.getBytes()); int nBytes = (int) (bytesWritten - position); groupIndex.put(group.getName(), new IndexEntry(position, nBytes)); } }
private int writeIndex() throws IOException { // compress and write BufferedByteWriter buff = new BufferedByteWriter(); buff.putInt(chrPositionMap.size()); for (Map.Entry<String, IndexEntry> entry : chrPositionMap.entrySet()) { IndexEntry ie = entry.getValue(); buff.putNullTerminatedString(entry.getKey()); buff.putLong(ie.position); buff.putInt(ie.size); } byte[] bytes = buff.getBytes(); write(bytes); return bytes.length; }
private void writeGroups() throws IOException { for (TDFGroup group : groupCache.values()) { long position = bytesWritten; BufferedByteWriter buffer = new BufferedByteWriter(); group.write(buffer); write(buffer.getBytes()); int nBytes = (int) (bytesWritten - position); groupIndex.put(group.getName(), new IndexEntry(position, nBytes)); } }
private void writeDatasets() throws IOException { for (TDFDataset dataset : datasetCache.values()) { long position = bytesWritten; BufferedByteWriter buffer = new BufferedByteWriter(); dataset.write(buffer); write(buffer.getBytes()); int nBytes = (int) (bytesWritten - position); datasetIndex.put(dataset.getName(), new IndexEntry(position, nBytes)); } }
private void writeIndex() throws IOException { BufferedByteWriter buffer = new BufferedByteWriter(); // Now write out dataset index buffer.putInt(datasetIndex.size()); for (Map.Entry<String, IndexEntry> entry : datasetIndex.entrySet()) { buffer.putNullTerminatedString(entry.getKey()); buffer.putLong(entry.getValue().position); buffer.putInt(entry.getValue().nBytes); } // group index log.info("Group idx: " + groupIndex.size()); buffer.putInt(groupIndex.size()); for (Map.Entry<String, IndexEntry> entry : groupIndex.entrySet()) { buffer.putNullTerminatedString(entry.getKey()); buffer.putLong(entry.getValue().position); buffer.putInt(entry.getValue().nBytes); } byte[] bytes = buffer.getBytes(); write(bytes); }
private void writeIndex() throws IOException { BufferedByteWriter buffer = new BufferedByteWriter(); // Now write out dataset index buffer.putInt(datasetIndex.size()); for (Map.Entry<String, IndexEntry> entry : datasetIndex.entrySet()) { buffer.putNullTerminatedString(entry.getKey()); buffer.putLong(entry.getValue().position); buffer.putInt(entry.getValue().nBytes); } // group index System.out.println("Group idx: " + groupIndex.size()); buffer.putInt(groupIndex.size()); for (Map.Entry<String, IndexEntry> entry : groupIndex.entrySet()) { buffer.putNullTerminatedString(entry.getKey()); buffer.putLong(entry.getValue().position); buffer.putInt(entry.getValue().nBytes); } byte[] bytes = buffer.getBytes(); write(bytes); }
currentChrBuffer = new BufferedByteWriter();
public void writeTile(String dsId, int tileNumber, TDFTile tile) throws IOException { TDFDataset dataset = datasetCache.get(dsId); if (dataset == null) { throw new java.lang.NoSuchFieldError("Dataset: " + dsId + " doese not exist. " + "Call createDataset first"); } long pos = bytesWritten; if (tileNumber < dataset.tilePositions.length) { dataset.tilePositions[tileNumber] = pos; // Write the tile contents to a byte buffer first, so we can optionally gzip it BufferedByteWriter buffer = new BufferedByteWriter(); tile.writeTo(buffer); byte[] bytes = buffer.getBytes(); if (compressed) { bytes = compressionUtils.compress(bytes); } write(bytes); int nBytes = bytes.length; dataset.tileSizes[tileNumber] = nBytes; } else { // The occasional tile number == tile array size is expected, but tile // numbers larger than that are not if (tileNumber > dataset.tilePositions.length) { System.out.println("Unexpected tile number: " + tileNumber + " (max of " + dataset.tilePositions.length + " expected)."); } } }
public void writeTile(String dsId, int tileNumber, TDFTile tile) throws IOException { TDFDataset dataset = datasetCache.get(dsId); if (dataset == null) { throw new java.lang.NoSuchFieldError("Dataset: " + dsId + " doese not exist. " + "Call createDataset first"); } long pos = bytesWritten; if (tileNumber < dataset.tilePositions.length) { dataset.tilePositions[tileNumber] = pos; // Write the tile contents to a byte buffer first, so we can optionally gzip it BufferedByteWriter buffer = new BufferedByteWriter(); tile.writeTo(buffer); byte[] bytes = buffer.getBytes(); if (compressed) { bytes = CompressionUtils.compress(bytes); } write(bytes); int nBytes = bytes.length; //tile.writeTo(fos); //int nBytes = (int) (fos.bytesWritten() - pos); // bytes.length; dataset.tileSizes[tileNumber] = nBytes; } else { // The occasional tile number == tile array size is expected, but tile // numbers larger than that are not if (tileNumber > dataset.tilePositions.length) { System.out.println("Unexpected tile number: " + tileNumber + " (max of " + dataset.tilePositions.length + " expected)."); } } }
public byte [] encodeBinary() throws IOException { BufferedByteWriter writer = new BufferedByteWriter(); writer.putNullTerminatedString(snp); writer.putNullTerminatedString(chr); writer.putInt(position); writer.putNullTerminatedString(geneId); writer.putNullTerminatedString(geneName); //writer.putFloat(tStat); writer.putFloat(pValue); //writer.putFloat(qValue); return writer.getBytes(); }
private void writeHeader() throws IOException { // Magic number -- 4 bytes byte[] magicNumber = new byte[]{'E', 'Q', 'T', 'L'}; BufferedByteWriter buffer = new BufferedByteWriter(); buffer.put(magicNumber); buffer.putInt(version); // Reserve space for the master index pointer and byte count. // The actual values will be written at the end indexPositionPosition = buffer.bytesWritten(); buffer.putLong(0l); // File position for start of index buffer.putInt(0); // Size in bytes of index final byte[] bytes = buffer.getBytes(); write(bytes); }
BufferedByteWriter buffer = new BufferedByteWriter(24); buffer.put(magicNumber); buffer.putInt(version); write(buffer.getBytes()); buffer = new BufferedByteWriter(24);
BufferedByteWriter buffer = new BufferedByteWriter(24); buffer.put(magicNumber); buffer.putInt(version); write(buffer.getBytes()); buffer = new BufferedByteWriter(24);