Java tutorial
/* * #%L * gitools-core * %% * Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/gpl-3.0.html>. * #L% */ package org.gitools.matrix.format; import org.apache.commons.io.IOUtils; import org.gitools.api.PersistenceException; import org.gitools.api.analysis.IProgressMonitor; import org.gitools.api.matrix.IMatrix; import org.gitools.api.matrix.MatrixDimensionKey; import org.gitools.api.resource.IResourceLocator; import org.gitools.matrix.model.compressmatrix.AbstractCompressor; import org.gitools.matrix.model.compressmatrix.CompressDimension; import org.gitools.matrix.model.compressmatrix.CompressMatrix; import org.gitools.matrix.model.compressmatrix.CompressRow; import org.gitools.resource.AbstractResourceFormat; import javax.enterprise.context.ApplicationScoped; import java.io.*; import java.util.HashMap; import java.util.Map; import java.util.regex.Pattern; import java.util.zip.GZIPInputStream; @ApplicationScoped public class CmatrixMatrixFormat extends AbstractResourceFormat<IMatrix> { public static final String EXTENSION = "cmatrix"; public CmatrixMatrixFormat() { super(EXTENSION, IMatrix.class); } @Override protected CompressMatrix readResource(IResourceLocator resourceLocator, IProgressMonitor progressMonitor) throws PersistenceException { try { DataInputStream in = new DataInputStream(resourceLocator.openInputStream(progressMonitor)); // Format version int formatVersion = in.readInt(); // Dictionary byte[] dictionary = readBuffer(in); // Columns String[] columns = splitBuffer(readBuffer(in)); // Rows String[] rows = splitBuffer(readBuffer(in)); // Headers String[] headers = splitBuffer(readBuffer(in)); // Values Map<Integer, CompressRow> values = new HashMap<>(rows.length); for (int i = 0; i < rows.length; i++) { int row = in.readInt(); int uncompressLength = in.readInt(); values.put(row, new CompressRow(uncompressLength, readBuffer(in))); } in.close(); CompressDimension rowDim = new CompressDimension(MatrixDimensionKey.ROWS, rows); CompressDimension colDim = new CompressDimension(MatrixDimensionKey.COLUMNS, columns); return new CompressMatrix(rowDim, colDim, dictionary, headers, values); } catch (IOException e) { throw new PersistenceException(e); } } @Override protected void writeResource(IResourceLocator resourceLocator, IMatrix resource, IProgressMonitor progressMonitor) throws PersistenceException { if (!(resource instanceof CompressMatrix)) { throw new UnsupportedOperationException("It is not possible to convert into a compress matrix"); } CompressMatrix matrix = (CompressMatrix) resource; try { DataOutputStream out = new DataOutputStream(resourceLocator.openOutputStream(progressMonitor)); int formatVersion = 0; out.writeInt(0); progressMonitor.begin("Writing dictionary...", 1); byte[] dictionary = matrix.getDictionary(); out.writeInt(dictionary.length); out.write(dictionary); progressMonitor.begin("Writing columns...", 1); byte[] buffer = AbstractCompressor.stringToByteArray(matrix.getColumns().getLabels()); out.writeInt(buffer.length); out.write(buffer); progressMonitor.begin("Writing rows...", 1); buffer = AbstractCompressor.stringToByteArray(matrix.getRows().getLabels()); out.writeInt(buffer.length); out.write(buffer); progressMonitor.begin("Writing headers...", 1); String[] headers = new String[resource.getLayers().size()]; for (int i = 0; i < resource.getLayers().size(); i++) { headers[i] = resource.getLayers().get(i).getId(); } buffer = AbstractCompressor.stringToByteArray(headers); out.writeInt(buffer.length); out.write(buffer); Map<Integer, CompressRow> compressRowMap = matrix.getCompressRows(); progressMonitor.begin("Writing values...", compressRowMap.size()); for (Map.Entry<Integer, CompressRow> value : compressRowMap.entrySet()) { progressMonitor.worked(1); // The row position out.writeInt(value.getKey()); // Compress the row CompressRow compressRow = value.getValue(); // Write the length of the buffer before compression out.writeInt(compressRow.getNotCompressedLength()); // The length of the compressed buffer with the columns out.writeInt(compressRow.getContent().length); // The buffer with all the columns out.write(compressRow.getContent()); } out.close(); } catch (IOException e) { throw new PersistenceException(e); } } /** * Read a byte array that starts with an integer that contains the buffer length to read. * * @param in the input stream * @return the byte array * @throws IOException */ public static byte[] readBuffer(DataInputStream in) throws IOException { int length = in.readInt(); return IOUtils.toByteArray(in, length); } private static Pattern TAB = Pattern.compile("\t"); private static String[] splitBuffer(byte[] buffer) throws UnsupportedEncodingException { String line = new String(buffer, "UTF-8"); return TAB.split(line); } public static String[] readHeader(File file) { try { DataInputStream in; if (file.getName().endsWith(".gz")) { in = new DataInputStream(new GZIPInputStream(new FileInputStream(file))); } else { in = new DataInputStream(new FileInputStream(file)); } // Format version int version = in.readInt(); // Dictionary byte[] dictionary = readBuffer(in); // Columns String[] columns = splitBuffer(readBuffer(in)); // Rows String[] rows = splitBuffer(readBuffer(in)); // Headers String[] headers = splitBuffer(readBuffer(in)); in.close(); return headers; } catch (IOException e) { throw new PersistenceException(e); } } }