List of usage examples for java.io DataInputStream readUTF
public final String readUTF() throws IOException
readUTF method of DataInput. From source file:org.apache.giraph.master.BspServiceMaster.java
/** * Read the finalized checkpoint file and associated metadata files for the * checkpoint. Modifies the {@link PartitionOwner} objects to get the * checkpoint prefixes. It is an optimization to prevent all workers from * searching all the files. Also read in the aggregator data from the * finalized checkpoint file and setting it. * * @param superstep Checkpoint set to examine. * @throws IOException// w ww.jav a 2 s . c o m * @throws InterruptedException * @throws KeeperException * @return Collection of generated partition owners. */ private Collection<PartitionOwner> prepareCheckpointRestart(long superstep) throws IOException, KeeperException, InterruptedException { List<PartitionOwner> partitionOwners = new ArrayList<>(); FileSystem fs = getFs(); String finalizedCheckpointPath = getSavedCheckpointBasePath(superstep) + CheckpointingUtils.CHECKPOINT_FINALIZED_POSTFIX; LOG.info("Loading checkpoint from " + finalizedCheckpointPath); DataInputStream finalizedStream = fs.open(new Path(finalizedCheckpointPath)); GlobalStats globalStats = new GlobalStats(); globalStats.readFields(finalizedStream); updateCounters(globalStats); SuperstepClasses superstepClasses = SuperstepClasses.createToRead(getConfiguration()); superstepClasses.readFields(finalizedStream); getConfiguration().updateSuperstepClasses(superstepClasses); int prefixFileCount = finalizedStream.readInt(); String checkpointFile = finalizedStream.readUTF(); for (int i = 0; i < prefixFileCount; ++i) { int mrTaskId = finalizedStream.readInt(); DataInputStream metadataStream = fs.open( new Path(checkpointFile + "." + mrTaskId + CheckpointingUtils.CHECKPOINT_METADATA_POSTFIX)); long partitions = metadataStream.readInt(); WorkerInfo worker = getWorkerInfoById(mrTaskId); for (long p = 0; p < partitions; ++p) { int partitionId = metadataStream.readInt(); PartitionOwner partitionOwner = new BasicPartitionOwner(partitionId, worker); partitionOwners.add(partitionOwner); LOG.info("prepareCheckpointRestart partitionId=" + partitionId + " assigned to " + partitionOwner); } metadataStream.close(); } //Ordering appears to be important as of right now we rely on this ordering //in WorkerGraphPartitioner Collections.sort(partitionOwners, new Comparator<PartitionOwner>() { @Override public int compare(PartitionOwner p1, PartitionOwner p2) { return Integer.compare(p1.getPartitionId(), p2.getPartitionId()); } }); globalCommHandler.getAggregatorHandler().readFields(finalizedStream); aggregatorTranslation.readFields(finalizedStream); masterCompute.readFields(finalizedStream); finalizedStream.close(); return partitionOwners; }
From source file:org.spout.engine.filesystem.WorldFiles.java
public static void readColumn(InputStream in, SpoutColumn column, AtomicInteger lowestY, BlockMaterial[][] topmostBlocks) { if (in == null) { //The inputstream is null because no height map data exists for (int x = 0; x < SpoutColumn.BLOCKS.SIZE; x++) { for (int z = 0; z < SpoutColumn.BLOCKS.SIZE; z++) { column.getAtomicInteger(x, z).set(Integer.MIN_VALUE); topmostBlocks[x][z] = null; column.setDirty(x, z);// w ww .j a va2 s.c om } } lowestY.set(Integer.MAX_VALUE); return; } DataInputStream dataStream = new DataInputStream(in); try { for (int x = 0; x < SpoutColumn.BLOCKS.SIZE; x++) { for (int z = 0; z < SpoutColumn.BLOCKS.SIZE; z++) { column.getAtomicInteger(x, z).set(dataStream.readInt()); } } @SuppressWarnings("unused") int version = dataStream.readInt(); lowestY.set(dataStream.readInt()); //Save heightmap StringMap global = ((SpoutEngine) Spout.getEngine()).getEngineItemMap(); StringMap itemMap = column.getWorld().getItemMap(); boolean warning = false; for (int x = 0; x < SpoutColumn.BLOCKS.SIZE; x++) { for (int z = 0; z < SpoutColumn.BLOCKS.SIZE; z++) { if (!dataStream.readBoolean()) { continue; } int blockState = dataStream.readInt(); short blockId = BlockFullState.getId(blockState); short blockData = BlockFullState.getData(blockState); blockId = (short) itemMap.convertTo(global, blockId); blockState = BlockFullState.getPacked(blockId, blockData); BlockMaterial m; try { m = (BlockMaterial) MaterialRegistry.get(blockState); } catch (ClassCastException e) { m = null; if (!warning) { Spout.getLogger().severe( "Error reading column topmost block information, block was not a valid BlockMaterial"); warning = false; } } if (m == null) { column.setDirty(x, z); } topmostBlocks[x][z] = m; } } //Save Biomes BiomeManager manager = null; try { //Biome manager is serialized with: // - boolean, if a biome manager exists // - String, the class name // - int, the number of bytes of data to read // - byte[], size of the above int in length boolean exists = dataStream.readBoolean(); if (exists) { String biomeManagerClass = dataStream.readUTF(); int biomeSize = dataStream.readInt(); byte[] biomes = new byte[biomeSize]; dataStream.readFully(biomes); //Attempt to create the biome manager class from the class name @SuppressWarnings("unchecked") Class<? extends BiomeManager> clazz = (Class<? extends BiomeManager>) Class .forName(biomeManagerClass); Class<?>[] params = { int.class, int.class }; manager = clazz.getConstructor(params).newInstance(column.getX(), column.getZ()); manager.deserialize(biomes); column.setBiomeManager(manager); } } catch (Exception e) { Spout.getLogger().log(Level.SEVERE, "Failed to read biome data for column", e); } } catch (IOException e) { Spout.getLogger() .severe("Error reading column height-map for column" + column.getX() + ", " + column.getZ()); } }
From source file:org.hyperic.hq.agent.server.AgentDListProvider.java
/** * DList info string is a series of properties seperated by '|' * Three properties are expected./*w ww . j ava 2 s. com*/ * * Directory to place the data files * Size in MB to start checking for unused blocks * Maximum percentage of free blocks allowed * * Default is 'data|20|50' */ public void init(String info) throws AgentStorageException { BufferedInputStream bIs; FileInputStream fIs = null; DataInputStream dIs; long nEnts; // Parse out configuration StringTokenizer st = new StringTokenizer(info, "|"); if (st.countTokens() != 5) { throw new AgentStorageException(info + " is an invalid agent storage provider configuration"); } keyVals = new HashMap<EncVal, EncVal>(); lists = new HashMap<String, DiskList>(); overloads = new HashMap<String, ListInfo>(); String dir = st.nextToken(); this.writeDir = new File(dir); this.keyValFile = new File(writeDir, "keyvals"); this.keyValFileBackup = new File(writeDir, "keyvals.backup"); String s = st.nextToken().trim(); long factor; if ("m".equalsIgnoreCase(s)) { factor = 1024 * 1024; } else if ("k".equalsIgnoreCase(s)) { factor = 1024; } else { throw new AgentStorageException(info + " is an invalid agent storage provider configuration"); } try { maxSize = Long.parseLong(st.nextToken().trim()) * factor; chkSize = Long.parseLong(st.nextToken().trim()) * factor; chkPerc = Integer.parseInt(st.nextToken().trim()); } catch (NumberFormatException e) { throw new AgentStorageException("Invalid agent storage provider " + "configuration: " + e); } if (this.writeDir.exists() == false) { // Try to create it this.writeDir.mkdir(); } if (this.writeDir.isDirectory() == false) { throw new AgentStorageException(dir + " is not a directory"); } try { fIs = new FileInputStream(this.keyValFile); bIs = new BufferedInputStream(fIs); dIs = new DataInputStream(bIs); nEnts = dIs.readLong(); while (nEnts-- != 0) { String encKey = dIs.readUTF(); String encVal = dIs.readUTF(); String key = SecurityUtil.isMarkedEncrypted(encKey) ? SecurityUtil.decryptRecursiveUnmark(encryptor, encKey) : encKey; String val = SecurityUtil.isMarkedEncrypted(encVal) ? SecurityUtil.decryptRecursiveUnmark(encryptor, encVal) : encVal; this.keyVals.put(new EncVal(encryptor, key, encKey), new EncVal(encryptor, val, encVal)); } } catch (FileNotFoundException exc) { // Normal when it doesn't exist log.debug("file not found (this is ok): " + exc); } catch (IOException exc) { log.error("Error reading " + this.keyValFile + " loading " + "last known good version"); // Close old stream close(fIs); // Fall back to last known good keyvals file try { fIs = new FileInputStream(this.keyValFileBackup); bIs = new BufferedInputStream(fIs); dIs = new DataInputStream(bIs); nEnts = dIs.readLong(); while (nEnts-- != 0) { String encKey = dIs.readUTF(); String encVal = dIs.readUTF(); String key = SecurityUtil.encrypt(this.encryptor, encKey); String val = SecurityUtil.encrypt(this.encryptor, encVal); this.keyVals.put(new EncVal(encryptor, key, encKey), new EncVal(encryptor, val, encVal)); } } catch (FileNotFoundException e) { log.warn(e); log.debug(e, e); } catch (IOException e) { AgentStorageException toThrow = new AgentStorageException( "Error reading " + this.keyValFile + ": " + e); toThrow.initCause(e); throw toThrow; } } finally { close(fIs); } }
From source file:com.android.launcher2.Launcher.java
private static void readConfiguration(Context context, LocaleConfiguration configuration) { DataInputStream in = null; try {/*from w w w. j a v a 2 s . c o m*/ in = new DataInputStream(context.openFileInput(PREFERENCES)); configuration.locale = in.readUTF(); configuration.mcc = in.readInt(); configuration.mnc = in.readInt(); } catch (FileNotFoundException e) { // Ignore } catch (IOException e) { // Ignore } finally { if (in != null) { try { in.close(); } catch (IOException e) { // Ignore } } } }
From source file:org.alfresco.repo.search.impl.lucene.index.IndexInfo.java
/** * Get the deletions for a given index (there is no check if they should be applied that is up to the calling layer) * /*from w w w . j a v a 2 s . c o m*/ * @param id String * @param fileName String * @return Set<String> * @throws IOException */ private Set<String> getDeletions(String id, String fileName) throws IOException { if (id == null) { throw new IndexerException("\"null\" is not a valid identifier for a transaction"); } // Check state Set<String> deletions = new HashSet<String>(); File location = new File(indexDirectory, id).getCanonicalFile(); File file = new File(location, fileName).getCanonicalFile(); if (!file.exists()) { if (s_logger.isDebugEnabled()) { s_logger.debug("No deletions for " + id); } return Collections.<String>emptySet(); } DataInputStream is = new DataInputStream(new BufferedInputStream(new FileInputStream(file))); int size = is.readInt(); for (int i = 0; i < size; i++) { String ref = is.readUTF(); deletions.add(ref); } is.close(); if (s_logger.isDebugEnabled()) { s_logger.debug("There are " + deletions.size() + " deletions for " + id); } return deletions; }
From source file:com.ocpsoft.pretty.faces.config.annotation.ByteCodeAnnotationFilter.java
/** * <p>//from w w w . ja v a2 s.co m * Checks whether that supplied {@link InputStream} contains a Java class * file that might contain PrettyFaces annotations. * </p> * <p> * The caller of this method is responsible to close the supplied * {@link InputStream}. This method won't do it! * </p> * * @param classFileStream * The stream to read the class file from. * @return <code>true</code> for files that should be further checked for * annotations * @throws IOException * for any kind of IO problem */ @SuppressWarnings("unused") public boolean accept(InputStream classFileStream) throws IOException { // open a DataInputStream DataInputStream in = new DataInputStream(classFileStream); // read magic and abort if it doesn't match int magic = in.readInt(); if (magic != CLASS_FILE_MAGIC) { if (log.isDebugEnabled()) { log.debug("Magic not found! Not a valid class file!"); } return false; } // check for at least JDK 1.5 int minor = in.readUnsignedShort(); int major = in.readUnsignedShort(); if (major < 49) { // JDK 1.4 or less if (log.isTraceEnabled()) { log.trace("Not a JDK5 class! It cannot contain annotations!"); } return false; } // this values is equal to the number entries in the constants pool + 1 int constantPoolEntries = in.readUnsignedShort() - 1; // loop over all entries in the constants pool for (int i = 0; i < constantPoolEntries; i++) { // the tag to identify the record type int tag = in.readUnsignedByte(); // process record according to its type switch (tag) { case CONSTANT_Class: /* * CONSTANT_Class_info { * u1 tag; * u2 name_index; * } */ in.readUnsignedShort(); break; case CONSTANT_Fieldref: case CONSTANT_Methodref: case CONSTANT_InterfaceMethodref: /* * CONSTANT_[Fieldref|Methodref|InterfaceMethodref]_info { * u1 tag; * u2 class_index; * u2 name_and_type_index; * } */ in.readUnsignedShort(); in.readUnsignedShort(); break; case CONSTANT_String: /* * CONSTANT_String_info { * u1 tag; * u2 string_index; * } */ in.readUnsignedShort(); break; case CONSTANT_Integer: case CONSTANT_Float: /* * CONSTANT_[Integer|Float]_info { * u1 tag; * u4 bytes; * } */ in.readInt(); break; case CONSTANT_Long: case CONSTANT_Double: /* * CONSTANT_Long_info { * u1 tag; * u4 high_bytes; * u4 low_bytes; * } */ in.readLong(); /* * We must increase the constant pool index because this tag * type takes two entries */ i++; break; case CONSTANT_NameAndType: /* * CONSTANT_NameAndType_info { * u1 tag; * u2 name_index; * u2 descriptor_index; * } */ in.readUnsignedShort(); in.readUnsignedShort(); break; case CONSTANT_Utf8: /* * CONSTANT_Utf8_info { * u1 tag; * u2 length; * u1 bytes[length]; * } */ String str = in.readUTF(); // check if this string sounds interesting if (str.contains(SEARCH_STRING)) { if (log.isTraceEnabled()) { log.trace("Found PrettyFaces annotation reference in constant pool: " + str); } return true; } break; default: /* * Unknown tag! Should not happen! We will scan the class in this case. */ if (log.isDebugEnabled()) { log.debug("Unknown constant pool tag found: " + tag); } return true; } } /* * We are finished with reading the interesting parts of the class file. * We stop here because the file doesn't seem to be interesting. */ if (log.isTraceEnabled()) { log.trace("No reference to PrettyFaces annotations found!"); } return false; }
From source file:UnicodeUtil.java
private static void loadCompositions(ClassLoader loader) { DataInputStream in = null; try {//w w w. j a v a 2 s. co m InputStream source = loader.getResourceAsStream("nu/xom/compositions.dat"); in = new DataInputStream(source); // ???? would it make sense to store a serialized HashMap instead???? compositions = new HashMap(); try { while (true) { String composed = in.readUTF(); String decomposed = in.readUTF(); compositions.put(decomposed, composed); } } catch (java.io.EOFException ex) { // finished } } catch (IOException ex) { return; } finally { try { if (in != null) in.close(); } catch (IOException ex) { // no big deal } } }
From source file:org.nd4j.linalg.factory.Nd4j.java
/** * Read in an ndarray from a data input stream * * @param dis the data input stream to read from * @return the ndarray//from w w w .j ava2 s . c o m * @throws IOException */ public static IComplexNDArray readComplex(DataInputStream dis) throws IOException { int dimensions = dis.readInt(); int[] shape = new int[dimensions]; int[] stride = new int[dimensions]; for (int i = 0; i < dimensions; i++) shape[i] = dis.readInt(); for (int i = 0; i < dimensions; i++) stride[i] = dis.readInt(); String dataType = dis.readUTF(); String type = dis.readUTF(); if (!type.equals("complex")) throw new IllegalArgumentException("Trying to read in a real ndarray"); if (dataType.equals("double")) { double[] data = ArrayUtil.readDouble(ArrayUtil.prod(shape), dis); return createComplex(data, shape, stride, 0); } double[] data = ArrayUtil.read(ArrayUtil.prod(shape), dis); return createComplex(data, shape, stride, 0); }
From source file:MiGA.StatsSelection.java
public void getCompoundPerfectSSRs(String[] organisms, int length, boolean flag, int gap) throws SQLException, ClassNotFoundException, FileNotFoundException, IOException { String statsfile = ""; for (int i = 0; i < organisms.length; i++) { boolean found = false; String buffer = new String(); int seekstart = 0; int seekend = 0; List<String> ssrs = new ArrayList<String>(); // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else//from w ww .j a v a 2 s . com indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here PrintWriter stats = null; PrintWriter html = null; PrintWriter out; DataOutputStream lt = null; if (filetype.contains("organism")) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter( new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compp"))); html = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("organisms/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "organisms/" + organisms[i] + "/results/allCompPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for organism: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + " - minimum SSR length (bp): " + length); } else { File f = new File("local/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compp"))); html = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("local/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "local/" + organisms[i] + "/results/allCompPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for project: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + " - minimum SSR length (bp): " + length); } int countpc = 0; int bpcount = 0, Aperc = 0, Tperc = 0, Gperc = 0, Cperc = 0; while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(files))); boolean eof = false; while (!eof) { try { SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); start = new ArrayList<Integer>(); int len = in.readInt(); int line = in.readInt(); for (int k = 0; k < len; k++) { String temp = in.readUTF(); if (!temp.contains("N")) { SSR.add(temp); EndOfSsr.add(in.readInt()); repeats.add(in.readInt()); int st = EndOfSsr.get(k) - (SSR.get(k).length() * repeats.get(k)); if (st >= 0) start.add(st); else start.add(0); } else { int junk = in.readInt(); junk = in.readInt(); } /* int real_end = end+(line-1)*20000; int start = real_end - (ssr.length()*reps); //SSR.add(ssr); repeats.add(in.readInt()); EndOfSsr.add(real_end); this.start.add(start); * */ } List<String> SSRlen = new ArrayList<String>(); List<Integer> Endlen = new ArrayList<Integer>(); List<Integer> repslen = new ArrayList<Integer>(); List<Integer> startlen = new ArrayList<Integer>(); for (int k = 0; k < SSR.size(); k++) { if (SSR.get(k).length() * repeats.get(k) >= length) { SSRlen.add(SSR.get(k)); Endlen.add(EndOfSsr.get(k)); repslen.add(repeats.get(k)); startlen.add(start.get(k)); } } List<Integer> sortedstart = new ArrayList<Integer>(); List<Integer> sortedend = new ArrayList<Integer>(); for (int t = 0; t < startlen.size(); t++) { sortedstart.add(startlen.get(t)); sortedend.add(Endlen.get(t)); } Collections.sort(sortedstart); Collections.sort(sortedend); for (int k = 0; k < sortedstart.size() - 2; k++) { found = false; ssrs = new ArrayList<String>(); if (sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { seekstart = sortedstart.get(k); while (k < sortedstart.size() - 1 && sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { for (int c = 0; c < startlen.size(); c++) { if (sortedstart.get(k) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); } if (sortedstart.get(k + 1) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); seekend = Endlen.get(c); found = true; } } k++; } k--; } boolean check = checkalldiff(ssrs); if (found && check) { BufferedReader stdin = null; String newdir = ""; if (flag) { String[] temp = files.split("/"); boolean type = CheckForKaryotype(organisms[i]); newdir = ""; if (type) { newdir = temp[0] + "/" + temp[1] + "/chrom-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + "-slices.txt"; } else { newdir = temp[0] + "/" + temp[1] + "/slice-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + ".txt"; } stdin = new BufferedReader(new FileReader(newdir)); } else { String[] temp = files.split("data/"); newdir = temp[0] + "/" + temp[1].substring(0, temp[1].lastIndexOf('.')) + ".txt"; stdin = new BufferedReader(new FileReader(newdir)); } buffer = ""; String prebuf = ""; for (int c = 0; c < line; c++) { buffer = stdin.readLine(); } stdin.close(); //System.out.println(buffer.length() + "\t" + seekstart + "\t" + seekend); int real_end = (line - 1) * 20000 + seekend; int real_start = (line - 1) * 20000 + seekstart; //tofile.add("SSR: "+buffer.substring(seekstart, seekend) + "start-end: "+ real_start + "-" +real_end ); countpc++; String tmp = ""; if (seekstart < 0) { stdin = new BufferedReader(new FileReader(newdir)); for (int c = 0; c < line - 1; c++) { prebuf = stdin.readLine(); } stdin.close(); tmp += prebuf.substring(prebuf.length() + seekstart); tmp += buffer.substring(0, seekend); } else tmp = buffer.substring(seekstart, seekend); bpcount += tmp.length(); if (tmp.contains("A")) { Aperc += StringUtils.countMatches(tmp, "A"); } if (tmp.contains("T")) { Tperc += StringUtils.countMatches(tmp, "T"); } if (tmp.contains("G")) { Gperc += StringUtils.countMatches(tmp, "G"); } if (tmp.contains("C")) { Cperc += StringUtils.countMatches(tmp, "C"); } out.println("SSR: " + tmp + " start-end: " + real_start + "-" + real_end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); } } } catch (EOFException e) { eof = true; } } in.close(); } out.close(); Runtime.getRuntime().exec("notepad " + statsfile); try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Connection con = null; try { con = DriverManager.getConnection("jdbc:mysql://localhost:3306", "biouser", "thesis2012"); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Statement st = null; try { st = con.createStatement(); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } st.executeUpdate("use lobid"); int seqcount = 0; if (filetype.contains("organisms")) { ResultSet rs = st.executeQuery( "SELECT end FROM slices INNER JOIN organism WHERE slices.org_id=organism.org_id AND organism.name='" + organisms[i] + "'"); while (rs.next()) { seqcount += Long.parseLong(rs.getString(1)); } } else if (filetype.contains("local")) { BufferedReader in = new BufferedReader(new FileReader("local/" + organisms[i] + "/index.txt")); int count = countlines("local/" + organisms[i] + "/index.txt"); for (int c = 0; c < count; c++) { String temp = in.readLine(); BufferedReader tmp = new BufferedReader( new FileReader("local/" + organisms[i] + "/" + temp + ".txt")); boolean eof = false; while (!eof) { String s = tmp.readLine(); if (s != null) { seqcount += s.length(); } else { eof = true; } } tmp.close(); } } DecimalFormat round = new DecimalFormat("#.###"); html.println("<html><h1>******* Compound Perfect SSRs *******</h1>"); html.println("<h4>Results for project: " + organisms[i] + "</h4><h4>Search Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + "</h4><h4>minimum SSR length (bp): " + length + "</h4>"); html.println( "<table border=\"1\"><tr><td> </td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); html.println("<tr><td><b>Compound Perf.</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr>"); html.println("<tr><td><b>TOTAL</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr></table></html>"); html.close(); stats.println("******* Compound Perfect SSRs *******"); stats.println("Results for project: " + organisms[i] + "\nSearch Parameters --> Maximum Inter-repeat Region for Perfect Compound SSRs (bp) : " + gap + "\nminimum SSR length (bp): " + length); stats.println( " ___________________________________________________________________________________________________________________ "); stats.println( "| | | | | | | | Relative | | Relative |"); stats.println( "| | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); stats.println( "|==============|=======|============|=======|=======|=======|=======|===============|===============|===============|"); stats.printf( "|Compound Perf.|" + cell(Integer.toString(countpc), 7) + "|" + cell(Integer.toString(bpcount), 12) + "|%s|%s|%s|%s|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|\n", cell((float) Aperc * 100 / bpcount, 7), cell((float) Tperc * 100 / bpcount, 7), cell((float) Cperc * 100 / bpcount, 7), cell((float) Gperc * 100 / bpcount, 7)); stats.println( "|--------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); lt.writeLong(seqcount); lt.writeInt(countpc); lt.writeInt(bpcount); lt.writeInt(Aperc); lt.writeInt(Tperc); lt.writeInt(Gperc); lt.writeInt(Cperc); stats.println("|TOTAL |" + cell(Integer.toString(countpc), 7) + "|" + cell(Long.toString(bpcount), 12) + "|" + cell((float) Aperc * 100 / bpcount, 7) + "|" + cell((float) Tperc * 100 / bpcount, 7) + "|" + cell((float) Cperc * 100 / bpcount, 7) + "|" + cell((float) Gperc * 100 / bpcount, 7) + "|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|"); stats.println( "|______________|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); stats.println("Genome length (bp): " + seqcount); stats.println("Relative Frequency: Count of each motif type / total SSR count"); stats.println("Abundance: bp of each motif type / total sequence bp"); stats.println("Relative Abundance: bp of each motif type / total microsatellites bp"); stats.println(); stats.println(); stats.close(); lt.close(); } }
From source file:MiGA.StatsSelection.java
public void getImPerfectCompoundSSRs(String[] organisms, int length, boolean flag, int gap) throws SQLException, ClassNotFoundException, FileNotFoundException, IOException { String statsfile = ""; for (int i = 0; i < organisms.length; i++) { boolean found = false; String buffer = new String(); int seekstart = 0; int seekend = 0; List<String> ssrs = new ArrayList<String>(); // 18/11/2013 added starting here String filetype = ""; String filepro = ""; if (flag) { filetype = "organisms"; filepro = "organisms/" + organisms[i] + "/data/"; int ret = getOrganismStatus(organisms[i]); if (ret == -1) indexer = new Indexer(chromosomelist); else//from w w w . ja va 2s .c om indexer = new Indexer(ret); } else { filetype = "local"; filepro = "local/" + organisms[i] + "/data/"; String indexfile = "local/" + organisms[i] + "/index.txt"; indexer = new Indexer(indexfile); } //List<String> files = getFiles(organisms[i], minlen, flag); // 18/11/2013 added ending here PrintWriter out; PrintWriter stats; PrintWriter html; DataOutputStream lt = null; if (filetype.contains("organism")) { File f = new File("organisms/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter( new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("organisms/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compim"))); html = new PrintWriter(new FileWriter("organisms/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("organisms/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } String toopen = "organisms/" + organisms[i] + "/results/allCompImPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for organism: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs(bp) : " + gap + " - minimum SSR length(bp): " + length); } else { File f = new File("local/" + organisms[i] + "/stats/"); if (!f.exists()) { f.mkdir(); } stats = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".txt", true)); lt = new DataOutputStream(new BufferedOutputStream(new FileOutputStream("local/" + organisms[i] + "/data/" + now.toString().replace(':', '_').replace(' ', '_') + ".compim"))); html = new PrintWriter(new FileWriter("local/" + organisms[i] + "/stats/" + "summary_statistics" + now.toString().replace(':', '_').replace(' ', '_') + ".html", true)); File fi = new File("local/" + organisms[i] + "/results/"); if (!fi.exists()) { fi.mkdir(); } Calendar calendar = Calendar.getInstance(); Date now = calendar.getTime(); String toopen = "local/" + organisms[i] + "/results/allCompImPerfect_" + now.toString().replace(':', '_').replace(' ', '_') + ".txt"; statsfile = toopen; out = new PrintWriter(toopen); out.println("Results for project: " + organisms[i] + "\t Search Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs(bp) : " + gap + " - minimum SSR length(bp): " + length); } int countpc = 0; int bpcount = 0, Aperc = 0, Tperc = 0, Gperc = 0, Cperc = 0; while (indexer.hasNext()) { String files = filepro + indexer.getNextFileName(); DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(files))); //PrintWriter out = new PrintWriter(files + "-minlentgh_" + length + "_ImPerfect.stats"); boolean eof = false; while (!eof) { try { SSR = new ArrayList<String>(); repeats = new ArrayList<Integer>(); EndOfSsr = new ArrayList<Integer>(); start = new ArrayList<Integer>(); int len = in.readInt(); int line = in.readInt(); for (int k = 0; k < len; k++) { //THIS String temp = in.readUTF(); if (!temp.contains("N")) { SSR.add(temp); EndOfSsr.add(in.readInt()); repeats.add(in.readInt()); start.add(EndOfSsr.get(k) - (SSR.get(k).length() * repeats.get(k))); } else { int junk = in.readInt(); junk = in.readInt(); } } List<String> SSRlen = new ArrayList<String>(); List<Integer> Endlen = new ArrayList<Integer>(); List<Integer> repslen = new ArrayList<Integer>(); List<Integer> startlen = new ArrayList<Integer>(); for (int k = 0; k < SSR.size(); k++) { if (SSR.get(k).length() * repeats.get(k) >= length) { SSRlen.add(SSR.get(k)); Endlen.add(EndOfSsr.get(k)); repslen.add(repeats.get(k)); startlen.add(start.get(k)); } } List<Integer> sortedstart = new ArrayList<Integer>(); List<Integer> sortedend = new ArrayList<Integer>(); for (int t = 0; t < startlen.size(); t++) { sortedstart.add(startlen.get(t)); sortedend.add(Endlen.get(t)); } Collections.sort(sortedstart); Collections.sort(sortedend); //List<String> tofile = new ArrayList<String>(); for (int k = 0; k < sortedstart.size() - 2; k++) { found = false; ssrs.clear(); ssrs = new ArrayList<String>(); if (sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { seekstart = sortedstart.get(k); while (k < sortedstart.size() - 1 && sortedstart.get(k + 1) - sortedend.get(k) <= gap && sortedstart.get(k + 1) - sortedend.get(k) >= 0) { for (int c = 0; c < startlen.size(); c++) { if (sortedstart.get(k) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); } if (sortedstart.get(k + 1) == startlen.get(c)) { ssrs.add(SSRlen.get(c)); seekend = Endlen.get(c); found = true; } } k++; } k--; } boolean check = checkallsame(ssrs); boolean check2 = checkalldiff(ssrs); if (found && !check && !check2) { BufferedReader stdin = null; if (flag) { String[] temp = files.split("/"); boolean type = CheckForKaryotype(organisms[i]); String newdir = ""; if (type) { newdir = temp[0] + "/" + temp[1] + "/chrom-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + "-slices.txt"; } else { newdir = temp[0] + "/" + temp[1] + "/slice-" + temp[3].substring(0, temp[3].lastIndexOf('.')) + ".txt"; } stdin = new BufferedReader(new FileReader(newdir)); } else { String[] temp = files.split("data/"); String newdir = temp[0] + "/" + temp[1].substring(0, temp[1].lastIndexOf('.')) + ".txt"; stdin = new BufferedReader(new FileReader(newdir)); } buffer = ""; for (int c = 0; c < line; c++) { buffer = stdin.readLine(); } //System.out.println(buffer.length() + "\t" + seekstart + "\t" + seekend); int real_end = (line - 1) * 20000 + seekend; int real_start = (line - 1) * 20000 + seekstart; //tofile.add("SSR: "+buffer.substring(seekstart, seekend) + "start-end: "+ real_start + "-" +real_end ); countpc++; if (seekstart < 0) seekstart++; String tmp = buffer.substring(seekstart, seekend); bpcount += tmp.length(); if (tmp.contains("A")) { Aperc += StringUtils.countMatches(tmp, "A"); } if (tmp.contains("T")) { Tperc += StringUtils.countMatches(tmp, "T"); } if (tmp.contains("G")) { Gperc += StringUtils.countMatches(tmp, "G"); } if (tmp.contains("C")) { Cperc += StringUtils.countMatches(tmp, "C"); } out.println("SSR: " + tmp + " start-end: " + real_start + "-" + real_end + " Path(../data/chromosome): " + files.substring(0, files.lastIndexOf('.'))); stdin.close(); } } } catch (EOFException e) { eof = true; } } in.close(); } out.close(); Runtime.getRuntime().exec("notepad " + statsfile); try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Connection con = null; try { con = DriverManager.getConnection("jdbc:mysql://localhost:3306", "biouser", "thesis2012"); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } Statement st = null; try { st = con.createStatement(); } catch (SQLException ex) { Logger.getLogger(StatsSelection.class.getName()).log(Level.SEVERE, null, ex); } st.executeUpdate("use lobid"); int seqcount = 0; if (filetype.contains("organisms")) { ResultSet rs = st.executeQuery( "SELECT end FROM slices INNER JOIN organism WHERE slices.org_id=organism.org_id AND organism.name='" + organisms[i] + "'"); while (rs.next()) { seqcount += Long.parseLong(rs.getString(1)); } } else if (filetype.contains("local")) { BufferedReader in = new BufferedReader(new FileReader("local/" + organisms[i] + "/index.txt")); int count = countlines("local/" + organisms[i] + "/index.txt"); for (int c = 0; c < count; c++) { String temp = in.readLine(); BufferedReader tmp = new BufferedReader( new FileReader("local/" + organisms[i] + "/" + temp + ".txt")); boolean eof = false; while (!eof) { String s = tmp.readLine(); if (s != null) { seqcount += s.length(); } else { eof = true; } } tmp.close(); } } DecimalFormat round = new DecimalFormat("#.###"); html.println("<html><h1>******* Compound Imperfect SSRs *******</h1>"); html.println("<h4>Results for project: " + organisms[i] + "</h4><h4>Search Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs (bp) : " + gap + "</h4><h4>minimum SSR length (bp): " + length + "</h4>"); html.println( "<table border=\"1\"><tr><td> </td><td><b>count</b></td><td><b>bp</b></td><td><b>A%</b></td><td><b>T%</b></td><td><b>C%</b></td><td><b>G%</b></td><td><b>Relative Frequency</b></td><td><b>Abundance</b></td><td><b>Relative Abundance</b></td></tr>"); html.println("<tr><td><b>Compound Imperf.</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr>"); html.println("<tr><td><b>TOTAL</b></td><td>" + countpc + "</td><td>" + bpcount + "</td><td>" + round.format((float) Aperc * 100 / bpcount) + "</td><td>" + round.format((float) Tperc * 100 / bpcount) + "</td><td>" + round.format((float) Cperc * 100 / bpcount) + "</td><td>" + round.format((float) Gperc * 100 / bpcount) + "</td><td>" + round.format((float) countpc / countpc) + "</td><td>" + round.format((float) bpcount / seqcount) + "</td><td>" + round.format((float) bpcount / bpcount) + "</td></tr></table></html>"); html.close(); stats.println("******* Compound Imperfect SSRs *******"); stats.println("Results for project: " + organisms[i] + "\nSearch Parameters --> Maximum Inter-repeat Region for Imperfect Compound SSRs(bp) : " + gap + "\nminimum SSR length(bp): " + length); stats.println( " ____________________________________________________________________________________________________________________ "); stats.println( "| | | | | | | | Relative | | Relative |"); stats.println( "| | count | bp | A% | T% | C% | G% | Frequency | Abundance | Abundance |"); stats.println( "|===============|=======|============|=======|=======|=======|=======|===============|===============|===============|"); stats.printf( "|Compound Imper.|" + cell(Integer.toString(countpc), 7) + "|" + cell(Integer.toString(bpcount), 12) + "|%s|%s|%s|%s|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|\n", cell((float) Aperc * 100 / bpcount, 7), cell((float) Tperc * 100 / bpcount, 7), cell((float) Cperc * 100 / bpcount, 7), cell((float) Gperc * 100 / bpcount, 7)); stats.println( "|---------------|-------|------------|-------|-------|-------|-------|---------------|---------------|---------------|"); lt.writeLong(seqcount); lt.writeInt(countpc); lt.writeInt(bpcount); lt.writeInt(Aperc); lt.writeInt(Tperc); lt.writeInt(Gperc); lt.writeInt(Cperc); stats.println("|TOTAL |" + cell(Integer.toString(countpc), 7) + "|" + cell(Long.toString(bpcount), 12) + "|" + cell((float) Aperc * 100 / bpcount, 7) + "|" + cell((float) Tperc * 100 / bpcount, 7) + "|" + cell((float) Cperc * 100 / bpcount, 7) + "|" + cell((float) Gperc * 100 / bpcount, 7) + "|" + cell((float) countpc / countpc, 15) + "|" + cell((float) bpcount / seqcount, 15) + "|" + cell((float) bpcount / bpcount, 15) + "|"); stats.println( "|_______________|_______|____________|_______|_______|_______|_______|_______________|_______________|_______________|"); stats.println("Genome length (bp): " + seqcount); stats.println("Relative Frequency: Count of each motif type / total SSR count"); stats.println("Abundance: bp of each motif type / total sequence bp"); stats.println("Relative Abundance: bp of each motif type / total microsatellites bp"); stats.println(); stats.println(); stats.close(); lt.close(); } }