List of usage examples for java.io DataInputStream read
public final int read(byte b[], int off, int len) throws IOException
len bytes of data from the contained input stream into an array of bytes. From source file:com.cohesionforce.dis.BinaryConverter.java
public void run() { int count = 0; System.out.println("Opening file to convert: " + inputFile); FileInputStream fis;/* w w w . j a v a2 s.co m*/ try { fis = new FileInputStream(inputFile); } catch (FileNotFoundException e1) { e1.printStackTrace(); return; } DataInputStream dis = new DataInputStream(fis); startWriters(); System.out.println("Starting to convert PDUs"); while (done == false) { byte buffer[] = new byte[MAX_PDU_SIZE]; byte pduType; try { pduType = dis.readByte(); int pduSize = dis.readInt(); int skip = dis.read(buffer, 0, 19); assert (skip == 19); int numberRead = dis.read(buffer, 0, pduSize); assert (numberRead == pduSize); ++count; // Convert the byte array to an object Object object; object = unmarshaller.getPdu(buffer); if (object != null) { logPdu(object, pduType); } } catch (EOFException e) { done = true; } catch (IOException e) { e.printStackTrace(); } catch (Exception e) { done = true; e.printStackTrace(); } if (count % 100000 == 0) { System.out.println("Converted " + count + " PDUs"); } } // end loop try { dis.close(); } catch (IOException e1) { e1.printStackTrace(); } System.out.print("Waiting on writers to clear their queues"); boolean emptyQueue = false; while (!emptyQueue) { emptyQueue = true; for (LogWriter<?> writer : writers) { // If any queue is not empty, sleep and check again if (!writer.getQueue().isEmpty()) { try { emptyQueue = false; System.out.print("."); Thread.sleep(1000); break; } catch (InterruptedException e) { e.printStackTrace(); } } } } System.out.println(""); System.out.println("PDUs converted: " + count); System.out.println("Shutting down logging threads"); threadGroup.interrupt(); int tries = 0; while (threadGroup.activeCount() > 0 && tries < 10) { try { Thread.sleep(2000); } catch (InterruptedException e) { } ++tries; } System.out.println("Completed logging threads shutdown"); }
From source file:ffx.xray.MTZFilter.java
/** * {@inheritDoc}// w w w. j a v a 2 s.c o m */ @Override public ReflectionList getReflectionList(File mtzFile, CompositeConfiguration properties) { ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis; DataInputStream dis; try { fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); byte headeroffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // eat "MTZ" title dis.read(bytes, offset, 4); String mtzstr = new String(bytes); // header offset dis.read(headeroffset, offset, 4); // machine stamp dis.read(bytes, offset, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); int stamp = bb.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } bb = ByteBuffer.wrap(headeroffset); int headeroffseti = bb.order(b).getInt(); // skip to header and parse dis.skipBytes((headeroffseti - 4) * 4); for (Boolean parsing = true; parsing; dis.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } } catch (EOFException eof) { System.out.println("EOF reached "); } catch (IOException ioe) { System.out.println("IO Exception: " + ioe.getMessage()); return null; } // column identifiers foString = sigfoString = rfreeString = null; if (properties != null) { foString = properties.getString("fostring", null); sigfoString = properties.getString("sigfostring", null); rfreeString = properties.getString("rfreestring", null); } h = k = l = fo = sigfo = rfree = -1; fplus = sigfplus = fminus = sigfminus = rfreeplus = rfreeminus = -1; fc = phic = -1; boolean print = false; parseColumns(print); parseFcColumns(print); if (fo < 0 && fplus < 0 && sigfo < 0 && sigfplus < 0 && fc < 0 && phic < 0) { logger.info( " The MTZ header contains insufficient information to generate the reflection list.\n For non-default column labels set fostring/sigfostring in the properties file."); return null; } Column c; if (fo > 0) { c = (Column) columns.get(fo); } else if (fplus > 0) { c = (Column) columns.get(fplus); } else { c = (Column) columns.get(fc); } Dataset d = (Dataset) datasets.get(c.id - dsetoffset); if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(String.format("\n Reading %s\n\n", mtzFile.getName())); sb.append(String.format(" Setting up reflection list based on MTZ file.\n")); sb.append(String.format(" Space group number: %d (name: %s)\n", sgnum, SpaceGroup.spaceGroupNames[sgnum - 1])); sb.append(String.format(" Resolution: %8.3f\n", 0.999999 * resHigh)); sb.append(String.format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", d.cell[0], d.cell[1], d.cell[2], d.cell[3], d.cell[4], d.cell[5])); logger.info(sb.toString()); } Crystal crystal = new Crystal(d.cell[0], d.cell[1], d.cell[2], d.cell[3], d.cell[4], d.cell[5], SpaceGroup.spaceGroupNames[sgnum - 1]); double sampling = 0.6; if (properties != null) { sampling = properties.getDouble("sampling", 0.6); } Resolution resolution = new Resolution(0.999999 * resHigh, sampling); return new ReflectionList(crystal, resolution, properties); }
From source file:org.tacografo.file.FileBlockTGD.java
/** * Lectura de los bloques con formato :tag(fid)-longitud-value * //from ww w .jav a2s. co m * @param entrada * @throws IOException * @throws ErrorFile ocurrido cuando no es un fichero tgd o falla en la lectura de algun bloque * porque no encuentre el tag(fid) */ private void lectura_bloque(DataInputStream entrada) throws IOException, ErrorFile { boolean existe_fid = true; while (existe_fid) { // la lectura tiene que ser con readUnsignedShort debido a que // los fid c108 y c100 // los detecta con signo y me los rellenas como ffffc108 y // ffffc100 int fid = entrada.readUnsignedShort(); existe_fid = this.existe_Fid(fid); if (existe_fid) { // tipo de archivo 0 = bloque de dato -- 1 = certificado byte tipo = entrada.readByte(); Integer longitud = Integer.valueOf(entrada.readChar()); byte[] datos = new byte[longitud]; entrada.read(datos, 0, longitud); // tipo de bloque if (tipo == 0) { CardBlock block = FactoriaBloques.getFactoria(fid, datos); if (block != null) { this.lista_bloque.put(block.getFID(), block); } } } else { throw new ErrorFile(); } } }
From source file:ffx.xray.MTZFilter.java
public boolean readFcs(File mtzFile, ReflectionList reflectionlist, DiffractionRefinementData fcdata, CompositeConfiguration properties) { int nread, nignore, nres, nfriedel, ncut; ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis;//from ww w .j a v a2 s.c o m DataInputStream dis; StringBuilder sb = new StringBuilder(); try { fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); byte headeroffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // eat "MTZ" title dis.read(bytes, offset, 4); String mtzstr = new String(bytes); // header offset dis.read(headeroffset, offset, 4); // machine stamp dis.read(bytes, offset, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); int stamp = bb.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } bb = ByteBuffer.wrap(headeroffset); int headeroffseti = bb.order(b).getInt(); // skip to header and parse dis.skipBytes((headeroffseti - 4) * 4); for (Boolean parsing = true; parsing; dis.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } // column identifiers fc = phic = fs = phis = -1; boolean print = true; parseFcColumns(print); if (h < 0 || k < 0 || l < 0) { String message = "Fatal error in MTZ file - no H K L indexes?\n"; logger.log(Level.SEVERE, message); return false; } // reopen to start at beginning fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); // skip initial header dis.skipBytes(80); float data[] = new float[nColumns]; HKL mate = new HKL(); // read in data ComplexNumber c = new ComplexNumber(); nread = nignore = nres = nfriedel = ncut = 0; for (int i = 0; i < nReflections; i++) { for (int j = 0; j < nColumns; j++) { dis.read(bytes, offset, 4); bb = ByteBuffer.wrap(bytes); data[j] = bb.order(b).getFloat(); } int ih = (int) data[h]; int ik = (int) data[k]; int il = (int) data[l]; boolean friedel = reflectionlist.findSymHKL(ih, ik, il, mate, false); HKL hkl = reflectionlist.getHKL(mate); if (hkl != null) { if (fc > 0 && phic > 0) { c.re(data[fc] * cos(toRadians(data[phic]))); c.im(data[fc] * sin(toRadians(data[phic]))); fcdata.setFc(hkl.index(), c); } if (fs > 0 && phis > 0) { c.re(data[fs] * cos(toRadians(data[phis]))); c.im(data[fs] * sin(toRadians(data[phis]))); fcdata.setFs(hkl.index(), c); } nread++; } else { HKL tmp = new HKL(ih, ik, il); if (!reflectionlist.resolution .inInverseResSqRange(Crystal.invressq(reflectionlist.crystal, tmp))) { nres++; } else { nignore++; } } } sb.append(String.format(" MTZ file type (machine stamp): %s\n", stampstr)); sb.append(String.format(" Fc HKL read in: %d\n", nread)); sb.append(String.format(" Fc HKL read as friedel mates: %d\n", nfriedel)); sb.append(String.format(" Fc HKL NOT read in (too high resolution): %d\n", nres)); sb.append(String.format(" Fc HKL NOT read in (not in internal list?): %d\n", nignore)); sb.append(String.format(" Fc HKL NOT read in (F/sigF cutoff): %d\n", ncut)); sb.append(String.format(" HKL in internal list: %d\n", reflectionlist.hkllist.size())); if (logger.isLoggable(Level.INFO)) { logger.info(sb.toString()); } } catch (EOFException eof) { System.out.println("EOF reached "); return false; } catch (IOException ioe) { System.out.println("IO Exception: " + ioe.getMessage()); return false; } return true; }
From source file:com.trigger_context.Main_Service.java
private void recvFile(DataInputStream in, String path) { Log.i("recvFile", "Start"); // path should end with "/" String Filename = null;// w w w . j av a2s .c om long size = 0; try { Filename = in.readUTF(); size = in.readLong(); } catch (IOException e1) { Log.i(Main_Service.LOG_TAG, "recvFile--error in readins file name and lngth"); } OutputStream outfile = null; // noti("path of recv folder:",path); try { outfile = new FileOutputStream(path + Filename); } catch (FileNotFoundException e1) { Log.i(Main_Service.LOG_TAG, "recvFile--Error file not found exception"); } byte[] buff = new byte[1024]; int readbytes; try { while (size > 0 && (readbytes = in.read(buff, 0, (int) Math.min(buff.length, size))) != -1) { try { outfile.write(buff, 0, readbytes); size -= readbytes; } catch (IOException e) { Log.i(Main_Service.LOG_TAG, "recvFile--Error file write"); } } } catch (IOException e) { Log.i(Main_Service.LOG_TAG, "recvFile--Error socket read"); e.printStackTrace(); } try { outfile.close(); } catch (IOException e) { Log.i(Main_Service.LOG_TAG, "recvFile--Erro oufile close"); } }
From source file:ffx.xray.parsers.MTZFilter.java
/** * {@inheritDoc}/*w w w . j ava2s .c o m*/ */ @Override public ReflectionList getReflectionList(File mtzFile, CompositeConfiguration properties) { ByteOrder byteOrder = ByteOrder.nativeOrder(); FileInputStream fileInputStream; DataInputStream dataInputStream; try { fileInputStream = new FileInputStream(mtzFile); dataInputStream = new DataInputStream(fileInputStream); byte headerOffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // Eat "MTZ" title. dataInputStream.read(bytes, offset, 4); String mtzstr = new String(bytes); // Header offset. dataInputStream.read(headerOffset, offset, 4); // Machine stamp. dataInputStream.read(bytes, offset, 4); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); int stamp = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) { byteOrder = ByteOrder.BIG_ENDIAN; } break; case '4': if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) { byteOrder = ByteOrder.LITTLE_ENDIAN; } break; } byteBuffer = ByteBuffer.wrap(headerOffset); int headerOffsetI = byteBuffer.order(byteOrder).getInt(); // skip to header and parse dataInputStream.skipBytes((headerOffsetI - 4) * 4); for (Boolean parsing = true; parsing; dataInputStream.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } } catch (EOFException e) { String message = " MTZ end of file reached."; logger.log(Level.WARNING, message, e); return null; } catch (IOException e) { String message = " MTZ IO exception."; logger.log(Level.WARNING, message, e); return null; } // column identifiers foString = sigFoString = rFreeString = null; if (properties != null) { foString = properties.getString("fostring", null); sigFoString = properties.getString("sigfostring", null); rFreeString = properties.getString("rfreestring", null); } h = k = l = fo = sigFo = rFree = -1; fPlus = sigFPlus = fMinus = sigFMinus = rFreePlus = rFreeMinus = -1; fc = phiC = -1; boolean print = false; parseColumns(print); parseFcColumns(print); if (fo < 0 && fPlus < 0 && sigFo < 0 && sigFPlus < 0 && fc < 0 && phiC < 0) { logger.info(" The MTZ header contains insufficient information to generate the reflection list."); logger.info(" For non-default column labels set fostring/sigfostring in the properties file."); return null; } Column column; if (fo > 0) { column = (Column) columns.get(fo); } else if (fPlus > 0) { column = (Column) columns.get(fPlus); } else { column = (Column) columns.get(fc); } Dataset dataSet = (Dataset) dataSets.get(column.id - dsetOffset); if (logger.isLoggable(Level.INFO)) { StringBuilder sb = new StringBuilder(); sb.append(format("\n Reading %s\n\n", mtzFile.getName())); sb.append(format(" Setting up reflection list based on MTZ file.\n")); sb.append(format(" Space group number: %d (name: %s)\n", spaceGroupNum, SpaceGroup.spaceGroupNames[spaceGroupNum - 1])); sb.append(format(" Resolution: %8.3f\n", 0.999999 * resHigh)); sb.append(format(" Cell: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", dataSet.cell[0], dataSet.cell[1], dataSet.cell[2], dataSet.cell[3], dataSet.cell[4], dataSet.cell[5])); logger.info(sb.toString()); } Crystal crystal = new Crystal(dataSet.cell[0], dataSet.cell[1], dataSet.cell[2], dataSet.cell[3], dataSet.cell[4], dataSet.cell[5], SpaceGroup.spaceGroupNames[spaceGroupNum - 1]); double sampling = 0.6; if (properties != null) { sampling = properties.getDouble("sampling", 0.6); } Resolution resolution = new Resolution(0.999999 * resHigh, sampling); return new ReflectionList(crystal, resolution, properties); }
From source file:org.apache.sshd.server.sftp.SftpSubsystem.java
public void run() { DataInputStream dis = null; try {// w w w. j a v a2 s. co m dis = new DataInputStream(in); while (true) { int length = dis.readInt(); if (length < 5) { throw new IllegalArgumentException(); } Buffer buffer = new Buffer(length + 4); buffer.putInt(length); int nb = length; while (nb > 0) { int l = dis.read(buffer.array(), buffer.wpos(), nb); if (l < 0) { throw new IllegalArgumentException(); } buffer.wpos(buffer.wpos() + l); nb -= l; } process(buffer); } } catch (Throwable t) { if (!closed && !(t instanceof EOFException)) { // Ignore han log.error("Exception caught in SFTP subsystem", t); } } finally { if (dis != null) { try { dis.close(); } catch (IOException ioe) { log.error("Could not close DataInputStream", ioe); } } if (handles != null) { for (Map.Entry<String, Handle> entry : handles.entrySet()) { Handle handle = entry.getValue(); try { handle.close(); } catch (IOException ioe) { log.error("Could not close open handle: " + entry.getKey(), ioe); } } } dis = null; callback.onExit(0); } }
From source file:ffx.xray.parsers.MTZFilter.java
/** * Read the structure factors./*from w w w .j a v a2 s . c o m*/ * * @param mtzFile * @param reflectionList * @param fcData * @param properties * @return */ public boolean readFcs(File mtzFile, ReflectionList reflectionList, DiffractionRefinementData fcData, CompositeConfiguration properties) { int nRead, nIgnore, nRes, nFriedel, nCut; ByteOrder byteOrder = ByteOrder.nativeOrder(); FileInputStream fileInputStream; DataInputStream dataInputStream; StringBuilder sb = new StringBuilder(); try { fileInputStream = new FileInputStream(mtzFile); dataInputStream = new DataInputStream(fileInputStream); byte headerOffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // Eat "MTZ" title. dataInputStream.read(bytes, offset, 4); String mtzString = null; // Header offset. dataInputStream.read(headerOffset, offset, 4); // Machine stamp. dataInputStream.read(bytes, offset, 4); ByteBuffer byteBuffer = ByteBuffer.wrap(bytes); int stamp = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt(); String stampString = Integer.toHexString(stamp); switch (stampString.charAt(0)) { case '1': case '3': if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) { byteOrder = ByteOrder.BIG_ENDIAN; } break; case '4': if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) { byteOrder = ByteOrder.LITTLE_ENDIAN; } break; } byteBuffer = ByteBuffer.wrap(headerOffset); int headerOffsetI = byteBuffer.order(byteOrder).getInt(); // Skip to header and parse. dataInputStream.skipBytes((headerOffsetI - 4) * 4); for (Boolean parsing = true; parsing; dataInputStream.read(bytes, offset, 80)) { mtzString = new String(bytes); parsing = parseHeader(mtzString); } // Column identifiers. fc = phiC = fs = phiS = -1; boolean print = true; parseFcColumns(print); if (h < 0 || k < 0 || l < 0) { String message = " Fatal error in MTZ file - no H K L indexes?\n"; logger.log(Level.SEVERE, message); return false; } // Reopen to start at beginning. fileInputStream = new FileInputStream(mtzFile); dataInputStream = new DataInputStream(fileInputStream); // Skip initial header. dataInputStream.skipBytes(80); float data[] = new float[nColumns]; HKL mate = new HKL(); // Read in data. ComplexNumber complexNumber = new ComplexNumber(); nRead = nIgnore = nRes = nFriedel = nCut = 0; for (int i = 0; i < nReflections; i++) { for (int j = 0; j < nColumns; j++) { dataInputStream.read(bytes, offset, 4); byteBuffer = ByteBuffer.wrap(bytes); data[j] = byteBuffer.order(byteOrder).getFloat(); } int ih = (int) data[h]; int ik = (int) data[k]; int il = (int) data[l]; boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, false); HKL hkl = reflectionList.getHKL(mate); if (hkl != null) { if (fc > 0 && phiC > 0) { complexNumber.re(data[fc] * cos(toRadians(data[phiC]))); complexNumber.im(data[fc] * sin(toRadians(data[phiC]))); fcData.setFc(hkl.index(), complexNumber); } if (fs > 0 && phiS > 0) { complexNumber.re(data[fs] * cos(toRadians(data[phiS]))); complexNumber.im(data[fs] * sin(toRadians(data[phiS]))); fcData.setFs(hkl.index(), complexNumber); } nRead++; } else { HKL tmp = new HKL(ih, ik, il); if (!reflectionList.resolution .inInverseResSqRange(Crystal.invressq(reflectionList.crystal, tmp))) { nRes++; } else { nIgnore++; } } } if (logger.isLoggable(Level.INFO)) { sb.append(format(" MTZ file type (machine stamp): %s\n", stampString)); sb.append(format(" Fc HKL read in: %d\n", nRead)); sb.append(format(" Fc HKL read as friedel mates: %d\n", nFriedel)); sb.append(format(" Fc HKL NOT read in (too high resolution): %d\n", nRes)); sb.append(format(" Fc HKL NOT read in (not in internal list?): %d\n", nIgnore)); sb.append(format(" Fc HKL NOT read in (F/sigF cutoff): %d\n", nCut)); sb.append( format(" HKL in internal list: %d\n", reflectionList.hkllist.size())); logger.info(sb.toString()); } } catch (EOFException e) { String message = " MTZ end of file reached."; logger.log(Level.WARNING, message, e); return false; } catch (IOException e) { String message = " MTZ IO Exception."; logger.log(Level.WARNING, message, e); return false; } return true; }
From source file:org.apache.jsp.fileUploader_jsp.java
private String UpdateToShare(byte[] bytes, String mimeType, String title, String description, String prevId, Set<String> communities, boolean isJson, String type, boolean newShare, HttpServletRequest request, HttpServletResponse response) {//from w w w . jav a2 s. c o m String charset = "UTF-8"; String url = ""; try { if (isJson) { //first check if bytes are actually json try { new JsonParser().parse(new String(bytes)); } catch (Exception ex) { return "Failed, file was not valid JSON"; } if (newShare) url = API_ROOT + "social/share/add/json/" + URLEncoder.encode(type, charset) + "/" + URLEncoder.encode(title, charset) + "/" + URLEncoder.encode(description, charset) + "/"; else url = API_ROOT + "social/share/update/json/" + prevId + "/" + URLEncoder.encode(type, charset) + "/" + URLEncoder.encode(title, charset) + "/" + URLEncoder.encode(description, charset) + "/"; } else { if (newShare) url = API_ROOT + "social/share/add/binary/" + URLEncoder.encode(title, charset) + "/" + URLEncoder.encode(description, charset) + "/"; else url = API_ROOT + "social/share/update/binary/" + prevId + "/" + URLEncoder.encode(title, charset) + "/" + URLEncoder.encode(description, charset) + "/"; } if (localCookie) CookieHandler.setDefault(cm); URLConnection connection = new URL(url).openConnection(); connection.setDoOutput(true); connection.setRequestProperty("Accept-Charset", charset); String cookieVal = getBrowserInfiniteCookie(request); if (cookieVal != null) { connection.addRequestProperty("Cookie", "infinitecookie=" + cookieVal); connection.setDoInput(true); connection.setDoOutput(true); connection.setRequestProperty("Accept-Charset", "UTF-8"); } if (mimeType != null && mimeType.length() > 0) connection.setRequestProperty("Content-Type", mimeType + ";charset=" + charset); DataOutputStream output = new DataOutputStream(connection.getOutputStream()); output.write(bytes); DataInputStream responseStream = new DataInputStream(connection.getInputStream()); ByteArrayOutputStream buffer = new ByteArrayOutputStream(); int nRead; byte[] data = new byte[16384]; while ((nRead = responseStream.read(data, 0, data.length)) != -1) { buffer.write(data, 0, nRead); } String json = buffer.toString(); String newCookie = getConnectionInfiniteCookie(connection); if (newCookie != null && response != null) { setBrowserInfiniteCookie(response, newCookie, request.getServerPort()); } buffer.flush(); buffer.close(); output.close(); responseStream.close(); if (isJson) { jsonResponse jr = new Gson().fromJson(json, jsonResponse.class); if (jr == null) { return "Failed: " + json; } if (jr.response.success == true) { if (jr.data != null && jr.data._id != null) { addRemoveCommunities(jr.data._id, communities, request, response); return jr.data._id; //When a new upload, mr.data contains the ShareID for the upload } } return "Upload Failed: " + jr.response.message; } else { modResponse mr = new Gson().fromJson(json, modResponse.class); if (mr == null) { return "Failed: " + json; } if (mr.response.success == true) { if (prevId != null && mr.data == null) { addRemoveCommunities(prevId, communities, request, response); return prevId; } else { addRemoveCommunities(mr.data, communities, request, response); return mr.data; //When a new upload, mr.data contains the ShareID for the upload } } else { return "Upload Failed: " + mr.response.message; } } } catch (IOException e) { e.printStackTrace(); return "Upload Failed: " + e.getMessage(); } }
From source file:ffx.xray.MTZFilter.java
/** * {@inheritDoc}/*from www.ja v a2 s .c o m*/ */ @Override public boolean readFile(File mtzFile, ReflectionList reflectionlist, DiffractionRefinementData refinementdata, CompositeConfiguration properties) { int nread, nignore, nres, nfriedel, ncut; ByteOrder b = ByteOrder.nativeOrder(); FileInputStream fis; DataInputStream dis; boolean transpose = false; StringBuilder sb = new StringBuilder(); //sb.append(String.format("\n Opening %s\n", mtzFile.getName())); try { fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); byte headeroffset[] = new byte[4]; byte bytes[] = new byte[80]; int offset = 0; // eat "MTZ" title dis.read(bytes, offset, 4); String mtzstr = new String(bytes); // header offset dis.read(headeroffset, offset, 4); // machine stamp dis.read(bytes, offset, 4); ByteBuffer bb = ByteBuffer.wrap(bytes); int stamp = bb.order(ByteOrder.BIG_ENDIAN).getInt(); String stampstr = Integer.toHexString(stamp); switch (stampstr.charAt(0)) { case '1': case '3': if (b.equals(ByteOrder.LITTLE_ENDIAN)) { b = ByteOrder.BIG_ENDIAN; } break; case '4': if (b.equals(ByteOrder.BIG_ENDIAN)) { b = ByteOrder.LITTLE_ENDIAN; } break; } bb = ByteBuffer.wrap(headeroffset); int headeroffseti = bb.order(b).getInt(); // skip to header and parse dis.skipBytes((headeroffseti - 4) * 4); for (Boolean parsing = true; parsing; dis.read(bytes, offset, 80)) { mtzstr = new String(bytes); parsing = parseHeader(mtzstr); } // column identifiers foString = sigfoString = rfreeString = null; if (properties != null) { foString = properties.getString("fostring", null); sigfoString = properties.getString("sigfostring", null); rfreeString = properties.getString("rfreestring", null); } h = k = l = fo = sigfo = rfree = -1; fplus = sigfplus = fminus = sigfminus = rfreeplus = rfreeminus = -1; boolean print = true; parseColumns(print); if (h < 0 || k < 0 || l < 0) { String message = "Fatal error in MTZ file - no H K L indexes?\n"; logger.log(Level.SEVERE, message); return false; } // reopen to start at beginning fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); // skip initial header dis.skipBytes(80); // check if HKLs need to be transposed or not float data[] = new float[nColumns]; HKL mate = new HKL(); int nposignore = 0; int ntransignore = 0; int nzero = 0; int none = 0; for (int i = 0; i < nReflections; i++) { for (int j = 0; j < nColumns; j++) { dis.read(bytes, offset, 4); bb = ByteBuffer.wrap(bytes); data[j] = bb.order(b).getFloat(); } int ih = (int) data[h]; int ik = (int) data[k]; int il = (int) data[l]; boolean friedel = reflectionlist.findSymHKL(ih, ik, il, mate, false); HKL hklpos = reflectionlist.getHKL(mate); if (hklpos == null) { nposignore++; } friedel = reflectionlist.findSymHKL(ih, ik, il, mate, true); HKL hkltrans = reflectionlist.getHKL(mate); if (hkltrans == null) { ntransignore++; } if (rfree > 0) { if (((int) data[rfree]) == 0) { nzero++; } else if (((int) data[rfree]) == 1) { none++; } } if (rfreeplus > 0) { if (((int) data[rfreeplus]) == 0) { nzero++; } else if (((int) data[rfreeplus]) == 1) { none++; } } if (rfreeminus > 0) { if (((int) data[rfreeminus]) == 0) { nzero++; } else if (((int) data[rfreeminus]) == 1) { none++; } } } if (nposignore > ntransignore) { transpose = true; } if (none > (nzero * 2) && refinementdata.rfreeflag < 0) { refinementdata.setFreeRFlag(0); sb.append(String.format(" Setting R free flag to %d based on MTZ file data.\n", refinementdata.rfreeflag)); } else if (nzero > (none * 2) && refinementdata.rfreeflag < 0) { refinementdata.setFreeRFlag(1); sb.append(String.format(" Setting R free flag to %d based on MTZ file data.\n", refinementdata.rfreeflag)); } else if (refinementdata.rfreeflag < 0) { refinementdata.setFreeRFlag(0); sb.append(String.format(" Setting R free flag to MTZ default: %d\n", refinementdata.rfreeflag)); } // reopen to start at beginning fis = new FileInputStream(mtzFile); dis = new DataInputStream(fis); // skip initial header dis.skipBytes(80); // read in data double anofsigf[][] = new double[refinementdata.n][4]; for (int i = 0; i < refinementdata.n; i++) { anofsigf[i][0] = anofsigf[i][1] = anofsigf[i][2] = anofsigf[i][3] = Double.NaN; } nread = nignore = nres = nfriedel = ncut = 0; for (int i = 0; i < nReflections; i++) { for (int j = 0; j < nColumns; j++) { dis.read(bytes, offset, 4); bb = ByteBuffer.wrap(bytes); data[j] = bb.order(b).getFloat(); } int ih = (int) data[h]; int ik = (int) data[k]; int il = (int) data[l]; boolean friedel = reflectionlist.findSymHKL(ih, ik, il, mate, transpose); HKL hkl = reflectionlist.getHKL(mate); if (hkl != null) { if (fo > 0 && sigfo > 0) { if (refinementdata.fsigfcutoff > 0.0) { if ((data[fo] / data[sigfo]) < refinementdata.fsigfcutoff) { ncut++; continue; } } if (friedel) { anofsigf[hkl.index()][2] = data[fo]; anofsigf[hkl.index()][3] = data[sigfo]; nfriedel++; } else { anofsigf[hkl.index()][0] = data[fo]; anofsigf[hkl.index()][1] = data[sigfo]; } } else { if (fplus > 0 && sigfplus > 0) { if (refinementdata.fsigfcutoff > 0.0) { if ((data[fplus] / data[sigfplus]) < refinementdata.fsigfcutoff) { ncut++; continue; } } anofsigf[hkl.index()][0] = data[fplus]; anofsigf[hkl.index()][1] = data[sigfplus]; } if (fminus > 0 && sigfminus > 0) { if (refinementdata.fsigfcutoff > 0.0) { if ((data[fminus] / data[sigfminus]) < refinementdata.fsigfcutoff) { ncut++; continue; } } anofsigf[hkl.index()][2] = data[fminus]; anofsigf[hkl.index()][3] = data[sigfminus]; } } if (rfree > 0) { refinementdata.setFreeR(hkl.index(), (int) data[rfree]); } else { if (rfreeplus > 0 && rfreeminus > 0) { // not sure what the correct thing to do here is? refinementdata.setFreeR(hkl.index(), (int) data[rfreeplus]); } else if (rfreeplus > 0) { refinementdata.setFreeR(hkl.index(), (int) data[rfreeplus]); } else if (rfreeminus > 0) { refinementdata.setFreeR(hkl.index(), (int) data[rfreeminus]); } } nread++; } else { HKL tmp = new HKL(ih, ik, il); if (!reflectionlist.resolution .inInverseResSqRange(Crystal.invressq(reflectionlist.crystal, tmp))) { nres++; } else { nignore++; } } } // set up fsigf from F+ and F- refinementdata.generate_fsigf_from_anofsigf(anofsigf); sb.append(String.format(" MTZ file type (machine stamp): %s\n", stampstr)); sb.append(String.format(" HKL data is %s\n", transpose ? "transposed" : "not transposed")); sb.append(String.format(" HKL read in: %d\n", nread)); sb.append(String.format(" HKL read as friedel mates: %d\n", nfriedel)); sb.append(String.format(" HKL NOT read in (too high resolution): %d\n", nres)); sb.append(String.format(" HKL NOT read in (not in internal list?): %d\n", nignore)); sb.append(String.format(" HKL NOT read in (F/sigF cutoff): %d\n", ncut)); sb.append( String.format(" HKL in internal list: %d\n", reflectionlist.hkllist.size())); if (logger.isLoggable(Level.INFO)) { logger.info(sb.toString()); } if (rfree < 0 && rfreeplus < 0 && rfreeminus < 0) { refinementdata.generateRFree(); } } catch (EOFException eof) { System.out.println("EOF reached "); return false; } catch (IOException ioe) { System.out.println("IO Exception: " + ioe.getMessage()); return false; } return true; }