--- /dev/null
+/* $RCSfile$
+ * $Date: 2006-03-18 15:59:33 -0600 (Sat, 18 Mar 2006) $
+ * $Revision: 4652 $
+ *
+ * Some portions of this file have been modified by Robert Hanson hansonr.at.stolaf.edu 2012-2017
+ * for use in SwingJS via transpilation into JavaScript using Java2Script.
+ *
+ * Copyright (C) 2003-2005 Miguel, Jmol Development, www.jmol.org
+ *
+ * Contact: hansonr@stolaf.edu
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library 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
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package javajs.util;
+
+
+import java.io.BufferedInputStream;
+import java.io.DataInputStream;
+import java.io.IOException;
+import java.util.Map;
+
+import javajs.api.GenericBinaryDocument;
+import javajs.api.GenericOutputChannel;
+
+/* a basic binary file reader (extended by CompoundDocument).
+ *
+ * Note that YOU are responsible for determining whether a file
+ * is bigEndian or littleEndian; the default is bigEndian.
+ *
+ * JavaScript note: readShort() malfunctioned because (short) (xx << 8)
+ * isn't the same as (int) (xx << 8); same problem in java.io.DataStream
+ *
+ *
+ */
+
+public class BinaryDocument extends BC implements GenericBinaryDocument {
+
+ public BinaryDocument() {
+ }
+
+
+ // called by reflection
+
+ protected DataInputStream stream;
+ protected boolean isRandom = false;
+ protected boolean isBigEndian = true;
+ protected BufferedInputStream bis;
+ protected long nBytes;
+ protected GenericOutputChannel out;
+
+
+ @Override
+ public void close() {
+ if (stream != null)
+ try {
+ stream.close();
+ } catch (IOException e) {
+ // ignore
+ }
+ if (out != null)
+ out.closeChannel();
+ }
+
+ @Override
+ public BinaryDocument setStream(BufferedInputStream bis, boolean isBigEndian) {
+ this.bis = bis;
+ if (bis != null) {
+ stream = new DataInputStream(bis);
+ }
+ this.isBigEndian = isBigEndian;
+ return this;
+ }
+
+ @Override
+ public BufferedInputStream getInputStream() {
+ return bis;
+ }
+
+ @Override
+ public void setStreamData(DataInputStream stream, boolean isBigEndian) {
+ if (stream != null)
+ this.stream = stream;
+ this.isBigEndian = isBigEndian;
+ }
+
+ @Override
+ public void setOutputChannel(GenericOutputChannel out) {
+ this.out = out;
+ }
+
+ public void setRandom(boolean TF) {
+ isRandom = TF;
+ //CANNOT be random for web
+ }
+
+ @Override
+ public byte readByte() throws IOException {
+ nBytes++;
+ return ioReadByte();
+ }
+
+ @Override
+ public int readUInt8() throws IOException {
+ nBytes++;
+ int b = stream.readUnsignedByte();
+ if (out != null)
+ out.writeByteAsInt(b);
+ return b;
+ }
+
+ private byte ioReadByte() throws IOException {
+ byte b = stream.readByte();
+ if (out != null)
+ out.writeByteAsInt(b);
+ return b;
+ }
+
+ @Override
+ public byte[] readBytes(int n) throws IOException {
+ byte[] b = new byte[n];
+ readByteArray(b, 0, n);
+ return b;
+ }
+
+ @Override
+ public int readByteArray(byte[] b, int off, int len) throws IOException {
+ int n = ioRead(b, off, len);
+ nBytes += n;
+ return n;
+ }
+
+ private int ioRead(byte[] b, int off, int len) throws IOException {
+ int m = 0;
+ while (len > 0) {
+ int n = stream.read(b, off, len);
+ m += n;
+ if (n > 0 && out != null)
+ out.write(b, off, n);
+ if (n >= len)
+ break;
+ off += n;
+ len -= n;
+ }
+ return m;
+ }
+
+ @Override
+ public String readString(int nChar) throws IOException {
+ byte[] temp = new byte[nChar];
+ int n = readByteArray(temp, 0, nChar);
+ return new String(temp, 0, n, "UTF-8");
+ }
+
+ @Override
+ public short readShort() throws IOException {
+ nBytes += 2;
+ short n = (isBigEndian ? ioReadShort()
+ : (short) ((ioReadByte() & 0xff)
+ | (ioReadByte() & 0xff) << 8));
+ /**
+ * @j2sNative
+ *
+ * return (n > 0x7FFF ? n - 0x10000 : n);
+ */
+ {
+ return n;
+ }
+ }
+
+ private short ioReadShort() throws IOException {
+ short b = stream.readShort();
+ if (out != null)
+ out.writeShort(b);
+ return b;
+ }
+
+
+ @Override
+ public int readIntLE() throws IOException {
+ nBytes += 4;
+ return readLEInt();
+ }
+
+ @Override
+ public int readInt() throws IOException {
+ nBytes += 4;
+ return (isBigEndian ? ioReadInt() : readLEInt());
+ }
+
+ private int ioReadInt() throws IOException {
+ int i = stream.readInt();
+ if (out != null)
+ out.writeInt(i);
+ return i;
+ }
+
+ @Override
+ public int swapBytesI(int n) {
+ return (((n >> 24) & 0xff)
+ | ((n >> 16) & 0xff) << 8
+ | ((n >> 8) & 0xff) << 16
+ | (n & 0xff) << 24);
+ }
+
+ @Override
+ public short swapBytesS(short n) {
+ return (short) ((((n >> 8) & 0xff)
+ | (n & 0xff) << 8));
+ }
+
+
+ @Override
+ public int readUnsignedShort() throws IOException {
+ nBytes += 2;
+ int a = (ioReadByte() & 0xff);
+ int b = (ioReadByte() & 0xff);
+ return (isBigEndian ? (a << 8) + b : (b << 8) + a);
+ }
+
+ @Override
+ public long readLong() throws IOException {
+ nBytes += 8;
+ return (isBigEndian ? ioReadLong()
+ : ((((long) ioReadByte()) & 0xff)
+ | (((long) ioReadByte()) & 0xff) << 8
+ | (((long) ioReadByte()) & 0xff) << 16
+ | (((long) ioReadByte()) & 0xff) << 24
+ | (((long) ioReadByte()) & 0xff) << 32
+ | (((long) ioReadByte()) & 0xff) << 40
+ | (((long) ioReadByte()) & 0xff) << 48
+ | (((long) ioReadByte()) & 0xff) << 54));
+ }
+
+ private long ioReadLong() throws IOException {
+ long b = stream.readLong();
+ if (out != null)
+ out.writeLong(b);
+ return b;
+ }
+
+ private int readLEInt() throws IOException {
+ ioRead(t8, 0, 4);
+ return bytesToInt(t8, 0, false);
+ }
+
+ byte[] t8 = new byte[8];
+
+ @Override
+ public float readFloat() throws Exception {
+ return intToFloat(readInt());
+ }
+
+ @SuppressWarnings("unused")
+ @Override
+ public double readDouble() throws IOException {
+ /**
+ *
+ * reading the float equivalent here in JavaScript
+ *
+ * @j2sNative
+ *
+ *
+ */
+ {
+ nBytes += 8;
+ if (true)
+ return (isBigEndian ? ioReadDouble()
+ : Double.longBitsToDouble(readLELong()));
+ }
+ // this is the JavaScript-only part
+ this.readByteArray(this.t8, 0, 8);
+ return bytesToDoubleToFloat(this.t8, 0, this.isBigEndian);
+ }
+
+ private double ioReadDouble() throws IOException {
+ double d = stream.readDouble();
+ if (out != null)
+ out.writeLong(Double.doubleToRawLongBits(d));
+ return d;
+ }
+
+ private long readLELong() throws IOException {
+ return ((((long) ioReadByte()) & 0xff)
+ | (((long) ioReadByte()) & 0xff) << 8
+ | (((long) ioReadByte()) & 0xff) << 16
+ | (((long) ioReadByte()) & 0xff) << 24
+ | (((long) ioReadByte()) & 0xff) << 32
+ | (((long) ioReadByte()) & 0xff) << 40
+ | (((long) ioReadByte()) & 0xff) << 48
+ | (((long) ioReadByte()) & 0xff) << 56);
+ }
+
+ @Override
+ public void seek(long offset) {
+ // slower, but all that is available using the applet
+ try {
+ if (offset == nBytes)
+ return;
+ if (offset < nBytes) {
+ stream.reset();
+ if (out != null && nBytes != 0)
+ out.reset();
+ nBytes = 0;
+ } else {
+ offset -= nBytes;
+ }
+ if (out == null) {
+ stream.skipBytes((int)offset);
+ } else {
+ readByteArray(new byte[(int)offset], 0, (int) offset);
+ }
+ nBytes += offset;
+ } catch (IOException e) {
+ System.out.println(e.toString());
+ }
+ }
+
+ @Override
+ public long getPosition() {
+ return nBytes;
+ }
+
+ @Override
+ public SB getAllDataFiles(String binaryFileList, String firstFile) {
+ return null;
+ }
+
+ @Override
+ public void getAllDataMapped(String replace, String string,
+ Map<String, String> fileData) {
+ }
+
+
+/* random access -- application only:
+ *
+ void seekFile(long offset) {
+ try {
+ file.seek(offset);
+ } catch (IOException e) {
+ System.out.println(e.getMessage());
+ }
+ }
+*/
+}
git://source.jalview.org / jalview.git / blobdiff