+++ /dev/null
-/* $RCSfile$
- * $Author: hansonr $
- * $Date: 2007-04-05 09:07:28 -0500 (Thu, 05 Apr 2007) $
- * $Revision: 7326 $
- *
- * 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 The Jmol Development Team
- *
- * Contact: jmol-developers@lists.sf.net
- *
- * 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.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.StringReader;
-import java.io.UnsupportedEncodingException;
-
-import java.util.Map;
-
-import javajs.api.Interface;
-
-
-import javajs.api.GenericCifDataParser;
-import javajs.api.GenericLineReader;
-import javajs.api.GenericZipTools;
-
-/**
- * A general helper class for a variety of stream and reader functionality
- * including:
- *
- * stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams
- *
- * various stream/reader methods, including UTF-encoded stream reading
- *
- * reflection-protected access to a CIF parser and ZIP tools
- *
- *
- *
- *
- */
-public class Rdr implements GenericLineReader {
-
- public static class StreamReader extends BufferedReader {
-
- private BufferedInputStream stream;
-
- public StreamReader(BufferedInputStream bis, String charSet) throws UnsupportedEncodingException {
- super(new InputStreamReader(bis, (charSet == null ? "UTF-8" : charSet)));
- stream = bis;
- }
-
- public BufferedInputStream getStream() {
- try {
- stream.reset();
- } catch (IOException e) {
- // ignore
- }
- return stream;
- }
-
- }
-
- BufferedReader reader;
-
- public Rdr(BufferedReader reader) {
- this.reader = reader;
- }
-
- @Override
- public String readNextLine() throws Exception {
- return reader.readLine();
- }
-
- public static Map<String, Object> readCifData(GenericCifDataParser parser, BufferedReader br) {
- return parser.set(null, br, false).getAllCifData();
- }
-
-
- ///////////
-
-
- /**
- *
- * Read a UTF-8 byte array fully, converting it to a String.
- * Called by Jmol's XMLReaders
- *
- * @param bytes
- * @return a UTF-8 string
- */
- public static String bytesToUTF8String(byte[] bytes) {
- return streamToUTF8String(new BufferedInputStream(new ByteArrayInputStream(bytes)));
- }
-
- /**
- *
- * Read a UTF-8 stream fully, converting it to a String.
- * Called by Jmol's XMLReaders
- *
- * @param bis
- * @return a UTF-8 string
- */
- public static String streamToUTF8String(BufferedInputStream bis) {
- String[] data = new String[1];
- try {
- readAllAsString(getBufferedReader(bis, "UTF-8"), -1, true, data, 0);
- } catch (IOException e) {
- }
- return data[0];
- }
-
- /**
- * Read an input stream fully, saving a byte array, then
- * return a buffered reader to those bytes converted to string form.
- *
- * @param bis
- * @param charSet
- * @return Reader
- * @throws IOException
- */
- public static BufferedReader getBufferedReader(BufferedInputStream bis, String charSet)
- throws IOException {
- // could also just make sure we have a buffered input stream here.
- if (getUTFEncodingForStream(bis) == Encoding.NONE)
- return new StreamReader(bis, (charSet == null ? "UTF-8" : charSet));
- byte[] bytes = getLimitedStreamBytes(bis, -1);
- bis.close();
- return getBR(charSet == null ? fixUTF(bytes) : new String(bytes, charSet));
- }
-
- /**
- * This method is specifically for strings that are marked for UTF 8 or 16.
- *
- * @param bytes
- * @return UTF-decoded bytes
- */
- public static String fixUTF(byte[] bytes) {
- Encoding encoding = getUTFEncoding(bytes);
- if (encoding != Encoding.NONE)
- try {
- String s = new String(bytes, encoding.name().replace('_', '-'));
- switch (encoding) {
- case UTF8:
- case UTF_16BE:
- case UTF_16LE:
- // extra byte at beginning removed
- s = s.substring(1);
- break;
- default:
- break;
- }
- return s;
- } catch (UnsupportedEncodingException e) {
- System.out.println(e);
- }
- return new String(bytes);
- }
-
- private static Encoding getUTFEncoding(byte[] bytes) {
- if (bytes.length >= 3 && (bytes[0] & 0xFF) == 0xEF && (bytes[1] & 0xFF) == 0xBB && (bytes[2] & 0xFF) == 0xBF)
- return Encoding.UTF8;
- if (bytes.length >= 4 && (bytes[0] & 0xFF) == 0 && (bytes[1] & 0xFF) == 0
- && (bytes[2] & 0xFF) == 0xFE && (bytes[3] & 0xFF) == 0xFF)
- return Encoding.UTF_32BE;
- if (bytes.length >= 4 && (bytes[0] & 0xFF) == 0xFF && (bytes[1] & 0xFF) == 0xFE
- && (bytes[2] & 0xFF) == 0 && (bytes[3] & 0xFF) == 0)
- return Encoding.UTF_32LE;
- if (bytes.length >= 2 && (bytes[0] & 0xFF) == 0xFF && (bytes[1] & 0xFF) == 0xFE)
- return Encoding.UTF_16LE;
- if (bytes.length >= 2 && (bytes[0] & 0xFF) == 0xFE && (bytes[1] & 0xFF) == 0xFF)
- return Encoding.UTF_16BE;
- return Encoding.NONE;
-
- }
-
- ////////// stream type checking //////////
-
-
- private static Encoding getUTFEncodingForStream(BufferedInputStream is) throws IOException {
- byte[] abMagic = new byte[4];
- abMagic[3] = 1;
- try{
- is.mark(5);
- } catch (Exception e) {
- return Encoding.NONE;
- }
- is.read(abMagic, 0, 4);
- is.reset();
- return getUTFEncoding(abMagic);
- }
-
- public static boolean isBase64(SB sb) {
- return (sb.indexOf(";base64,") == 0);
- }
-
- public static boolean isCompoundDocumentS(InputStream is) {
- return isCompoundDocumentB(getMagic(is, 8));
- }
-
- public static boolean isCompoundDocumentB(byte[] bytes) {
- return (bytes.length >= 8 && (bytes[0] & 0xFF) == 0xD0
- && (bytes[1] & 0xFF) == 0xCF && (bytes[2] & 0xFF) == 0x11
- && (bytes[3] & 0xFF) == 0xE0 && (bytes[4] & 0xFF) == 0xA1
- && (bytes[5] & 0xFF) == 0xB1 && (bytes[6] & 0xFF) == 0x1A
- && (bytes[7] & 0xFF) == 0xE1);
- }
-
- public static boolean isBZip2S(InputStream is) {
- return isBZip2B(getMagic(is, 3));
- }
-
- public static boolean isGzipS(InputStream is) {
- return isGzipB(getMagic(is, 2));
- }
-
- public static boolean isBZip2B(byte[] bytes) {
- return (bytes != null && bytes.length >= 3 // BZh
- && (bytes[0] & 0xFF) == 0x42 && (bytes[1] & 0xFF) == 0x5A && (bytes[2] & 0xFF) == 0x68);
-}
-
- public static boolean isGzipB(byte[] bytes) {
- return (bytes != null && bytes.length >= 2
- && (bytes[0] & 0xFF) == 0x1F && (bytes[1] & 0xFF) == 0x8B);
- }
-
- public static boolean isPickleS(InputStream is) {
- return isPickleB(getMagic(is, 2));
- }
-
- public static boolean isPickleB(byte[] bytes) {
- return (bytes != null && bytes.length >= 2
- && (bytes[0] & 0xFF) == 0x7D && (bytes[1] & 0xFF) == 0x71);
- }
-
- public static boolean isMessagePackS(InputStream is) {
- return isMessagePackB(getMagic(is, 2));
- }
-
- public static boolean isMessagePackB(byte[] bytes) {
- // look for 'map' start, but PNG files start with 0x89, which is
- // the MessagePack start for a 9-member map, so in that case we have
- // to check that the next byte is not "P" as in <89>PNG
- int b;
-
- return (bytes != null && bytes.length >= 1 && (((b = bytes[0] & 0xFF)) == 0xDE || (b & 0xE0) == 0x80 && bytes[1] != 0x50));
- }
-
- public static boolean isPngZipStream(InputStream is) {
- return isPngZipB(getMagic(is, 55));
- }
-
- public static boolean isPngZipB(byte[] bytes) {
- // \0PNGJ starting at byte 50
- return (bytes[50] == 0 && bytes[51] == 0x50 && bytes[52] == 0x4E && bytes[53] == 0x47 && bytes[54] == 0x4A);
- }
-
- /**
- * Check for a ZIP input stream - starting with "PK<03><04>"
- * @param is
- * @return true if a ZIP stream
- */
- public static boolean isZipS(InputStream is) {
- return isZipB(getMagic(is, 4));
- }
-
- public static boolean isZipB(byte[] bytes) {
- return (bytes.length >= 4
- && bytes[0] == 0x50 //PK<03><04>
- && bytes[1] == 0x4B
- && bytes[2] == 0x03
- && bytes[3] == 0x04);
- }
-
- public static byte[] getMagic(InputStream is, int n) {
- byte[] abMagic = new byte[n];
- try {
- is.mark(n + 1);
- is.read(abMagic, 0, n);
- } catch (IOException e) {
- }
- try {
- is.reset();
- } catch (IOException e) {
- }
- return abMagic;
- }
-
- public static String guessMimeTypeForBytes(byte[] bytes) {
- // only options here are JPEG, PNG, GIF, and BMP
- switch (bytes.length < 2 ? -1 : bytes[1]) {
- case 0:
- return "image/jpg"; // 0xFF 0x00 ...
- case 0x49:
- return "image/gif"; // GIF89a...
- case 0x4D:
- return "image/BMP"; // BM...
- case 0x50:
- return "image/png";
- default:
- return "image/unknown";
- }
- }
-
-
- ////////// stream/byte methods ///////////
-
- public static BufferedInputStream getBIS(byte[] bytes) {
- return new BufferedInputStream(new ByteArrayInputStream(bytes));
- }
-
- public static BufferedReader getBR(String string) {
- return new BufferedReader(new StringReader(string));
- }
-
-
- public static BufferedInputStream toBIS(Object o) {
- return (AU.isAB(o) ? getBIS((byte[]) o)
- : o instanceof SB ? getBIS(Rdr.getBytesFromSB((SB) o))
- : o instanceof String ? getBIS(((String) o).getBytes()) : null);
- }
-
-
- /**
- * Drill down into a GZIP stack until no more layers.
- * @param jzt
- *
- * @param bis
- * @return non-gzipped buffered input stream.
- *
- * @throws IOException
- */
- public static BufferedInputStream getUnzippedInputStream(GenericZipTools jzt, BufferedInputStream bis) throws IOException {
- while (isGzipS(bis))
- bis = new BufferedInputStream(jzt.newGZIPInputStream(bis));
- return bis;
- }
-
- public static BufferedInputStream getUnzippedInputStreamBZip2(GenericZipTools jzt,
- BufferedInputStream bis) throws IOException {
- while (isBZip2S(bis))
- bis = new BufferedInputStream(jzt.newBZip2InputStream(bis));
- return bis;
- }
-
-
- /**
- * Allow for base64-encoding check.
- *
- * @param sb
- * @return byte array
- */
- public static byte[] getBytesFromSB(SB sb) {
- return (isBase64(sb) ? Base64.decodeBase64(sb.substring(8)) : sb.toBytes(0, -1));
- }
-
- /**
- * Read a an entire BufferedInputStream for its bytes, and
- * either return them or leave them in the designated output channel.
- *
- * @param bis
- * @param out a destination output channel, or null
- * @return byte[] (if out is null) or a message indicating length (if not)
- *
- * @throws IOException
- */
- public static Object getStreamAsBytes(BufferedInputStream bis,
- OC out) throws IOException {
- byte[] buf = new byte[1024];
- byte[] bytes = (out == null ? new byte[4096] : null);
- int len = 0;
- int totalLen = 0;
- while ((len = bis.read(buf, 0, 1024)) > 0) {
- totalLen += len;
- if (out == null) {
- if (totalLen >= bytes.length)
- bytes = AU.ensureLengthByte(bytes, totalLen * 2);
- System.arraycopy(buf, 0, bytes, totalLen - len, len);
- } else {
- out.write(buf, 0, len);
- }
- }
- bis.close();
- if (out == null) {
- return AU.arrayCopyByte(bytes, totalLen);
- }
- return totalLen + " bytes";
- }
-
- /**
- * Read a possibly limited number of bytes (when n > 0) from a stream,
- * leaving the stream open.
- *
- * @param is an input stream, not necessarily buffered.
- * @param n the maximum number of bytes to read, or -1 for all
- * @return the bytes read
- *
- * @throws IOException
- */
- public static byte[] getLimitedStreamBytes(InputStream is, long n)
- throws IOException {
-
- //Note: You cannot use InputStream.available() to reliably read
- // zip data from the web.
-
- int buflen = (n > 0 && n < 1024 ? (int) n : 1024);
- byte[] buf = new byte[buflen];
- byte[] bytes = new byte[n < 0 ? 4096 : (int) n];
- int len = 0;
- int totalLen = 0;
- if (n < 0)
- n = Integer.MAX_VALUE;
- while (totalLen < n && (len = is.read(buf, 0, buflen)) > 0) {
- totalLen += len;
- if (totalLen > bytes.length)
- bytes = AU.ensureLengthByte(bytes, totalLen * 2);
- System.arraycopy(buf, 0, bytes, totalLen - len, len);
- if (n != Integer.MAX_VALUE && totalLen + buflen > bytes.length)
- buflen = bytes.length - totalLen;
-
- }
- if (totalLen == bytes.length)
- return bytes;
- buf = new byte[totalLen];
- System.arraycopy(bytes, 0, buf, 0, totalLen);
- return buf;
- }
-
- /**
- * This method fills data[i] with string data from a file that may or may not
- * be binary even though it is being read by a reader. It is meant to be used
- * simple text-based files only.
- *
- * @param br
- * @param nBytesMax
- * @param allowBinary
- * @param data
- * @param i
- * @return true if data[i] holds the data; false if data[i] holds an error message.
- */
- public static boolean readAllAsString(BufferedReader br, int nBytesMax, boolean allowBinary, String[] data, int i) {
- try {
- SB sb = SB.newN(8192);
- String line;
- if (nBytesMax < 0) {
- line = br.readLine();
- if (allowBinary || line != null && line.indexOf('\0') < 0
- && (line.length() != 4 || line.charAt(0) != 65533
- || line.indexOf("PNG") != 1)) {
- sb.append(line).appendC('\n');
- while ((line = br.readLine()) != null)
- sb.append(line).appendC('\n');
- }
- } else {
- int n = 0;
- int len;
- while (n < nBytesMax && (line = br.readLine()) != null) {
- if (nBytesMax - n < (len = line.length()) + 1)
- line = line.substring(0, nBytesMax - n - 1);
- sb.append(line).appendC('\n');
- n += len + 1;
- }
- }
- br.close();
- data[i] = sb.toString();
- return true;
- } catch (Exception ioe) {
- data[i] = ioe.toString();
- return false;
- }
- }
-
-
- /////////// PNGJ support /////////////
-
-
- /**
- * Look at byte 50 for "\0PNGJxxxxxxxxx+yyyyyyyyy" where xxxxxxxxx is a byte
- * offset to the JMOL data and yyyyyyyyy is the length of the data.
- *
- * @param bis
- * @return same stream or byte stream
- */
-
- /**
- * Retrieve the two numbers in a PNG iTXt tag indicating the
- * file pointer for the start of the ZIP data as well as its length.
- *
- * @param bis
- * @param pt_count
- */
- static void getPngZipPointAndCount(BufferedInputStream bis, int[] pt_count) {
- bis.mark(75);
- try {
- byte[] data = getLimitedStreamBytes(bis, 74);
- bis.reset();
- int pt = 0;
- for (int i = 64, f = 1; --i > 54; f *= 10)
- pt += (data[i] - '0') * f;
- int n = 0;
- for (int i = 74, f = 1; --i > 64; f *= 10)
- n += (data[i] - '0') * f;
- pt_count[0] = pt;
- pt_count[1] = n;
- } catch (Throwable e) {
- pt_count[1] = 0;
- }
- }
-
- /**
- * Either advance a PNGJ stream to its zip file data or pull out the ZIP data
- * bytes and create a new stream for them from which a ZIP utility can start
- * extracting files.
- *
- * @param bis
- * @param asNewStream
- * @return new buffered ByteArrayInputStream, possibly with no data if there is an error
- */
- public static BufferedInputStream getPngZipStream(BufferedInputStream bis, boolean asNewStream) {
- if (!isPngZipStream(bis))
- return bis;
- byte[] data = new byte[0];
- bis.mark(75);
- try {
- int pt_count[] = new int[2];
- getPngZipPointAndCount(bis, pt_count);
- if (pt_count[1] != 0) {
- int pt = pt_count[0];
- while (pt > 0)
- pt -= bis.skip(pt);
- if (!asNewStream)
- return bis;
- data = getLimitedStreamBytes(bis, pt_count[1]);
- }
- } catch (Throwable e) {
- } finally {
- try {
- if (asNewStream)
- bis.close();
- } catch (Exception e) {
- // ignore
- }
- }
- return getBIS(data);
- }
-
- /** We define a request for zip file extraction by vertical bar:
- * zipName|interiorFileName. These may be nested if there is a
- * zip file contained in a zip file.
- *
- * @param fileName
- * @return filename trimmed of interior fileName
- *
- */
- public static String getZipRoot(String fileName) {
- int pt = fileName.indexOf("|");
- return (pt < 0 ? fileName : fileName.substring(0, pt));
- }
-
- public static BufferedWriter getBufferedWriter(OutputStream os, String charSetName) {
- OutputStreamWriter osw = (OutputStreamWriter) Interface.getInstanceWithParams("java.io.OutputStreamWriter",
- new Class<?>[] { java.io.OutputStream.class, String.class },
- new Object[] { os, charSetName == null ? "UTF-8" : charSetName });
-
- return new BufferedWriter(osw);
- }
-
-
-}
-
git://source.jalview.org / jalview.git / blobdiff