X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=srcjar%2Fjavajs%2Futil%2FRdr.java;fp=srcjar%2Fjavajs%2Futil%2FRdr.java;h=0000000000000000000000000000000000000000;hb=5152dafd5d71c877156621def8463d437c9c5453;hp=3ff08b76499c6410c9b9c444e4518fb9ff8cea92;hpb=c4cf7aa546ede43930f9a17fec5060119984da41;p=jalview.git diff --git a/srcjar/javajs/util/Rdr.java b/srcjar/javajs/util/Rdr.java deleted file mode 100644 index 3ff08b7..0000000 --- a/srcjar/javajs/util/Rdr.java +++ /dev/null @@ -1,591 +0,0 @@ -/* $RCSfile$ - * $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 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); - } - - -} -