src.it.unimi.dsi.big.util.LongBigListSignedStringMap Maven / Gradle / Ivy
Show all versions of dsiutils Show documentation
/*
* DSI utilities
*
* Copyright (C) 2013-2020 Sebastiano Vigna
*
* 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 3 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 program; if not, see The purpose of this map is identical to that of a {@link ShiftAddXorSignedStringMap}, but
* Shift-Add-Xor signatures are 64-bit and stored in a {@link LongBigList}. This approach makes it possible to
* store the signatures in a file and read them by memory mapping using a {@link ByteBufferLongBigList}.
* If the map has a very large number of keys but the access pattern is strongly skewed towards a relatively
* small number of entries, using memory mapping might be advantageous.
*
*
The intended usage pattern is as follows:
*
*
*
* - first, you {@linkplain #sign(Iterator, Object2LongFunction) generate a file of signatures} (note that
* for this phase it might be necessary to keep the signatures in main memory; see {@link #sign(Iterator, String)} for some elaboration);
*
*
- then, when you want to use the signed map you map the file using {@link ByteBufferLongBigList#map(java.nio.channels.FileChannel)}
* and {@linkplain #LongBigListSignedStringMap(Object2LongFunction, LongBigList) create on the fly a signed map}.
*
*
*
* To simplify the process, there is a {@linkplain #LongBigListSignedStringMap(Object2LongFunction, String) constructor} that will do the mapping for you.
*
* @author Sebastiano Vigna
* @since 2.0.13
* @deprecated There are much better and faster hash functions.
*/
@Deprecated
public class LongBigListSignedStringMap extends AbstractObject2LongFunction implements StringMap, Serializable {
private static final long serialVersionUID = 0L;
/** The underlying map. */
protected final Object2LongFunction function;
/** Signatures. */
protected final LongBigList signatures;
/** Generates a 64-bit signatures big array using a given function and string sequence.
*
* The resulting big array can be saved using {@link BinIO#storeLongs(long[][], CharSequence)}
* or similar {@link BinIO} methods.
*
* @param iterator an iterator over a list of strings.
* @param function the function to be signed.
* @return a big array of 64-bit signatures.
*/
public static long[][] sign(final Iterator iterator, final Object2LongFunction function) {
return sign(iterator, function, null);
}
/** Generates a 64-bit signatures big array using a given function and string sequence.
*
*
The resulting big array can be saved using {@link BinIO#storeLongs(long[][], CharSequence)}
* or similar {@link BinIO} methods.
*
* @param iterator an iterator over a list of strings.
* @param function the function to be signed.
* @param pl a progress logger, or {@code null}.
* @return a big array of 64-bit signatures.
*/
public static long[][] sign(final Iterator iterator, final Object2LongFunction function , final ProgressLogger pl) {
final long n = function instanceof Size64 ? ((Size64)function).size64() : function .size();
final long[][] signature = LongBigArrays.newBigArray(n);
if (pl != null) {
pl.expectedUpdates = n;
pl.start("Signing...");
}
CharSequence s;
for(long i = 0; i < n; i++) {
s = iterator.next();
LongBigArrays.set(signature, function .getLong(s), signature(s));
if (pl != null) pl.lightUpdate();
}
if (iterator.hasNext()) throw new IllegalStateException("Iterator provides more than " + n + " elements");
if (pl != null) pl.done();
return signature;
}
/** Creates a signed string map using a given hash map and a big list of 64-bit signatures.
*
* @param function a minimal perfect hash for the strings enumerated by iterator; it must support {@link Function#size() size()}.
* and have default return value -1.
* @param signatures a big list of 64-bit signatures generated by {@link #sign(Iterator, Object2LongFunction, ProgressLogger)}.
*/
public LongBigListSignedStringMap(final Object2LongFunction function, final LongBigList signatures) {
final long n = function instanceof Size64 ? ((Size64)function).size64() : function.size();
if (n != signatures.size64()) throw new IllegalStateException("The size of the function differs from that of the signature list: " + n + " != " + signatures.size64());
this.function = function;
this.signatures = signatures;
defaultReturnValue(-1);
}
/** Generates an on-disk list 64-bit signatures big array using a given string sequence.
*
*
This methods generates on-disk signatures in the same order of the strings returned by
* the provided iterator. Thus, the signature file can be only used with a function that
* maps each string returned by the iterator in its ordinal position. This happens, for instance,
* if you have a sorted set of string and you use a monotone minimal perfect hash function.
*
* @param iterator an iterator over a list of strings.
* @param signatureFile the file name of the resulting signature file.
*/
public static void sign(final Iterator iterator, final String signatureFile) throws IOException {
sign(iterator, signatureFile, null);
}
/** Generates an on-disk list 64-bit signatures big array using a given string sequence.
*
* @param iterator an iterator over a list of strings.
* @param signatureFile the file name of the resulting signature file.
* @param pl a progress logger, or {@code null}.
* @see #sign(Iterator, DataOutput, ProgressLogger)
*/
public static void sign(final Iterator iterator, final String signatureFile, final ProgressLogger pl) throws IOException {
final DataOutputStream dos = new DataOutputStream(new FastBufferedOutputStream(new FileOutputStream(signatureFile)));
sign(iterator, dos, pl);
dos.close();
}
/** Generates an on-disk list 64-bit signatures big array using a given string sequence.
*
*
This methods generates on-disk signatures in the same order of the strings returned by
* the provided iterator. Thus, the generated signatures can be only used with a function that
* maps each string returned by the iterator in its ordinal position. This happens, for instance,
* if you have a sorted set of string and you use a
* monotone minimal perfect hash function.
*
* @param iterator an iterator over a list of strings.
* @param signatures a {@link DataOutput} where the signatures will be written.
* @param pl a progress logger, or {@code null}.
*/
public static void sign(final Iterator iterator, final DataOutput signatures, final ProgressLogger pl) throws IOException {
if (pl != null) pl.start("Signing...");
CharSequence s;
while(iterator.hasNext()) {
s = iterator.next();
signatures.writeLong(signature(s));
if (pl != null) pl.lightUpdate();
}
if (pl != null) pl.done();
}
/** Creates a signed string map using a given hash map and a big list of 64-bit signatures.
*
* @param function a minimal perfect hash for the strings enumerated by iterator; it must support {@link Function#size() size()}.
* and have default return value -1.
* @param signatures a file containing a list of 64-bit signatures
* generated by {@link #sign(Iterator, Object2LongFunction, ProgressLogger)} and stored in {@link DataOutput} format.
*/
@SuppressWarnings("resource")
public LongBigListSignedStringMap(final Object2LongFunction function, final String signatures) throws FileNotFoundException, IOException {
final long n = function instanceof Size64 ? ((Size64)function).size64() : function.size();
final long signatureSize = new File(signatures).length() / Long.BYTES;
if (n != signatureSize) throw new IllegalStateException("The size of the function differs from that of the signature list: " + n + " != " + signatureSize);
this.function = function;
this.signatures = ByteBufferLongBigList.map(new FileInputStream(signatures).getChannel());
defaultReturnValue(-1);
}
private static long signature(final CharSequence s) {
int i;
final int l = s.length();
long h = 42;
for (i = l; i-- != 0;) h ^= (h << 5) + s.charAt(i) + (h >>> 2);
return h;
}
private boolean checkSignature(final CharSequence s, final long index) {
return index >= 0 && index < function.size() && signatures.getLong(index) == signature(s);
}
@Override
public long getLong(final Object o) {
final CharSequence s = (CharSequence)o;
final long index = function.getLong(s);
return checkSignature(s, index) ? index : defRetValue;
}
@Override
public Long get(final Object o) {
final CharSequence s = (CharSequence)o;
final long index = function.getLong(s);
return checkSignature(s, index) ? Long.valueOf(index) : null;
}
@Override
public boolean containsKey(final Object o) {
final CharSequence s = (CharSequence)o;
return checkSignature(s, function.getLong(s));
}
@Override
@Deprecated
public int size() {
return signatures.size();
}
@Override
public long size64() {
return signatures.size64();
}
@Override
public ObjectBigList list() {
return null;
}
@SuppressWarnings("unchecked")
public static void main(final String[] arg) throws NoSuchMethodException, IOException, JSAPException, ClassNotFoundException {
final SimpleJSAP jsap = new SimpleJSAP(LongBigListSignedStringMap.class.getName(), "Generates a 64-bit signature file by reading a newline-separated list of strings and a function built on the same list of strings.",
new Parameter[] {
new FlaggedOption("bufferSize", JSAP.INTSIZE_PARSER, "64Ki", JSAP.NOT_REQUIRED, 'b', "buffer-size", "The size of the I/O buffer used to read strings."),
new FlaggedOption("encoding", ForNameStringParser.getParser(Charset.class), "UTF-8", JSAP.NOT_REQUIRED, 'e', "encoding", "The string file encoding."),
new Switch("zipped", 'z', "zipped", "The string list is compressed in gzip format."),
new UnflaggedOption("function", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the function to be signed, or - for writing signatures in the same order of the strings."),
new UnflaggedOption("signatures", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, JSAP.NOT_GREEDY, "The filename of the resulting signatures."),
new UnflaggedOption("stringFile", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, JSAP.NOT_GREEDY, "Read strings from this file instead of standard input."),
});
final JSAPResult jsapResult = jsap.parse(arg);
if (jsap.messagePrinted()) return;
final int bufferSize = jsapResult.getInt("bufferSize");
final String functionName = jsapResult.getString("function");
final String signaturesName = jsapResult.getString("signatures");
final String stringFile = jsapResult.getString("stringFile");
final Charset encoding = (Charset)jsapResult.getObject("encoding");
final boolean zipped = jsapResult.getBoolean("zipped");
final InputStream inputStream = stringFile != null ? new FileInputStream(stringFile) : System.in;
final Iterator iterator = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(inputStream) : inputStream, encoding), bufferSize));
final Object2LongFunction function = "-".equals(functionName) ? null : (Object2LongFunction)BinIO.loadObject(functionName);
final Logger logger = LoggerFactory.getLogger(LongBigListSignedStringMap.class);
final ProgressLogger pl = new ProgressLogger(logger);
if (function != null) BinIO.storeLongs(sign(iterator, function, pl), signaturesName);
else sign(iterator, signaturesName, pl);
if (stringFile != null) inputStream.close();
}
}