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459 lines
17 KiB
459 lines
17 KiB
// kelondroAttrSeq.java
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// -----------------------
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// part of YaCy
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// (C) by Michael Peter Christen; mc@anomic.de
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// first published on http://www.anomic.de
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// Frankfurt, Germany, 2005
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// Created 15.11.2005
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//
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// $LastChangedDate: 2005-10-22 15:28:04 +0200 (Sat, 22 Oct 2005) $
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// $LastChangedRevision: 968 $
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// $LastChangedBy: theli $
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//
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// This program is free software; you can redistribute it and/or modify
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// it under the terms of the GNU General Public License as published by
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// the Free Software Foundation; either version 2 of the License, or
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// (at your option) any later version.
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//
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// This program is distributed in the hope that it will be useful,
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// but WITHOUT ANY WARRANTY; without even the implied warranty of
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// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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// GNU General Public License for more details.
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//
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// You should have received a copy of the GNU General Public License
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// along with this program; if not, write to the Free Software
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// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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//
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// Using this software in any meaning (reading, learning, copying, compiling,
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// running) means that you agree that the Author(s) is (are) not responsible
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// for cost, loss of data or any harm that may be caused directly or indirectly
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// by usage of this softare or this documentation. The usage of this software
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// is on your own risk. The installation and usage (starting/running) of this
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// software may allow other people or application to access your computer and
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// any attached devices and is highly dependent on the configuration of the
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// software which must be done by the user of the software; the author(s) is
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// (are) also not responsible for proper configuration and usage of the
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// software, even if provoked by documentation provided together with
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// the software.
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//
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// Any changes to this file according to the GPL as documented in the file
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// gpl.txt aside this file in the shipment you received can be done to the
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// lines that follows this copyright notice here, but changes must not be
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// done inside the copyright notive above. A re-distribution must contain
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// the intact and unchanged copyright notice.
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// Contributions and changes to the program code must be marked as such.
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package de.anomic.kelondro;
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import java.io.File;
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import java.io.BufferedReader;
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import java.io.InputStreamReader;
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import java.io.FileInputStream;
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import java.io.IOException;
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import java.util.Map;
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import java.util.HashMap;
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import java.util.TreeMap;
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import java.util.Iterator;
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import java.util.ArrayList;
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import java.util.StringTokenizer;
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import java.util.zip.GZIPInputStream;
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import java.util.logging.Logger;
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import de.anomic.server.serverCodings;
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import de.anomic.server.serverFileUtils;
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public class kelondroAttrSeq {
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// class objects
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private File file;
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private Map entries;
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private Structure structure;
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private String name;
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private long created;
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// optional logger
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protected Logger theLogger = null;
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public kelondroAttrSeq(File file, boolean tree) throws IOException {
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this.file = file;
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this.structure = null;
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this.created = -1;
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this.name = "";
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this.entries = (tree) ? (Map) new TreeMap() : (Map) new HashMap();
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readAttrFile(file);
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}
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public kelondroAttrSeq(String name, String struct, boolean tree) {
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this.file = null;
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this.structure = new Structure(struct);
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this.created = System.currentTimeMillis();
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this.name = name;
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this.entries = (tree) ? (Map) new TreeMap() : (Map) new HashMap();
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}
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public void setLogger(Logger newLogger) {
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this.theLogger = newLogger;
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}
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public void logInfo(String message) {
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if (this.theLogger == null)
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System.err.println("ATTRSEQ INFO for file " + this.file + ": " + message);
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else
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this.theLogger.info("ATTRSEQ INFO for file " + this.file + ": " + message);
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}
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public void logWarning(String message) {
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if (this.theLogger == null)
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System.err.println("ATTRSEQ WARNING for file " + this.file + ": " + message);
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else
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this.theLogger.warning("ATTRSEQ WARNING for file " + this.file + ": " + message);
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}
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private void readAttrFile(File loadfile) throws IOException {
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BufferedReader br = null;
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int p;
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if (loadfile.toString().endsWith(".gz")) {
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br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(loadfile))));
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} else {
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br = new BufferedReader(new InputStreamReader(new FileInputStream(loadfile)));
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}
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String line;
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String key;
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while ((line = br.readLine()) != null) {
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line = line.trim();
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if (line.length() == 0) continue;
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if (line.startsWith("#")) {
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if (line.startsWith("# Structure=")) {
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structure = new Structure(line.substring(12));
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}
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if (line.startsWith("# Name=")) {
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name = line.substring(7);
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}
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if (line.startsWith("# Created=")) {
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created = Long.parseLong(line.substring(10));
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}
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continue;
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}
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if ((p = line.indexOf('=')) > 0) {
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key = line.substring(0, p).trim();
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if (entries.containsKey(key)) {
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logWarning("read PropFile " + loadfile.toString() + ", key " + key + ": double occurrence");
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} else {
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entries.put(key, line.substring(p + 1).trim());
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}
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}
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}
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br.close();
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if (structure == null) throw new IOException("file contains no structure tag");
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if (name == null) throw new IOException("file contains no name tag");
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if (created == -1) throw new IOException("file contains no created tag");
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}
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public int size() {
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return entries.size();
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}
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public long created() {
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return this.created;
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}
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public void toFile(File out) throws IOException {
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// generate header
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StringBuffer sb = new StringBuffer(2000);
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sb.append("# Name=" + this.name); sb.append((char) 13); sb.append((char) 10);
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sb.append("# Created=" + this.created); sb.append((char) 13); sb.append((char) 10);
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sb.append("# Structure=" + this.structure.toString()); sb.append((char) 13); sb.append((char) 10);
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sb.append("# ---"); sb.append((char) 13); sb.append((char) 10);
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Iterator i = entries.entrySet().iterator();
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Map.Entry entry;
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String k;
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Object v;
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while (i.hasNext()) {
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entry = (Map.Entry) i.next();
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k = (String) entry.getKey();
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v = entry.getValue();
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sb.append(k); sb.append('=');
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if (v instanceof String) sb.append((String) v);
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if (v instanceof Entry) sb.append(((Entry) v).toString());
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sb.append((char) 13); sb.append((char) 10);
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}
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if (out.toString().endsWith(".gz")) {
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serverFileUtils.writeAndZip(sb.toString().getBytes(), out);
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} else {
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serverFileUtils.write(sb.toString().getBytes(), out);
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}
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}
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public Iterator keys() {
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return entries.keySet().iterator();
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}
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public Entry newEntry(String pivot, boolean tree) {
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return new Entry(pivot, new HashMap(), (tree) ? (Map) new TreeMap() : (Map) new HashMap());
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}
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public Entry newEntry(String pivot, HashMap props, Map seq) {
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return new Entry(pivot, props, seq);
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}
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/*
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public void putEntry(String pivot, String attrseq) {
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entries.put(pivot, attrseq);
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}
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*/
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public void putEntry(Entry entry) {
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if (shortmem())
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entries.put(entry.pivot, entry.toString());
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else
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entries.put(entry.pivot, entry);
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}
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public void putEntrySmall(Entry entry) {
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entries.put(entry.pivot, entry.toString());
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}
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public Entry getEntry(String pivot) {
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Object e = entries.get(pivot);
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if (e == null) return null;
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if (e instanceof String) return new Entry(pivot, (String) e, false);
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if (e instanceof Entry) return (Entry) e;
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return null;
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}
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public Entry removeEntry(String pivot) {
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Object e = entries.remove(pivot);
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if (e == null) return null;
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if (e instanceof String) return new Entry(pivot, (String) e, false);
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if (e instanceof Entry) return (Entry) e;
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return null;
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}
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public class Structure {
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protected String pivot_name = null;
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protected int pivot_len = -1;
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protected String[] prop_names = null;
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protected int[] prop_len = null, prop_pos = null;
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protected String[] seq_names = null;
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protected int[] seq_len = null, seq_pos = null;
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// example:
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//# Structure=<pivot-12>,'=',<UDate-3>,<VDate-3>,<LCount-2>,<GCount-2>,<ICount-2>,<DCount-2>,<TLength-3>,<WACount-3>,<WUCount-3>,<Flags-1>,'|',*<Anchor-12>
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public Structure(String structure) {
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// parse a structure string
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// parse pivot definition:
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int p = structure.indexOf(",'='");
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if (p < 0) return;
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String pivot = structure.substring(0, p);
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structure = structure.substring(p + 5);
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Object[] a = atom(pivot);
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if (a == null) return;
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pivot_name = (String) a[0];
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pivot_len = ((Integer) a[1]).intValue();
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// parse property part definition:
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p = structure.indexOf(",'|'");
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if (p < 0) return;
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ArrayList l = new ArrayList();
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String attr = structure.substring(0, p);
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String seqs = structure.substring(p + 5);
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StringTokenizer st = new StringTokenizer(attr, ",");
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while (st.hasMoreTokens()) {
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a = atom(st.nextToken());
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if (a == null) break;
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l.add(a);
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}
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prop_names = new String[l.size()];
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prop_len = new int[l.size()];
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prop_pos = new int[l.size()];
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p = 0;
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for (int i = 0; i < l.size(); i++) {
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a = (Object[]) l.get(i);
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prop_names[i] = (String) a[0];
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prop_len[i] = ((Integer) a[1]).intValue();
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prop_pos[i] = p;
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p += prop_len[i];
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}
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// parse sequence definition:
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if (seqs.startsWith("*")) seqs = seqs.substring(1);
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l = new ArrayList();
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st = new StringTokenizer(seqs, ",");
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while (st.hasMoreTokens()) {
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a = atom(st.nextToken());
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if (a == null) break;
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l.add(a);
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}
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seq_names = new String[l.size()];
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seq_len = new int[l.size()];
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seq_pos = new int[l.size()];
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p = 0;
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for (int i = 0; i < l.size(); i++) {
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a = (Object[]) l.get(i);
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seq_names[i] = (String) a[0];
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seq_len[i] = ((Integer) a[1]).intValue();
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seq_pos[i] = p;
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p += seq_len[i];
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}
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}
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private Object[] atom(String a) {
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if (a.startsWith("<")) {
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a = a.substring(1);
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} else return null;
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if (a.endsWith(">")) {
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a = a.substring(0, a.length() - 1);
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} else return null;
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int p = a.indexOf('-');
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if (p < 0) return null;
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String atomname = a.substring(0, p);
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try {
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int x = Integer.parseInt(a.substring(p + 1));
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return new Object[]{atomname, new Integer(x)};
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} catch (NumberFormatException e) {
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return null;
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}
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}
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public String toString() {
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StringBuffer sb = new StringBuffer(100);
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sb.append('<'); sb.append(pivot_name); sb.append('-'); sb.append(Integer.toString(pivot_len)); sb.append(">,'=',");
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if (prop_names.length > 0) {
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for (int i = 0; i < prop_names.length; i++) {
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sb.append('<'); sb.append(prop_names[i]); sb.append('-'); sb.append(Integer.toString(prop_len[i])); sb.append(">,");
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}
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}
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sb.append("'|'");
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if (seq_names.length > 0) {
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for (int i = 0; i < seq_names.length; i++) {
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sb.append(",<"); sb.append(seq_names[i]); sb.append('-'); sb.append(Integer.toString(seq_len[i])); sb.append('>');
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}
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}
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return sb.toString();
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}
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}
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public class Entry {
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String pivot;
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HashMap attrs;
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Map seq;
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public Entry(String pivot, HashMap attrs, Map seq) {
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this.pivot = pivot;
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this.attrs = attrs;
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this.seq = seq;
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}
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public Entry(String pivot, String attrseq, boolean tree) {
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this.pivot = pivot;
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attrs = new HashMap();
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seq = (tree) ? (Map) new TreeMap() : (Map) new HashMap();
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for (int i = 0; i < structure.prop_names.length; i++) {
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attrs.put(structure.prop_names[i], new Long(serverCodings.enhancedCoder.decodeBase64Long(attrseq.substring(structure.prop_pos[i], structure.prop_pos[i] + structure.prop_len[i]))));
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}
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int p = attrseq.indexOf('|') + 1;
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long[] seqattrs = new long[structure.seq_names.length - 1];
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String seqname;
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while (p + structure.seq_len[0] <= attrseq.length()) {
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seqname = attrseq.substring(p, p + structure.seq_len[0]);
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p += structure.seq_len[0];
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for (int i = 1; i < structure.seq_names.length; i++) {
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seqattrs[i - 1] = serverCodings.enhancedCoder.decodeBase64Long(attrseq.substring(p, p + structure.seq_len[i]));
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p += structure.seq_len[i];
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}
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seq.put(seqname, seqattrs);
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}
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}
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public HashMap getAttrs() {
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return attrs;
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}
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public long getAttr(String key, long dflt) {
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Long i = (Long) attrs.get(key);
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if (i == null) return dflt;
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return i.longValue();
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}
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public void setAttr(String key, long attr) {
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attrs.put(key, new Long(attr));
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}
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public Map getSeq() {
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return seq;
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}
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public void setSeq(Map seq) {
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this.seq = seq;
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}
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public void addSeq(String s, long[] seqattrs) {
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this.seq.put(s, seqattrs);
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}
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public String toString() {
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// creates only the attribute field and the sequence, not the pivot
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StringBuffer sb = new StringBuffer(100 + structure.seq_len[0] * seq.size());
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Long val;
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for (int i = 0; i < structure.prop_names.length; i++) {
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val = (Long) attrs.get(structure.prop_names[i]);
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sb.append(serverCodings.enhancedCoder.encodeBase64LongSmart((val == null) ? 0 : val.longValue(), structure.prop_len[i]));
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}
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sb.append('|');
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Iterator q = seq.entrySet().iterator();
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Map.Entry entry;
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long[] seqattrs;
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while (q.hasNext()) {
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entry = (Map.Entry) q.next();
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sb.append((String) entry.getKey());
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seqattrs = (long[]) entry.getValue();
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for (int i = 1; i < structure.seq_names.length; i++) {
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sb.append(serverCodings.enhancedCoder.encodeBase64Long(seqattrs[i - 1], structure.seq_len[i]));
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}
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}
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return sb.toString();
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}
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}
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private static final Runtime runtime = Runtime.getRuntime();
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private static final long cc = 0;
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private static boolean shortmemstate = false;
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private static boolean shortmem() {
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if ((cc % 300) == 0) {
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shortmemstate = (runtime.freeMemory() < 20000000L);
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}
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return shortmemstate;
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}
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public static void transcode(File from_file, File to_file) throws IOException {
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kelondroAttrSeq crp = new kelondroAttrSeq(from_file, true);
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//crp.toFile(new File(args[1]));
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kelondroAttrSeq cro = new kelondroAttrSeq(crp.name + "/Transcoded from " + crp.file.getName(), crp.structure.toString(), true);
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Iterator i = crp.entries.keySet().iterator();
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String key;
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kelondroAttrSeq.Entry entry;
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while (i.hasNext()) {
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key = (String) i.next();
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entry = crp.getEntry(key);
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cro.putEntry(entry);
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}
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cro.toFile(to_file);
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}
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public static void main(String[] args) {
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// java -classpath source de.anomic.kelondro.kelondroPropFile -transcode DATA/RANKING/GLOBAL/CRG-test-unsorted-original.cr DATA/RANKING/GLOBAL/CRG-test-generated.cr
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try {
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if ((args.length == 3) && (args[0].equals("-transcode"))) {
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transcode(new File(args[1]), new File(args[2]));
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}
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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}
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