// kelondroAttrSeq.java
// -----------------------
// part of YaCy
// (C) by Michael Peter Christen; mc@anomic.de
// first published on http://www.anomic.de
// Frankfurt, Germany, 2005
// Created 15.11.2005
//
// $LastChangedDate: 2005-10-22 15:28:04 +0200 (Sat, 22 Oct 2005) $
// $LastChangedRevision: 968 $
// $LastChangedBy: theli $
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// This program 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 General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// Using this software in any meaning (reading, learning, copying, compiling,
// running) means that you agree that the Author(s) is (are) not responsible
// for cost, loss of data or any harm that may be caused directly or indirectly
// by usage of this softare or this documentation. The usage of this software
// is on your own risk. The installation and usage (starting/running) of this
// software may allow other people or application to access your computer and
// any attached devices and is highly dependent on the configuration of the
// software which must be done by the user of the software; the author(s) is
// (are) also not responsible for proper configuration and usage of the
// software, even if provoked by documentation provided together with
// the software.
//
// Any changes to this file according to the GPL as documented in the file
// gpl.txt aside this file in the shipment you received can be done to the
// lines that follows this copyright notice here, but changes must not be
// done inside the copyright notive above. A re-distribution must contain
// the intact and unchanged copyright notice.
// Contributions and changes to the program code must be marked as such.
package de.anomic.kelondro;
import java.io.File;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.HashSet;
import java.util.Map;
import java.util.HashMap;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.Iterator;
import java.util.ArrayList;
import java.util.StringTokenizer;
import java.util.zip.GZIPInputStream;
import java.util.logging.Logger;
import de.anomic.server.serverFileUtils;
import de.anomic.server.serverMemory;
public class kelondroAttrSeq {
// class objects
private File file;
private Map entries;
protected Structure structure;
private String name;
private long created;
// optional logger
protected Logger theLogger = null;
public kelondroAttrSeq(File file, boolean tree) throws IOException {
this.file = file;
this.structure = null;
this.created = -1;
this.name = "";
this.entries = (tree) ? (Map) new TreeMap() : (Map) new HashMap();
readAttrFile(file);
}
public kelondroAttrSeq(String name, String struct, boolean tree) {
this.file = null;
this.structure = new Structure(struct);
this.created = System.currentTimeMillis();
this.name = name;
this.entries = (tree) ? (Map) new TreeMap() : (Map) new HashMap();
}
public void setLogger(Logger newLogger) {
this.theLogger = newLogger;
}
public void logInfo(String message) {
if (this.theLogger == null)
System.err.println("ATTRSEQ INFO for file " + this.file + ": " + message);
else
this.theLogger.info("ATTRSEQ INFO for file " + this.file + ": " + message);
}
public void logWarning(String message) {
if (this.theLogger == null)
System.err.println("ATTRSEQ WARNING for file " + this.file + ": " + message);
else
this.theLogger.warning("ATTRSEQ WARNING for file " + this.file + ": " + message);
}
private void readAttrFile(File loadfile) throws IOException {
BufferedReader br = null;
int p;
if (loadfile.toString().endsWith(".gz")) {
br = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(loadfile))));
} else {
br = new BufferedReader(new InputStreamReader(new FileInputStream(loadfile)));
}
String line, key, oldvalue, newvalue;
while ((line = br.readLine()) != null) {
line = line.trim();
if (line.length() == 0) continue;
if (line.startsWith("#")) {
if (line.startsWith("# Structure=")) {
structure = new Structure(line.substring(12));
}
if (line.startsWith("# Name=")) {
name = line.substring(7);
}
if (line.startsWith("# Created=")) {
created = Long.parseLong(line.substring(10));
}
continue;
}
if ((p = line.indexOf('=')) > 0) {
key = line.substring(0, p).trim();
newvalue = line.substring(p + 1).trim();
oldvalue = (String) entries.get(key);
if (oldvalue != null) {
if (newvalue.equals(oldvalue)) {
//logWarning("key " + key + ": double occurrence. values are equal. second appearance is ignored");
} else {
if (newvalue.length() < oldvalue.length()) {
if (oldvalue.substring(0, newvalue.length()).equals(newvalue)) {
logWarning("key " + key + ": double occurrence. new value is subset of old value. second appearance is ignored");
} else {
logWarning("key " + key + ": double occurrence. new value is shorter than old value, but not a subsequence. old = " + oldvalue + ", new = " + newvalue);
}
} else if (newvalue.length() > oldvalue.length()) {
if (newvalue.substring(0, oldvalue.length()).equals(oldvalue)) {
logWarning("key " + key + ": double occurrence. old value is subset of new value. first appearance is ignored");
} else {
logWarning("key " + key + ": double occurrence. old value is shorter than new value, but not a subsequence. old = " + oldvalue + ", new = " + newvalue);
}
entries.put(key, newvalue);
} else {
logWarning("key " + key + ": double occurrence. old and new value have equal length but are not equal. old = " + oldvalue + ", new = " + newvalue);
//entries.put(key, newvalue);
}
}
} else {
entries.put(key, newvalue);
}
}
}
br.close();
if (structure == null) throw new IOException("file contains no structure tag");
if (name == null) throw new IOException("file contains no name tag");
if (created == -1) throw new IOException("file contains no created tag");
}
public int size() {
return entries.size();
}
public long created() {
return this.created;
}
public void toFile(File out) throws IOException {
// generate header
StringBuffer sb = new StringBuffer(2000);
sb.append("# Name=" + this.name); sb.append((char) 13); sb.append((char) 10);
sb.append("# Created=" + this.created); sb.append((char) 13); sb.append((char) 10);
sb.append("# Structure=" + this.structure.toString()); sb.append((char) 13); sb.append((char) 10);
sb.append("# ---"); sb.append((char) 13); sb.append((char) 10);
Iterator i = entries.entrySet().iterator();
Map.Entry entry;
String k;
Object v;
while (i.hasNext()) {
entry = (Map.Entry) i.next();
k = (String) entry.getKey();
v = entry.getValue();
sb.append(k); sb.append('=');
if (v instanceof String) sb.append((String) v);
if (v instanceof Entry) sb.append(((Entry) v).toString());
sb.append((char) 13); sb.append((char) 10);
}
if (out.toString().endsWith(".gz")) {
serverFileUtils.writeAndGZip(sb.toString().getBytes(), out);
} else {
serverFileUtils.write(sb.toString().getBytes(), out);
}
}
public Iterator keys() {
return entries.keySet().iterator();
}
public Entry newEntry(String pivot, boolean tree) {
return new Entry(pivot, new HashMap(), (tree) ? (Set) new TreeSet() : (Set) new HashSet());
}
public Entry newEntry(String pivot, HashMap props, Set seq) {
return new Entry(pivot, props, seq);
}
/*
public void putEntry(String pivot, String attrseq) {
entries.put(pivot, attrseq);
}
*/
public void putEntry(Entry entry) {
if (shortmem())
entries.put(entry.pivot, entry.toString());
else
entries.put(entry.pivot, entry);
}
public void putEntrySmall(Entry entry) {
entries.put(entry.pivot, entry.toString());
}
public Entry getEntry(String pivot) {
Object e = entries.get(pivot);
if (e == null) return null;
if (e instanceof String) return new Entry(pivot, (String) e, false);
if (e instanceof Entry) return (Entry) e;
return null;
}
public Entry removeEntry(String pivot) {
Object e = entries.remove(pivot);
if (e == null) return null;
if (e instanceof String) return new Entry(pivot, (String) e, false);
if (e instanceof Entry) return (Entry) e;
return null;
}
public class Structure {
protected String pivot_name = null;
protected int pivot_len = -1;
protected String[] prop_names = null;
protected int[] prop_len = null, prop_pos = null;
protected String[] seq_names = null;
protected int[] seq_len = null, seq_pos = null;
protected kelondroRow seqrow;
// example:
//# 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>
public Structure(String structure) {
// parse a structure string
// parse pivot definition:
int p = structure.indexOf(",'='");
if (p < 0) return;
String pivot = structure.substring(0, p);
structure = structure.substring(p + 5);
kelondroColumn a = new kelondroColumn(pivot);
pivot_name = a.nickname();
pivot_len = a.cellwidth();
// parse property part definition:
p = structure.indexOf(",'|'");
if (p < 0) return;
ArrayList l = new ArrayList();
String attr = structure.substring(0, p);
String seqs = structure.substring(p + 5);
StringTokenizer st = new StringTokenizer(attr, ",");
while (st.hasMoreTokens()) {
a = new kelondroColumn(st.nextToken());
if (a == null) break;
l.add(a);
}
prop_names = new String[l.size()];
prop_len = new int[l.size()];
prop_pos = new int[l.size()];
p = 0;
for (int i = 0; i < l.size(); i++) {
a = (kelondroColumn) l.get(i);
prop_names[i] = a.nickname();
prop_len[i] = a.cellwidth();
prop_pos[i] = p;
p += prop_len[i];
}
// parse sequence definition:
if (seqs.startsWith("*")) seqs = seqs.substring(1);
l = new ArrayList();
st = new StringTokenizer(seqs, ",");
while (st.hasMoreTokens()) {
a = new kelondroColumn(st.nextToken());
if (a == null) break;
l.add(a);
}
seq_names = new String[l.size()];
seq_len = new int[l.size()];
seq_pos = new int[l.size()];
p = 0;
for (int i = 0; i < l.size(); i++) {
a = (kelondroColumn) l.get(i);
seq_names[i] = a.nickname();
seq_len[i] = a.cellwidth();
seq_pos[i] = p;
p += seq_len[i];
}
// generate rowdef for seq row definition
StringBuffer rowdef = new StringBuffer();
rowdef.append("byte[] ");
rowdef.append(seq_names[0]);
rowdef.append('-');
rowdef.append(seq_len[0]);
for (int i = 1; i < seq_names.length; i++) {
rowdef.append(", byte[] ");
rowdef.append(seq_names[i]);
rowdef.append('-');
rowdef.append(seq_len[i]);
}
seqrow = new kelondroRow(new String(rowdef));
}
public String toString() {
StringBuffer sb = new StringBuffer(100);
sb.append('<'); sb.append(pivot_name); sb.append('-'); sb.append(Integer.toString(pivot_len)); sb.append(">,'=',");
if (prop_names.length > 0) {
for (int i = 0; i < prop_names.length; i++) {
sb.append('<'); sb.append(prop_names[i]); sb.append('-'); sb.append(Integer.toString(prop_len[i])); sb.append(">,");
}
}
sb.append("'|'");
if (seq_names.length > 0) {
for (int i = 0; i < seq_names.length; i++) {
sb.append(",<"); sb.append(seq_names[i]); sb.append('-'); sb.append(Integer.toString(seq_len[i])); sb.append('>');
}
}
return sb.toString();
}
}
public class Entry {
String pivot;
HashMap attrs;
Set seq;
public Entry(String pivot, HashMap attrs, Set seq) {
this.pivot = pivot;
this.attrs = attrs;
this.seq = seq;
}
public Entry(String pivot, String attrseq, boolean tree) {
this.pivot = pivot;
attrs = new HashMap();
seq = (tree) ? (Set) new TreeSet() : (Set) new HashSet();
for (int i = 0; i < structure.prop_names.length; i++) {
attrs.put(structure.prop_names[i], new Long(kelondroBase64Order.enhancedCoder.decodeLong(attrseq.substring(structure.prop_pos[i], structure.prop_pos[i] + structure.prop_len[i]))));
}
int p = attrseq.indexOf('|') + 1;
//long[] seqattrs = new long[structure.seq_names.length - 1];
String seqname;
while (p + structure.seq_len[0] <= attrseq.length()) {
seqname = attrseq.substring(p, p + structure.seq_len[0]);
p += structure.seq_len[0];
for (int i = 1; i < structure.seq_names.length; i++) {
//seqattrs[i - 1] = kelondroBase64Order.enhancedCoder.decodeLong(attrseq.substring(p, p + structure.seq_len[i]));
p += structure.seq_len[i];
}
seq.add(seqname/*, seqattrs*/);
}
}
public HashMap getAttrs() {
return attrs;
}
public long getAttr(String key, long dflt) {
Long i = (Long) attrs.get(key);
if (i == null) return dflt;
return i.longValue();
}
public void setAttr(String key, long attr) {
attrs.put(key, new Long(attr));
}
public Set getSeqSet() {
return seq;
}
public kelondroRowCollection getSeqCollection() {
kelondroRowCollection collection = new kelondroRowCollection(structure.seqrow, seq.size());
Iterator i = seq.iterator();
while (i.hasNext()) {
collection.add(structure.seqrow.newEntry(((String) i.next()).getBytes()));
}
return collection;
}
public void setSeq(Set seq) {
this.seq = seq;
}
public void addSeq(String s/*, long[] seqattrs*/) {
this.seq.add(s/*, seqattrs*/);
}
public String toString() {
// creates only the attribute field and the sequence, not the pivot
StringBuffer sb = new StringBuffer(100 + structure.seq_len[0] * seq.size());
Long val;
for (int i = 0; i < structure.prop_names.length; i++) {
val = (Long) attrs.get(structure.prop_names[i]);
sb.append(kelondroBase64Order.enhancedCoder.encodeLongSmart((val == null) ? 0 : val.longValue(), structure.prop_len[i]));
}
sb.append('|');
Iterator q = seq.iterator();
//long[] seqattrs;
while (q.hasNext()) {
sb.append((String) q.next());
//seqattrs = (long[]) entry.getValue();
/*
for (int i = 1; i < structure.seq_names.length; i++) {
sb.append(kelondroBase64Order.enhancedCoder.encodeLong(seqattrs[i - 1], structure.seq_len[i]));
}
*/
}
return sb.toString();
}
}
private static final long cc = 0;
private static boolean shortmemstate = false;
private static boolean shortmem() {
if ((cc % 300) == 0) {
shortmemstate = (serverMemory.available() < 20000000L);
}
return shortmemstate;
}
public static void transcode(File from_file, File to_file) throws IOException {
kelondroAttrSeq crp = new kelondroAttrSeq(from_file, true);
//crp.toFile(new File(args[1]));
kelondroAttrSeq cro = new kelondroAttrSeq(crp.name + "/Transcoded from " + crp.file.getName(), crp.structure.toString(), true);
Iterator i = crp.entries.keySet().iterator();
String key;
kelondroAttrSeq.Entry entry;
while (i.hasNext()) {
key = (String) i.next();
entry = crp.getEntry(key);
cro.putEntry(entry);
}
cro.toFile(to_file);
}
public static void main(String[] args) {
// java -classpath source de.anomic.kelondro.kelondroPropFile -transcode DATA/RANKING/GLOBAL/CRG-test-unsorted-original.cr DATA/RANKING/GLOBAL/CRG-test-generated.cr
try {
if ((args.length == 3) && (args[0].equals("-transcode"))) {
transcode(new File(args[1]), new File(args[2]));
}
} catch (IOException e) {
e.printStackTrace();
}
}
}