package erminer.algo;
/* Copyright (c) 2008-2013 Philippe Fournier-Viger
*
* This file is part of the SPMF DATA MINING SOFTWARE
* (http://www.philippe-fournier-viger.com/spmf).
*
* SPMF 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 3 of the License, or (at your option) any later
* version.
*
* SPMF 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
* SPMF. If not, see <http://www.gnu.org/licenses/>.
*/
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* Implementation of a sequence database, where each sequence is implemented
* as a list of integers and should have a unique id.
*
* @see Sequence
* @author Philipe-Fournier-Viger
*/
public class SequenceDatabase {
// variable that contains the sequences of this database
private final List<Sequence> sequences = new ArrayList<Sequence>();
/**
* Method to load a sequence database from a text file in SPMF format.
* @param path the input file path.
* @throws IOException exception if error while reading the file.
*/
public void loadFile(String path) throws IOException {
String thisLine; // variable to read each line.
BufferedReader myInput = null;
try {
FileInputStream fin = new FileInputStream(new File(path));
myInput = new BufferedReader(new InputStreamReader(fin));
// for each line until the end of the file
int i=0;
while ((thisLine = myInput.readLine()) != null) {
// if the line is not a comment, is not empty or is not other
// kind of metadata
if (thisLine.isEmpty() == false &&
thisLine.charAt(0) != '#' && thisLine.charAt(0) != '%'
&& thisLine.charAt(0) != '@') {
// split this line according to spaces and process the line
addSequence(thisLine.split(" "));
}
}
} catch (Exception e) {
e.printStackTrace();
} finally {
if (myInput != null) {
myInput.close();
}
}
}
/**
* Method to process a line from the input file
* @param tokens A list of tokens from the line (which were separated by spaces in the original file).
*/
public void addSequence(String[] tokens) {
// create a new Sequence to store the sequence
Sequence sequence = new Sequence(sequences.size());
// create a list of strings for the first itemset.
List<Integer> itemset = new ArrayList<Integer>();
// for each token in this line
for (String token : tokens) {
// if the token start with "<", it indicates a timestamp.
// We just ignore it because algorithms that use this class
// don't need it.
if (token.codePointAt(0) == '<') {
// we ignore
}
// if the token is -1, it means that we reached the end of an itemset.
else if (token.equals("-1")) {
// add the current itemset to the sequence
sequence.addItemset(itemset);
// create a new itemset
itemset = new ArrayList<Integer>();
}
// if the token is -2, it means that we reached the end of
// the sequence.
else if (token.equals("-2")) {
// we add it to the list of sequences
sequences.add(sequence);
} else {
// otherwise it is an item.
// we parse it as an integer and add it to
// the current itemset.
itemset.add(Integer.parseInt(token));
}
}
}
/**
* Method to add a sequence to this sequence database
* @param sequence A sequence of type "Sequence".
*/
public void addSequence(Sequence sequence) {
sequences.add(sequence);
}
/**
* Print this sequence database to System.out.
*/
public void print() {
System.out.println("============ SEQUENCE DATABASE ==========");
for (Sequence sequence : sequences) { // pour chaque objet
System.out.print(sequence.getId() + ": ");
sequence.print();
System.out.println("");
}
}
/**
* Print statistics about this database.
*/
public void printDatabaseStats() {
System.out.println("============ STATS ==========");
System.out.println("Number of sequences : " + sequences.size());
// Calculate the average size of sequences in this database
long size = 0;
for(Sequence sequence : sequences){
size += sequence.size();
}
double meansize = ((float)size) / ((float)sequences.size());
System.out.println("mean size" + meansize);
}
/**
* Return a string representation of this sequence database.
*/
public String toString() {
StringBuilder r = new StringBuilder();
// for each sequence
for (Sequence sequence : sequences) {
r.append(sequence.getId());
r.append(": ");
r.append(sequence.toString());
r.append('\n');
}
return r.toString();
}
/**
* Get the sequence count in this database.
* @return the sequence count.
*/
public int size() {
return sequences.size();
}
/**
* Get the sequences from this sequence database.
* @return A list of sequences (Sequence).
*/
public List<Sequence> getSequences() {
return sequences;
}
/**
* Get the list of sequence IDs for this database.
* @return A set containing the sequence IDs of sequence in this
* database.
*/
public Set<Integer> getSequenceIDs() {
// create a set
Set<Integer> set = new HashSet<Integer>();
// for each sequence
for (Sequence sequence : getSequences()) {
set.add(sequence.getId()); // add the id to the set.
}
return set; // return the set.
}
// public void loadFileKosarakFormat(String filepath, int nblinetoread)
// throws IOException {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(filepath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// int i = 0;
// while ((thisLine = myInput.readLine()) != null) {
// // ajoute une s�quence
// String[] split = thisLine.split(" ");
// i++;
// if (nblinetoread == i) {
// break;
// }
// Sequence sequence = new Sequence(sequences.size());
// for (String value : split) {
// List<Integer> itemset = new ArrayList<Integer>();
// itemset.add(Integer.parseInt(value));
// sequence.addItemset(itemset);
// }
// sequences.add(sequence);
//
// }
// } catch (Exception e) {
// e.printStackTrace();
// } finally {
// if (myInput != null) {
// myInput.close();
// }
// }
// }
//
//
// public void loadFileKosarakFormatV2(String filepath, int nblinetoread)
// throws IOException {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(filepath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// int i = 0;
// while ((thisLine = myInput.readLine()) != null) {
// // ajoute une s�quence
// String[] split = thisLine.split(" ");
// i++;
//// if (nblinetoread == i) {
//// break;
//// }
// if(split.length < 25){
// continue;
// }
// Sequence sequence = new Sequence(sequences.size());
// int count=0;
// List<Integer> itemset = new ArrayList<Integer>();
// for (String value : split) {
// itemset.add(Integer.parseInt(value));
// count++;
// if(count == 3){
// sequence.addItemset(itemset);
// itemset = new ArrayList<Integer>();
// count =0;
// }
// }
// if(sequence.size() >10 ){
// sequences.add(sequence);
// }
//
// }
// } catch (Exception e) {
// e.printStackTrace();
// } finally {
// if (myInput != null) {
// myInput.close();
// }
// }
// }
//
// public void loadFileWebViewFOrmat(String filepath, int nbLine) {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(filepath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// int realID = 0;
// int lastId = 0;
// Sequence sequence = null;
// while ((thisLine = myInput.readLine()) != null) {
// // ajoute une s�quence
// String[] split = thisLine.split(" ");
// int id = Integer.parseInt(split[0]);
// int val = Integer.parseInt(split[1]);
//
// if(lastId != id){
// if(lastId!=0 ){ //&& sequence.size() >=2
// sequences.add(sequence);
// realID++;
// }
// sequence = new Sequence(realID);
// lastId = id;
// }
// List<Integer> itemset = new ArrayList<Integer>();
// itemset.add(val);
// sequence.addItemset(itemset);
// }
// myInput.close();
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
//
// public void loadFileSignLanguage(String fileToPath, int i) {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(fileToPath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// String oldUtterance = "-1";
// Sequence sequence = null;
// int seqid =0;
// while ((thisLine = myInput.readLine()) != null) {
// if(thisLine.length() >= 1 && thisLine.charAt(0) != '#'){
// String []tokens = thisLine.split(" ");
// String currentUtterance = tokens[0];
// if(!currentUtterance.equals(oldUtterance)){
// if(sequence != null){
// sequences.add(sequence);
// }
// sequence = new Sequence(seqid++);
// oldUtterance = currentUtterance;
// }
// for(int j=1; j< tokens.length; j++){
// int character = Integer.parseInt(tokens[j]);
// if(character == -11 || character == -12){
// continue;
// }
// List<Integer> itemset = new ArrayList<Integer>();
// itemset.add(character);
// sequence.addItemset(itemset);
// }
// }
// }
// sequences.add(sequence);
// System.out.println(sequence.toString());
// myInput.close();
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
//
// public void loadFileWebViewFOrmatV2(String filepath, int nbLine) {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(filepath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// int realID = 0;
// int lastId = 0;
// Sequence sequence = null;
// while ((thisLine = myInput.readLine()) != null) {
// // ajoute une s�quence
// String[] split = thisLine.split(" ");
// int id = Integer.parseInt(split[0]);
// int val = Integer.parseInt(split[1]);
//
// if(lastId != id){
// if(lastId!=0 && sequence.size() >=5){
// sequences.add(sequence);
// realID++;
// }
// sequence = new Sequence(realID);
// lastId = id;
// }
// List<Integer> itemset = new ArrayList<Integer>();
// itemset.add(val);
// sequence.addItemset(itemset);
// }
// myInput.close();
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
//
// public void loadSnakeDataset(String filepath, int nbLine) {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(filepath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// int realID = 0;
// while ((thisLine = myInput.readLine()) != null) {
// if(thisLine.length() >= 50){
// Sequence sequence = new Sequence(realID++);
// for(int i=0; i< thisLine.length(); i++){
// List<Integer> itemset = new ArrayList<Integer>();
// int character = thisLine.toCharArray()[i] - 65;
// System.out.println(thisLine.toCharArray()[i] + " " + character);
// itemset.add(character);
// sequence.addItemset(itemset);
// }
// sequences.add(sequence);
// }
// }
// myInput.close();
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
//
//
// public void loadFileMSNBCFormat(String filepath, int nblinetoread)
// throws IOException {
// String thisLine;
// BufferedReader myInput = null;
// try {
// FileInputStream fin = new FileInputStream(new File(filepath));
// myInput = new BufferedReader(new InputStreamReader(fin));
// int i = 0;
// while ((thisLine = myInput.readLine()) != null) {
// // ajoute une s�quence
// String[] split = thisLine.split(" ");
// i++;
// if (nblinetoread == i) {
// break;
// }
// Sequence sequence = new Sequence(sequences.size());
// for (String value : split) {
// Itemset itemset = new Itemset();
// itemset.addItem(Integer.parseInt(value));
// sequence.addItemset(itemset);
// }
// if(sequence.size() > 4){
// sequences.add(sequence);
// }
//
// }
// } catch (Exception e) {
// e.printStackTrace();
// } finally {
// if (myInput != null) {
// myInput.close();
// }
// }
// }
}