Java Index Out of Bounds Exception - java

I'm getting an IndexOutOfBoundsException at the line that calls for my custom fonction:
motCars = remplaceTirets(motAlea, motCars, lettreDon);.
This function is supposed to turn one or more of the dashes into the letter if the given letter equals the letter in the word) and a line in the actual function where it says:
tempo += tirets.charAt(j);
The result is: _ _ _ _ _ _ _ (the amount of these dashes depends on the word chosen by the program, which works and then it asks to give a letter but when I give a letter I get:
Exception in thread 'main' java.lang.String IndexOutOfBoundsException. String Index out of range: 1.
It's partly in french because I live in Quebec. But I'm hoping that it doesn't matter because the french words just concern the strings and words, not the logic of java. I'm a beginner and overwhelmed with all the advice on all the forums on Java. Any specific advice will be welcome.
Thanks in advance for taking the time to have a look !
Anita
import java.util.Scanner;
class Tp {
public static void main( String[] args ) throws Exception {
Scanner clavier = new Scanner(System.in);
String motAlea = "";
String motCars = "";
char lettreDon = Character.UNASSIGNED;
String tempo = "";
String invite = "";
String tirets = "";
int l = 0;
int m = 0;
final String ANNONCE = "J'ai choisi un mot a deviner\n";
final String INSTRUCT = "Entrez une lettre a la fois. L'indice d'essais: 15.\n";
final String INVITE = "\tEntrez une lettre: ";
final String BRAVO = "BRAVO ! Le mot a deviner etait: ";
final String DESOLE = "DESOLE...Vous avez perdu...";
String[] vingtMots = { "WATTHEUREMETRE", "HELIOGRAPH", "GRENOUILLERE", "CONTRAROTATIF",
"CUISSARDE", "BRIGANTINE", "AVITAILLEUR", "ENTREDOUBLURE",
"GALLETAGE", "OEUILLERE", "CREMAILLERE", "HALTEROPHILIE",
"MARTINGALE", "EMPENNAGE", "ENCOCHAGE", "DECLENCHEUR",
"BIMETALLIQUE", "PIVOTEMENT", "DECLINAISON", "CROISILLON"
}; // tableau string
int indexAlea = 0;
indexAlea = (int)(Math.random() * 20) + 1;
motAlea = vingtMots[indexAlea];
for (l = 0; l < motAlea.length(); l++) {
tempo += "_";
motCars = tempo;
} // for
System.out.print(ANNONCE);
System.out.print(INSTRUCT);
l = 0;
do {
if (motCars.equals(motAlea)) {
System.out.print(BRAVO + motAlea + ", " + "devine en " + m +
" tentatives");
System.exit(0);
} // if
if (l == 15) {
System.out.print("\n" + DESOLE + "Le mot a devine etait: " +
motAlea + ". " + "Au revoir... ");
System.exit(0);
} // if
for (int i = 0; i < motAlea.length(); i++) {
System.out.print(motCars.charAt(i) + " ");
} // for
m = l + 1;
invite = "\t" + INVITE + m + "> :";
lettreDon = lecture(invite);
motCars = remplaceTirets(motAlea, motCars, lettreDon);
l++;
} // do
while (l < 16); {
System.out.print("\n" + DESOLE + "Le mot a devine etait: " + motAlea + ". "
+ "Au revoir... ");
} // while
} //main(...)
public static char lecture(String invite1){
Scanner clavier = new Scanner(System.in);
final String ERREUR = "La valeur entree est erronnee !\nReprenez-vous...";
final String VIDE = " ";
String retour = "";
do {
try {
System.out.print(invite1);
retour = clavier.nextLine().trim(); // Mise en forme;
for (int k = 0; k < retour.length(); k++) {
if(Character.isLetter(retour.charAt(k))) {
return retour.toUpperCase().charAt(0);
} // if
} // for
} // try
catch (Exception e) {
System.out.print(ERREUR);
}
}// do
while (!retour.equals(VIDE)); {
retour = "X";
return retour.charAt(0);
} // while
} // lecture(...)
public static String remplaceTirets(String motAlea1, String tirets,
char lettre) {
String retour;
String tempo = "";
for (int j = 0; j < motAlea1.length(); j++) {
String lettre1 = Character.toString(lettre);
if (motAlea1.charAt(j) != lettre1.charAt(0)) {
tempo += tirets.charAt(j);
} // if
else {
tempo += lettre1.charAt(0);
} // else
tirets = tempo;
} // for
return retour = tirets;
} //remplaceTirets(...)
}//Tp

The line
tirets = tempo;
should be out of the for loop.
change your code to
for (int j = 0; j < motAlea1.length(); j++) {
String lettre1 = Character.toString(lettre);
if (motAlea1.charAt(j) != lettre1.charAt(0)) {
tempo += tirets.charAt(j);
} // if
else {
tempo += lettre1.charAt(0);
} // else
//tirets = tempo; //REMOVE THIS LINE
} // for
tirets = tempo; //ADD THIS LINE

You are accessing a position in tirets based on the length of motAlea1. I expect that motAlea1.length() > tirets.length().
for (int j = 0; j < motAlea1.length(); j++) {
String lettre1 = Character.toString(lettre);
if (motAlea1.charAt(j) != lettre1.charAt(0)) {
tempo += tirets.charAt(j); //THIS COULD FAIL!!!
}else{
tempo += lettre1.charAt(0);
}
tirets = tempo;
}

In this loop:
for (int j = 0; j < motAlea1.length(); j++) {
String lettre1 = Character.toString(lettre);
if (motAlea1.charAt(j) != lettre1.charAt(0)) {
tempo += tirets.charAt(j);
} // if
else {
tempo += lettre1.charAt(0);
} // else
tirets = tempo;
} // for
String tirets is shorter than motAlea1 and so you're trying to retrieve a character beyond its end.

Related

how to save screen actions and motions on a text file for academic purpose?

I have the following code to show motion events on screen phone android :
private String MotionToString(MotionEvent ev){
String bank = " ";
String Wrap = "\n";
StringBuilder msg = new StringBuilder();
msg.append(MotionEvent.actionToString(ev.getAction())).append(bank);
save(msg.append(MotionEvent.actionToString(ev.getAction())).append(bank));
msg.append("ActionButton: "+ ev.getActionButton()).append(Wrap);
save(msg.append("ActionButton: "+ ev.getActionButton()).append(Wrap));
msg.append("Flags: 0x"+Integer.toHexString(ev.getFlags())).append(bank).append("EdgeFlags: 0x"+Integer.toHexString(ev.getEdgeFlags())).append(Wrap);
save(msg.append("Flags: 0x"+Integer.toHexString(ev.getFlags())).append(bank).append("EdgeFlags: 0x"+Integer.toHexString(ev.getEdgeFlags())).append(Wrap));
msg.append("EventTime: "+ev.getEventTime()).append(bank).append("DownTime: "+ev.getDownTime()).append(Wrap);
save(msg.append("EventTime: "+ev.getEventTime()).append(bank).append("DownTime: "+ev.getDownTime()).append(Wrap));
final int pointerCount = ev.getPointerCount();
for (int i = 0; i < pointerCount; i++) {
msg.append("PointerId[" + i + "]="+ev.getPointerId(i)).append(bank);
int x = (int)ev.getX(i);
int y = (int)ev.getY(i);
if ( x != 0f || y != 0f) {
msg.append("x[").append(i).append("]=").append(x).append(bank);
msg.append("y[").append(i).append("]=").append(y).append(bank);
}
msg.append("toolType[" + i + "]=" + ev.getToolType(i)).append(Wrap);
}
final int historySize = ev.getHistorySize();
msg.append("HistorySize: "+ historySize).append(Wrap);
for(int i = 0; i < historySize; i++){
msg.append("EventTime: "+ev.getHistoricalEventTime(i)).append(Wrap);
for(int j = 0;j< pointerCount;j++){
int x = (int)ev.getHistoricalX(j,i);
int y = (int)ev.getHistoricalY(j,i);
if ( x != 0f || y != 0f) {
msg.append("x[").append(j).append("]=").append(x).append(bank);
msg.append("y[").append(j).append("]=").append(y).append(Wrap);
}
}
}
return msg.toString();
}
the source code from : https://github.com/anlory/MotionEvent
I am trying to save all these Motion Event on a text file for a academic purpose , any thoughts how can I do it. thank you in advance

Problem with reading textfiles with scanner in Java and ArrayLists

I'm having a problem where I read a textfile named "songs.txt" with Scanner in a function called loadFiles() which every line is:
Music ID # Song Name # Release Date
And with this I create a Song object, and then store said object in a ArrayList. After reading the file, I clone this ArrayList so I can return a ArrayList with the songs read and clear the first ArrayList to prevent the cases where for exemple:
(PS: I use the ArrayLists as global variables)
songs.txt has this structure:
1oYYd2gnWZYrt89EBXdFiO#Message In A Bottle#1979
7zxc7dmd82nd92nskDInds#Sweet Child of Mine#1980
And the loadFiles() is called 2 times, the ArrayList would have a size of 4 instead of 2 as it should be. So that's why after songs.txt is read I copy the arrayList and then clear the first ArrayList that way the ArrayList that's returned only has the size of 2.
This is my code:
package pt.ulusofona.aed.deisiRockstar2021;
import java.io.IOException;
import java.util.Scanner;
import java.io.*;
import java.util.ArrayList;
public class Main {
public static ArrayList < Song > teste6 = new ArrayList < > ();
public static ArrayList < Song > getSongsArray = new ArrayList < > ();
public static ArrayList < Artista > testeSongArtists = new ArrayList < > ();
public static ParseInfo parseInfoSongsTxT = new ParseInfo(0, 0);
public static ParseInfo parseInfoSongsArtistsTxT = new ParseInfo(0, 0);
public static ParseInfo parseInfoSongsDetailsTxT = new ParseInfo(0, 0);
public static void main(String[] args) throws IOException {
ArrayList < Song > teste7 = new ArrayList < Song > ();
loadFiles();
loadFiles();
teste7 = getSongs();
ParseInfo teste8 = getParseInfo("songs.txt");
System.out.println("\n----------------------TESTE DO MAIN----------------------");
System.out.println(teste7.toString());
System.out.println(teste8.toString());
System.out.println(getSongsArray.size());
}
public static void loadFiles() throws IOException {
//Aqui lê-se o ficheiro songs.txt
System.out.println("----------------------LEITURA DO FICHEIRO songs.txt------------");
String nomeFicheiro = "songs.txt";
try {
File ficheiro = new File(nomeFicheiro);
FileInputStream fis = new FileInputStream(ficheiro);
Scanner leitorFicheiro = new Scanner(fis);
while (leitorFicheiro.hasNextLine()) {
String linha = leitorFicheiro.nextLine();
String dados[] = linha.split("#");
if (dados.length != 3) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[0].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[1].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[2].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
//Meter para ignorar a acabar com espaço
parseInfoSongsTxT.NUM_LINHAS_OK += 1;
String idTemaMusical = dados[0];
String nome = dados[1];
int anoLancamento = Integer.parseInt(dados[2]);
Song song = new Song(idTemaMusical, nome, null, anoLancamento, 0, false, 0, 0, 0, 0);
teste6.add(song);
}
leitorFicheiro.close();
getSongsArray = (ArrayList < Song > ) teste6.clone();
teste6.clear();
} catch (FileNotFoundException exception) {
String mensagem = "Erro: o ficheiro " + nomeFicheiro + " nao foi encontrado.";
System.out.println(mensagem);
}
System.out.println(teste6.toString());
System.out.println("Ok: " + parseInfoSongsTxT.NUM_LINHAS_OK + ", Ignored: " + parseInfoSongsTxT.NUM_LINHAS_IGNORED + "\n");
System.out.println("----------------------LEITURA DO FICHEIRO song_artists.txt------------");
//Aqui é lido o ficheiro song_artists.txt, mas falta ver se é preciso separar vários artistas com o mesmo ID para posições diferentes no ArrayList
String nomeFicheiro2 = "song_artists.txt";
try {
File song_artists = new File(nomeFicheiro2);
FileInputStream fis2 = new FileInputStream(song_artists);
Scanner leitorFicheiro2 = new Scanner(fis2);
while (leitorFicheiro2.hasNextLine()) {
String linha = leitorFicheiro2.nextLine();
String dados[] = linha.split("#");
if (dados.length != 2) {
parseInfoSongsArtistsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[0].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[1].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
parseInfoSongsArtistsTxT.NUM_LINHAS_OK += 1;
String idTemaMusical = dados[0];
String artista = dados[1];
Artista artista2 = new Artista(idTemaMusical, artista);
testeSongArtists.add(artista2);
}
leitorFicheiro2.close();
} catch (FileNotFoundException exception) {
String mensagem = "Erro: o ficheiro " + nomeFicheiro2 + " não foi encontrado.";
System.out.println(mensagem);
}
System.out.println(testeSongArtists.toString());
System.out.println("Ok: " + parseInfoSongsArtistsTxT.NUM_LINHAS_OK + ", Ignored: " + parseInfoSongsArtistsTxT.NUM_LINHAS_IGNORED + "\n");
System.out.println("----------------------LEITURA DO FICHEIRO song_details.txt------------");
//Aqui lê-se o ficheiro song_details.txt
boolean letra = false;
ArrayList < Song > testeSongDetails = new ArrayList < Song > ();
String nomeFicheiro3 = "song_details.txt";
try {
File song_details = new File(nomeFicheiro3);
FileInputStream fis3 = new FileInputStream(song_details);
Scanner leitorFicheiro3 = new Scanner(fis3);
while (leitorFicheiro3.hasNextLine()) {
String linha = leitorFicheiro3.nextLine();
String dados[] = linha.split("#");
if (dados.length != 7) {
parseInfoSongsDetailsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[0].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[1].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[3].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[4].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[5].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
if (Character.isWhitespace(dados[6].charAt(0))) {
parseInfoSongsTxT.NUM_LINHAS_IGNORED += 1;
continue;
}
parseInfoSongsDetailsTxT.NUM_LINHAS_OK += 1;
String idTemaMusical = dados[0];
//System.out.println(idTemaMusical);
int duracao = Integer.parseInt(dados[1]);
//System.out.println(duracao);
int letraExplicita = Integer.parseInt(dados[2]);
//System.out.println(letraExplicita);
if (letraExplicita == 0) {
letra = false;
} else {
letra = true;
}
//System.out.println(letra);
int populariedade = Integer.parseInt(dados[3]);
//System.out.println(populariedade);
double dancabilidade = Double.parseDouble(dados[4]);
//System.out.println(dancabilidade);
double vivacidade = Double.parseDouble(dados[5]);
//System.out.println(vivacidade);
double volumeMedio = Double.parseDouble(dados[6]);
//System.out.println(volumeMedio);
Song song = new Song(idTemaMusical, null, null, 0, duracao, letra, populariedade, dancabilidade, vivacidade, volumeMedio);
testeSongDetails.add(song);
}
leitorFicheiro3.close();
} catch (FileNotFoundException exception) {
String mensagem = "Erro: o ficheiro " + nomeFicheiro3 + " não foi encontrado.";
System.out.println(mensagem);
}
System.out.println("Ok: " + parseInfoSongsDetailsTxT.NUM_LINHAS_OK + ", Ignored: " + parseInfoSongsDetailsTxT.NUM_LINHAS_IGNORED);
}
public static ArrayList < Song > getSongs() {
return getSongsArray;
}
public static ParseInfo getParseInfo(String fileName) {
if (fileName == "songs.txt") {
return parseInfoSongsTxT;
}
if (fileName == "song_artists.txt") {
return parseInfoSongsArtistsTxT;
}
if (fileName == "song_details.txt") {
return parseInfoSongsDetailsTxT;
}
return null;
}
}
The problem is that when I made a test to check the function where the ArrayList is returned to see the size of the ArrayList it always comes as 0.
I think it's because only the function the returns the ArrayList is tested so loadFiles() isn't executed so the ArrayListo never gets cloned and that makes the ArrayList that is returned stay the same.
I thought about calling loadFiles() inside getSongs() and that way I would guarantee that the ArrayList is cloned but that would make getSongs use "throws IOException" and since I have to respect the school's project guide and getSongs doesn't include "throws IOException" i can't put it there.
But the more I think about it, that doesn't even make sense because how can they test it with a file of their own and loadFiles() isn't executed?
I'm out of ideas how to solve this problem, any help is welcome thank you.

Properties file and array

Good afternoon, I have a problem. When reading a property file, and passing it to an array, it looks like the array is repeated until you finish reading the document, as shown in the image
I'm supposed to read the properties from a txt file that contains them and pass the artist's name to an array of size 10.
Here the methods used by the program
/**
* Carga la información inicial del karaoke.
*/
private void cargarKaraoke() {
try {
Properties datos = new Properties();
FileInputStream in = new FileInputStream(RUTA_ARCHIVO);
datos.load(in);
in.close();
int numArtistas = Integer.parseInt(datos.getProperty("total.artistas"));
for(int i = 1; i <= numArtistas; i++) {
String nombre = datos.getProperty("artista" + i + ".nombre");
String categoria = datos.getProperty("artista" + i + ".categoria");
String imagen = datos.getProperty("artista" + i + ".imagen");
karaoke.agregarArtista(nombre, categoria, imagen);
int numCanciones = Integer.parseInt(datos.getProperty("artista"
+ i + ".total.canciones"));
for(int j = 1; j <= numCanciones; j++) {
String cancion = datos.getProperty("artista" + i + ".cancion"
+ j + ".nombre");
int duracion = Integer.parseInt(datos.getProperty("artista"
+ i + ".cancion" + j + ".duracion"));
String letra = datos.getProperty("artista" + i + ".cancion"
+ j + ".letra");
int dificultad = Integer.parseInt(datos.getProperty( "artista"
+ i + ".cancion" + j + ".dificultad"));
String genero = datos.getProperty("artista" + i + ".cancion"
+ j + ".genero");
String ruta = datos.getProperty("artista" + i + ".cancion"
+ j + ".ruta");
karaoke.agregarCancion(nombre, cancion, duracion, letra,
dificultad, genero, ruta);
}
}
}
catch(Exception e) {
JOptionPane.showMessageDialog(this, "No fue posible cargar la información "
+ "inicial del karaoke " + e.getMessage(), "Error",
JOptionPane.ERROR_MESSAGE);
}
}
public void agregarArtista(String nombreArtista, String categoria, String imagen) {
for (int i = 0; i < artistas.length; i++) {
artistas[i] = new Artista(nombreArtista, categoria, imagen);
}
System.out.println(Arrays.toString(artistas));
}
public int agregarCancion(String nombre, int duracion, String letra, int dificultad,
String genero, String ruta) {
canciones.add(new Cancion(dificultad, duracion, genero, nombre, letra, ruta));
return 1;
}
But at the time of testing the results of the image appear.
Personally I think the problem is in the method to add artist, but I can not identify the problem.
Does anyone have any idea what's going on?
You can save all Artista obejcts in a List List<Artista> artistas = new ArrayList<Artista>() and change the Method agregarArtista to fill the list with the Artists Data:
public void agregarArtista(String nombreArtista, String categoria, String imagen) {
artistas.add(new Artista(nombreArtista, categoria, imagen));
System.out.println(artistas);
}
If You want only first 10 Artists then You could change the Method as below:
public void agregarArtista(String nombreArtista, String categoria, String imagen) {
if (artistas.size() < 10) {
artistas.add(new Artista(nombreArtista, categoria, imagen));
}
System.out.println(artistas);
}
If the result should be in a Array then You could convert List to an Array like this:
Artista[] artistasArray = artistas.toArray(new Artista[0]);

Error message for StorageResource type

I've been trying to work on this problem for a while now but to no avail. When I run the code I get this error message: incompatible types: edu.duke.StorageResource cannot be converted to java.lang.String on line String geneList = FMG.storeAll(dna);. Does this mean I'm trying to make edu.duke object work with a java.lang.String type object? What would we go about resolving this issue?
Here's my code so far:
package coursera_java_duke;
import java.io.*;
import edu.duke.FileResource;
import edu.duke.StorageResource;
import edu.duke.DirectoryResource;
public class FindMultiGenes5 {
public int findStopIndex(String dna, int index) {
int stop1 = dna.indexOf("TGA", index);
if (stop1 == -1 || (stop1 - index) % 3 != 0) {
stop1 = dna.length();
}
int stop2 = dna.indexOf("TAA", index);
if (stop2 == -1 || (stop2 - index) % 3 != 0) {
stop2 = dna.length();
}
int stop3 = dna.indexOf("TAG", index);
if (stop3 == -1 || (stop3 - index) % 3 != 0) {
stop3 = dna.length();
}
return Math.min(stop1, Math.min(stop2, stop3));
}
public StorageResource storeAll(String dna) {
//CATGTAATAGATGAATGACTGATAGATATGCTTGTATGCTATGAAAATGTGAAATGACCCAdna = "CATGTAATAGATGAATGACTGATAGATATGCTTGTATGCTATGAAAATGTGAAATGACCCA";
String geneAL = new String();
String sequence = dna.toUpperCase();
StorageResource store = new StorageResource();
int index = 0;
while (true) {
index = sequence.indexOf("ATG", index);
if (index == -1)
break;
int stop = findStopIndex(sequence, index + 3);
if (stop != sequence.length()) {
String gene = dna.substring(index, stop + 3);
store.add(gene);
//index = sequence.substring(index, stop + 3).length();
index = stop + 3; // start at the end of the stop codon
}else{ index = index + 3;
}
}
return store;//System.out.println(sequence);
}
public void testStorageFinder() {
DirectoryResource dr = new DirectoryResource();
StorageResource dnaStore = new StorageResource();
for (File f : dr.selectedFiles()) {
FileResource fr = new FileResource(f);
String s = fr.asString();
dnaStore = storeAll(s);
printGenes(dnaStore);
}
System.out.println("size = " + dnaStore.size());
}
public String readStrFromFile(){
FileResource readFile = new FileResource();
String DNA = readFile.asString();
//System.out.println("DNA: " + DNA);
return DNA;
}//end readStrFromFile() method;
public float calCGRatio(String gene){
gene = gene.toUpperCase();
int len = gene.length();
int CGCount = 0;
for(int i=0; i<len; i++){
if(gene.charAt(i) == 'C' || gene.charAt(i) == 'G')
CGCount++;
}//end for loop
System.out.println("CGCount " + CGCount + " Length: " + len + " Ratio: " + (float)CGCount/len);
return (float)CGCount/len;
}//end of calCGRatio() method;
public void printGenes(StorageResource sr){
//create a FindMultiGenesFile object FMG
FindMultiGenes5 FMG = new FindMultiGenes5();
//read a DNA sequence from file
String dna = FMG.readStrFromFile();
String geneList = FMG.storeAll(dna);
//store all genes into a document
StorageResource dnaStore = new StorageResource();
System.out.println("\n There are " + geneList.size() + " genes. ");
int longerthan60 = 0;
int CGGreaterthan35 = 0;
for(int i=0; i<geneList.size(); i++){
if(!dnaStore.contains(geneList.get(i)))
dnaStore.add(geneList.get(i));
if(geneList.get(i).length() > 60) longerthan60++;
if(FMG.calCGRatio(geneList.get(i)) > 0.35) CGGreaterthan35++;
}
System.out.println("dnaStore.size: " + dnaStore.size());
System.out.println("\n There are " + dnaStore.size() + " genes. ");
System.out.println("There are " + longerthan60 + " genes longer than 60.");
System.out.println("There are " + CGGreaterthan35 + " genes with CG ratio greater than 0.35.");
}//end main();
}
I found your post as I am also doing a similar course at Duke using those edu.duke libraries.
When I get that error message it is because I'm using the wrong method to access it.
Try FMD.data() to get an iterable of all of the gene strings.

Sentence comparison with NLP

I used lingpipe for sentence detection but I don't have any idea if there is a better tool. As far as I have understood, there is no way to compare two sentences and see if they mean the same thing.
Is there anyother good source where I can have a pre-built method for comparing two sentences and see if they are similar?
My requirement is as below:
String sent1 = "Mary and Meera are my classmates.";
String sent2 = "Meera and Mary are my classmates.";
String sent3 = "I am in Meera and Mary's class.";
// several sentences will be formed and basically what I need to do is
// this
boolean bothAreEqual = compareOf(sent1, sent2);
sop(bothAreEqual); // should print true
boolean bothAreEqual = compareOf(sent2, sent3);
sop(bothAreEqual);// should print true
How to test if the meaning of two sentences are the same: this would be a too open-ended question.
However, there are methods for comparing two sentences and see if they are similar. There are many possible definition for similarity that can be tested with pre-built methods.
See for example http://en.wikipedia.org/wiki/Levenshtein_distance
Distance between
'Mary and Meera are my classmates.'
and 'Meera and Mary are my classmates.':
6
Distance between
'Mary and Meera are my classmates.'
and 'Alice and Bobe are not my classmates.':
14
Distance between
'Mary and Meera are my classmates.'
and 'Some totally different sentence.':
29
code:
public class LevenshteinDistance {
private static int minimum(int a, int b, int c) {
return Math.min(Math.min(a, b), c);
}
public static int computeDistance(CharSequence str1,
CharSequence str2) {
int[][] distance = new int[str1.length() + 1][str2.length() + 1];
for (int i = 0; i <= str1.length(); i++){
distance[i][0] = i;
}
for (int j = 0; j <= str2.length(); j++){
distance[0][j] = j;
}
for (int i = 1; i <= str1.length(); i++){
for (int j = 1; j <= str2.length(); j++){
distance[i][j] = minimum(
distance[i - 1][j] + 1,
distance[i][j - 1] + 1,
distance[i - 1][j - 1]
+ ((str1.charAt(i - 1) == str2.charAt(j - 1)) ? 0 : 1));
}
}
int result = distance[str1.length()][str2.length()];
//log.debug("distance:"+result);
return result;
}
public static void main(String[] args) {
String sent1="Mary and Meera are my classmates.";
String sent2="Meera and Mary are my classmates.";
String sent3="Alice and Bobe are not my classmates.";
String sent4="Some totally different sentence.";
System.out.println("Distance between \n'"+sent1+"' \nand '"+sent2+"': \n"+computeDistance(sent1, sent2));
System.out.println("Distance between \n'"+sent1+"' \nand '"+sent3+"': \n"+computeDistance(sent1, sent3));
System.out.println("Distance between \n'"+sent1+"' \nand '"+sent4+"': \n"+computeDistance(sent1, sent4));
}
}
Here is wat i have come up with. this is just a substitute till i get to the real thing but it might be of some help to people out there..
package com.examples;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import com.aliasi.sentences.MedlineSentenceModel;
import com.aliasi.sentences.SentenceModel;
import com.aliasi.tokenizer.IndoEuropeanTokenizerFactory;
import com.aliasi.tokenizer.Tokenizer;
import com.aliasi.tokenizer.TokenizerFactory;
import com.aliasi.util.Files;
import com.sun.accessibility.internal.resources.accessibility;
public class SentenceWordAnalysisAndLevenshteinDistance {
private static int minimum(int a, int b, int c) {
return Math.min(Math.min(a, b), c);
}
public static int computeDistance(CharSequence str1, CharSequence str2) {
int[][] distance = new int[str1.length() + 1][str2.length() + 1];
for (int i = 0; i <= str1.length(); i++) {
distance[i][0] = i;
}
for (int j = 0; j <= str2.length(); j++) {
distance[0][j] = j;
}
for (int i = 1; i <= str1.length(); i++) {
for (int j = 1; j <= str2.length(); j++) {
distance[i][j] = minimum(
distance[i - 1][j] + 1,
distance[i][j - 1] + 1,
distance[i - 1][j - 1]
+ ((str1.charAt(i - 1) == str2.charAt(j - 1)) ? 0
: 1));
}
}
int result = distance[str1.length()][str2.length()];
return result;
}
static final TokenizerFactory TOKENIZER_FACTORY = IndoEuropeanTokenizerFactory.INSTANCE;
static final SentenceModel SENTENCE_MODEL = new MedlineSentenceModel();
public static void main(String[] args) {
try {
ArrayList<String> sentences = null;
sentences = new ArrayList<String>();
// Reading from text file
// sentences = readSentencesInFile("D:\\sam.txt");
// Giving sentences
// ArrayList<String> sentences = new ArrayList<String>();
sentences.add("Mary and Meera are my classmates.");
sentences.add("Mary and Meera are my classmates.");
sentences.add("Meera and Mary are my classmates.");
sentences.add("Alice and Bobe are not my classmates.");
sentences.add("Some totally different sentence.");
// Self-implemented
wordAnalyser(sentences);
// Internet referred
// levenshteinDistance(sentences);
} catch (Exception e) {
// TODO: handle exception
e.printStackTrace();
}
}
private static ArrayList<String> readSentencesInFile(String path) {
ArrayList<String> sentencesList = new ArrayList<String>();
try {
System.out.println("Reading file from : " + path);
File file = new File(path);
String text = Files.readFromFile(file, "ISO-8859-1");
System.out.println("INPUT TEXT: ");
System.out.println(text);
List<String> tokenList = new ArrayList<String>();
List<String> whiteList = new ArrayList<String>();
Tokenizer tokenizer = TOKENIZER_FACTORY.tokenizer(
text.toCharArray(), 0, text.length());
tokenizer.tokenize(tokenList, whiteList);
System.out.println(tokenList.size() + " TOKENS");
System.out.println(whiteList.size() + " WHITESPACES");
String[] tokens = new String[tokenList.size()];
String[] whites = new String[whiteList.size()];
tokenList.toArray(tokens);
whiteList.toArray(whites);
int[] sentenceBoundaries = SENTENCE_MODEL.boundaryIndices(tokens,
whites);
System.out.println(sentenceBoundaries.length
+ " SENTENCE END TOKEN OFFSETS");
if (sentenceBoundaries.length < 1) {
System.out.println("No sentence boundaries found.");
return new ArrayList<String>();
}
int sentStartTok = 0;
int sentEndTok = 0;
for (int i = 0; i < sentenceBoundaries.length; ++i) {
sentEndTok = sentenceBoundaries[i];
System.out.println("SENTENCE " + (i + 1) + ": ");
StringBuffer sentenceString = new StringBuffer();
for (int j = sentStartTok; j <= sentEndTok; j++) {
sentenceString.append(tokens[j] + whites[j + 1]);
}
System.out.println(sentenceString.toString());
sentencesList.add(sentenceString.toString());
sentStartTok = sentEndTok + 1;
}
} catch (IOException e) {
// TODO: handle exception
e.printStackTrace();
}
return sentencesList;
}
private static void levenshteinDistance(ArrayList<String> sentences) {
System.out.println("\nLevenshteinDistance");
for (int i = 0; i < sentences.size(); i++) {
System.out.println("Distance between \n'" + sentences.get(0)
+ "' \nand '" + sentences.get(i) + "': \n"
+ computeDistance(sentences.get(0),
sentences.get(i)));
}
}
private static void wordAnalyser(ArrayList<String> sentences) {
System.out.println("No.of Sentences : " + sentences.size());
List<String> stopWordsList = getStopWords();
List<String> tokenList = new ArrayList<String>();
ArrayList<List<String>> filteredSentences = new ArrayList<List<String>>();
for (int i = 0; i < sentences.size(); i++) {
tokenList = new ArrayList<String>();
List<String> whiteList = new ArrayList<String>();
Tokenizer tokenizer = TOKENIZER_FACTORY.tokenizer(sentences.get(i)
.toCharArray(), 0, sentences.get(i).length());
tokenizer.tokenize(tokenList, whiteList);
System.out.print("Sentence " + (i + 1) + ": " + tokenList.size()
+ " TOKENS, ");
System.out.println(whiteList.size() + " WHITESPACES");
filteredSentences.add(filterStopWords(tokenList, stopWordsList));
}
for (int i = 0; i < sentences.size(); i++) {
System.out.println("\n" + (i + 1) + ". Comparing\n '"
+ sentences.get(0) + "' \nwith\n '" +
sentences.get(i)
+ "' : \n");
System.out.println(filteredSentences.get(0) + "\n and \n"
+ filteredSentences.get(i));
System.out.println("Percentage of similarity: "
+ calculateSimilarity(filteredSentences.get(0),
filteredSentences.get(i))
+ "%");
}
}
private static double calculateSimilarity(List<String> list1,
List<String> list2) {
int length1 = list1.size();
int length2 = list2.size();
int count1 = 0;
int count2 = 0;
double result1 = 0.0;
double result2 = 0.0;
int least, highest;
if (length2 > length1) {
least = length1;
highest = length2;
} else {
least = length2;
highest = length1;
}
// computing result1
for (String string1 : list1) {
if (list2.contains(string1))
count1++;
}
result1 = (count1 * 100) / length1;
// computing result2
for (String string2 : list2) {
if (list1.contains(string2))
count2++;
}
result2 = (count2 * 100) / length2;
double avg = (result1 + result2) / 2;
return avg;
}
private static List<String> getStopWords() {
String stopWordsString = ".,a,able,about,across,after,all,almost,also,am,among,an,and,any,are,as,at,be,because,been,but,by,can,cannot,could,dear,did,do,does,either,else,ever,every,for,from,get,got,had,has,have,he,her,hers,him,his,how,however,i,if,in,into,is,it,its,just,least,let,like,likely,may,me,might,most,must,my,neither,no,nor,not,of,off,often,on,only,or,other,our,own,rather,said,say,says,she,should,since,so,some,than,that,the,their,them,then,there,these,they,this,tis,to,too,twas,us,wants,was,we,were,what,when,where,which,while,who,whom,why,will,with,would,yet,you,your";
List<String> stopWordsList = new ArrayList<String>();
List<String> stopWordTokenList = new ArrayList<String>();
List<String> whiteList = new ArrayList<String>();
Tokenizer tokenizer = TOKENIZER_FACTORY.tokenizer(
stopWordsString.toCharArray(), 0, stopWordsString.length());
tokenizer.tokenize(stopWordTokenList, whiteList);
for (int i = 0; i < stopWordTokenList.size(); i++) {
// System.out.println((i + 1) + ":" + tokenList.get(i));
if (!stopWordTokenList.get(i).equals(",")) {
stopWordsList.add(stopWordTokenList.get(i));
}
}
System.out.println("No.of stop words: " + stopWordsList.size());
return stopWordsList;
}
private static List<String> filterStopWords(List<String> tokenList,
List<String> stopWordsList) {
List<String> filteredSentenceWords = new ArrayList<String>();
for (String sentenceToken : tokenList) {
if (!stopWordsList.contains(sentenceToken)) {
filteredSentenceWords.add(sentenceToken);
}
}
return filteredSentenceWords;
}
}

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