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How to continue processing a file when I reach a null String [duplicate]

This question already has an answer here:
What is a StringIndexOutOfBoundsException? How can I fix it?
(1 answer)
Closed 4 years ago.
I'm trying to read in a file that contains a sequence of DNA. And within my program I want to read in each subsequence of that DNA of length 4, and store it in my hashmap to count the occurence of each subsequence. For example if I have the sequence CCACACCACACCCACACACCCAC, and I want every subsequence of length 4, the first 3 subsequences would be:
CCAC, CACA, ACAC, etc.
So in order to do this I have to iterate over the string several times, here is my implementation
try
{
String file = sc.nextLine();
BufferedReader reader = new BufferedReader(new FileReader(file + ".fasta"));
Map<String, Integer> frequency = new HashMap<>();
String line = reader.readLine();
while(line != null)
{
System.out.println("Processing Line: " + line);
String [] kmer = line.split("");
for(String nucleotide : kmer)
{
System.out.print(nucleotide);
int sequence = nucleotide.length();
for(int i = 0; i < sequence; i++)
{
String subsequence = nucleotide.substring(i, i+5);
if(frequency.containsKey(subsequence))
{
frequency.put(subsequence, frequency.get(subsequence) +1);
}
else
{
frequency.put(subsequence, 1);
}
}
}
System.out.println();
line = reader.readLine();
}
System.out.println(frequency);
}
catch(StringIndexOutOfBoundsException e)
{
System.out.println();
}
I have a problem when reaching the end of the string, it won't continue to process due to the error. How would I go about getting around that?

You are calling substring(i, i + 5). At the end of the string i + 5 goes out of bounds. Let's say your string is "ABCDEFGH", length 8, your loop will go from i = 0 to i = 7. When i reaches 4 substring(4, 9) cannot be computed and the exception is raised.
Try this:
for(int i = 0; i < sequence - 4; i++)

You can directly read each line and extract first 4 sub-chars without
the need to splitting it up each time when you read a line.
The error you are getting because when the Program is looping through the splitted characters then it is possible that there are less than 4 characters left altogether at the end to be extracted. Less than 4 chars are responsible which is throwing the error. e.g. suppose you have a line CCACACC then grouping in 4 chars you would get 1st group as complete i.e., CCAC and 2nd group as ACC which is incomplete. So in your code when the line nucleotide.substring(i, i+5); is encountered then probably there is no group of complete 4 characters left at the end that can be extracted and hence the Program throws error. And to extract 4 chars you need to add 4, not 5.
So the work around the code will be to put the extraction line in a try block as given below in the edited code. Replace the loop body with the below code.
while(reader.hasNextLine())
{
line = reader.nextLine();
for(int i = 0; i < line.length; i++)
{
String subsequence = "";
// put the extract operation in a try block
// to avoid crashing
try
{
subsequence = nucleotide.substring(i, i+4);
}
catch(Exception e)
{
// just leave blank to pass the error
}
if(frequency.containsKey(subsequence))
{
frequency.put(subsequence, frequency.get(subsequence) +1);
}
else
{
frequency.put(subsequence, 1);
}
}

Based on the title of your post...try changing the condition for your while loop. Instead of using the current:
String line = reader.readLine();
while(line != null) {
// ...... your code .....
}
use this code:
String line;
while((line = reader.readLine()) != null) {
// If file line is blank then skip to next file line.
if (line.trim().equals("")) {
continue;
}
// ...... your code .....
}
That would cover handling blank file lines.
Now about the StringIndexOutOfBoundsException exception you are experiencing. I believe by now you already basically know why you are receiving this exception and therefore you need to decide what you want to do about it. When a string is to be split into specific length chunks and that length is not equally divisible against the overall length if a specific file line characters then there are obviously a few options available:
Ignore the remaining characters at the end of the file line. Although an easy solution it's not very feasible since it would produce incomplete data. I don't know anything about DNA but I'm certain this would not be the route to take.
Add the remaining DNA sequence (even though it's short) to the Map. Again, I know nothing about DNA and I'm not sure if even this wouldn't be a viable solution. Perhaps it is, I simply don't know.
Add the remaining short DNA sequence to the beginning of the next
incoming file line and carry on breaking that line into 4 character
chunks. Continue doing this until the end of file is reached at which
point if the final DNA sequence is determined to be short then add
that to the Map (or not).
There may of course be other options and whatever they might be it's something you will need to decide. To assist you however, here is code to cover the three options I've mentioned:
Ignore the remaining characters:
Map<String, Integer> frequency = new HashMap<>();
String subsequence;
String line;
try (BufferedReader reader = new BufferedReader(new FileReader("DNA.txt"))) {
while ((line = reader.readLine()) != null) {
// If file line is blank then skip to next file line.
if (line.trim().equals("")) {
continue;
}
for (int i = 0; i < line.length(); i += 4) {
// Get out of loop - Don't want to deal with remaining Chars
if ((i + 4) > (line.length() - 1)) {
break;
}
subsequence = line.substring(i, i + 4);
if (frequency.containsKey(subsequence)) {
frequency.put(subsequence, frequency.get(subsequence) + 1);
}
else {
frequency.put(subsequence, 1);
}
}
}
}
catch (IOException ex) {
ex.printStackTrace();
}
Add the remaining DNA sequence (even though it's short) to the Map:
Map<String, Integer> frequency = new HashMap<>();
String subsequence;
String line;
try (BufferedReader reader = new BufferedReader(new FileReader("DNA.txt"))) {
while ((line = reader.readLine()) != null) {
// If file line is blank then skip to next file line.
if (line.trim().equals("")) {
continue;
}
String lineRemaining = "";
for (int i = 0; i < line.length(); i += 4) {
// Get out of loop - Don't want to deal with remaining Chars
if ((i + 4) > (line.length() - 1)) {
lineRemaining = line.substring(i);
break;
}
subsequence = line.substring(i, i + 4);
if (frequency.containsKey(subsequence)) {
frequency.put(subsequence, frequency.get(subsequence) + 1);
}
else {
frequency.put(subsequence, 1);
}
}
if (lineRemaining.length() > 0) {
subsequence = lineRemaining;
if (frequency.containsKey(subsequence)) {
frequency.put(subsequence, frequency.get(subsequence) + 1);
}
else {
frequency.put(subsequence, 1);
}
}
}
}
catch (IOException ex) {
ex.printStackTrace();
}
Add the remaining short DNA sequence to the beginning of the next incoming file line:
Map<String, Integer> frequency = new HashMap<>();
String lineRemaining = "";
String subsequence;
String line;
try (BufferedReader reader = new BufferedReader(new FileReader("DNA.txt"))) {
while ((line = reader.readLine()) != null) {
// If file line is blank then skip to next file line.
if (line.trim().equals("")) {
continue;
}
// Add remaining portion of last line to new line.
if (lineRemaining.length() > 0) {
line = lineRemaining + line;
lineRemaining = "";
}
for (int i = 0; i < line.length(); i += 4) {
// Get out of loop - Don't want to deal with remaining Chars
if ((i + 4) > (line.length() - 1)) {
lineRemaining = line.substring(i);
break;
}
subsequence = line.substring(i, i + 4);
if (frequency.containsKey(subsequence)) {
frequency.put(subsequence, frequency.get(subsequence) + 1);
}
else {
frequency.put(subsequence, 1);
}
}
}
// If any Chars remaining at end of file then
// add to MAP
if (lineRemaining.length() > 0) {
frequency.put(lineRemaining, 1);
}
}
catch (IOException ex) {
ex.printStackTrace();
}

It is not clear at all from the question description, but I'll guess your input file ends with an empty line.
Try removing the last newline in your input file, or alternatively check against empty in your while loop:
while (line != null && !line.isEmpty())

Java replace characters in a TextFile - Alice In Wonderland

I'm trying to make a compressor for TextFiles and I get stuck at replacing characters.
This is my code:
compress.setOnAction(event ->
{
String line;
try(BufferedReader reader = new BufferedReader(new FileReader(newFile)))
{
while ((line = reader.readLine()) != null)
{
int length = line.length();
String newLine = "";
for (int i = 1; i < length; i++)
{
int c = line.charAt(i);
if (c == line.charAt(i - 1))
{
}
}
}
}
catch (IOException ex)
{
ex.printStackTrace();
}
});
So what I want to do is: I want to find all the words where two characters are equal, if they are aside (Like 'Took'). When the if statement is true, I want to replace the first letter of the two equals characters, so it would look like: 'T2ok'.
I've tried a lot of things and I get an ArrayOutOfbounds, StringOutOfbounds, and so on, all the time...
Hope someone has a great answer :-)
Regards

Create a method that compress one String as follows:
Loop throu every character using a while loop. Count the duplicates in another nested while loop that increments the current index while duplicates are found and skips them from being written to output. Additionally this counts their occurence.
public String compress(String input){
int length = input.length(); // length of input
int ix = 0; // actual index in input
char c; // actual read character
int ccounter; // occurrence counter of actual character
StringBuilder output = // the output
new StringBuilder(length);
// loop over every character in input
while(ix < length){
// read character at actual index then inc index
c = input.charAt(ix++);
// we count one occurrence of this character here
ccounter = 1;
// while not reached end of line and next character
// is the same as previously read
while(ix < length && input.charAt(ix) == c){
// inc index means skip this character
ix++;
// and inc character occurence counter
ccounter++;
}
// if more than one character occurence is counted
if(ccounter > 1){
// print the character count
output.append(ccounter);
}
// print the actual character
output.append(c);
}
// return the full compressed output
return output.toString();
}
Now you can use this method to create a file input to output stream using java8 techniques.
// create input stream that reads line by line, create output writer
try (Stream<String> input = Files.lines(Paths.get("input.txt"));
PrintWriter output = new PrintWriter("output.txt", "UTF-8")){
// compress each input stream line, and print to output
input.map(s -> compress(s)).forEachOrdered(output::println);
} catch (IOException e) {
e.printStackTrace();
}
If you really want to. You can remove the input file and rename the output file afterwards with
Files.move(Paths.get("output.txt"), Paths.get("input.txt"),StandardCopyOption.REPLACE_EXISTING);
I think this is the most efficient way to do what you want.

try this:
StringBuilder sb = new StringBuilder();
String line;
try(BufferedReader reader = new BufferedReader(new FileReader(newFile)))
{
while ((line = reader.readLine()) != null)
{
if (!line.isEmpty()) {
//clear states
boolean matchedPreviously = false;
char last = line.charAt(0);
sb.setLength(0);
sb.append(last);
for (int i = 1; i < line.length(); i++) {
char c = line.charAt(i);
if (!matchedPreviously && c == last) {
sb.setLength(sb.length()-1);
sb.append(2);
matchedPreviously = true;
} else matchedPreviously = false;
sb.append(last = c);
}
System.out.println(sb.toString());
}
}
}
catch (IOException ex)
{
ex.printStackTrace();
}
This solution uses only a single loop, but can only find occurrences of length 2

How to modify my readFile function so it does not stop at first line (java)

the following code will only read the first line of a text file and it will stop there. I've been experimenting with loops but i cannot get it to successfully update the line until there are no more lines in the file. can anyone help? thanks
public void readFile(){
try {
BufferedReader in = new BufferedReader(new FileReader("test1.txt"));
words = new ArrayList<Word>();
int lineNum = 1; // we read first line in start
// delimeters of line in this example only "space"
char [] parse = {' '};
String delims = new String(parse);
String line = in.readLine();
String [] lineWords = line.split(delims);
// split the words and create word object
for (int i = 0; i < lineWords.length; i++) {
Word w = new Word(lineWords[i]);
words.add(w);
}
lineNum++; // pass the next line
line = in.readLine();
in.close();
} catch (IOException e) {
}
}

Basically, you want to keep reading until you run out of lines, at which time BufferedReader will return null
char[] parse = {' '};
String delims = new String(parse);
String line = null;
while ((line = in.readLine()) != null) {
String[] lineWords = line.split(delims);
// split the words and create word object
for (int i = 0; i < lineWords.length; i++) {
Word w = new Word(lineWords[i]);
words.add(w);
}
lineNum++; // pass the next line
}
You should be managing your resources better, if you open it, you should make all reasonable attempts to close. Currently, if your code fails for some reason, the in.close line will never be called. Also, you shouldn't ignore exceptions
Luckily, in Java 8, this is easy to manage...
try (BufferedReader in = new BufferedReader(new FileReader("test1.txt"))) {
//...
} catch (IOException e) {
e.printStackTrace();
}
Take a closer look at Basic I/O, The try-with-resources Statement and BufferedReader JavaDocs, especially BufferedReader#readLine
You may also want to take a look at LineNumberReader ;)

while((line = in.readLine()) != null){
//process line
}
This nested statement reads a line from the BufferedReader and stores it in line. At the end of the file, readLine() will return null and stop the loop.

Why isn't the text file completly read?

So I am trying to extract a piece of code from a txtfile ,the start of the piece being indicated by "# EMPIRES" and the end being indicated by another string starting with a '#'. My program however never finds the start of the piece and keeps on going until it reaches the end of the file.
To try and find out what the problem was I tried first to print every line that it finds.
And here I encountered another problem. My code already stops finding new lines,long before
"# EMPIRES" is even reached.
public String getEmpirestxt(String fileName) {
Scanner sc;
try {
sc = new Scanner(new File(fileName));
String currentLine = sc.nextLine();
StringBuilder empiresText = new StringBuilder(currentLine);
while (!currentLine.startsWith("# EMPIRES")) {
currentLine = sc.nextLine();
System.out.println(currentLine);
}
currentLine = sc.nextLine();
while (sc.hasNextLine() && currentLine.charAt(0)!='#') {
empiresText.append("\n").append(sc.nextLine());
}
return empiresText.toString();
} catch (FileNotFoundException ex) {
System.out.println("Landed_Titles.txt not found.");
}
return null;
}
The textfile itself :
https://www.wetransfer.com/downloads/a1093792d5ac54b6ccce04afecb9357f20140402095042/505fca

Here is my solution to your problem. I used newBufferedReader instead of the Scanner to read the file. This example works with Java 7.
public String getEmpirestxt2(String fileName) {
Charset charset = Charset.forName("ISO-8859-1");
Path filePath = Paths.get(fileName);
try (BufferedReader reader = Files.newBufferedReader(filePath, charset)) {
String line = null;
// find the start of the piece
while ((line = reader.readLine()) != null && !line.equals(START)) {
}
System.out.println("START: " + line);
// getting the piece
StringBuilder sb = new StringBuilder();
while ((line = reader.readLine()) != null && !line.startsWith(END)) {
sb.append(line);
}
System.out.println("END: " + line);
return sb.toString();
} catch (IOException x) {
System.err.format("IOException: %s%n", x);
}
return null;
}
The constants in the method are:
private static final String START = "# EMPIRES";
private static final String END = "#";
I tested it with your file and it works fine. It also prints the starting and end points of the required piece:
START: # EMPIRES
END: # color={ 144 80 60 }

String currentLine = sc.nextLine();
you are starting reading from the next Line.

The condition:
while (sc.hasNextLine() && currentLine.charAt(0)!='#')
may terminate even if the file has more lines to read, because of the second predicate. If currentLine.charAt(0)!='#' is fales, the while loop ends. This does not mean there are no more lines to read.

In your second while loop you never set currentLine
This part:
currentLine = sc.nextLine();
while (sc.hasNextLine() && currentLine.charAt(0)!='#') {
empiresText.append("\n").append(sc.nextLine());
}
should be:
do{
currentLine=sc.nextLine();
empiresText.append("\n").append(sc.nextLine());
}while(sc.hasNextLine() && currentLine.charAt(0)!='#');
Otherwise the line right after # EMPIRES won't be read and the code while loop will never stop because the currentLine is not getting updated.

Append currentLine instead of sc.nextLine() in the second while loop :
while (sc.hasNextLine() && currentLine.charAt(0) != '#') {
empiresText.append("\n").append(currentLine);
currentLine = sc.nextLine();
}
Otherwise you can use a single loop like below :
while (sc.hasNextLine()){
if(sc.nextLine().startsWith("# EMPIRES")){
currentLine = sc.nextLine();
while (sc.hasNextLine() && currentLine.charAt(0) != '#') {
empiresText.append("\n").append(currentLine);
currentLine = sc.nextLine();
}
}
}

Take Strings from Text file and assign each line to value (2 at a time and insert into LinkedHashMap)

What I'm trying to do is, load a Text file, then take the values from each line and assign them to a variable in my program. Every two lines, I will insert them into a LinkedHashMap (As a pair)
The problem with a buffered reader is, all I can seem to do is, read one line at a time.
Here is my current code:
public static void receiver(String firstArg) {// Receives
// Input
// File
String cipherText;
String key;
String inFile = new File(firstArg).getAbsolutePath();
Path file = new File(inFile).toPath();
// File in = new File(inFile);
try (InputStream in = Files.newInputStream(file);
BufferedReader reader = new BufferedReader(
new InputStreamReader(in))) {
String line = null;
while ((line = reader.readLine()) != null) {
// System.out.println(line);
String[] arrayLine = line.split("\n"); // here you are
// splitting
// with whitespace
cipherText = arrayLine[0];
// key = arrayLine[1];
System.out.println(arrayLine[0] + " " + arrayLine[1]);
cipherKeyPairs.put(arrayLine[0], arrayLine[1]);
}
} catch (IOException x) {
System.err.println(x);
}
The problem is, it can't find the arrayLine[1] (for obvious reasons). I need it to read two lines at a time without the array going out of bounds.
Any idea how to do this, so that I can store them into my LinkedHashMap, two lines at a time as separate values.

You can overcome this issue by inserting in the List every 2 lines reading.
A description for this code is that: "Bold is the true case"
Read the first line (count is 0)
If (secondLine is false) ==> Save the line to CipherText variable, make secondLine = true
Else If (secondLine is true) ==> Add to list (CipherText, line), make secondLine = false
Read the second line (count is 1)
If (secondLine is false) ==> Save the line to CipherText variable, make secondLine = true
Else If (secondLine is true) ==> Add to list (CipherText, line), make secondLine = false
String cipherText;
boolean secondLine = false;
String inFile = new File(firstArg).getAbsolutePath();
Path file = new File(inFile).toPath();
try {
InputStream in = Files.newInputStream(file);
BufferedReader reader = new BufferedReader(new InputStreamReader(in))) {
String line = null;
while ((line = reader.readLine()) != null) {
if (!secondLine) //first line reading
{
cipherText = line;
secondLine = true;
}
else if (secondLine) //second line reading
{
cipherKeyPairs.put(cipherText, line);
secondLine = false;
}
}
} catch (IOException x) {
System.err.println(x);
}

See if this works for you. I just edited your code. it might not be the best answer.
public static void receiver(String firstArg) {// Receives
// Input
// File
String cipherText;
String key;
String inFile = new File(firstArg).getAbsolutePath();
Path file = new File(inFile).toPath();
// File in = new File(inFile);
try (InputStream in = Files.newInputStream(file);
BufferedReader reader = new BufferedReader(
new InputStreamReader(in))) {
String line = null;
List<String> lines = new ArrayList();
while ((line = reader.readLine()) != null) {
lines.add(line);//trim line first though and check for empty string
}
for(int i=1;i<lines.size();i++){
cipherText = arrayLine[i];
// key = arrayLine[1];
System.out.println(arrayLine[i] + " " + arrayLine[i-1]);
cipherKeyPairs.put(arrayLine[i-1], arrayLine[i]);
}
} catch (IOException x) {
System.err.println(x);
}
}