FASTA format: Difference between revisions

This implementation presumes the data-file is well-formed

<syntaxhighlight lang="java">

import java.io.BufferedReader;

import java.io.FileReader;

import java.io.IOException;

import java.util.ArrayList;

import java.util.List;

</syntaxhighlight>

<syntaxhighlight lang="java">

public static void main(String[] args) throws IOException {

List<FASTA> fastas = readFile("fastas.txt");

for (FASTA fasta : fastas)

System.out.println(fasta);

}

static List<FASTA> readFile(String path) throws IOException {

try (BufferedReader reader = new BufferedReader(new FileReader(path))) {

List<FASTA> list = new ArrayList<>();

StringBuilder lines = null;

String newline = System.lineSeparator();

String line;

while ((line = reader.readLine()) != null) {

if (line.startsWith(">")) {

if (lines != null)

list.add(parseFASTA(lines.toString()));

lines = new StringBuilder();

lines.append(line).append(newline);

} else {

lines.append(line);

}

}

list.add(parseFASTA(lines.toString()));

return list;

}

}

static FASTA parseFASTA(String string) {

String description;

char[] sequence;

int indexOf = string.indexOf(System.lineSeparator());

description = string.substring(1, indexOf);

/* using 'stripLeading' will remove any additional line-separators */

sequence = string.substring(indexOf + 1).stripLeading().toCharArray();

return new FASTA(description, sequence);

}

/* using a 'char' array seems more logical */

record FASTA(String description, char[] sequence) {

@Override

public String toString() {

return "%s: %s".formatted(description, new String(sequence));

}

}

</syntaxhighlight>

<pre>

Rosetta_Example_1: THERECANBENOSPACE

Rosetta_Example_2: THERECANBESEVERALLINESBUTTHEYALLMUSTBECONCATENATED

</pre>

<br />

An alternate demonstration