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POJava looping through array - Optimization
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copied!<p>I've got some Java code that runs quite the expected way, but it's taking some amount of time -some seconds- even if the job is just looping through an array.</p> <p>The input file is a Fasta file as shown in the image below. The file I'm using is 2.9Mo, and there are some other Fasta file that can take up to 20Mo.</p> <p><img src="https://i.stack.imgur.com/I1uaS.gif" alt="enter image description here"></p> <p>And in the code im trying to loop through it by bunches of threes, e.g: AGC TTT TCA ... etc The code has no functional sens for now but what I want is to append each Amino Acid to it's equivalent bunch of Bases. Example :</p> <p>AGC - Ser / CUG Leu / ... etc</p> <p>So what's wrong with the code ? and Is there any way to do it better ? Any optimization ? Looping through the whole String is taking some time, maybe just seconds, but need to find a better way to do it.</p> <pre><code>import java.io.BufferedReader; import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; public class fasta { public static void main(String[] args) throws IOException { File fastaFile; FileReader fastaReader; BufferedReader fastaBuffer = null; StringBuilder fastaString = new StringBuilder(); try { fastaFile = new File("res/NC_017108.fna"); fastaReader = new FileReader(fastaFile); fastaBuffer = new BufferedReader(fastaReader); String fastaDescription = fastaBuffer.readLine(); String line = fastaBuffer.readLine(); while (line != null) { fastaString.append(line); line = fastaBuffer.readLine(); } System.out.println(fastaDescription); System.out.println(); String currentFastaAcid; for (int i = 0; i < fastaString.length(); i+=3) { currentFastaAcid = fastaString.toString().substring(i, i + 3); System.out.println(currentFastaAcid); } } catch (NullPointerException e) { System.out.println(e.getMessage()); } catch (FileNotFoundException e) { System.out.println(e.getMessage()); } catch (IOException e) { System.out.println(e.getMessage()); } finally { fastaBuffer.close(); } } } </code></pre>

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