Question

I have a file that looks like this (but is much bigger):

>some text
ABC
DEF
GHI
>some more text
JKL
MNO
PQR

I have been playing around with it in Java for some time and have been able to build arrays with the lines, etc. The lines with ‘>’ are usually one line but sometimes could be 2, 3 or more lines. The lines that don’t begin with ‘>’ are the same length in characters but there may be 10, 20 or 30 or more of these lines. I am at the point now where I want to create an string array, where each string in the array contains a string of the lines that don’t begin with ‘>’ like so:

array element 1 = ABCDEFGHI
array element 2 = JKLMONPQR

I feel like I am close but need a small kick in the butt to get me going. I’m sure this is easy for a pro, but I am still new to Java.

Specific problem is related to other posts I made on this board. It’s a FASTA file:

>3BHS_BOVIN (P14893) 3 beta-hydroxysteroid
AGWSCLVTGGGGFLGQRIICLLVEEKDLQEIRVLDKVFRPEVREEFSKLQSKIKLTLLEG
DILDEQCLKGACQGTSVVIHTASVIDVRNAVPRETIMNVNVKGTQLLLEACVQASVPVFI
>41_BOVIN (Q9N179) Protein 4.1 
MHCKVSLLDDTVYECVVEKHAKGQDLLKRVCEHLNLLEEDYFGLAIWDNATSKTWLDSAK
EIKKQVRGVPWNFTFNVKFYPPDPAQLTEDITRYYLCLQLRQDIVSGRLPCSFATLALLG
SYTIQSELGDYDPELHGADYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLEN
>5NTD_BOVIN (Q05927) 5'-nucleotidase 
MNPGAARTPALRILPLGALLWPAARPWELTILHTNDVHSRLEQTSEDSSKCVNASRCVGG
VARLATKVHQIRRAEPHVLLLDAGDQYQGTIWFTVYKGTEVAHFMNALGYESMALGNHEF
DNGVEGLIDPLLKEVNFPILSANIKAKGPLASKISGLYSPYKILTVGDEVVGIVGYTSKE
TPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEVDKLIAQKVKGVDVVV

I ultimately need the sequences in their own array element so that I can manipulate them later.

Answer 1

Assuming you can iterate over the lines:

List<String> array = new ArrayList<String>();
StringBuilder buf = new StringBuilder();
for (String line : lines) {
  if (line.startsWith(">")) {
    if (buf.length() > 0) {
      array.add(buf.toString());
      buf.setLength(0);
    }
  } else {
    buf.append(line);
  }
}
if (buf.length() > 0) { // Add the final text element(s).
  array.add(buf.toString());
}