package com.cbrc.pipeline2; import java.io.BufferedReader; import java.io.BufferedWriter; import java.io.DataInputStream; import java.io.FileInputStream; import java.io.FileWriter; import java.io.InputStreamReader; public class Test { String foldIn; String fnmFasta; String foldOut; String fnmOut; void init(String rootIn, String rootOut, String fnmInFasta, String fOut) { this.foldIn = rootIn; this.fnmFasta = this.foldIn + fnmInFasta; this.foldOut = rootOut; this.foldOut = this.foldOut + fOut; } void loadFasta(){ try { FileInputStream fstream = new FileInputStream(fnmFasta); DataInputStream in = new DataInputStream(fstream); BufferedReader br = new BufferedReader(new InputStreamReader(in)); String befTrim , strLine; while ((befTrim = br.readLine()) != null) { strLine = befTrim.trim(); } br.close();