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package fileIO;
import java.io.File;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import structures.ListNum;
/**
* Accepts multiple input files.
* Reads them each sequentially, and outputs everything to a single output file.
* Generically, it can be used to concatenate files while recompressing them
* and avoiding the use of stdio.
* @author Brian Bushnell
* @date January 21, 2025
*
*/
public class Concatenate {
public static void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
Concatenate x=new Concatenate(args);
//Run the object
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public Concatenate(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Parser parser=new Parser();
parser.out1=out1;
for(int i=0; i<args.length; i++){
String arg=args[i];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(b!=null && b.equalsIgnoreCase("null")){b=null;}
if(a.equals("parse_flag_goes_here")){
//Set a variable here
}else if(a.equals("in")){
in.clear();
String[] b2=(b==null) ? null : (new File(b).exists() ? new String[] {b} : b.split(","));
for(String b3 : b2){in.add(b3);}
}else if(b==null && new File(arg).exists()){
in.add(arg);
}else if(parser.parse(arg, a, b)){
//do nothing
}else{
assert(false) : "Unknown parameter "+args[i];
outstream.println("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
out1=parser.out1;
}
ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, true, false, false);
}
void process(Timer t){
final ByteStreamWriter bsw;
if(out1!=null){
final int buff=4;
for(String s : in) {
assert(!out1.equalsIgnoreCase(s)) : "Input file and output file have same name.";
}
bsw=ByteStreamWriter.makeBSW(ffout1);
}else{bsw=null;}
for(String s : in) {
processInner(s, bsw);
}
bsw.poisonAndWait();
if(verbose){outstream.println("Finished.");}
t.stop();
Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 12);
}
void processInner(String fname, ByteStreamWriter bsw) {
FileFormat ffin=FileFormat.testInput(fname, FileFormat.TXT, null, true, true);
final ByteFile bf=ByteFile.makeByteFile(ffin);
ListNum<byte[]> ln;
while((ln=bf.nextList())!=null) {
for(byte[] line : ln.list) {
linesProcessed++;
bytesProcessed+=(line.length+1);
if(bsw!=null) {bsw.println(line);}
}
}
bf.close();
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private ArrayList<String> in=new ArrayList<String>();
private String out1="stdout.txt";
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private long maxReads=-1;
private long linesProcessed=0, bytesProcessed=0;
/*--------------------------------------------------------------*/
private java.io.PrintStream outstream=System.err;
public static boolean verbose=false;
}
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