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package stream;
import java.util.ArrayList;
import dna.Data;
import fileIO.ByteFile;
import fileIO.FileFormat;
import shared.Shared;
import shared.Tools;
import structures.ByteBuilder;
public class GbkReadInputStream extends ReadInputStream {
public static void main(String[] args){
GbkReadInputStream fris=new GbkReadInputStream(args[0], true);
Read r=fris.next();
System.out.println(r.toText(false));
}
public GbkReadInputStream(String fname, boolean allowSubprocess_){
this(FileFormat.testInput(fname, FileFormat.GBK, null, allowSubprocess_, false));
}
public GbkReadInputStream(FileFormat ff){
if(verbose){System.err.println("FastqReadInputStream("+ff+")");}
flag=(Shared.AMINO_IN ? Read.AAMASK : 0);
stdin=ff.stdio();
if(!ff.gbk()){
System.err.println("Warning: Did not find expected fastq file extension for filename "+ff.name());
}
bf=ByteFile.makeByteFile(ff);
// assert(false) : interleaved;
}
@Override
public void start() {
// if(cris!=null){cris.start();}
}
@Override
public boolean hasMore() {
if(buffer==null || next>=buffer.size()){
if(bf.isOpen()){
fillBuffer();
}else{
assert(generated>0) : "Was the file empty?";
}
}
return (buffer!=null && next<buffer.size());
}
@Override
public Read next() {
if(!hasMore()){return null;}
Read r=buffer.set(next, null);
next++;
consumed++;
return r;
}
@Override
public synchronized ArrayList<Read> nextList() {
if(next!=0){throw new RuntimeException("'next' should not be used when doing blockwise access.");}
if(buffer==null || next>=buffer.size()){fillBuffer();}
ArrayList<Read> list=buffer;
buffer=null;
if(list!=null && list.size()==0){list=null;}
consumed+=(list==null ? 0 : list.size());
return list;
}
private synchronized void fillBuffer(){
assert(buffer==null || next>=buffer.size());
buffer=null;
next=0;
buffer=toReadList(bf, BUF_LEN, nextReadID, flag);
int bsize=(buffer==null ? 0 : buffer.size());
nextReadID+=bsize;
if(bsize<BUF_LEN){bf.close();}
generated+=bsize;
if(buffer==null){
if(!errorState){
errorState=true;
System.err.println("Null buffer in FastqReadInputStream.");
}
}
}
public static ArrayList<Read> toReadList(final ByteFile bf, final int maxReadsToReturn, long numericID, final int flag){
ArrayList<Read> list=new ArrayList<Read>(Data.min(8192, maxReadsToReturn));
int added=0;
String idLine=null;
ByteBuilder bb=new ByteBuilder();
for(byte[] s=bf.nextLine(); s!=null; s=bf.nextLine()){
// if(Tools.startsWith(s, "ID")){
// idLine=new String(s, 2, s.length-2).trim();
// }else
if(Tools.startsWith(s, "ORIGIN")){
// System.err.println(new String(s));
byte[] line=null;
for(line=bf.nextLine(); line!=null && line[0]!='/'; line=bf.nextLine()){
for(byte b : line){
if(Tools.isLetter(b)){
bb.append(Tools.toUpperCase(b));
}
}
}
assert(line==null || Tools.startsWith(line, "//")) : new String(line);
Read r=new Read(bb.toBytes(), null, idLine==null ? ""+numericID : idLine, numericID, flag);
list.add(r);
added++;
numericID++;
bb.clear();
idLine=null;
if(added>=maxReadsToReturn){break;}
}
}
assert(list.size()<=maxReadsToReturn);
return list;
}
@Override
public boolean close(){
if(verbose){System.err.println("Closing "+this.getClass().getName()+" for "+bf.name()+"; errorState="+errorState);}
errorState|=bf.close();
if(verbose){System.err.println("Closed "+this.getClass().getName()+" for "+bf.name()+"; errorState="+errorState);}
return errorState;
}
@Override
public synchronized void restart() {
generated=0;
consumed=0;
next=0;
nextReadID=0;
buffer=null;
bf.reset();
}
@Override
public boolean paired() {return false;}
@Override
public String fname(){return bf.name();}
/** Return true if this stream has detected an error */
@Override
public boolean errorState(){return errorState || FASTQ.errorState();}
private ArrayList<Read> buffer=null;
private int next=0;
private final ByteFile bf;
private final int flag;
private final int BUF_LEN=Shared.bufferLen();;
private final long MAX_DATA=Shared.bufferData(); //TODO - lot of work for unlikely case of super-long fastq reads. Must be disabled for paired-ends.
public long generated=0;
public long consumed=0;
private long nextReadID=0;
public final boolean stdin;
public static boolean verbose=false;
}
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