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package stream;
import java.util.ArrayList;
import dna.AminoAcid;
import dna.ChromosomeArray;
import dna.Data;
import shared.KillSwitch;
import shared.Shared;
import shared.Tools;
public class SequentialReadInputStream extends ReadInputStream {
public SequentialReadInputStream(long maxReads_, int readlen_, int minreadlen_, int overlap_, boolean alternateStrand_){
maxReads=(maxReads_<0 ? Long.MAX_VALUE : maxReads_);
readlen=readlen_;
minReadlen=minreadlen_;
POSITION_INCREMENT=readlen;
overlap=overlap_;
alternateStrand=alternateStrand_;
assert(overlap<POSITION_INCREMENT);
maxPosition=Data.chromLengths[1];
maxChrom=Data.numChroms;
restart();
}
@Override
public void start(){}
@Override
public void restart(){
position=0;
chrom=1;
generated=0;
consumed=0;
next=0;
buffer=null;
}
@Override
public boolean paired() {
return false;
}
@Override
public boolean close() {return false;}
@Override
public boolean hasMore() {
if(verbose){
System.out.println("Called hasMore(): "+(id>=maxReads)+", "+(chrom<maxChrom)+", "+(position<=maxPosition)+", "+(buffer==null || next>=BUF_LEN));
System.out.println(id+", "+maxReads+", "+chrom+", "+maxChrom+", "+position+", "+maxPosition+", "+buffer+", "+next+", "+(buffer==null ? -1 : BUF_LEN));
}
// if(buffer==null || next>=buffer.size()){
// if(tf.isOpen()){
// fillBuffer();
// }else{
// assert(generated>0) : "Was the file empty?";
// }
// }
// return (buffer!=null && next<buffer.size());
if(id>=maxReads){return false;}
if(chrom<maxChrom){return true;}
if(position<=maxPosition){return true;}
if(buffer==null || next>=buffer.size()){return false;}
return true;
}
@Override
public Read next() {
if(!hasMore()){return null;}
if(buffer==null || next>=buffer.size()){fillBuffer();}
Read r=buffer.get(next);
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(!hasMore()){return null;}
if(buffer==null || next>=buffer.size()){fillBuffer();}
ArrayList<Read> r=buffer;
buffer=null;
if(r!=null && r.size()==0){r=null;}
consumed+=(r==null ? 0 : r.size());
return r;
}
private synchronized void fillBuffer(){
// System.out.println("fill "+chrom+", "+position);
buffer=null;
if(chrom>maxChrom){return;}
ChromosomeArray cha=Data.getChromosome(chrom);
next=0;
if(position==0){
while(position<=maxPosition && !AminoAcid.isFullyDefined((char)cha.get(position))){position++;}
}
ArrayList<Read> reads=new ArrayList<Read>(BUF_LEN);
int index=0;
while(position<=maxPosition && index<buffer.size() && id<maxReads){
int start=position;
int stop=Tools.min(position+readlen-1, cha.maxIndex);
byte[] s=cha.getBytes(start, stop);
// assert(s.length==readlen) : s.length+", "+readlen;
if(s.length<1 || !AminoAcid.isFullyDefined(s)){
int firstGood=-1, lastGood=-1;
for(int i=0; i<s.length; i++){
if(AminoAcid.isFullyDefined(s[i])){
lastGood=i;
if(firstGood==-1){firstGood=i;}
}
}
if(lastGood-firstGood+1>=minReadlen){
start=start+firstGood;
stop=stop-(s.length-lastGood-1);
s=KillSwitch.copyOfRange(s, firstGood, lastGood+1);
assert(s.length==lastGood-firstGood+1);
}else{
s=null;
}
}
if(s!=null){
Read r=new Read(s, null, id, chrom, start, stop, Shared.PLUS);
if(alternateStrand && (r.numericID&1)==1){r.reverseComplement();}
r.setSynthetic(true);
// System.out.println("Made read: "+r);
// assert(id!=54406) : "\n"+r.toString()+"\nbases: "+s.length+"\nstart: "+start+"\nstop: "+stop+"\nminlen: "+minReadlen+"\n";
reads.add(r);
index++;
position+=(POSITION_INCREMENT-overlap);
id++;
}else{
//Move to the next defined position
while(AminoAcid.isFullyDefined((char)cha.get(position))){position++;}
while(position<=maxPosition && !AminoAcid.isFullyDefined((char)cha.get(position))){position++;}
}
}
// System.out.println("got "+index+" from "+chrom+", "+position);
if(index==0){
if(UNLOAD && chrom>0){Data.unload(chrom, true);}
chrom++;
position=0;
buffer=null;
fillBuffer();
return;
}
generated+=index;
buffer=reads;
}
@Override
public String fname(){return "sequential";}
private long id=0;
public int position=0;
public int maxPosition;
private int chrom;
private ArrayList<Read> buffer=null;
private int next=0;
private final int BUF_LEN=Shared.bufferLen();;
public static boolean UNLOAD=false;
public long generated=0;
public long consumed=0;
public final long maxReads;
public final int readlen;
public final int POSITION_INCREMENT;
public final int minReadlen;
public final int maxChrom;
public final int overlap;
public final boolean alternateStrand;
public static boolean verbose=false;
}
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