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package stream;
import java.util.ArrayList;
import java.util.Comparator;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import sort.ReadComparatorClump;
import sort.ReadComparatorTopological5Bit;
import structures.ListNum;
public class CrisContainer implements Comparable<CrisContainer> {
public CrisContainer(String fname, Comparator<Read> comparator_, boolean allowSubprocess){
comparator=comparator_;
genKmer=(comparator==ReadComparatorTopological5Bit.comparator);
clump=(comparator==ReadComparatorClump.comparator);
FileFormat ff=FileFormat.testInput(fname, FileFormat.FASTQ, null, allowSubprocess, true);
cris=ConcurrentReadInputStream.getReadInputStream(-1, true, ff, null, null, null);
// System.err.println(genKmer+", "+clump+", "+comparator.getClass());
cris.start();
fetch();
}
public CrisContainer(ConcurrentReadInputStream cris_, Comparator<Read> comparator_){
comparator=comparator_;
genKmer=(comparator==ReadComparatorTopological5Bit.comparator);
clump=(comparator==ReadComparatorClump.comparator);
cris=cris_;
// System.err.println(genKmer+", "+clump+", "+comparator.getClass());
fetch();
}
public ArrayList<Read> fetch(){
final ArrayList<Read> old=list;
fetchInner();
return old;
}
private void fetchInner(){
ListNum<Read> ln=cris.nextList();
list=(ln==null ? null : ln.list);
if(list.size()<1){list=null;}
else if(genKmer){
for(Read r : list){ReadComparatorTopological5Bit.genKmer(r);}
}else if(clump){
for(Read r : list){ReadComparatorClump.set(r);}
}
read=(list==null ? null : list.get(0));
if(lastNum>=0){cris.returnList(lastNum, list==null);}
if(ln!=null){lastNum=ln.id;}
assert((read==null)==(list==null || list.size()==0));
// if(count>0 && list!=null){
// for(Read r : list){
// assert(remainingReads>=0) : remainingReads+", "+count+", "+r.numericID;
// double remaining=(count-sum);
// double mult=2*(remaining/remainingReads);
// sum=sum+randy.nextDouble()*mult;
// r.rand=sum;
//// System.err.println(r.rand);
// remainingReads--;
// }
// }
}
public boolean close(){
return ReadWrite.closeStream(cris);
}
public Read peek(){return read;}
@Override
public int compareTo(CrisContainer other) {
assert(read!=null);
assert(other.read!=null);
return comparator.compare(read, other.read);
}
public int compareTo(Read other) {
return comparator.compare(read, other);
}
public boolean hasMore(){
return read!=null;
}
public ConcurrentReadInputStream cris(){return cris;}
final ConcurrentReadInputStream cris;
private Read read;
private long lastNum=-1;
private ArrayList<Read> list;
private final Comparator<Read> comparator;
private final boolean genKmer, clump;
// private double sum=0;
// final int count;
// private final Random randy;
// private int remainingReads;
}
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