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package clump;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import sort.SortByName;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import structures.ListNum;
public class StreamToOutput {
public StreamToOutput(FileFormat ffin1, FileFormat ffin2, ConcurrentReadOutputStream[] rosa_, KmerComparator old, boolean sortByName_, boolean incrementComparator){
final ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ffin1, ffin2, null, null);
cris.start();
rosa=rosa_;
kc=(incrementComparator ? new KmerComparator(old.k, old.seed+1, old.border-1, old.hashes, false, false) : old);
sortByName=sortByName_;
}
public StreamToOutput(ConcurrentReadInputStream cris_, ConcurrentReadOutputStream[] rosa_, KmerComparator old, boolean sortByName_, boolean incrementComparator){
cris=cris_;
rosa=rosa_;
kc=(incrementComparator ? new KmerComparator(old.k, old.seed+1, old.border-1, old.hashes, false, false) : old);
sortByName=sortByName_;
}
public boolean process(){
if(rosa==null || rosa.length==0){return errorState;}
File temp=null;
if(sortByName){
try {
temp=File.createTempFile("temp_namesort_", ".fq.gz");
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
SortByName sbn=new SortByName(new String[] {"out="+temp.getAbsolutePath()});
sbn.processInner(cris);
FileFormat ff=FileFormat.testInput(temp.getAbsolutePath(), null, false);
cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null, null, null);
}
if(rosa.length==1){
processSingle(cris);
}else{
processMulti(cris);
}
errorState|=ReadWrite.closeStream(cris);
if(temp!=null){
temp.delete();
}
return errorState;
}
public void processSingle(ConcurrentReadInputStream cris){
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
if(rosa!=null){rosa[0].add(reads, ln.id);}
for(Read r : reads){
readsIn+=r.pairCount();
basesIn+=r.pairLength();
}
cris.returnList(ln);
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(ln!=null){
cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
}
}
public void processMulti(ConcurrentReadInputStream cris){
final int groups=rosa.length;
@SuppressWarnings("unchecked")
final ArrayList<Read>[] out=new ArrayList[groups];
for(int i=0; i<out.length; i++){
out[i]=new ArrayList<Read>();
}
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
for(Read r : reads){
long kmer=kc.hash(r, null, 0, false);
int group=(int)(kmer%groups);
out[group].add(r);
readsIn+=r.pairCount();
basesIn+=r.pairLength();
}
for(int group=0; group<groups; group++){
rosa[group].add(out[group], ln.id);
out[group]=new ArrayList<Read>();
}
cris.returnList(ln);
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(ln!=null){
cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
}
}
long readsIn=0;
long basesIn=0;
// final FileFormat ffin1;
// final FileFormat ffin2;
ConcurrentReadInputStream cris;
ConcurrentReadOutputStream[] rosa;
final KmerComparator kc;
final boolean sortByName;
boolean errorState=false;
}
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