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package stream;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import structures.ListNum;
public abstract class ReadInputStream {
public static final ArrayList<Read> toReads(String fname, int defaultFormat, long maxReads){
if(fname==null){return null;}
FileFormat ff=FileFormat.testInput(fname, defaultFormat, null, false, true);
return toReads(ff, maxReads);
}
public static final Read[] toReadArray(FileFormat ff, long maxReads){
ArrayList<Read> list=toReads(ff, maxReads);
return list==null ? null : list.toArray(new Read[0]);
}
public static final ArrayList<Read> toReads(FileFormat ff, long maxReads){
ArrayList<Read> list=new ArrayList<Read>();
/* Start an input stream */
ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(maxReads, false, ff, null);
cris.start(); //4567
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
/* Iterate through read lists from the input stream */
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
list.addAll(reads);
/* Dispose of the old list and fetch a new one */
cris.returnList(ln);
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
/* Cleanup */
cris.returnList(ln);
ReadWrite.closeStream(cris);
return list;
}
public abstract Read next();
// public final ArrayList<Read> fetchAll(){
// ArrayList<Read> out=new ArrayList<Read>();
// for(ArrayList<Read> list=nextList(); list!=null && list.size()>0; list=nextList()){
// out.addAll(list);
// }
// close();
// return out;
// }
public abstract ArrayList<Read> nextList();
public abstract boolean hasMore();
public abstract void restart();
/** Returns true if there was an error, false otherwise */
public abstract boolean close();
public abstract boolean paired();
protected static final ArrayList<Read> toList(Read[] array){
if(array==null || array.length==0){return null;}
ArrayList<Read> list=new ArrayList<Read>(array.length);
for(int i=0; i<array.length; i++){list.add(array[i]);}
return list;
}
/** Return true if this stream has detected an error */
public boolean errorState(){return errorState;}
/** TODO */
protected boolean errorState=false;
public final boolean preferLists(){return true;}
public abstract void start();
public abstract String fname();
}
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