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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package bref;
import blbutil.FileUtil;
import blbutil.Filter;
import blbutil.SampleFileIt;
import blbutil.Utilities;
import java.io.BufferedInputStream;
import java.io.DataInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayDeque;
import java.util.Deque;
import java.util.NoSuchElementException;
import vcf.Marker;
import vcf.RefGTRec;
import vcf.Samples;
/**
* <p>Class {@code Bref3It} represents an iterator whose {@code next()} which
* returns records from a bref version 3 file.
* </p>
* <p>Instances of class {@code Bref3It} are not thread-safe.
* </p>
* <p>Methods of this class will terminate the Java Virtual Machine with
* an error message if an I/O error or file format error is detected.
* </p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public final class Bref3It implements SampleFileIt<RefGTRec> {
private final File brefFile;
private final DataInputStream bref;
private final Bref3Reader bref3Reader;
private final Deque<RefGTRec> buffer;
/**
* Constructs a new {@code Bref3It} instance.
* @param brefFile a bref version 3 file or {@code null} if the
* bref version 3 file is to be read from standard input
*
* @throws IllegalArgumentException if a format error is detected in a
* line of the specified bref file
*/
public Bref3It(File brefFile) {
this(brefFile, Filter.acceptAllFilter());
}
/**
* Constructs a new {@code Bref4It} instance.
* @param brefFile a bref v4 file
* @param markerFilter a marker filter or {@code null}
*
* @throws IllegalArgumentException if a format error is detected in a
* line of the specified bref v3 file
* @throws NullPointerException if {@code file == null}
*/
public Bref3It(File brefFile, Filter<Marker> markerFilter) {
if (markerFilter == null) {
markerFilter = Filter.acceptAllFilter();
}
InputStream is = null;
if (brefFile==null) {
is = new BufferedInputStream(System.in);
}
else {
is = FileUtil.bufferedInputStream(brefFile);
}
this.brefFile = brefFile;
this.bref = new DataInputStream(is);
this.bref3Reader = new Bref3Reader(bref, markerFilter);
this.buffer = new ArrayDeque<>(500);
bref3Reader.readBlock(bref, buffer);
}
/**
* Returns {@code true} if the iteration has more elements, and returns
* {@code false} otherwise.
* @return {@code true} if the iteration has more elements
*/
@Override
public boolean hasNext() {
return !buffer.isEmpty();
}
/**
* Returns the next element in the iteration.
* @return the next element in the iteration
* @throws NoSuchElementException if the iteration has no more elements
*/
@Override
public RefGTRec next() {
if (hasNext()==false) {
throw new NoSuchElementException();
}
RefGTRec rec = buffer.removeFirst();
if (buffer.isEmpty()) {
bref3Reader.readBlock(bref, buffer);
}
return rec;
}
@Override
public void close() {
try {
bref.close();
} catch (IOException ex) {
Utilities.exit(ex, "Error closing file");
}
buffer.clear();
}
@Override
public File file() {
return brefFile;
}
@Override
public Samples samples() {
return bref3Reader.samples();
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder(80);
sb.append(this.getClass().toString());
sb.append(" : ");
sb.append(brefFile);
return sb.toString();
}
}
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