/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.cli_plugin;
import org.apache.log4j.Logger;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.Feature;
import htsjdk.tribble.readers.AsciiLineReader;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.LineIteratorImpl;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.*;
/**
* Decoder for Ascii features
* User: jacob
* Date: 2012-Sep-27
*/
public class AsciiDecoder<D extends Feature> implements FeatureDecoder<D> {
private static Logger log = Logger.getLogger(AsciiDecoder.class);
protected LineFeatureDecoder<D> lineFeatureDecoder;
public AsciiDecoder() {
}
public AsciiDecoder(LineFeatureDecoder<D> lineFeatureDecoder) {
this.lineFeatureDecoder = lineFeatureDecoder;
}
public Iterator<D> decodeAll(InputStream is, boolean strictParsing) throws IOException {
List<D> featuresList = new ArrayList<D>();
String line;
D feat;
LineIterator lrw = new LineIteratorImpl(new AsciiLineReader(is));
lineFeatureDecoder.readActualHeader(lrw);
while (lrw.hasNext()) {
line = lrw.next();
try {
feat = decode(line);
if (feat != null) {
featuresList.add(feat);
}
} catch (Exception e) {
log.error(e.getMessage(), e);
if (strictParsing) {
throw new RuntimeException(e);
}
}
}
is.close();
return featuresList.iterator();
}
public D decode(String line) {
return this.lineFeatureDecoder.decode(line);
}
@Override
public void setAttributes(List<Map<String, Object>> attributes) {
}
@Override
public void setInputs(List<String> commands, Map<Argument, Object> argumentMap) {
}
/**
* Wrap an AsciiFeatureCodec into implementing LineFeatureDecoder
*
* @param <T>
*/
public static class DecoderWrapper<T extends Feature> extends AsciiDecoder<T> implements LineFeatureDecoder<T> {
private AsciiFeatureCodec<T> wrappedCodec;
public DecoderWrapper(AsciiFeatureCodec<T> wrappedCodec) {
this.wrappedCodec = wrappedCodec;
this.lineFeatureDecoder = this;
}
@Override
public T decode(String line) {
return wrappedCodec.decode(line);
}
@Override
public Object readActualHeader(LineIterator reader) throws IOException{
return wrappedCodec.readHeader(reader);
}
}
/**
* The purpose of this class is 2-fold:
* 0. Wrap a BufferedReader in a LineIterator so the interface works
* 1. Keep track of read lines so reading the header doesn't throw away potential data
* When the QueuingLineReader is set to {@code queueing}, it queues each readLine.
* Once {@code queueing} is turned off the queued lines are returned. The queue is
* cleared when {@code queueing} is toggled on the theory that only blocks
* will want to be read.
* @author jacob
* @since 3 Jul 2013
* @deprecated Using {@link htsjdk.tribble.readers.LineIterator#peek()} should
* remove the need for this class
*/
@Deprecated
private static class QueuingLineReader implements LineIterator{
private BufferedReader wrappedReader;
private Queue<String> lineBuffer = new ArrayDeque<String>();
private boolean queueing = false;
private String next = null;
private boolean iterating = false;
QueuingLineReader(BufferedReader lineReader){
this.wrappedReader = lineReader;
}
/**
* Toggle whether we are queuing lines or not
* @param queueing
*/
void setQueueing(boolean queueing){
boolean wasQueuing = this.queueing;
this.queueing = queueing;
if(this.queueing) {
lineBuffer.clear();
}else{
this.iterating = false;
this.next = null;
}
}
private String readLine() throws IOException {
String line;
if(queueing){
line = this.wrappedReader.readLine();
if(line != null) lineBuffer.add(line);
}else{
line = lineBuffer.poll();
if(line == null) line = this.wrappedReader.readLine();
}
return line;
}
public void close() {
this.lineBuffer = null;
try {
this.wrappedReader.close();
} catch (IOException e) {
log.error(e.getMessage(), e);
}
}
protected String advance() {
String next = null;
try {
next = readLine();
} catch (IOException e) {
log.error(e.getMessage(), e);
}
return next;
}
@Override
public boolean hasNext() {
// If this is the start of iteration, queue up the first item
if (!iterating) {
next = advance();
iterating = true;
}
return next != null;
}
@Override
public String peek() {
return this.next;
}
@Override
public String next() {
if (!hasNext()) {
throw new NoSuchElementException();
}
String ret = next;
next = advance();
return ret;
}
@Override
public void remove() {
throw new UnsupportedOperationException("remove() not supported");
}
}
}