private void loadAnnotations(String annotationFilename) { try { LineIterator lines = new LineIterator(new FastBufferedReader(new FileReader(annotationFilename))); for (MutableString line : lines.allLines()) { if (line.startsWith("#")) continue; String tokens[] = line.toString().split("\t"); final String chromosome = tokens[0]; int position = Integer.parseInt(tokens[1]); // convert to zero-based position used by goby/variationanalysis: position -= 1; Int2ObjectAVLTreeMap<Annotation> perPositionMap = annotations.getOrDefault(chromosome, new Int2ObjectAVLTreeMap<>()); Annotation a = new Annotation(); a.position = position; a.toBase = tokens.length >= 3 ? tokens[2] : null; a.frequency = tokens.length >= 4 ? Float.parseFloat(tokens[3]) : null; perPositionMap.put(position, a); annotations.put(chromosome, perPositionMap); } } catch (FileNotFoundException e) { throw new RuntimeException("Unable to find annotation filename:" + annotationFilename, e); } }
/** Returns all lines remaining in this iterator as a list. * * @return all lines remaining in this iterator as a list. */ public List<MutableString> allLines() { final ObjectArrayList<MutableString> result = new ObjectArrayList<MutableString>(); while( hasNext() ) result.add( next().copy() ); return result; } }
final ProgressLogger pl = new ProgressLogger(); pl.itemsName = "URIs"; final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( System.in, "UTF-8" ), bufferSize ), pl ); while( termIterator.hasNext() ) { uri = termIterator.next(); if ( uniqueURIs ) makeUnique( filter, uri ); termList.add( uri.copy() ); pl.itemsName = "URIs"; pl.start( "Copying URIs..." ); final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( new FileInputStream( termFile ) ), bufferSize ), pl ); File temp = File.createTempFile( URLMPHVirtualDocumentResolver.class.getName(), ".uniqueuris" ); temp.deleteOnExit(); final FastBufferedOutputStream outputStream = new FastBufferedOutputStream( new FileOutputStream( termFile ), bufferSize ); MutableString uri; while( termIterator.hasNext() ) { uri = termIterator.next(); makeUnique( filter, uri ); uri.writeUTF8( outputStream );
System.exit(1); predictionLine = new LineIterator(new FastBufferedReader(predReader));
public MutableString next() { if ( ! hasNext() ) throw new NoSuchElementException(); toAdvance = true; if ( pl != null ) pl.update(); return s[ k ]; }
final ProgressLogger pl = new ProgressLogger(); pl.itemsName = "URIs"; final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( System.in, "UTF-8" ), bufferSize ), pl ); while( termIterator.hasNext() ) { uri = termIterator.next(); if ( uniqueURIs ) makeUnique( filter, uri ); termList.add( uri.copy() ); pl.itemsName = "URIs"; pl.start( "Copying URIs..." ); final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( new FileInputStream( termFile ) ), bufferSize ), pl ); File temp = File.createTempFile( URLMPHVirtualDocumentResolver.class.getName(), ".uniqueuris" ); temp.deleteOnExit(); final FastBufferedOutputStream outputStream = new FastBufferedOutputStream( new FileOutputStream( termFile ), bufferSize ); MutableString uri; while( termIterator.hasNext() ) { uri = termIterator.next(); makeUnique( filter, uri ); uri.writeUTF8( outputStream );
pl.itemsName = "words"; pl.start( "Reading words..." ); final FrontCodedStringList frontCodedStringList = new FrontCodedStringList( new LineIterator( new FastBufferedReader( new InputStreamReader( zipped ? new GZIPInputStream( System.in ) : System.in, encoding ), bufferSize ), pl ), ratio, utf8 ); pl.done();
@Override public MutableString next() { if (! hasNext()) throw new NoSuchElementException(); toAdvance = true; if (pl != null) pl.update(); return s[k]; }
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
final ProgressLogger pl = new ProgressLogger(); pl.itemsName = "URIs"; final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( System.in, "UTF-8" ), bufferSize ), pl ); while( termIterator.hasNext() ) { uri = termIterator.next(); if ( uniqueURIs ) makeUnique( filter, uri ); termList.add( uri.copy() ); pl.itemsName = "URIs"; pl.start( "Copying URIs..." ); final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( new FileInputStream( termFile ) ), bufferSize ), pl ); File temp = File.createTempFile( URLMPHVirtualDocumentResolver.class.getName(), ".uniqueuris" ); temp.deleteOnExit(); final FastBufferedOutputStream outputStream = new FastBufferedOutputStream( new FileOutputStream( termFile ), bufferSize ); MutableString uri; while( termIterator.hasNext() ) { uri = termIterator.next(); makeUnique( filter, uri ); uri.writeUTF8( outputStream );
/** Returns all lines remaining in this iterator as a list. * * @return all lines remaining in this iterator as a list. */ public List<MutableString> allLines() { final ObjectArrayList<MutableString> result = new ObjectArrayList<MutableString>(); while( hasNext() ) result.add( next().copy() ); return result; } }
final Iterator<MutableString> iterator = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(inputStream) : inputStream, encoding), bufferSize)); final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject(functionName); final Logger logger = LoggerFactory.getLogger(ShiftAddXorSignedStringMap.class);
public MutableString next() { if ( ! hasNext() ) throw new NoSuchElementException(); toAdvance = true; if ( pl != null ) pl.update(); return s[ k ]; }
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
final ProgressLogger pl = new ProgressLogger(); pl.itemsName = "URIs"; final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( System.in, "UTF-8" ), bufferSize ), pl ); while( termIterator.hasNext() ) { uri = termIterator.next(); if ( uniqueURIs ) makeUnique( filter, uri ); termList.add( uri.copy() ); pl.itemsName = "URIs"; pl.start( "Copying URIs..." ); final LineIterator termIterator = new LineIterator( new FastBufferedReader( new InputStreamReader( new FileInputStream( termFile ) ), bufferSize ), pl ); File temp = File.createTempFile( URLMPHVirtualDocumentResolver.class.getName(), ".uniqueuris" ); temp.deleteOnExit(); final FastBufferedOutputStream outputStream = new FastBufferedOutputStream( new FileOutputStream( termFile ), bufferSize ); MutableString uri; while( termIterator.hasNext() ) { uri = termIterator.next(); makeUnique( filter, uri ); uri.writeUTF8( outputStream );
pl.itemsName = "strings"; pl.start("Reading strings..."); final FrontCodedStringList frontCodedStringList = new FrontCodedStringList(new LineIterator(new FastBufferedReader( new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding), bufferSize), pl), ratio, utf8); pl.done();
pl.displayFreeMemory = true; pl.start("Loading strings..."); collection = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(System.in) : System.in, encoding)), pl).allLines(); pl.done();
/** * Obtain the next selectedIndex from prediction line that is strictly larger than currentIndex. * If predictionLine is null (option -p was not given), return currentIndex. * * @param predictionLine * @param selectedIndex * @param currentIndex * @return */ private int getNextIndex(LineIterator predictionLine, int selectedIndex, int currentIndex) { if (predictionLine == null) return currentIndex; if (selectedIndex >= currentIndex) { return selectedIndex; } while (selectedIndex < currentIndex && predictionLine.hasNext()) { // find the next selected index in the prediction file. MutableString line = predictionLine.next(); if (line.startsWith("index")) continue; int tabIndex = line.indexOf('\t'); if (tabIndex == -1) { tabIndex = line.length(); } if (tabIndex > 0) { selectedIndex = Integer.parseInt(line.subSequence(0, tabIndex).toString()); } } return selectedIndex; }
final Iterator<MutableString> iterator = new LineIterator(new FastBufferedReader(new InputStreamReader(zipped ? new GZIPInputStream(inputStream) : inputStream, encoding), bufferSize)); final Object2LongFunction<CharSequence> function = (Object2LongFunction<CharSequence>)BinIO.loadObject(functionName); final Logger logger = LoggerFactory.getLogger(ShiftAddXorSignedStringMap.class);