/** For any given TileTemplateRead, we want to make sure that there is only a single TilePhasingValue */ private static Collection<TilePhasingValue> ensureSoleTilePhasingValuesPerRead(final Collection<TilePhasingValue> tilePhasingValues) { final Map<TileTemplateRead, List<TilePhasingValue>> partitionedMap = tilePhasingValues.stream().collect(Collectors.groupingBy(TilePhasingValue::getTileTemplateRead)); final Collection<TilePhasingValue> newTilePhasingValues = new LinkedList<>(); for (final TileTemplateRead read : partitionedMap.keySet()) { newTilePhasingValues.add(CollectionUtil.getSoleElement(partitionedMap.get(read))); } return newTilePhasingValues; } }
/** For any given TileTemplateRead, we want to make sure that there is only a single TilePhasingValue */ private static Collection<TilePhasingValue> ensureSoleTilePhasingValuesPerRead(final Collection<TilePhasingValue> tilePhasingValues) { final Map<TileTemplateRead, List<TilePhasingValue>> partitionedMap = tilePhasingValues.stream().collect(Collectors.groupingBy(TilePhasingValue::getTileTemplateRead)); final Collection<TilePhasingValue> newTilePhasingValues = new LinkedList<>(); for (final TileTemplateRead read : partitionedMap.keySet()) { newTilePhasingValues.add(CollectionUtil.getSoleElement(partitionedMap.get(read))); } return newTilePhasingValues; } }
/** Reads all of the stream into a String, decoding with the provided {@link java.nio.charset.Charset} then closes the stream quietly. */ public static String slurp(final InputStream is, final Charset charSet) { final List<String> tokenOrEmpty = tokenSlurp(is, charSet, "\\A"); return tokenOrEmpty.isEmpty() ? StringUtil.EMPTY_STRING : CollectionUtil.getSoleElement(tokenOrEmpty); }
/** Reads all of the stream into a String, decoding with the provided {@link java.nio.charset.Charset} then closes the stream quietly. */ public static String slurp(final InputStream is, final Charset charSet) { final List<String> tokenOrEmpty = tokenSlurp(is, charSet, "\\A"); return tokenOrEmpty.isEmpty() ? StringUtil.EMPTY_STRING : CollectionUtil.getSoleElement(tokenOrEmpty); }
/** Reads all of the stream into a String, decoding with the provided {@link java.nio.charset.Charset} then closes the stream quietly. */ public static String slurp(final InputStream is, final Charset charSet) { final List<String> tokenOrEmpty = tokenSlurp(is, charSet, "\\A"); return tokenOrEmpty.isEmpty() ? StringUtil.EMPTY_STRING : CollectionUtil.getSoleElement(tokenOrEmpty); }
private static Collection<Tile> getTileClusterRecordsV3( final Map<String, ? extends Collection<IlluminaTileMetrics>> locationToMetricsMap, final Map<Integer, Map<Integer, Collection<TilePhasingValue>>> phasingValues, final float density) { final Collection<Tile> tiles = new LinkedList<>(); for (final Map.Entry<String, ? extends Collection<IlluminaTileMetrics>> entry : locationToMetricsMap.entrySet()) { final Collection<IlluminaTileMetrics> tileRecords = entry.getValue(); final IlluminaTileMetrics record = CollectionUtil.getSoleElement(tileRecords); //only create for cluster records if (record.isClusterRecord()) { final Collection<TilePhasingValue> tilePhasingValues = phasingValues.get(record.getLaneNumber()).get(record.getTileNumber()); tiles.add(new Tile(record.getLaneNumber(), record.getTileNumber(), density, record.getMetricValue(), tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()]))); } } return Collections.unmodifiableCollection(tiles); }
private static Collection<Tile> getTileClusterRecordsV3( final Map<String, ? extends Collection<IlluminaTileMetrics>> locationToMetricsMap, final Map<Integer, Map<Integer, Collection<TilePhasingValue>>> phasingValues, final float density) { final Collection<Tile> tiles = new LinkedList<>(); for (final Map.Entry<String, ? extends Collection<IlluminaTileMetrics>> entry : locationToMetricsMap.entrySet()) { final Collection<IlluminaTileMetrics> tileRecords = entry.getValue(); final IlluminaTileMetrics record = CollectionUtil.getSoleElement(tileRecords); //only create for cluster records if (record.isClusterRecord()) { final Collection<TilePhasingValue> tilePhasingValues = phasingValues.get(record.getLaneNumber()).get(record.getTileNumber()); tiles.add(new Tile(record.getLaneNumber(), record.getTileNumber(), density, record.getMetricValue(), tilePhasingValues.toArray(new TilePhasingValue[tilePhasingValues.size()]))); } } return Collections.unmodifiableCollection(tiles); }
phasingValue = CollectionUtil.getSoleElement(codeMetricsMap.get(phasingCode)).getMetricValue(); prePhasingValue = CollectionUtil.getSoleElement(codeMetricsMap.get(prePhasingCode)).getMetricValue(); } else { final String message = String.format(
phasingValue = CollectionUtil.getSoleElement(codeMetricsMap.get(phasingCode)).getMetricValue(); prePhasingValue = CollectionUtil.getSoleElement(codeMetricsMap.get(prePhasingCode)).getMetricValue(); } else { final String message = String.format(
IlluminaMetricsCode.CLUSTER_ID.getMetricsCode(), IlluminaMetricsCode.DENSITY_ID.getMetricsCode(), entry.getKey(), observedCodes)); final IlluminaTileMetrics densityRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.DENSITY_ID.getMetricsCode())); final IlluminaTileMetrics clusterRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode()));
IlluminaMetricsCode.CLUSTER_ID.getMetricsCode(), IlluminaMetricsCode.DENSITY_ID.getMetricsCode(), entry.getKey(), observedCodes)); final IlluminaTileMetrics densityRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.DENSITY_ID.getMetricsCode())); final IlluminaTileMetrics clusterRecord = CollectionUtil.getSoleElement(codeMetricsMap.get(IlluminaMetricsCode.CLUSTER_ID.getMetricsCode()));