List of usage examples for org.apache.commons.lang3 ArrayUtils toPrimitive
public static boolean[] toPrimitive(final Boolean[] array)
Converts an array of object Booleans to primitives.
This method returns null for a null input array.
From source file:org.mskcc.shenkers.control.alignment.AlignmentPolygon.java
public Polygon getPolygon() { Stack<Double> ends = new Stack<>(); Stack<Double> heights = new Stack<>(); List<Double> points = new ArrayList<>(); for (int i = 0; i < span.size(); i++) { GenomeSpan s = span.get(i);/*from w w w. j a va 2 s .c om*/ GenomeSpan d = displayedSpans.get(i); double displayedSpanWidth = d.length() + 0.; double relativeWidth = s.length() / displayedSpanWidth; int distanceFromStart = d.isNegativeStrand() ? d.getEnd() - s.getEnd() : s.getStart() - d.getStart(); // int distanceFromStart = d.isNegativeStrand() ? d.getEnd() : d.getStart(); double relativeStart = (distanceFromStart) / displayedSpanWidth; double relativeHeight = weight.get(i); points.add(relativeStart); points.add(relativeHeight); ends.push(relativeStart + relativeWidth); heights.push(relativeHeight); } while (ends.size() > 0) { points.add(ends.pop()); points.add(heights.pop()); } logger.info(points); return new Polygon(ArrayUtils.toPrimitive(points.toArray(new Double[0]))); }
From source file:org.mskcc.shenkers.control.track.bam.BamView1.java
public Pane get(SamReader SAMReader, String chr, int start, int end) { LineHistogramView lhv = new LineHistogramView(); logger.info("calculating coverage for region {}:{}-{}", chr, start, end); SAMRecordIterator sri = SAMReader.query(chr, start, end, false); int length = 1 + end - start; int[] cov = new int[length]; try {// www. jav a2 s . c o m while (sri.hasNext()) { SAMRecord sr = sri.next(); // logger.info("read: " + sr); int alignmentPosition = sr.getAlignmentStart(); // logger.info("ap {} lastStart {}", alignmentPosition, lastStart); // // // update all positions for which we won't see any more reads // for (int i = lastStart; i < alignmentPosition; i++) { // max = Math.max(max, cov[i-start]); // final int j = i; // final double MAX = Math.max(max, cov[i-start]); // logger.info("emitting: " + cov[j - start]); // // ); // } // lastStart = alignmentPosition; // } Cigar cigar = sr.getCigar(); for (int i = 0; i < cigar.numCigarElements(); i++) { CigarElement cigarElement = cigar.getCigarElement(i); if (cigarElement.getOperator().consumesReferenceBases()) { boolean consumesReadBases = cigarElement.getOperator().consumesReadBases(); for (int j = 0; j < cigarElement.getLength(); j++) { if (consumesReadBases && alignmentPosition >= start && alignmentPosition <= end) { cov[alignmentPosition - start]++; } alignmentPosition++; } } } } // Platform.runLater(() -> { //// double MAX = 0; //// for (double d : cov) { //// MAX = Math.max(d, MAX); //// lhv.addData(d); //// } // // double[] data = ArrayUtils.toPrimitive(IntStream.of(cov).mapToDouble(j -> j + 0.).boxed().collect(Collectors.toList()).toArray(new Double[0])); // lhv.setData(data); // IntStream.of(cov).max().ifPresent(m -> lhv.setMax(m)); // // }); } catch (Exception e) { e.printStackTrace(); } sri.close(); double[] data = ArrayUtils.toPrimitive(IntStream.of(cov).mapToDouble(j -> j + 0.).boxed() .collect(Collectors.toList()).toArray(new Double[0])); lhv.setData(data, null); IntStream.of(cov).max().ifPresent(m -> lhv.setMax(m)); // if(lastStart<end) // for (int i = lastStart; i <= end; i++) { // final int j = i; // final double MAX = Math.max(max, cov[i]); // logger.info("emitting: "+cov[j-start]); // Platform.runLater(() -> { // lhv.addData(cov[j - start]); // lhv.setMax(MAX); // } // ); // } // Platform.runLater(() -> { // lhv.setMin(0); // lhv.setMax(1); // }); // while (true) { // Platform.runLater(() // -> lhv.addData(Math.random())); // try { // Thread.sleep(1000); // } catch (InterruptedException e) { // if (isCancelled()) { // break; // } // } // } return lhv.getGraphic(); }
From source file:org.neo4j.ogm.typeconversion.ByteArrayWrapperBase64Converter.java
@Override public String toGraphProperty(Byte[] value) { if (value == null) return null; return Base64.getEncoder().encodeToString(ArrayUtils.toPrimitive(value)); }
From source file:org.opendaylight.openflowplugin.pyretic.Utils.OutputUtils.java
/** * @param nodeId/*from w w w . j a v a 2 s .co m*/ * @param payload * @param outPort * @param inPort * @return * */ public synchronized static TransmitPacketInput createPacketOut(final String nodeId, final byte[] payload, final String outPort, final String inPort) { ArrayList<Byte> list = new ArrayList<Byte>(40); // FIXME payload should be added to packet for (byte b : payload) { list.add(b); } /* System.out.print("My super duper payload: "); for (int i = 0; i < list.size(); i++) System.out.printf("%02x ",0xff & list.get(i)); System.out.println(""); */ NodeRef ref = createNodeRef(nodeId); NodeConnectorRef nEgressConfRef = new NodeConnectorRef(createNodeConnRef(nodeId, outPort)); NodeConnectorRef nIngressConRef = new NodeConnectorRef(createNodeConnRef(nodeId, inPort)); TransmitPacketInputBuilder tPackBuilder = new TransmitPacketInputBuilder(); final ArrayList<Byte> _converted_list = list; byte[] _primitive = ArrayUtils.toPrimitive(_converted_list.toArray(new Byte[0])); List<Action> actionList = new ArrayList<Action>(); ActionBuilder ab = new ActionBuilder(); OutputActionBuilder output = new OutputActionBuilder(); output.setMaxLength(Integer.valueOf(0xffff)); Uri value = new Uri(OutputPortValues.NORMAL.toString()); output.setOutputNodeConnector(value); ab.setAction(new OutputActionCaseBuilder().setOutputAction(output.build()).build()); ab.setOrder(0); ab.setKey(new ActionKey(0)); actionList.add(ab.build()); tPackBuilder.setConnectionCookie(null); tPackBuilder.setAction(actionList); tPackBuilder.setPayload(_primitive); tPackBuilder.setNode(ref); tPackBuilder.setEgress(nEgressConfRef); tPackBuilder.setIngress(nIngressConRef); tPackBuilder.setBufferId(Long.valueOf(0xffffffffL)); return tPackBuilder.build(); }
From source file:org.openestate.tool.helloworld.db.hsql.HSqlDbHelloWorldHandler.java
@Override public long[] getObjectIds(Connection c) throws SQLException { PreparedStatement statement = null; ResultSet result = null;/* www .j a v a 2 s . c o m*/ try { statement = c.prepareStatement("SELECT " + FIELD_HELLOWORLD_ID + " " + "FROM " + VIEW_HELLOWORLD + " " + "ORDER BY " + FIELD_HELLOWORLD_ID + " ASC;"); result = statement.executeQuery(); List<Long> ids = new ArrayList<>(); while (result.next()) { ids.add(result.getLong(FIELD_HELLOWORLD_ID)); } return ArrayUtils.toPrimitive(ids.toArray(new Long[0])); } finally { JdbcUtils.closeQuietly(result); JdbcUtils.closeQuietly(statement); } }
From source file:org.openml.webapplication.fantail.dc.DCUntils.java
public static double[] computeAttributeEntropy(Instances data) { List<Double> attributeEntropy = new ArrayList<Double>(); for (int attIndex = 0; attIndex < data.numAttributes(); attIndex++) { if (data.attribute(attIndex).isNominal() && (data.classIndex() != attIndex)) { double[] attValueCounts = new double[data.numDistinctValues(attIndex)]; for (int i = 0; i < data.numInstances(); i++) { Instance inst = data.instance(i); attValueCounts[(int) inst.value(attIndex)]++; }// w w w . j a va 2 s . c o m double attEntropy = 0; for (int c = 0; c < data.attribute(attIndex).numValues(); c++) { if (attValueCounts[c] > 0) { double prob_c = attValueCounts[c] / data.numInstances(); attEntropy += prob_c * (Utils.log2(prob_c)); } } attEntropy = attEntropy * -1.0; attributeEntropy.add(attEntropy); } } return ArrayUtils.toPrimitive(attributeEntropy.toArray(new Double[attributeEntropy.size()])); }
From source file:org.openml.webapplication.fantail.dc.DCUntils.java
public static double[] computeMutualInformation(Instances data) { List<Double> mutualInformation = new ArrayList<Double>(); for (int attIndex = 0; attIndex < data.numAttributes(); attIndex++) { if (data.attribute(attIndex).isNominal() && (data.classIndex() != attIndex)) { // System.out.println(data.attribute(attIndex)); double infoGain = computeInfoGain(data, data.attribute(attIndex)); infoGain = Math.round(infoGain * Math.pow(10, 14)) / Math.pow(10, 14); mutualInformation.add(infoGain); }//from w w w . j a va 2 s. c om } return ArrayUtils.toPrimitive(mutualInformation.toArray(new Double[mutualInformation.size()])); }
From source file:org.openml.webapplication.fantail.dc.statistical.Statistical.java
@Override public Map<String, Double> characterize(Instances instances) { int attrib_count = instances.numAttributes() - 1, numeric_count = 0; for (int i = 0; i < attrib_count; i++) { if (instances.attribute(i).isNumeric()) { numeric_count++;/*from ww w . j a v a 2s . c o m*/ final double mean = instances.meanOrMode(i); final double stddev = Math.sqrt(instances.variance(i)); final double kurtosis = findKurtosis(instances, mean, stddev, i); final double skewness = findSkewness(instances, mean, stddev, i); meanList.add(mean); stdDevList.add(stddev); kurtosisList.add(kurtosis); skewnessList.add(skewness); } } if (0 == numeric_count) { Map<String, Double> qualities = new HashMap<String, Double>(); qualities.put(ids[0], 0.0); qualities.put(ids[1], 0.0); qualities.put(ids[2], 0.0); qualities.put(ids[3], 0.0); qualities.put(ids[4], 0.0); qualities.put(ids[5], 0.0); qualities.put(ids[6], 0.0); qualities.put(ids[7], 0.0); qualities.put(ids[8], 0.0); qualities.put(ids[9], 0.0); qualities.put(ids[10], 0.0); qualities.put(ids[11], 0.0); qualities.put(ids[12], 0.0); qualities.put(ids[13], 0.0); qualities.put(ids[14], 0.0); qualities.put(ids[15], 0.0); qualities.put(ids[16], 0.0); qualities.put(ids[17], 0.0); qualities.put(ids[18], 0.0); qualities.put(ids[19], 0.0); qualities.put(ids[20], 0.0); qualities.put(ids[21], 0.0); qualities.put(ids[22], 0.0); qualities.put(ids[23], 0.0); return qualities; } else { double[] meansArray = ArrayUtils.toPrimitive(meanList.toArray(new Double[numeric_count])); double[] stdDevsArray = ArrayUtils.toPrimitive(stdDevList.toArray(new Double[numeric_count])); double[] kurtosisArray = ArrayUtils.toPrimitive(kurtosisList.toArray(new Double[numeric_count])); double[] skewnessArray = ArrayUtils.toPrimitive(skewnessList.toArray(new Double[numeric_count])); Map<String, Double> qualities = new HashMap<String, Double>(); qualities.put(ids[0], StatUtils.mean(meansArray)); qualities.put(ids[1], StatUtils.mean(stdDevsArray)); qualities.put(ids[2], StatUtils.mean(kurtosisArray)); qualities.put(ids[3], StatUtils.mean(skewnessArray)); qualities.put(ids[4], StatUtils.min(meansArray)); qualities.put(ids[5], StatUtils.min(stdDevsArray)); qualities.put(ids[6], StatUtils.min(kurtosisArray)); qualities.put(ids[7], StatUtils.min(skewnessArray)); qualities.put(ids[8], StatUtils.max(meansArray)); qualities.put(ids[9], StatUtils.max(stdDevsArray)); qualities.put(ids[10], StatUtils.max(kurtosisArray)); qualities.put(ids[11], StatUtils.max(skewnessArray)); qualities.put(ids[12], StatUtils.percentile(meansArray, 25)); qualities.put(ids[13], StatUtils.percentile(stdDevsArray, 25)); qualities.put(ids[14], StatUtils.percentile(kurtosisArray, 25)); qualities.put(ids[15], StatUtils.percentile(skewnessArray, 25)); qualities.put(ids[16], StatUtils.percentile(meansArray, 50)); qualities.put(ids[17], StatUtils.percentile(stdDevsArray, 50)); qualities.put(ids[18], StatUtils.percentile(kurtosisArray, 50)); qualities.put(ids[19], StatUtils.percentile(skewnessArray, 50)); qualities.put(ids[20], StatUtils.percentile(meansArray, 75)); qualities.put(ids[21], StatUtils.percentile(stdDevsArray, 75)); qualities.put(ids[22], StatUtils.percentile(kurtosisArray, 75)); qualities.put(ids[23], StatUtils.percentile(skewnessArray, 75)); return qualities; } }
From source file:org.orcid.frontend.web.forms.PublicationsTaskForm.java
public int[] getPositions() { List<Integer> positionsToDelete = new ArrayList<Integer>(publications.size()); int position = 0; for (Publication publication : publications) { if (publication.isSelected()) { positionsToDelete.add(position); }//ww w .j a v a 2 s .co m position++; } return ArrayUtils.toPrimitive(positionsToDelete.toArray(new Integer[0])); }
From source file:org.pdfsam.ui.selection.multiple.move.MultipleSelectionAndFocus.java
public int[] getRows() { // TODO this sucks return ArrayUtils.toPrimitive(rows.toArray(new Integer[rows.size()])); }