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500697_10
public static Map<Study, Treatment> findStudyBaselines(Collection<Study> studies, UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph) { return new DepthFirstSearch<Map<Study, Treatment>>().search(new InconsistencyBaselineSearchProblem(studies, cGraph)); }
500697_11
public static Tree<Treatment, FoldedEdge<Treatment, Study>> findSpanningTree(Collection<Study> studies, UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph) { boolean hasCompleteBaseline = findStudyBaselines(studies, cGraph) != null; int nFunctional = cGraph.getEdgeCount() - cGraph.getVertexCount() + 1; ...
500697_12
@Override public boolean equals(Object obj) { if (obj instanceof Partition) { Partition other = (Partition) obj; return other.d_parts.equals(d_parts); } return false; }
500697_13
public Partition reduce() { if (d_reduced) { return this; } UndirectedGraph<Treatment, Part> graph = buildGraph(d_parts); if (graph == null) { return this; } // Start at an arbitrary part connected to the least vertex. // If we don't start at the least vertex, the result might vary for cycles that reduce...
500697_14
public Partition reduce() { if (d_reduced) { return this; } UndirectedGraph<Treatment, Part> graph = buildGraph(d_parts); if (graph == null) { return this; } // Start at an arbitrary part connected to the least vertex. // If we don't start at the least vertex, the result might vary for cycles that reduce...
500697_15
public String getName() { return "w." + StringUtils.join(CollectionHelper.transform(d_cycle.subList(0, d_cycle.size() - 1), s_idTransformer), "."); }
500697_16
@Override public boolean equals(Object obj) { if (obj instanceof InconsistencyParameter) { InconsistencyParameter other = (InconsistencyParameter) obj; return d_cycle.equals(other.d_cycle); } return false; }
500697_17
public static Tree<Treatment, FoldedEdge<Treatment, Study>> findSpanningTree(UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph) { MinimumDiameterSpanningTree<Treatment, FoldedEdge<Treatment, Study>> mdst = new MinimumDiameterSpanningTree<Treatment, FoldedEdge<Treatment, Study>>(cGraph, TreatmentComparato...
500697_18
public static Map<Study, Treatment> findStudyBaselines(Hypergraph<Treatment, Study> studyGraph, Tree<Treatment, FoldedEdge<Treatment, Study>> tree) { Map<Study, Treatment> map = new HashMap<Study, Treatment>(); for (Study s : studyGraph.getEdges()) { map.put(s, findMaxDegreeVertex(tree, studyGraph.getIncidentVertic...
500697_19
public static List<BasicParameter> getSplittableNodes(Network network) { Hypergraph<Treatment, Study> studyGraph = NetworkModel.createStudyGraph(network); UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph = NetworkModel.createComparisonGraph(studyGraph); return getSplittableNodes(studyGraph, cGraph); }
500697_20
public static List<BasicParameter> getSplittableNodes(Network network) { Hypergraph<Treatment, Study> studyGraph = NetworkModel.createStudyGraph(network); UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph = NetworkModel.createComparisonGraph(studyGraph); return getSplittableNodes(studyGraph, cGraph); }
500697_21
public static List<BasicParameter> getSplittableNodes(Network network) { Hypergraph<Treatment, Study> studyGraph = NetworkModel.createStudyGraph(network); UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph = NetworkModel.createComparisonGraph(studyGraph); return getSplittableNodes(studyGraph, cGraph); }
500697_22
public static Tree<Treatment, FoldedEdge<Treatment, Study>> findSpanningTree(UndirectedGraph<Treatment, FoldedEdge<Treatment, Study>> cGraph, BasicParameter split) { UndirectedSparseGraph<Treatment, FoldedEdge<Treatment, Study>> graph = new UndirectedSparseGraph<Treatment, FoldedEdge<Treatment, Study>>(); GraphUtil.c...
500697_23
@Override public Map<NetworkParameter, Integer> parameterize(Treatment ta, Treatment tb) { if (d_splitNode.getBaseline().equals(ta) && d_splitNode.getSubject().equals(tb)) { Map<NetworkParameter, Integer> map = new HashMap<NetworkParameter, Integer>(); map.put(getDirectParameter(), 1); return map; } if (d_spli...
500697_24
@Override public List<List<Pair<Treatment>>> parameterizeStudy(Study s) { Pair<Treatment> split = new Pair<Treatment>(d_splitNode.getBaseline(), d_splitNode.getSubject()); if (s.getTreatments().size() == 2 || !s.getTreatments().containsAll(split)) { return super.parameterizeStudy(s); } List<Pair<Treatment>> param...
500697_25
public static double generate(InconsistencyParameter w, InconsistencyParameterization pmtz, StartingValueGenerator generator, Map<BasicParameter, Double> basicValues) { double x = 0.0; final List<Treatment> c = w.getCycle(); for (int i = 1; i < c.size(); ++i) { BasicParameter p = new BasicParameter(c.get(i - 1),...
500697_26
public String getName() { return "d." + d_base.getId() + "." + d_subj.getId() + "." + (d_direct ? "dir" : "ind"); }
500697_27
@Override public boolean equals(Object obj) { if (obj instanceof SplitParameter) { SplitParameter other = (SplitParameter) obj; return d_base.equals(other.d_base) && d_subj.equals(other.d_subj) && d_direct == other.d_direct; } return false; }
500697_28
public int compareTo(SplitParameter other) { TreatmentComparator tc = TreatmentComparator.INSTANCE; if (tc.compare(d_base, other.d_base) != 0) { return tc.compare(d_base, other.d_base); } if (tc.compare(d_subj, other.d_subj) != 0) { return tc.compare(d_subj, other.d_subj); } if (d_direct) { return other.d_d...
500697_29
public int compare(Parameter o1, Parameter o2) { int par1Type = classes.indexOf(o1.getClass()); int par2Type = classes.indexOf(o2.getClass()); if (par1Type < 0 | par2Type < 0) { throw new IllegalArgumentException("Attempt to compare unknown Parameter class : " + o1.getClass()); } if (par1Type != par2Type) { ...
500697_30
public int compare(Parameter o1, Parameter o2) { int par1Type = classes.indexOf(o1.getClass()); int par2Type = classes.indexOf(o2.getClass()); if (par1Type < 0 | par2Type < 0) { throw new IllegalArgumentException("Attempt to compare unknown Parameter class : " + o1.getClass()); } if (par1Type != par2Type) { ...
500697_31
public int compare(Parameter o1, Parameter o2) { int par1Type = classes.indexOf(o1.getClass()); int par2Type = classes.indexOf(o2.getClass()); if (par1Type < 0 | par2Type < 0) { throw new IllegalArgumentException("Attempt to compare unknown Parameter class : " + o1.getClass()); } if (par1Type != par2Type) { ...
500697_32
public int compare(Parameter o1, Parameter o2) { int par1Type = classes.indexOf(o1.getClass()); int par2Type = classes.indexOf(o2.getClass()); if (par1Type < 0 | par2Type < 0) { throw new IllegalArgumentException("Attempt to compare unknown Parameter class : " + o1.getClass()); } if (par1Type != par2Type) { ...
500697_33
@Override public boolean equals(Object obj) { if (obj instanceof Part) { Part other = (Part) obj; return d_treatments.equals(other.d_treatments) && d_studies.equals(other.d_studies); } return false; }
500697_34
public String getName() { return "d." + d_base.getId() + "." + d_subj.getId(); }
500697_35
@Override public boolean equals(Object o) { if (o instanceof BasicParameter) { BasicParameter other = (BasicParameter) o; return d_base.equals(other.d_base) && d_subj.equals(other.d_subj); } return false; }
500697_36
@SuppressWarnings("rawtypes") @Override public int getRowIndex(Comparable key) { if (!(key instanceof String)) { return -1; } String str = (String) key; int idx = Integer.parseInt(str.substring(5)) - 1; if (idx < 0 || idx >= d_summary.getTreatments().size()) { return -1; } return idx; }
500697_37
@SuppressWarnings("rawtypes") @Override public int getColumnIndex(Comparable key) { if (!(key instanceof String) && !(key instanceof Treatment)) { return -1; } String treatment = key instanceof String ? (String) key : ((Treatment)key).getId(); int idx = 0; for (Treatment t : d_summary.getTreatments()) { if (t....
500697_38
@SuppressWarnings("rawtypes") @Override public int getRowIndex(Comparable key) { if (!(key instanceof String)) { return -1; } String str = (String) key; int idx = Integer.parseInt(str.substring(5)) - 1; if (idx < 0 || idx >= d_summary.getTreatments().size()) { return -1; } return idx; }
500697_39
@SuppressWarnings("rawtypes") @Override public int getColumnIndex(Comparable key) { if (!(key instanceof String) && !(key instanceof Treatment)) { return -1; } String treatment = key instanceof String ? (String) key : ((Treatment)key).getId(); int idx = 0; for (Treatment t : d_summary.getTreatments()) { if (t....
500697_40
@Override public String getRowKey(int row) { return "Rank " + (row + 1); }
500697_41
@Override public String getColumnKey(int column) { return d_summary.getTreatments().get(column).format(d_preferDescription); }
500697_42
@Override public List<String> getRowKeys() { List<String> keys = new ArrayList<String>(); for (int i = 0; i < d_summary.getTreatments().size(); ++i) { keys.add("Rank " + (i+1)); } return keys; }
500697_43
@Override public List<String> getColumnKeys() { List<String> keys = new ArrayList<String>(); for (Treatment t : d_summary.getTreatments()) { keys.add(t.getId()); } return keys; }
500697_44
@Override public int getRowCount() { return d_summary.getTreatments().size(); }
500697_45
@Override public int getColumnCount() { return d_summary.getTreatments().size(); }
500697_46
@Override public Number getValue(int row, int column) { return d_summary.getValue(d_summary.getTreatments().get(column), row + 1); }
500697_47
public int getColumnCount() { return d_summary.getTreatments().size() + 1; }
500697_48
public int getRowCount() { return d_summary.getTreatments().size(); }
500697_49
public Object getValueAt(int rowIndex, int columnIndex) { Treatment treatment = d_summary.getTreatments().get(rowIndex); if (columnIndex == 0) { return treatment.format(d_preferDescription); } else { return d_summary.getDefined() ? d_summary.getValue(treatment, columnIndex) : ""; } }
500697_50
@Override public String getColumnName(int column) { if (column == 0) { return "Drug"; } else { return "Rank " + column; } }
500697_51
@Override public Class<?> getColumnClass(int column) { if (column == 0) { return String.class; } else { return Double.class; } }
500697_52
public Object getValueAt(int rowIndex, int columnIndex) { Treatment treatment = d_summary.getTreatments().get(rowIndex); if (columnIndex == 0) { return treatment.format(d_preferDescription); } else { return d_summary.getDefined() ? d_summary.getValue(treatment, columnIndex) : ""; } }
500697_53
public Boolean getValue() { return d_val; }
500697_54
public Boolean getValue() { return d_val; }
500697_55
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_56
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_57
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_58
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_59
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_60
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_61
public String getValue() { NumberFormat format = new DecimalFormat("0.0"); if(d_results.getNumberOfSamples() > 0) { if(getKiloByteSize() < 100) { return format.format(getKiloByteSize()) + " KB"; } return format.format(getKiloByteSize() / 1000.0) + " MB"; } return "0.0 KB"; }
500697_62
public int[] getCounts(int series) { return d_counts[series]; }
500697_63
public int[] getCounts(int series) { return d_counts[series]; }
500697_64
public double[] getDensities(int series) { return d_densities[series]; }
500697_65
public double[] getDensities(int series) { return d_densities[series]; }
500697_66
public Double getX(int series, int bin) { if (series < 0 || series >= d_nSeries) throw new IndexOutOfBoundsException(); return (0.5 + bin) * d_interval + d_bottom; }
500697_67
public int[] getCounts(int series) { return d_counts[series]; }
500697_68
public double[] getDensities(int series) { return d_densities[series]; }
500697_69
public int getRowCount() { return d_studyIndex.get(d_studies.size()); }
500697_70
public Object getValueAt(int row, int col) { int i = findStudyIndex(row); if (i < 0) { return null; } Study s = d_studies.get(i); if (row == d_studyIndex.get(i)) { // study description row if (col == 0) { return s; } else { return null; } } else { Treatment t = s.getMeasurements().get(row - d_stud...
500697_71
public Object getValueAt(int row, int col) { int i = findStudyIndex(row); if (i < 0) { return null; } Study s = d_studies.get(i); if (row == d_studyIndex.get(i)) { // study description row if (col == 0) { return s; } else { return null; } } else { Treatment t = s.getMeasurements().get(row - d_stud...
500697_72
public Object getValueAt(int row, int col) { int i = findStudyIndex(row); if (i < 0) { return null; } Study s = d_studies.get(i); if (row == d_studyIndex.get(i)) { // study description row if (col == 0) { return s; } else { return null; } } else { Treatment t = s.getMeasurements().get(row - d_stud...
500697_73
@Override public boolean isCellEditable(int row, int col) { if (col == 0) { return false; } int i = findStudyIndex(row); if (i < 0 || row == d_studyIndex.get(i)) { return false; } return true; }
500697_74
public Component getTableCellRendererComponent(JTable table, Object cellContents, boolean isSelected, boolean hasFocus, int row, int column) { return (new DefaultTableCellRenderer()).getTableCellRendererComponent(table, getCellText(cellContents), isSelected, hasFocus, row, column); }
500697_75
public Component getTableCellRendererComponent(JTable table, Object cellContents, boolean isSelected, boolean hasFocus, int row, int column) { return (new DefaultTableCellRenderer()).getTableCellRendererComponent(table, getCellText(cellContents), isSelected, hasFocus, row, column); }
500697_76
public void clear() { final ArrayList<ModelType> nodes = new ArrayList<ModelType>(d_nodes.keySet()); d_nodes.clear(); fireTreeNodesRemoved(nodes); }
500697_77
public void replace(ModelType type, MCMCPresentation oldPresentation, MCMCPresentation newPresentation) { d_nodes.get(type).remove(oldPresentation); d_nodes.get(type).add(newPresentation); fireNodeReplaced(type, oldPresentation, newPresentation); }
500697_78
public static <V, E> void copyGraph(Graph<V, E> source, Graph<V, E> target) { addVertices(target, source.getVertices()); for (E e : source.getEdges()) { target.addEdge(e, source.getIncidentVertices(e), source.getEdgeType(e)); } }
500697_79
public static <V, E> void copyTree(Tree<V, E> source, Tree<V, E> target) { target.addVertex(source.getRoot()); LinkedList<E> toAdd = new LinkedList<E>(source.getChildEdges(source.getRoot())); while (!toAdd.isEmpty()) { E e = toAdd.removeFirst(); target.addEdge(e, source.getSource(e), source.getDest(e)); toAdd....
500697_80
public static <V, E> boolean isWeaklyConnected(Hypergraph<V, E> graph) { if (graph.getVertexCount() == 0) { return true; } else { HashSet<V> visited = new HashSet<V>(); // already visited vertices LinkedList<V> fringe = new LinkedList<V>(); // directly reachable vertices fringe.add(graph.getVertices().iterato...
500697_81
public static <V,E> boolean areVerticesWeaklyConnected(Hypergraph<V, E> studyGraph, V first, V second) { Set<V> visited = new HashSet<V>(); LinkedList<V> fringe = new LinkedList<V>(); fringe.add(first); while (!fringe.isEmpty()) { V v = fringe.removeFirst(); if (v.equals(second)) { return true; } visited...
500697_82
public static <V, E> boolean isSimpleCycle(UndirectedGraph<V, E> graph) { if (graph.getVertexCount() < 3 || graph.getEdgeCount() < graph.getVertexCount()) { return false; } V v = graph.getVertices().iterator().next(); Set<V> visited = new HashSet<V>(); visited.add(v); while (graph.getNeighborCount(v) == 2 && !v...
500697_83
public static <V, E> V findCommonAncestor(Tree<V, E> tree, V u, V v) { while (tree.getDepth(u) > tree.getDepth(v)) { u = tree.getParent(u); } while (tree.getDepth(v) > tree.getDepth(u)) { v = tree.getParent(v); } while (!u.equals(v)) { v = tree.getParent(v); u = tree.getParent(u); } return v; }
500697_84
public static <V, E> List<V> findPath(Tree<V, E> tree, V u, V v) { LinkedList<V> path = new LinkedList<V>(); while (tree.getDepth(u) > tree.getDepth(v)) { path.add(u); u = tree.getParent(u); } int idx = path.size(); while (tree.getDepth(v) > tree.getDepth(u)) { path.add(idx, v); v = tree.getParent(v); } ...
500697_85
public Iterator<Tree<V, E>> iterator() { return new SpanningTreeIterator(); }
500697_86
public Iterator<Tree<V, E>> iterator() { return new SpanningTreeIterator(); }
500697_87
public Tree<V, E> getMinimumDiameterSpanningTree() { PointOnEdge<V, E> center = new AbsoluteOneCenter<V, E>(d_graph, d_edgeLength, d_distance, d_vertexComparator).getCenter(); DelegateTree<V,E> tree = new DelegateTree<V, E>(); // add the center edge // choose the one closest to the absolute one center, or the "fi...
500697_88
public Tree<V, E> getMinimumDiameterSpanningTree() { PointOnEdge<V, E> center = new AbsoluteOneCenter<V, E>(d_graph, d_edgeLength, d_distance, d_vertexComparator).getCenter(); DelegateTree<V,E> tree = new DelegateTree<V, E>(); // add the center edge // choose the one closest to the absolute one center, or the "fi...
500697_89
public Tree<V, E> getMinimumDiameterSpanningTree() { PointOnEdge<V, E> center = new AbsoluteOneCenter<V, E>(d_graph, d_edgeLength, d_distance, d_vertexComparator).getCenter(); DelegateTree<V,E> tree = new DelegateTree<V, E>(); // add the center edge // choose the one closest to the absolute one center, or the "fi...
500697_90
static <V> Double intersect(final Distance<V> distance, final V e0, final V e1, final double l, final V u, final V v) { final double lu = distance.getDistance(e0, u).doubleValue(); final double ru = distance.getDistance(e1, u).doubleValue(); final double lv = distance.getDistance(e0, v).doubleValue(); final double ...
500697_91
static <V> List<V> distanceOrderedVertices(final Distance<V> distance, final V v, final Comparator<V> comparator) { final Map<V, Number> map = distance.getDistanceMap(v); List<V> list = new ArrayList<V>(map.keySet()); Collections.sort(list, new Comparator<V>() { public int compare(V a, V b) { if (map.get(a).equ...
500697_92
public PointOnEdge<V, E> getCenter() { LocalCenter<V, E> localCenter = new LocalCenter<V, E>(d_graph, d_edgeLength, d_distance, d_comparator); Center<V, E> c = null; for (E e : d_graph.getEdges()) { Center<V, E> lc = localCenter.transform(e); if (c == null || lc.getRadius() < c.getRadius() || (lc.getRadius...
500697_93
public PointOnEdge<V, E> getCenter() { LocalCenter<V, E> localCenter = new LocalCenter<V, E>(d_graph, d_edgeLength, d_distance, d_comparator); Center<V, E> c = null; for (E e : d_graph.getEdges()) { Center<V, E> lc = localCenter.transform(e); if (c == null || lc.getRadius() < c.getRadius() || (lc.getRadius...
500697_94
public PointOnEdge<V, E> getCenter() { LocalCenter<V, E> localCenter = new LocalCenter<V, E>(d_graph, d_edgeLength, d_distance, d_comparator); Center<V, E> c = null; for (E e : d_graph.getEdges()) { Center<V, E> lc = localCenter.transform(e); if (c == null || lc.getRadius() < c.getRadius() || (lc.getRadius...
500697_95
public boolean getDefined() { return d_isDefined; }
500697_96
public boolean getDefined() { return d_defined; }
500697_97
public boolean getDefined() { return d_defined; }
500697_98
public boolean getDefined() { return d_defined; }
500697_99
public double getScaleReduction() { return d_convergence; }
500806_10
@Override public void validateMessage(Message receivedMessage, Message controlMessage, TestContext context, ValidationContext validationContext) throws ValidationException { if (controlMessage == null || controlMessage.getPayload() == null) { log.debug("Skip message payload valid...
500806_11
@Override public void validateMessage(Message receivedMessage, Message controlMessage, TestContext context, ValidationContext validationContext) throws ValidationException { if (controlMessage == null || controlMessage.getPayload() == null) { log.debug("Skip message payload valid...
500806_12
@Override public void validateMessage(Message receivedMessage, Message controlMessage, TestContext context, ValidationContext validationContext) throws ValidationException { if (controlMessage == null || controlMessage.getPayload() == null) { log.debug("Skip message payload valid...
500806_13
@Override public void validateMessage(Message receivedMessage, Message controlMessage, TestContext context, ValidationContext validationContext) throws ValidationException { if (receivedMessage.getPayload() instanceof byte[]) { try (GZIPInputStream gzipInputStream = new GZIPInput...
500806_14
@Override public void validateMessage(Message receivedMessage, Message controlMessage, TestContext context, ValidationContext validationContext) throws ValidationException { if (receivedMessage.getPayload() instanceof byte[]) { try (GZIPInputStream gzipInputStream = new GZIPInput...
500806_15
@Override public void validateMessage(Message receivedMessage, Message controlMessage, TestContext context, ValidationContext validationContext) throws ValidationException { if (receivedMessage.getPayload() instanceof byte[]) { try (GZIPInputStream gzipInputStream = new GZIPInput...
500806_16
@Override public void processMessage(Message message, TestContext context) { if (message.getPayload() == null || !StringUtils.hasText(message.getPayload(String.class))) { return; } String jsonPathExpression; try { JSONParser parser = new JSONParser(JSONParser.MODE_JSON_SIMPLE); O...
500806_17
@Override public void processMessage(Message message, TestContext context) { if (message.getPayload() == null || !StringUtils.hasText(message.getPayload(String.class))) { return; } String jsonPathExpression; try { JSONParser parser = new JSONParser(JSONParser.MODE_JSON_SIMPLE); O...
500806_18
@Override public void processMessage(Message message, TestContext context) { if (message.getPayload() == null || !StringUtils.hasText(message.getPayload(String.class))) { return; } String jsonPathExpression; try { JSONParser parser = new JSONParser(JSONParser.MODE_JSON_SIMPLE); O...
500806_19
@Override public void processMessage(Message message, TestContext context) { if (message.getPayload() == null || !StringUtils.hasText(message.getPayload(String.class))) { return; } String jsonPathExpression; try { JSONParser parser = new JSONParser(JSONParser.MODE_JSON_SIMPLE); O...