Method emdHatImplLongLongInt has a Cognitive Complexity of 68 (exceeds 5 allowed). Consider refactoring.

Open

    private static long emdHatImplLongLongInt(java.util.Vector<Long> pc, java.util.Vector<Long> qc,
                                              java.util.Vector<java.util.Vector<Long>> c, long extraMassPenalty) {

        int n = pc.size();
        assert qc.size() == n;

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Function aggregate has a Cognitive Complexity of 64 (exceeds 5 allowed). Consider refactoring.

Open

def aggregate(latex):
    aggregation = []
    subgroups = [aggregation]
    insert_before_last_item = False
    environment = None

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CMMLInfoBase has 68 methods (exceeds 20 allowed). Consider refactoring.

Open

class CMMLInfoBase {
    @SuppressWarnings("all")
    Document cmmlDoc;
    public final Node adoptNode(Node node) throws DOMException {
        return cmmlDoc.adoptNode(node);

Method compute has a Cognitive Complexity of 63 (exceeds 5 allowed). Consider refactoring.

Open

    public long compute(java.util.Vector<Long> e, java.util.Vector<java.util.List<Edge>> c,
                        java.util.Vector<java.util.List<EdgeFlow>> x) {
        assert e.size() == c.size();
        assert x.size() == c.size();

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Function tokenize has a Cognitive Complexity of 55 (exceeds 5 allowed). Consider refactoring.

Open

def tokenize(string):
    _buffer = ''
    environments = []
    iterable = iter(range(len(string)))
    for i in iterable:

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Method compactForm has a Cognitive Complexity of 43 (exceeds 5 allowed). Consider refactoring.

Open

    private static MyNode compactForm(MyNode n) {
        if (n.node.getNodeType() == Node.TEXT_NODE) {
            n.out = n.node.getNodeValue().trim();
        } else {
            n.out = n.node.getNodeName();

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Method emdHatImplLongLongInt has 163 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    private static long emdHatImplLongLongInt(java.util.Vector<Long> pc, java.util.Vector<Long> qc,
                                              java.util.Vector<java.util.Vector<Long>> c, long extraMassPenalty) {

        int n = pc.size();
        assert qc.size() == n;

Method computeShortestPath has a Cognitive Complexity of 41 (exceeds 5 allowed). Consider refactoring.

Open

    void computeShortestPath(java.util.Vector<Long> d, java.util.Vector<Integer> prev,
                             int from, java.util.Vector<java.util.List<ReducedEdge>> costForward,
                             java.util.Vector<java.util.List<ResidualReducedEdge>> costBackward,
                             java.util.Vector<Long> e, int[] l) {
        // Making heap (all inf except 0, so we are saving comparisons...)

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Method generateConstraint has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.

Open

    private String generateConstraint(Node node, boolean isRoot) {
        int i = 0;
        String out = "";
        boolean hasText = false;
        if (node == null) {

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Method generateSimpleConstraints has a Cognitive Complexity of 38 (exceeds 5 allowed). Consider refactoring.

Open

    private String generateSimpleConstraints(Node node, boolean isRoot) {
        //Index of child node
        int childElementIndex = 0;
        final StringBuilder out = new StringBuilder();
        boolean queryHasText = false;

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File XMLHelper.java has 372 lines of code (exceeds 250 allowed). Consider refactoring.

Open

package com.formulasearchengine.mathmltools.helper;

import com.formulasearchengine.mathmltools.io.XmlDocumentReader;
import com.formulasearchengine.mathmltools.io.XmlDocumentWriter;
import com.formulasearchengine.mathmltools.xml.NonWhitespaceNodeList;

Method compute has 122 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    public long compute(java.util.Vector<Long> e, java.util.Vector<java.util.List<Edge>> c,
                        java.util.Vector<java.util.List<EdgeFlow>> x) {
        assert e.size() == c.size();
        assert x.size() == c.size();

Method isIdenticalTree has a Cognitive Complexity of 32 (exceeds 5 allowed). Consider refactoring.

Open

    boolean isIdenticalTree(MathNode aTree, MathNode bTree) {
        // first check if they have the same number of children
        if (aTree.equals(bTree) && aTree.getChildren().size() == bTree.getChildren().size()) {
            if (aTree.isOrderSensitive()) {
                // all children order sensitive

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File CMMLInfo.java has 364 lines of code (exceeds 250 allowed). Consider refactoring.

Open

package com.formulasearchengine.mathmltools.mml;

import com.formulasearchengine.mathmltools.helper.XMLHelper;
import com.formulasearchengine.mathmltools.querygenerator.FirstXQueryGenerator;
import com.formulasearchengine.mathmltools.querygenerator.QVarXQueryGenerator;

Function _convert_array_content has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

Open

def _convert_array_content(param, parent, alignment=None):
    if '|' in alignment:
        _alignment, columnlines = [], []
        for i in alignment:
            if i == '|':

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XMLHelper has 33 methods (exceeds 20 allowed). Consider refactoring.

Open

@SuppressWarnings("UnusedDeclaration")
public final class XMLHelper {
    public static final String NS_MATHML = "http://www.w3.org/1998/Math/MathML";
    public static final Pattern ANNOTATION_XML_PATTERN = Pattern.compile("annotation(-xml)?");
    public static final Pattern XML_DECLARATION = Pattern.compile("<\\?[xX][mM][lL].*\\?>", Pattern.DOTALL);

Method compareNode has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

    public static boolean compareNode(Node nQ, Node nN, Boolean considerLength, Map<String, Node> qvars) throws Exception {
        if (qvars == null) {
            throw new Exception("qvars array must not be null");
        }
        if (nQ.hasChildNodes()) {

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JsonGouldiBean has 28 methods (exceeds 20 allowed). Consider refactoring.

Open

@SuppressWarnings("unused")
@JsonIgnoreProperties(ignoreUnknown = true)
@JsonPropertyOrder({
        "definitions",
        "constraints",

Method abstractNodeDT has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

    private void abstractNodeDT(Node node, Integer applies) {
        Set<String> levelGenerators = Sets.newHashSet("apply", "bind");
        Map<String, Integer> dTa = new HashMap<>();
        Boolean rename = false;
        dTa.put("cn", 0);

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Method toString has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring.

Open

    public String toString() {
        Node mainElement = getMainElement();
        if (mainElement == null) {
            return null;
        }

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