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A Java library for collating textual sources, for example, to produce an apparatus.

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package eu.interedition.collatex.suffixtree;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.Map;

/**
 * @author Max Garfinkel
 */
public class Utils {

    /**
     * Appends a SequenceTerminal element to a supplied array.
     *
     * @param sequence          The sequence to which we are applying the terminating object.
     * @param terminatingObject The instance of the terminating object.
     * @return A new sequence with an extra element at the end containing the
     * terminating object.
     */
    static > Object[] addTerminalToSequence(S sequence,
                                                                     SequenceTerminal terminatingObject) {

        ArrayList list = new ArrayList();
        for (I item : sequence)
            list.add(item);

        Object[] newSequence = new Object[list.size() + 1];

        int i = 0;
        for (; i < list.size(); i++)
            newSequence[i] = list.get(i);
        newSequence[i] = terminatingObject;
        return newSequence;
    }

    static > String printTreeForGraphViz(SuffixTree tree) {
        return printTreeForGraphViz(tree, true);
    }

    /**
     * Generates a .dot format string for visualizing a suffix tree.
     *
     * @param tree The tree for which we are generating a dot file.
     * @return A string containing the contents of a .dot representation of the
     * tree.
     */
    static > String printTreeForGraphViz(SuffixTree tree, boolean printSuffixLinks) {
        LinkedList> stack = new LinkedList<>();
        stack.add(tree.getRoot());
        Map, Integer> nodeMap = new HashMap<>();
        nodeMap.put(tree.getRoot(), 0);
        int nodeId = 1;

        StringBuilder sb = new StringBuilder(
            "\ndigraph suffixTree{\n node [shape=circle, label=\"\", fixedsize=true, width=0.1, height=0.1]\n");

        while (stack.size() > 0) {
            LinkedList> childNodes = new LinkedList<>();
            for (Node node : stack) {

                // List edges = node.getEdges();
                for (Edge edge : node) {
                    int id = nodeId++;
                    if (edge.isTerminating()) {
                        childNodes.push(edge.getTerminal());
                        nodeMap.put(edge.getTerminal(), id);
                    }

                    sb.append(nodeMap.get(node)).append(" -> ").append(id)
                        .append(" [label=\"");

                    for (T item : edge) {
                        //if(item != null)
                        sb.append(item.toString());
                    }
                    sb.append("\"];\n");
                }
            }
            stack = childNodes;
        }
        if (printSuffixLinks) {
            // loop again to find all suffix links.
            sb.append("edge [color=red]\n");
            for (Map.Entry, Integer> entry : nodeMap.entrySet()) {
                Node n1 = entry.getKey();
                int id1 = entry.getValue();

                if (n1.hasSuffixLink()) {
                    Node n2 = n1.getSuffixLink();
                    Integer id2 = nodeMap.get(n2);
                    // if(id2 != null)
                    sb.append(id1).append(" -> ").append(id2).append(" ;\n");
                }
            }
        }
        sb.append("}");
        return (sb.toString());
    }
}
 















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