Examples with MappingTest org.edamontology.edammap.core.benchmarking.MappingTest used on opensource projects

Example 1 with MappingTest

use of org.edamontology.edammap.core.benchmarking.MappingTest in project edammap by edamontology.

the class Txt method out.

static void out(QueryType type, PrintStream ps, Map<EdamUri, Concept> concepts, List<Query> queries, List<MappingTest> mappings) throws IOException {
    ps.print("query_id");
    ps.print(SEP);
    ps.print("query_name");
    ps.print(SEP);
    ps.print("edam_branch");
    ps.print(SEP);
    ps.print("edam_uri");
    ps.print(SEP);
    ps.print("edam_label");
    ps.print(SEP);
    ps.print("edam_obsolete");
    ps.print(SEP);
    ps.print("best_one_query");
    ps.print(SEP);
    ps.print("best_one_edam");
    ps.print(SEP);
    ps.print("best_one_score");
    ps.print(SEP);
    ps.print("without_path_score");
    ps.print(SEP);
    ps.print("score");
    ps.print(SEP);
    ps.print("test");
    ps.println();
    for (int i = 0; i < queries.size(); ++i) {
        Query query = queries.get(i);
        MappingTest mapping = mappings.get(i);
        for (Branch branch : Branch.values()) {
            for (MatchTest matchTest : mapping.getMatches(branch)) {
                Match match = matchTest.getMatch();
                Concept concept = concepts.get(match.getEdamUri());
                ps.print(query.getId() != null ? query.getId() : "");
                ps.print(SEP);
                ps.print(query.getName() != null ? query.getName() : "");
                ps.print(SEP);
                ps.print(branch);
                ps.print(SEP);
                ps.print(match.getEdamUri());
                ps.print(SEP);
                ps.print(concept.getLabel());
                ps.print(SEP);
                ps.print(concept.isObsolete());
                ps.print(SEP);
                ps.print(match.getQueryMatch().getType().name());
                ps.print(SEP);
                ps.print(match.getConceptMatch().getType().name());
                ps.print(SEP);
                ps.print(match.getBestOneScore() > -1 ? match.getBestOneScore() : "");
                ps.print(SEP);
                ps.print(match.getWithoutPathScore() > -1 ? match.getWithoutPathScore() : "");
                ps.print(SEP);
                ps.print(match.getScore());
                ps.print(SEP);
                ps.print(matchTest.getTest().name());
                ps.println();
            }
        }
    }
}