Examples with Citation dr.util.Citation used on opensource projects

Example 1 with Citation

use of dr.util.Citation in project beast-mcmc by beast-dev.

the class BeastParser method executingRunnable.

@Override
protected void executingRunnable() {
    Logger.getLogger("dr.apps.beast").info("\nCitations for this analysis: ");
    Map<String, Set<Pair<String, String>>> categoryMap = new LinkedHashMap<String, Set<Pair<String, String>>>();
    // force the Framework category to be first...
    categoryMap.put("Framework", new LinkedHashSet<Pair<String, String>>());
    for (Pair<String, String> keyPair : getCitationStore().keySet()) {
        Set<Pair<String, String>> pairSet = categoryMap.get(keyPair.fst);
        if (pairSet == null) {
            pairSet = new LinkedHashSet<Pair<String, String>>();
            categoryMap.put(keyPair.fst, pairSet);
        }
        pairSet.add(keyPair);
    }
    for (String category : categoryMap.keySet()) {
        Logger.getLogger("dr.apps.beast").info("\n" + category.toUpperCase());
        Set<Pair<String, String>> pairSet = categoryMap.get(category);
        for (Pair<String, String> keyPair : pairSet) {
            Logger.getLogger("dr.apps.beast").info(keyPair.snd + ":");
            for (Citation citation : getCitationStore().get(keyPair)) {
                Logger.getLogger("dr.apps.beast").info("\t" + citation.toString());
            }
        }
    }
    // clear the citation store so all the same citations don't get cited again
    getCitationStore().clear();
    Logger.getLogger("dr.apps.beast").info("\n");
}

Example 2 with Citation

use of dr.util.Citation in project beast-mcmc by beast-dev.

the class AbstractMultivariateTraitLikelihood method getCitations.

@Override
public List<Citation> getCitations() {
    List<Citation> citations = new ArrayList<Citation>();
    citations.add(CommonCitations.LEMEY_2010_PHYLOGEOGRAPHY);
    if (doAscertainmentCorrect) {
        citations.add(new Citation(new Author[] { new Author("MA", "Suchard"), new Author("J", "Novembre"), new Author("B", "von Holdt"), new Author("G", "Cybis") }, Citation.Status.IN_PREPARATION));
    }
    return citations;
}

Example 3 with Citation

use of dr.util.Citation in project beast-mcmc by beast-dev.

the class GeoSpatialDistribution method getCitations.

public List<Citation> getCitations() {
    List<Citation> citationList = new ArrayList<Citation>();
    citationList.add(new Citation(new Author[] { new Author("S", "Nylinder"), new Author("P", "Lemey"), new Author("M", "de Bruyn"), new Author("MA", "Suchard"), new Author("BE", "Pfeil"), new Author("N", "Walsh"), new Author("AA", "Anderberg") }, "On the biogeography of Centipeda: a species-tree diffusion approach", 2014, "Systematic Biology", 63, 178, 191, Citation.Status.PUBLISHED));
    return citationList;
}

Example 4 with Citation

use of dr.util.Citation in project beast-mcmc by beast-dev.

the class IntegratedMultivariateTraitLikelihood method getCitations.

public List<Citation> getCitations() {
    List<Citation> citationList = new ArrayList<Citation>(super.getCitations());
    citationList.add(new Citation(new Author[] { new Author("OG", "Pybus"), new Author("MA", "Suchard"), new Author("P", "Lemey"), new Author("F", "Bernadin"), new Author("A", "Rambaut"), new Author("FW", "Crawford"), new Author("RR", "Gray"), new Author("N", "Arinaminpathy"), new Author("S", "Stramer"), new Author("MP", "Busch"), new Author("E", "Delwart") }, "Unifying the spatial epidemiology and evolution of emerging epidemics", 2012, "Proceedings of the National Academy of Sciences", 109, 15066, 15071, Citation.Status.PUBLISHED));
    return citationList;
}