Example usage for com.google.common.collect Multimap putAll

Introduction

In this page you can find the example usage for com.google.common.collect Multimap putAll.

Prototype

boolean putAll(Multimap<? extends K, ? extends V> multimap);

Source Link

Document

Stores all key-value pairs of multimap in this multimap, in the order returned by multimap.entries() .

Usage

From source file:de.hzi.helmholtz.Compare.PathwayComparisonUsingModules.java

public Multimap<Double, String> SubsetsMatching(final PathwayUsingModules firstPathway,
        final PathwayUsingModules secondPathway, BiMap<String, Integer> newSourceGeneIdToPositionMap,
        BiMap<String, Integer> newTargetGeneIdToPositionMap, int Yes) {
    Multimap<Double, String> resultPerfect = TreeMultimap.create(Ordering.natural().reverse(),
            Ordering.natural());/*from  ww  w  .  j av  a2  s .  co  m*/
    PathwayUsingModules firstPathwayCopy = new PathwayUsingModules(firstPathway);// Copy of the Query pathway
    PathwayUsingModules secondPathwayCopy = new PathwayUsingModules(secondPathway);// Copy of the Target pathway'
    // PathwayUsingModules secondPathwayCopy1 = new PathwayUsingModules(secondPathway);
    int currentQueryGene = 0;
    Iterator<Module> sourceGeneIt = firstPathway.geneIterator();
    List<String> QueryToRemove = new ArrayList<String>();
    List<String> TargetToRemove = new ArrayList<String>();
    while (sourceGeneIt.hasNext()) {
        currentQueryGene++;
        Module queryGene = sourceGeneIt.next();

        int currentTargetGene = 0;
        Multiset<String> qfunction = LinkedHashMultiset.create();
        List<String> qfunctionList = new ArrayList<String>();
        List<String> qactivity = new ArrayList<String>();
        List<Set<String>> qsubstrate = new ArrayList<Set<String>>();
        for (Domain d : queryGene.getDomains()) {
            qfunction.add(d.getDomainFunctionString());
            qfunctionList.add(d.getDomainFunctionString());
            qactivity.add(d.getStatus().toString());
            qsubstrate.add(d.getSubstrates());
        }
        Iterator<Module> targetGeneIt = secondPathway.geneIterator();

        while (targetGeneIt.hasNext()) {
            currentTargetGene++;
            Module targetGene = targetGeneIt.next();
            Multiset<String> tfunction = LinkedHashMultiset.create();
            List<String> tfunctionList = new ArrayList<String>();
            List<String> tactivity = new ArrayList<String>();
            List<Set<String>> tsubstrate = new ArrayList<Set<String>>();
            for (Domain d : targetGene.getDomains()) {
                tfunctionList.add(d.getDomainFunctionString());
                tfunction.add(d.getDomainFunctionString());
                tactivity.add(d.getStatus().toString());
                tsubstrate.add(d.getSubstrates());
            }
            Multiset<String> DomainsCovered = Multisets.intersection(qfunction, tfunction);
            if (DomainsCovered.size() == qfunction.size() && DomainsCovered.size() == tfunction.size()) {
                Multimap<Double, Multimap<String, Integer>> activityscores = myFunction.calculate(qactivity,
                        tactivity);
                Multimap<String, Integer> Functionscores = ArrayListMultimap.create();

                int TranspositionDomains = LevenshteinDistance.computeLevenshteinDistance(qfunctionList,
                        tfunctionList);
                if (TranspositionDomains > 0) {
                    TranspositionDomains = 1;
                }

                Functionscores.put(qfunction.size() + "-0", TranspositionDomains);
                Multimap<Double, Multimap<String, Integer>> substratescore = myFunction
                        .calculate(getSubstrateList(qsubstrate), getSubstrateList(tsubstrate));
                Object activityScore = activityscores.asMap().keySet().toArray()[0];
                Object substrateScore = substratescore.asMap().keySet().toArray()[0];
                double finalScore = Math
                        .round((((2.9 * 1.0) + (0.05 * Double.parseDouble(activityScore.toString().trim()))
                                + (0.05 * Double.parseDouble(substrateScore.toString().trim()))) / 3) * 100.0)
                        / 100.0;
                String ConvertedGeneIDs = "";
                if (Yes == 0) {
                    ConvertedGeneIDs = reconstructWithGeneId(Integer.toString(currentQueryGene),
                            newSourceGeneIdToPositionMap) + "->"
                            + reconstructWithGeneId(Integer.toString(currentTargetGene),
                                    newTargetGeneIdToPositionMap);
                } else {
                    ConvertedGeneIDs = reconstructWithGeneId(Integer.toString(currentTargetGene),
                            newTargetGeneIdToPositionMap) + "->"
                            + reconstructWithGeneId(Integer.toString(currentQueryGene),
                                    newSourceGeneIdToPositionMap);
                }
                resultPerfect.put(finalScore, ConvertedGeneIDs);
                ScoreFunctionMatchMisMatch.put(ConvertedGeneIDs, Functionscores);
                ScoreStatusMatchMisMatch.putAll(ConvertedGeneIDs, activityscores.values());
                ScoreSubstrateMatchMisMatch.putAll(ConvertedGeneIDs, substratescore.values());

                TargetToRemove.add(reconstructWithGeneId(Integer.toString(currentTargetGene),
                        newTargetGeneIdToPositionMap));
                QueryToRemove.add(reconstructWithGeneId(Integer.toString(currentQueryGene),
                        newSourceGeneIdToPositionMap));
            }
        }

    }
    for (String i : TargetToRemove) {
        secondPathwayCopy.removeModule(i);
    }
    for (String i : QueryToRemove) {
        firstPathwayCopy.removeModule(i);
    }
    if (firstPathwayCopy.size() > 0 && secondPathwayCopy.size() > 0) {
        // Re-construct the bimaps
        newSourceGeneIdToPositionMap = HashBiMap.create();
        int temp = 0;
        for (Module e : firstPathwayCopy.getModules()) {
            temp = temp + 1;
            newSourceGeneIdToPositionMap.put(e.getModuleId(), temp);
        }
        newTargetGeneIdToPositionMap = HashBiMap.create();
        temp = 0;
        for (Module e : secondPathwayCopy.getModules()) {
            temp = temp + 1;
            newTargetGeneIdToPositionMap.put(e.getModuleId(), temp);
        }
        resultPerfect.putAll(SubsetIdentification(firstPathwayCopy, secondPathwayCopy,
                newSourceGeneIdToPositionMap, newTargetGeneIdToPositionMap, Yes));
    }
    ////System.out.println(resultPerfect);
    return resultPerfect;
}