Example usage for java.util Set retainAll

Introduction

In this page you can find the example usage for java.util Set retainAll.

Prototype

boolean retainAll(Collection<?> c);

Source Link

Document

Retains only the elements in this set that are contained in the specified collection (optional operation).

Usage

From source file:Main.java

public static void main(String[] argv) throws Exception {
    Set set1 = new HashSet();
    Set set2 = new HashSet();

    set1.retainAll(set2);

    // Remove all elements from a set
    set1.clear();//  w w w . j  a  v  a  2  s  . co m

}

---

From source file:MainClass.java

public static void main(String[] args) {

    // Create two sets.
    Set s1 = new HashSet();
    s1.add("A");/*from   ww w. ja va  2 s  . c  o m*/
    s1.add("B");
    s1.add("C");

    Set s2 = new HashSet();
    s2.add("A");
    s2.add("B");

    Set union = new TreeSet(s1);
    union.addAll(s2); // now contains the union

    print("union", union);

    Set intersect = new TreeSet(s1);
    intersect.retainAll(s2);

    print("intersection", intersect);

}

---

From source file:SetStuff.java

public static void main(String[] args) {

    // Create two sets.
    Set s1 = new HashSet();
    s1.add("Ian Darwin");
    s1.add("Bill Dooley");
    s1.add("Jesse James");

    Set s2 = new HashSet();
    s2.add("Ian Darwin");
    s2.add("Doolin' Dalton");

    Set union = new TreeSet(s1);
    union.addAll(s2); // now contains the union

    print("union", union);

    Set intersect = new TreeSet(s1);
    intersect.retainAll(s2);

    print("intersection", intersect);

}

---

From source file:ubic.pubmedgate.resolve.focusedAnalysis.CreateNIFBulkDump.java

/**
 * @param args//from   www . ja v  a 2 s  . c o  m
 */
public static void main(String[] args) throws Exception {

    // training or unsupervised
    boolean allComp = true;
    // if training then check for accepted
    Model modelLoad = ModelFactory.createDefaultModel();
    String fileProperty;

    if (allComp) {
        fileProperty = "resolve.Lexicon.resolution.RDF.allComp";
        modelLoad.read(new FileInputStream(Config.config.getString(fileProperty)), null);
    }

    fileProperty = "resolve.Lexicon.resolution.RDF";
    modelLoad.read(new FileInputStream(Config.config.getString(fileProperty)), null);

    boolean reason = true;
    EvaluationRDFModel model = new EvaluationRDFModel(modelLoad, reason);

    int count = 0;
    int rejected = 0;
    String result = "pmid,mention,concept";
    log.info("total number of pmids:" + model.getPMIDs().size());
    Set<Resource> NIFSTDConcepts = model.getNIFSTDConcepts();
    Set<Resource> allTerms = model.getTerms();
    int passedPMIDs = 0;
    StopWatch s = new StopWatch();
    s.start();
    Set<Resource> PMIDs = model.getPMIDs();
    for (Resource pmid : PMIDs) {

        log.info("Time per PMID:" + (s.getTime() / ++passedPMIDs) + " processed:" + passedPMIDs + " of "
                + PMIDs.size());

        String pmidID = pmid.getURI().substring(pmid.getURI().lastIndexOf(':') + 1);
        log.info(pmidID);
        // PMID -> Mention -> Concept
        Set<Resource> mentions = model.getMentionsInPMID(pmid);
        for (Resource mention : mentions) {
            Set<Resource> terms = model.getLinkedResources(mention);
            // it's all resources before it's filtered
            terms.retainAll(allTerms);

            String mentionString = JenaUtil.getLabel(mention);
            for (Resource term : terms) {
                Set<Resource> concepts = model.getConceptsFromTerms(term);
                String termString = JenaUtil.getLabel(term);

                concepts.retainAll(NIFSTDConcepts);

                for (Resource concept : concepts) {
                    if (!model.rejected(mention, concept)) {
                        String conceptLabel = JenaUtil.getLabel(concept);
                        String conceptURI = "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#"
                                + concept.getLocalName();
                        log.info("  " + mentionString + "->" + termString + "->" + conceptLabel + "  "
                                + conceptURI);
                        // write mention, concept and pubmed abstract
                        result += "\r\n" + pmidID + ",\"" + mentionString + "\"," + conceptURI;
                        count++;
                    } else {
                        rejected++;
                    }
                }
            }
        }
    }
    log.info("Number printed:" + count);
    log.info("Number rejected:" + rejected);
    FileTools.stringToFile(result,
            new File(Config.config.getString("whitetext.resolve.results.folder") + "forNIFAll.txt"));

}

---

From source file:ubic.BAMSandAllen.RankedGeneListLoader.java

public static void main(String[] args) throws Exception {

    // RankedGeneListLoader jesseIdea = new RankedGeneListLoader(
    // "/grp/java/workspace/BAMSandAllen/data/rankedGenes/ranked once/Incoming.partialcon.genes.txt" );

    boolean removeNonExp = true;
    boolean useVirtual = true;
    boolean keepSign = true;

    // ERG, gene info top ten results varies for direction
    Direction direction = AnalyzeBAMSandAllenGenes.Direction.ANYDIRECTION;

    ConnectivityAndAllenExpressionMatrixPair pair = ExpressionMatrixPairFactory
            .connectivityAndExpression(direction, useVirtual, removeNonExp);
    // ConnectivityAndAllenExpressionMatrixPair pair = ExpressionMatrixPairFactory.connectivityPartial( direction,
    // false, RegressMatrix.CONNECTIVITY, useVirtual, removeNonExp, true );

    // need a partialcon pair
    // jesseIdea.writeCorrelationBasedData( pair );
    // System.exit( 1 );
    // pair.applyGeneFilter( new PrefixGeneFilter( "Drd" ) );
    // log.info( "Genes:" + Util.getUniqueGenes( pair.getMatrixBDataRows() ) );
    // log.info( pair.getCorrelation() );
    // pair.writeImages();
    ////  w  w w. java  2s . c  o  m
    // System.exit( 1 );

    // processDirectoryNoMissing( "/grp/java/workspace/BAMSandAllen/data/rankedGenes/direct increasing", pair );

    // processDirectoryNoMissing( "/grp/java/workspace/BAMSandAllen/data/rankedGenes/near final nobed", pair );
    processDirectoryNoMissing("/grp/java/workspace/BAMSandAllen/data/rankedGenes/LitCon", pair);
    System.exit(1);

    // LOOGenesInOrder.out.partialcon.txt.329.0.014448.topGenes.txt
    // LOOGenesInOrder.in.partialcon.txt.410.0.018005.topGenes.txt
    // LOOGenesInOrder.space.7.txt.435.0.019093.topGenes.txt

    /*
     * RankedGeneListLoader aLook = new RankedGeneListLoader(
     * "/grp/java/workspace/BAMSandAllen/data/rankedGenes/near final
     * nobed/LOOGenesInOrder.space.7.txt.435.0.019093.topGenes.txt" );
     */
    // ConnectivityAndAllenExpressionMatrixPair.NewEnergies.incoming.rOrder
    // ConnectivityAndAllenExpressionMatrixPair.NewEnergies.space.rOrder
    // ConnectivityAndAllenExpressionMatrixPair.NewEnergies.outgoing.rOrder
    // LOOGenesInOrder.out.partialcon.txt.329.0.014448.topGenes.txt
    // LOOGenesInOrder.in.partialcon.txt.410.0.018005.topGenes.txt
    // LOOGenesInOrder.space.7.txt.435.0.019093.topGenes.txt
    RankedGeneListLoader aLook = new RankedGeneListLoader(
            "/grp/java/workspace/BAMSandAllen/data/rankedGenes/near final nobed/LOOGenesInOrder.out.partialcon.txt.329.0.014448.topGenes.txt");
    pair.setMatrixBDataRows(aLook.lines);
    // log.info( pair.getCorrelation() );
    // pair.writeRMatrices();
    // pair.writeImages();
    pair.orderDataRows(aLook.lines);
    log.info(pair.getCorrelation());
    System.exit(1);
    pair.writeRMatrices();
    pair.writeImages();

    ExploreRegionNames explore = new ExploreRegionNames(pair);
    StringToStringSetMap parents = explore.getParents();

    String focusRegion = "Midbrain";
    Set<String> ROIs = parents.get(focusRegion);
    // some may have no exp
    ROIs.retainAll(pair.getAllenDataColNames());
    pair.removeAllenCols(ROIs);
    // Hindbrain
    // Interbrain
    // Midbrain
    // Cerebrum
    pair.run();

    log.info(focusRegion + ":" + pair.getCorrelation());
    pair.test(1000);

    System.exit(1);

    List<String> lines = aLook.lines;
    lines.remove(0);
    lines.remove(1);
    lines.remove(2);
    lines.remove(3);
    lines.remove(4);
    lines.remove(5);
    lines.remove(6);
    lines.remove(7);
    lines.remove(8);
    lines.remove(9);
    pair.setMatrixBDataRows(aLook.lines);
    log.info(pair.getCorrelation());
    log.info(lines.size());

    // processDirectoryNoMissing( "/grp/java/workspace/BAMSandAllen/data/rankedGenes/for Ray", pair );
    // processDirectoryNoMissing( "/grp/java/workspace/BAMSandAllen/data/rankedGenes/near final 962 regions", pair
    // );
    // processDirectoryNoMissing( "/grp/java/workspace/BAMSandAllen/data/rankedGenes/decreasing after lab meeting",
    // pair, keepSign );

}

---

From source file:ubic.pubmedgate.resolve.focusedAnalysis.PickNeuroLexRegions.java

/**
 * @param args/*ww w . j a va 2s  .c om*/
 */
public static void main(String[] args) throws Exception {
    // has human species
    // has spec to gen match to NIFSTD
    // no rejections
    // sort by occurances
    // get PMID references

    // common.add( "species:ncbi:9606" ); // human

    Model modelLoad = ModelFactory.createDefaultModel();
    String fileProperty;
    fileProperty = "resolve.Lexicon.resolution.RDF.allComp";
    modelLoad.read(new FileInputStream(Config.config.getString(fileProperty)), null);
    log.info(modelLoad.size());
    fileProperty = "resolve.Lexicon.resolution.RDF";
    modelLoad.read(new FileInputStream(Config.config.getString(fileProperty)), null);
    log.info(modelLoad.size());

    boolean reason = true;
    EvaluationRDFModel model = new EvaluationRDFModel(modelLoad, reason);
    Set<Resource> humanMentions = model.getMentionsForSpecies("9606");
    Set<Resource> commonSpeciesMentions = new HashSet<Resource>();
    Set<String> commonSpecies = SpeciesCounter.getCommonSpeciesLinStrings();
    Set<Resource> commonSpeciesPMIDs = new HashSet<Resource>();

    for (String common : commonSpecies) {
        common = common.substring(common.lastIndexOf(":") + 1);
        Set<Resource> mentionsForSpecies = model.getMentionsForSpecies(common);
        commonSpeciesMentions.addAll(mentionsForSpecies);

        commonSpeciesPMIDs.addAll(model.getPMIDsForSpecies(common));

    }

    log.info("Common mentions:" + commonSpeciesMentions.size());
    commonSpeciesMentions.retainAll(model.getMatchedMentions());

    log.info("Common pmids:" + commonSpeciesPMIDs.size());

    log.info("Matched common mentions:" + commonSpeciesMentions.size());

    log.info("Human mentions:" + humanMentions.size());
    Set<Resource> BIRNConcepts = model.getNIFSTDConcepts();
    Set<Resource> NNConcepts = model.getNNConcepts();
    humanMentions.retainAll(model.getMatchedMentions());

    log.info("Matched Human mentions:" + humanMentions.size());

    Set<Resource> finalRegionMentions = new HashSet<Resource>();
    int occuranceThreshold = 0;
    int count = 0;
    int nnLinks = 0;
    int birnConcepts = 0;
    ParamKeeper keeper = new ParamKeeper();

    ParamKeeper finalKeeper = new ParamKeeper();

    for (Resource commonMention : commonSpeciesMentions) {
        Set<Resource> concepts = model.getMentionEvaluations(commonMention);
        // there's going to be two of these properties - get the larger? should have number of unseen occurances
        int occurances = commonMention.getProperty(Vocabulary.number_of_occurances).getInt();
        // int abstractCount = commonMention.getProperty( Vocabulary.number_of_abstracts ).getInt();
        Set<Resource> pmids = model.getPMIDs(commonMention);
        Set<Resource> commonPmids = (Set<Resource>) Util.intersect(commonSpeciesPMIDs, pmids);
        // filter pmids for common species
        // if the pmid has link to one of common

        // StmtIterator statements = neuromention.listProperties( Vocabulary.in_PMID );
        // Resource taxon = model.createResource( "http://bio2rdf.org/taxon:" + species );
        // ResIterator resIt = model.listResourcesWithProperty( Vocabulary.mentions_species, taxon );

        int abstractCount = pmids.size();
        int commonAbstractCount = commonPmids.size();

        for (Resource concept : concepts) {
            if (BIRNConcepts.contains(concept)) {
                birnConcepts++;
                // how do I know it's spec to gen? -need to create automatic evaluations!
                if (model.specToGen(commonMention, concept) && commonAbstractCount > 1) {
                    Map<String, String> params = new HashMap<String, String>();
                    params.put("mention URI", commonMention.getURI());
                    String mentionLabel = JenaUtil.getLabel(commonMention);
                    mentionLabel = mentionLabel.substring(0, 1).toUpperCase() + mentionLabel.substring(1);
                    params.put("mention label", mentionLabel);
                    params.put("parent concept URI", concept.getURI());
                    params.put("parent concept label", "\"" + JenaUtil.getLabel(concept) + "\"");
                    params.put("abstract count", abstractCount + "");
                    params.put("common abstract count", commonAbstractCount + "");

                    params.put("PubMed link",
                            "HYPERLINK(\"" + model.getNCBIPMIDLink(commonPmids) + "\",\"PubMed Link\")");

                    count++;
                    finalRegionMentions.add(commonMention);

                    log.info(abstractCount + " " + commonAbstractCount + " " + JenaUtil.getLabel(commonMention)
                            + " < " + JenaUtil.getLabel(concept));

                    // TODO get birnlex IDs? - are they exact?
                    if (Util.intersectSize(NNConcepts, concepts) > 0) {
                        nnLinks++;
                        params.put("hasNNlink", "true");
                    } else {
                        params.put("hasNNlink", "false");
                    }

                    keeper.addParamInstance(params);

                    Map<String, String> finalParams = new HashMap<String, String>();
                    finalParams.put("Label", mentionLabel);
                    finalParams.put("Is part of", JenaUtil.getLabel(concept));
                    finalParams.put("Has role", "Brain Subdivisions based on automated term selection");
                    finalParams.put("Id", "");
                    String pmidComaString = "\"" + model.getComaSepPMIDs(commonPmids, 140) + "\"";
                    finalParams.put("PMID", pmidComaString);
                    finalKeeper.addParamInstance(finalParams);
                }
            }
        }
    }
    log.info("Number printed:" + count);
    log.info("Number in set:" + finalRegionMentions.size());
    log.info("Has NN links:" + nnLinks);
    log.info("Birn concepts:" + birnConcepts);

    keeper.writeExcel(Config.config.getString("whitetext.resolve.results.folder") + "forNeuroLex.xls");
    finalKeeper
            .writeExcel(Config.config.getString("whitetext.resolve.results.folder") + "forNeuroLexFinal.xls");

    // printMentionCountForPaper( finalRegionMentions, true );
    // printMentionCountForPaper( finalRegionMentions, false );
}

---

From source file:Main.java

public static <T> Set<T> intersect(Collection<T> l1, Collection<T> l2) {
    Set<T> nl = new HashSet<T>(l1);
    nl.retainAll(l2);
    return nl;/*from   w  w w . java 2  s.c  om*/
}

---

From source file:Main.java

public static <E> Set<E> intersection(final Set<E> set1, final Set<E> set2) {
    Set<E> set = new HashSet<>(set1);
    set.retainAll(set2);
    return Collections.unmodifiableSet(set);
}

---

From source file:Main.java

public static void performIntersection(Set<String> s1, Set<String> s2) {
    Set<String> s1Intersections2 = new HashSet<>(s1);
    s1Intersections2.retainAll(s2);
    System.out.println("s1 intersection  s2: " + s1Intersections2);
}

---

From source file:Main.java

/**
 * Returns the intersection of the given Collections.
 *
 * @param c1  the first Collection.//w w  w .  j  a v a 2  s.  co m
 * @param c2  the second Collection.
 * @param <T> the type.
 * @return the intersection of the Collections.
 */
public static <T> Collection<T> intersection(Collection<T> c1, Collection<T> c2) {
    Set<T> set1 = new HashSet<>(c1);
    set1.retainAll(new HashSet<>(c2));
    return set1;
}

---

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