Examples with SetOfGeneSets org.baderlab.csplugins.enrichmentmap.model.SetOfGeneSets used on opensource projects

Example 1 with SetOfGeneSets

use of org.baderlab.csplugins.enrichmentmap.model.SetOfGeneSets in project EnrichmentMapApp by BaderLab.

the class LegacySessionLoader method loadSession.

/**
	 * Restore Enrichment maps
	 *
	 * @param pStateFileList - list of files associated with thie session
	 */
@SuppressWarnings("unchecked")
public void loadSession(CySession session) {
    Map<Long, EnrichmentMapParameters> paramsMap = new HashMap<>();
    Map<Long, EnrichmentMap> enrichmentMapMap = new HashMap<>();
    List<File> fileList = session.getAppFileListMap().get(CyActivator.APP_NAME);
    try {
        //go through the prop files first to create the correct objects to be able to add other files to.
        for (File prop_file : fileList) {
            if (prop_file.getName().contains(".props")) {
                InputStream reader = streamUtil.getInputStream(prop_file.getAbsolutePath());
                String fullText = new Scanner(reader, "UTF-8").useDelimiter("\\A").next();
                //Given the file with all the parameters create a new parameter
                EnrichmentMapParameters params = enrichmentMapParametersFactory.create(fullText);
                EnrichmentMap em = new EnrichmentMap(params.getCreationParameters(), serviceRegistrar);
                //get the network name
                String param_name = em.getName();
                //TODO:distinguish between GSEA and EM saved sessions
                String props_name = (prop_file.getName().split("\\."))[0];
                String networkName = param_name;
                //related to bug ticket #49
                if (!props_name.equalsIgnoreCase(param_name))
                    networkName = props_name;
                //after associated the properties with the network
                //initialized each Dataset that we have files for
                HashMap<String, DataSetFiles> files = params.getFiles();
                for (Iterator<String> j = params.getFiles().keySet().iterator(); j.hasNext(); ) {
                    String current_dataset = j.next();
                    Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
                    em.createDataSet(current_dataset, method, files.get(current_dataset));
                }
                CyNetwork network = getNetworkByName(networkName);
                Long suid = network.getSUID();
                em.setNetworkID(suid);
                paramsMap.put(suid, params);
                enrichmentMapMap.put(suid, em);
            }
        }
        // go through the rest of the files
        for (File propFile : fileList) {
            FileNameParts parts = ParseFileName(propFile);
            if (parts == null || propFile.getName().contains(".props"))
                continue;
            CyNetwork net = getNetworkByName(parts.name);
            EnrichmentMap em = net == null ? null : enrichmentMapMap.get(net.getSUID());
            EnrichmentMapParameters params = paramsMap.get(net.getSUID());
            Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
            if (em == null) {
                System.out.println("network for file" + propFile.getName() + " does not exist.");
            } else if ((!propFile.getName().contains(".props")) && (!propFile.getName().contains(".expression1.txt")) && (!propFile.getName().contains(".expression2.txt"))) {
                HashMap<String, String> props = params.getProps();
                //if this a dataset specific file make sure there is a dataset object for it
                if (!(parts.dataset == null) && em.getDataSet(parts.dataset) == null && !parts.dataset.equalsIgnoreCase("signature"))
                    em.createDataSet(parts.dataset, method, params.getFiles().get(parts.dataset));
                if (parts.type == null)
                    System.out.println("Sorry, unable to determine the type of the file: " + propFile.getName());
                //read the file
                InputStream reader = streamUtil.getInputStream(propFile.getAbsolutePath());
                String fullText = new Scanner(reader, "UTF-8").useDelimiter("\\A").next();
                //if the file is empty then skip it
                if (fullText == null || fullText.equalsIgnoreCase(""))
                    continue;
                if (propFile.getName().contains(".gmt")) {
                    HashMap<String, GeneSet> gsMap = (HashMap<String, GeneSet>) params.repopulateHashmap(fullText, 1);
                    if (propFile.getName().contains(".signature.gmt")) {
                        // TODO Find a better way to serialize EMSignatureDataSet
                        String sdsName = propFile.getName().replace(".signature.gmt", "");
                        sdsName = NamingUtil.getUniqueName(sdsName, em.getSignatureDataSets().keySet());
                        EMSignatureDataSet sigDataSet = new EMSignatureDataSet(sdsName);
                        em.addSignatureDataSet(sigDataSet);
                        SetOfGeneSets sigGeneSets = sigDataSet.getGeneSetsOfInterest();
                        gsMap.forEach((k, v) -> sigGeneSets.addGeneSet(k, v));
                    } else if (propFile.getName().contains(".set2.gmt")) {
                        // account for legacy session files
                        if (em.getAllGeneSets().containsKey(LegacySupport.DATASET2)) {
                            SetOfGeneSets gs = new SetOfGeneSets(LegacySupport.DATASET2, props);
                            gs.setGeneSets(gsMap);
                        }
                    } else {
                        SetOfGeneSets gs = new SetOfGeneSets(parts.dataset, props);
                        gs.setGeneSets(gsMap);
                        em.getDataSets().get(parts.dataset).setSetOfGeneSets(gs);
                    }
                }
                if (propFile.getName().contains(".genes.txt")) {
                    HashMap<String, Integer> genes = params.repopulateHashmap(fullText, 2);
                    genes.forEach(em::addGene);
                    //ticket #188 - unable to open session files that have empty enrichment maps.
                    if (genes != null && !genes.isEmpty())
                        // Ticket #107 : restore also gene count (needed to determine the next free hash in case we do PostAnalysis with a restored session)
                        em.setNumberOfGenes(Math.max(em.getNumberOfGenes(), Collections.max(genes.values()) + 1));
                }
                if (propFile.getName().contains(".hashkey2genes.txt")) {
                    HashMap<Integer, String> hashkey2gene = params.repopulateHashmap(fullText, 5);
                    //ticket #188 - unable to open session files that have empty enrichment maps.
                    if (hashkey2gene != null && !hashkey2gene.isEmpty())
                        // Ticket #107 : restore also gene count (needed to determine the next free hash in case we do PostAnalysis with a restored session)
                        em.setNumberOfGenes(Math.max(em.getNumberOfGenes(), Collections.max(hashkey2gene.keySet()) + 1));
                }
                if ((parts.type != null && (parts.type.equalsIgnoreCase("ENR") || (parts.type.equalsIgnoreCase("SubENR")))) || propFile.getName().contains(".ENR1.txt") || propFile.getName().contains(".SubENR1.txt")) {
                    SetOfEnrichmentResults enrichments;
                    int temp = 1;
                    //check to see if this dataset has enrichment results already
                    if (parts.dataset != null && em.getDataSet(parts.dataset).getEnrichments() != null) {
                        enrichments = em.getDataSet(parts.dataset).getEnrichments();
                    } else if (parts.dataset == null) {
                        enrichments = em.getDataSet(LegacySupport.DATASET1).getEnrichments();
                    /*enrichments = new SetOfEnrichmentResults(EnrichmentMap.DATASET1,props);
                			em.getDataset(EnrichmentMap.DATASET1).setEnrichments(enrichments);*/
                    } else {
                        enrichments = new SetOfEnrichmentResults(parts.dataset, props);
                        em.getDataSet(parts.dataset).setEnrichments(enrichments);
                    }
                    if (parts.type.equalsIgnoreCase("ENR") || propFile.getName().contains(".ENR1.txt")) {
                        if (params.getMethod().equalsIgnoreCase(EnrichmentMapParameters.method_GSEA))
                            enrichments.setEnrichments(params.repopulateHashmap(fullText, 3));
                        else
                            enrichments.setEnrichments(params.repopulateHashmap(fullText, 4));
                    }
                }
                //it would only happen for sessions saved with version 0.8
                if (propFile.getName().contains(".RANKS1.txt") || propFile.getName().contains(".RANKS1Genes.txt")) {
                    Ranking new_ranking;
                    //Check to see if there is already GSEARanking
                    if (em.getDataSet(LegacySupport.DATASET1).getExpressionSets().getAllRanksNames().contains(Ranking.GSEARanking)) {
                        new_ranking = em.getDataSet(LegacySupport.DATASET1).getExpressionSets().getRanksByName(Ranking.GSEARanking);
                    } else {
                        new_ranking = new Ranking();
                        em.getDataSet(LegacySupport.DATASET1).getExpressionSets().addRanks(Ranking.GSEARanking, new_ranking);
                    }
                    if (propFile.getName().contains(".RANKS1.txt")) {
                        Map<Integer, Rank> ranks = (Map<Integer, Rank>) params.repopulateHashmap(fullText, 7);
                        ranks.forEach(new_ranking::addRank);
                    }
                //						if(prop_file.getName().contains(".RANKS1Genes.txt"))
                //							new_ranking.setRank2gene(em.getParams().repopulateHashmap(fullText,7));
                //						if(prop_file.getName().contains(".RANKS1.txt"))
                //							new_ranking.setRanking(em.getParams().repopulateHashmap(fullText,6));
                }
                if (propFile.getName().contains(".RANKS.txt")) {
                    if (parts.ranks_name == null) {
                        //we need to get the name of this set of rankings
                        // network_name.ranking_name.ranks.txt --> split by "." and get 2
                        String[] file_name_tokens = (propFile.getName()).split("\\.");
                        if ((file_name_tokens.length == 4) && (file_name_tokens[1].equals("Dataset 1 Ranking") || file_name_tokens[1].equals("Dataset 2 Ranking")) || (propFile.getName().contains(Ranking.GSEARanking)))
                            parts.ranks_name = Ranking.GSEARanking;
                        else //this is an extra rank file for backwards compatability.  Ignore it.
                        if ((file_name_tokens.length == 4) && (file_name_tokens[1].equals("Dataset 1") || file_name_tokens[1].equals("Dataset 2")) && file_name_tokens[2].equals("RANKS"))
                            continue;
                        else
                            //file name is not structured properly --> default to file name
                            parts.ranks_name = propFile.getName();
                    }
                    Ranking new_ranking = new Ranking();
                    Map<Integer, Rank> ranks = (Map<Integer, Rank>) params.repopulateHashmap(fullText, 6);
                    ranks.forEach(new_ranking::addRank);
                    if (parts.dataset != null)
                        em.getDataSet(parts.dataset).getExpressionSets().addRanks(parts.ranks_name, new_ranking);
                    else
                        em.getDataSet(LegacySupport.DATASET1).getExpressionSets().addRanks(parts.ranks_name, new_ranking);
                }
                //Deal with legacy issues                    
                if (params.isTwoDatasets()) {
                    //make sure there is a Dataset2
                    if (!em.getDataSets().containsKey(LegacySupport.DATASET2))
                        em.createDataSet(LegacySupport.DATASET2, method, new DataSetFiles());
                    if (propFile.getName().contains(".ENR2.txt") || propFile.getName().contains(".SubENR2.txt")) {
                        SetOfEnrichmentResults enrichments;
                        //check to see if this dataset has enrichment results already
                        if (em.getDataSet(LegacySupport.DATASET2).getEnrichments() != null) {
                            enrichments = em.getDataSet(LegacySupport.DATASET2).getEnrichments();
                        } else {
                            enrichments = new SetOfEnrichmentResults(LegacySupport.DATASET2, props);
                            em.getDataSet(LegacySupport.DATASET2).setEnrichments(enrichments);
                        }
                        if (propFile.getName().contains(".ENR2.txt")) {
                            if (params.getMethod().equalsIgnoreCase(EnrichmentMapParameters.method_GSEA))
                                enrichments.setEnrichments(params.repopulateHashmap(fullText, 3));
                            else
                                enrichments.setEnrichments(params.repopulateHashmap(fullText, 4));
                        }
                    }
                    //it would only happen for sessions saved with version 0.8
                    if (propFile.getName().contains(".RANKS2.txt") || propFile.getName().contains(".RANKS2Genes.txt")) {
                        Ranking new_ranking;
                        // Check to see if there is already GSEARanking
                        if (em.getDataSet(LegacySupport.DATASET2).getExpressionSets().getAllRanksNames().contains(Ranking.GSEARanking)) {
                            new_ranking = em.getDataSet(LegacySupport.DATASET2).getExpressionSets().getRanksByName(Ranking.GSEARanking);
                        } else {
                            new_ranking = new Ranking();
                            em.getDataSet(LegacySupport.DATASET2).getExpressionSets().addRanks(Ranking.GSEARanking, new_ranking);
                        }
                        if (propFile.getName().contains(".RANKS2.txt")) {
                            Map<Integer, Rank> ranks = (Map<Integer, Rank>) params.repopulateHashmap(fullText, 6);
                            ranks.forEach(new_ranking::addRank);
                        }
                    }
                }
            }
        }
        //info from the parameters
        for (int i = 0; i < fileList.size(); i++) {
            File prop_file = fileList.get(i);
            FileNameParts parts_exp = ParseFileName(prop_file);
            //unrecognized file
            if ((parts_exp == null) || (parts_exp.name == null))
                continue;
            CyNetwork net = getNetworkByName(parts_exp.name);
            EnrichmentMap map = net == null ? null : enrichmentMapMap.get(net.getSUID());
            EnrichmentMapParameters params = paramsMap.get(net.getSUID());
            Map<String, String> props = params.getProps();
            if (parts_exp.type != null && parts_exp.type.equalsIgnoreCase("expression")) {
                if (map.getDataSets().containsKey(parts_exp.dataset)) {
                    EMDataSet ds = map.getDataSet(parts_exp.dataset);
                    ds.getDataSetFiles().setExpressionFileName(prop_file.getAbsolutePath());
                    ds.getExpressionSets().setFilename(prop_file.getAbsolutePath());
                    ExpressionFileReaderTask expressionFile1 = new ExpressionFileReaderTask(ds);
                    GeneExpressionMatrix matrix = expressionFile1.parse();
                    matrix.restoreProps(parts_exp.dataset, props);
                }
            }
            //Deal with legacy session files.
            if (prop_file.getName().contains("expression1.txt")) {
                EMDataSet ds1 = map.getDataSet(LegacySupport.DATASET1);
                ds1.getDataSetFiles().setExpressionFileName(prop_file.getAbsolutePath());
                ds1.getExpressionSets().setFilename(prop_file.getAbsolutePath());
                ExpressionFileReaderTask expressionFile1 = new ExpressionFileReaderTask(ds1);
                expressionFile1.parse();
            }
            if (prop_file.getName().contains("expression2.txt")) {
                EMDataSet ds2 = map.getDataSet(LegacySupport.DATASET2);
                ds2.getDataSetFiles().setExpressionFileName(prop_file.getAbsolutePath());
                ds2.getExpressionSets().setFilename(prop_file.getAbsolutePath());
                ExpressionFileReaderTask expressionFile2 = new ExpressionFileReaderTask(ds2);
                expressionFile2.parse();
                //are dealing with two distinct expression files.
                if (map.getDataSet(LegacySupport.DATASET2) != null && map.getDataSet(LegacySupport.DATASET2).getGeneSetsOfInterest() != null && !map.getDataSet(LegacySupport.DATASET2).getGeneSetsOfInterest().getGeneSets().isEmpty()) {
                    map.setDistinctExpressionSets(true);
                    map.getDataSet(LegacySupport.DATASET1).setDataSetGenes(new HashSet<Integer>((Set<Integer>) map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getGeneIds()));
                    map.getDataSet(LegacySupport.DATASET2).setDataSetGenes(new HashSet<Integer>((Set<Integer>) map.getDataSet(LegacySupport.DATASET2).getExpressionSets().getGeneIds()));
                }
            }
        }
        //iterate over the networks
        for (Iterator<Long> j = enrichmentMapMap.keySet().iterator(); j.hasNext(); ) {
            Long id = j.next();
            EnrichmentMap map = enrichmentMapMap.get(id);
            //only initialize objects if there is a map for this network
            if (map != null) {
                if (map.getDataSets().size() > 1) {
                    Set<Integer> dataset1_genes = map.getDataSets().get(LegacySupport.DATASET1).getDataSetGenes();
                    Set<Integer> dataset2_genes = map.getDataSets().get(LegacySupport.DATASET2).getDataSetGenes();
                    if (!dataset1_genes.equals(dataset2_genes))
                        map.setDistinctExpressionSets(true);
                }
                //initialize the Genesets (makes sure the leading edge is set correctly)
                //Initialize the set of genesets and GSEA results that we want to compute over
                InitializeGenesetsOfInterestTask genesets_init = new InitializeGenesetsOfInterestTask(map);
                // MKTODO really?
                genesets_init.setThrowIfMissing(false);
                genesets_init.initializeSets(null);
            //					//for each map compute the similarity matrix, (easier than storing it) compute the geneset similarities
            //					ComputeSimilarityTask similarities = new ComputeSimilarityTask(map, ComputeSimilarityTask.ENRICHMENT);
            //					Map<String, GenesetSimilarity> similarity_results = similarities.computeGenesetSimilarities(null);
            //					map.setGenesetSimilarity(similarity_results);
            //
            //					// also compute geneset similarities between Enrichment- and Signature Genesets (if any)
            //					if (! map.getSignatureGenesets().isEmpty()){
            //						ComputeSimilarityTask sigSimilarities = new ComputeSimilarityTask(map, ComputeSimilarityTask.SIGNATURE);
            //						Map<String, GenesetSimilarity> sig_similarity_results = sigSimilarities.computeGenesetSimilarities(null);
            //						map.getGenesetSimilarity().putAll(sig_similarity_results);
            //					}
            }
        //end of if(map != null)
        }
        for (Iterator<Long> j = enrichmentMapMap.keySet().iterator(); j.hasNext(); ) {
            Long id = j.next();
            CyNetwork currentNetwork = cyNetworkManager.getNetwork(id);
            EnrichmentMap map = enrichmentMapMap.get(id);
            map.setLegacy(true);
            emManager.registerEnrichmentMap(map);
            if (!j.hasNext()) {
                //set the last network to be the one viewed and initialize the parameters panel
                cyApplicationManager.setCurrentNetwork(currentNetwork);
            }
        }
    } catch (Exception ee) {
        ee.printStackTrace();
    }
}

Example 2 with SetOfGeneSets

use of org.baderlab.csplugins.enrichmentmap.model.SetOfGeneSets in project EnrichmentMapApp by BaderLab.

the class LoadSignatureSetsActionListener method actionPerformed.

@Override
public void actionPerformed(ActionEvent event) {
    // make sure that the minimum information is set in the current set of parameters
    if (file.canRead()) {
        // MKTODO warning LoadSignatureGMTFilesTask is side-effecting, it pulls the loaded genes into the EnrichmentMap object
        LoadSignatureGMTFilesTask loadGMTs = new LoadSignatureGMTFilesTask(file, map, filterMetric);
        TaskObserver taskObserver = new ResultTaskObserver() {

            private SetOfGeneSets resultGeneSets;

            private Set<String> filteredSignatureSets;

            @Override
            public void taskFinished(ObservableTask task) {
                if (task instanceof FilterSignatureGSTask) {
                    resultGeneSets = task.getResults(SetOfGeneSets.class);
                    filteredSignatureSets = task.getResults(Set.class);
                }
            }

            @Override
            public void allFinished(FinishStatus finishStatus) {
                geneSetCallback.accept(resultGeneSets);
                filteredSignatureSetsCallback.accept(filteredSignatureSets);
            }
        };
        taskManager.execute(loadGMTs.createTaskIterator(), taskObserver);
    } else {
        JOptionPane.showMessageDialog(application.getJFrame(), "Signature GMT file name not valid.\n", "Invalid File", JOptionPane.WARNING_MESSAGE);
    }
}

Example 3 with SetOfGeneSets

use of org.baderlab.csplugins.enrichmentmap.model.SetOfGeneSets in project EnrichmentMapApp by BaderLab.

the class LoadSignatureGMTFilesTask method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    TaskIterator tasks = new TaskIterator();
    String name = file.getName();
    if (name.toLowerCase().endsWith(FILE_EXT))
        name = name.substring(0, name.length() - FILE_EXT.length()).trim();
    // this is an out-paramter for GMTFileReaderTask and an in-parameter for FilterSignatureGSTask
    // MKTODO: find a better way to pass data from one task to another
    // doesn't this need to be made available to paParams?
    SetOfGeneSets setOfGeneSets = new SetOfGeneSets(name);
    tasks.append(new GMTFileReaderTask(map, file.getAbsolutePath(), setOfGeneSets));
    tasks.append(new FilterSignatureGSTask(map, setOfGeneSets, filterMetric));
    return tasks;
}