Examples with BidiMap org.apache.commons.collections4.BidiMap used on opensource projects

Example 1 with BidiMap

use of org.apache.commons.collections4.BidiMap in project sling by apache.

the class ResourceResolverFactoryActivator method activate.

// ---------- SCR Integration ---------------------------------------------
/**
     * Activates this component (called by SCR before)
     */
@Activate
protected void activate(final BundleContext bundleContext, final ResourceResolverFactoryConfig config) {
    this.bundleContext = bundleContext;
    this.config = config;
    final BidiMap virtuals = new TreeBidiMap();
    for (int i = 0; config.resource_resolver_virtual() != null && i < config.resource_resolver_virtual().length; i++) {
        final String[] parts = Mapping.split(config.resource_resolver_virtual()[i]);
        virtuals.put(parts[0], parts[2]);
    }
    virtualURLMap = virtuals;
    final List<Mapping> maps = new ArrayList<>();
    for (int i = 0; config.resource_resolver_mapping() != null && i < config.resource_resolver_mapping().length; i++) {
        maps.add(new Mapping(config.resource_resolver_mapping()[i]));
    }
    final Mapping[] tmp = maps.toArray(new Mapping[maps.size()]);
    // check whether direct mappings are allowed
    if (config.resource_resolver_allowDirect()) {
        final Mapping[] tmp2 = new Mapping[tmp.length + 1];
        tmp2[0] = Mapping.DIRECT;
        System.arraycopy(tmp, 0, tmp2, 1, tmp.length);
        mappings = tmp2;
    } else {
        mappings = tmp;
    }
    // from configuration if available
    searchPath = config.resource_resolver_searchpath();
    if (searchPath != null && searchPath.length > 0) {
        for (int i = 0; i < searchPath.length; i++) {
            // ensure leading slash
            if (!searchPath[i].startsWith("/")) {
                searchPath[i] = "/" + searchPath[i];
            }
            // ensure trailing slash
            if (!searchPath[i].endsWith("/")) {
                searchPath[i] += "/";
            }
        }
    }
    if (searchPath == null) {
        searchPath = new String[] { "/" };
    }
    // the root of the resolver mappings
    mapRoot = config.resource_resolver_map_location();
    mapRootPrefix = mapRoot + '/';
    final String[] paths = config.resource_resolver_map_observation();
    this.observationPaths = new Path[paths.length];
    for (int i = 0; i < paths.length; i++) {
        this.observationPaths[i] = new Path(paths[i]);
    }
    // vanity path white list
    this.vanityPathWhiteList = null;
    String[] vanityPathPrefixes = config.resource_resolver_vanitypath_whitelist();
    if (vanityPathPrefixes != null) {
        final List<String> prefixList = new ArrayList<>();
        for (final String value : vanityPathPrefixes) {
            if (value.trim().length() > 0) {
                if (value.trim().endsWith("/")) {
                    prefixList.add(value.trim());
                } else {
                    prefixList.add(value.trim() + "/");
                }
            }
        }
        if (prefixList.size() > 0) {
            this.vanityPathWhiteList = prefixList.toArray(new String[prefixList.size()]);
        }
    }
    // vanity path black list
    this.vanityPathBlackList = null;
    vanityPathPrefixes = config.resource_resolver_vanitypath_blacklist();
    if (vanityPathPrefixes != null) {
        final List<String> prefixList = new ArrayList<>();
        for (final String value : vanityPathPrefixes) {
            if (value.trim().length() > 0) {
                if (value.trim().endsWith("/")) {
                    prefixList.add(value.trim());
                } else {
                    prefixList.add(value.trim() + "/");
                }
            }
        }
        if (prefixList.size() > 0) {
            this.vanityPathBlackList = prefixList.toArray(new String[prefixList.size()]);
        }
    }
    // check for required property
    Set<String> requiredResourceProvidersLegacy = getStringSet(config.resource_resolver_required_providers());
    Set<String> requiredResourceProviderNames = getStringSet(config.resource_resolver_required_providernames());
    boolean hasLegacyRequiredProvider = false;
    if (requiredResourceProvidersLegacy != null) {
        hasLegacyRequiredProvider = requiredResourceProvidersLegacy.remove(ResourceResolverFactoryConfig.LEGACY_REQUIRED_PROVIDER_PID);
        if (!requiredResourceProvidersLegacy.isEmpty()) {
            logger.error("ResourceResolverFactory is using deprecated required providers configuration (resource.resolver.required.providers" + "). Please change to use the property resource.resolver.required.providernames for values: " + requiredResourceProvidersLegacy);
        } else {
            requiredResourceProvidersLegacy = null;
        }
    }
    if (hasLegacyRequiredProvider) {
        final boolean hasRequiredProvider;
        if (requiredResourceProviderNames != null) {
            hasRequiredProvider = !requiredResourceProviderNames.add(ResourceResolverFactoryConfig.REQUIRED_PROVIDER_NAME);
        } else {
            hasRequiredProvider = false;
            requiredResourceProviderNames = Collections.singleton(ResourceResolverFactoryConfig.REQUIRED_PROVIDER_NAME);
        }
        if (hasRequiredProvider) {
            logger.warn("ResourceResolverFactory is using deprecated required providers configuration (resource.resolver.required.providers" + ") with value '" + ResourceResolverFactoryConfig.LEGACY_REQUIRED_PROVIDER_PID + ". Please remove this configuration property. " + ResourceResolverFactoryConfig.REQUIRED_PROVIDER_NAME + " is already contained in the property resource.resolver.required.providernames.");
        } else {
            logger.warn("ResourceResolverFactory is using deprecated required providers configuration (resource.resolver.required.providers" + ") with value '" + ResourceResolverFactoryConfig.LEGACY_REQUIRED_PROVIDER_PID + ". Please remove this configuration property and add " + ResourceResolverFactoryConfig.REQUIRED_PROVIDER_NAME + " to the property resource.resolver.required.providernames.");
        }
    }
    // for testing: if we run unit test, both trackers are set from the outside
    if (this.resourceProviderTracker == null) {
        this.resourceProviderTracker = new ResourceProviderTracker();
        this.changeListenerWhiteboard = new ResourceChangeListenerWhiteboard();
        this.preconds.activate(this.bundleContext, requiredResourceProvidersLegacy, requiredResourceProviderNames, resourceProviderTracker);
        this.changeListenerWhiteboard.activate(this.bundleContext, this.resourceProviderTracker, searchPath);
        this.resourceProviderTracker.activate(this.bundleContext, this.eventAdmin, new ChangeListener() {

            @Override
            public void providerAdded() {
                if (factoryRegistration == null) {
                    checkFactoryPreconditions(null, null);
                }
            }

            @Override
            public void providerRemoved(final String name, final String pid, final boolean stateful, final boolean isUsed) {
                if (factoryRegistration != null) {
                    if (isUsed && (stateful || config.resource_resolver_providerhandling_paranoid())) {
                        unregisterFactory();
                    }
                    checkFactoryPreconditions(name, pid);
                }
            }
        });
    } else {
        this.preconds.activate(this.bundleContext, requiredResourceProvidersLegacy, requiredResourceProviderNames, resourceProviderTracker);
        this.checkFactoryPreconditions(null, null);
    }
}

Example 2 with BidiMap

use of org.apache.commons.collections4.BidiMap in project polyGembler by c-zhou.

the class Traceable method main.

public static void main(String[] args) {
    final BidiMap<String, Integer> bidi = new TreeBidiMap<String, Integer>();
    bidi.put("a", 1);
    bidi.put("a", 2);
    bidi.put("b", 2);
    System.out.println(bidi.size());
    final DirectedWeightedPseudograph<TraceableVertex<String>, DefaultWeightedEdge> razor = new DirectedWeightedPseudograph<TraceableVertex<String>, DefaultWeightedEdge>(DefaultWeightedEdge.class);
    // JGraphModelAdapter<TraceableVertex<String>, DefaultWeightedEdge> jgAdapter =
    // new JGraphModelAdapter<TraceableVertex<String>, DefaultWeightedEdge>(razor);
    // JGraph jgraph = new JGraph(jgAdapter);
    TraceableVertex<String> a = new TraceableVertex<String>("a");
    TraceableVertex<String> b = new TraceableVertex<String>("b");
    TraceableVertex<String> c = new TraceableVertex<String>("c");
    TraceableVertex<String> d = new TraceableVertex<String>("d");
    razor.addVertex(a);
    razor.addVertex(b);
    razor.addVertex(c);
    razor.addVertex(d);
    razor.setEdgeWeight(razor.addEdge(a, a), 1);
    razor.setEdgeWeight(razor.addEdge(a, b), 1);
    razor.setEdgeWeight(razor.addEdge(a, c), 1);
    razor.setEdgeWeight(razor.addEdge(a, d), 1);
    razor.setEdgeWeight(razor.addEdge(b, a), 1);
    razor.setEdgeWeight(razor.addEdge(b, b), 1);
    razor.setEdgeWeight(razor.addEdge(b, c), 1);
    razor.setEdgeWeight(razor.addEdge(b, d), 1);
    razor.setEdgeWeight(razor.addEdge(c, a), 1);
    razor.setEdgeWeight(razor.addEdge(c, b), 1);
    razor.setEdgeWeight(razor.addEdge(c, c), 1);
    razor.setEdgeWeight(razor.addEdge(c, d), 1);
    razor.setEdgeWeight(razor.addEdge(d, a), 1);
    razor.setEdgeWeight(razor.addEdge(d, b), 1);
    razor.setEdgeWeight(razor.addEdge(d, c), 1);
    razor.setEdgeWeight(razor.addEdge(d, d), 1);
    // JFrame frame = new JFrame();
    // frame.getContentPane().add(jgraph);
    // frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    // frame.pack();
    // frame.setVisible(true);
    Set<TraceableVertex<String>> visited = new HashSet<TraceableVertex<String>>();
    Deque<TraceableVertex<String>> queue = new ArrayDeque<TraceableVertex<String>>();
    queue.push(a);
    visited.add(a);
    a.setScore(10);
    Set<DefaultWeightedEdge> out_edges;
    double max_score = Double.NEGATIVE_INFINITY, source_score, target_score, score;
    int source_ln;
    TraceableVertex<String> max_vertex = null;
    boolean isLeaf;
    TraceableVertex<String> source_vertex, target_vertex;
    double edge_weight;
    while (!queue.isEmpty()) {
        source_vertex = queue.pop();
        source_ln = 10;
        source_score = source_vertex.getScore() - source_ln;
        isLeaf = true;
        out_edges = razor.outgoingEdgesOf(source_vertex);
        for (DefaultWeightedEdge out : out_edges) {
            target_vertex = razor.getEdgeTarget(out);
            target_score = target_vertex.getScore();
            edge_weight = razor.getEdgeWeight(out);
            score = source_score + edge_weight;
            if (visited.contains(target_vertex) && (score <= target_score || isLoopback(razor, source_vertex, target_vertex)))
                continue;
            isLeaf = false;
            target_vertex.setBackTrace(source_vertex);
            target_vertex.setScore(score);
            queue.push(target_vertex);
            visited.add(target_vertex);
        }
        if (isLeaf && source_vertex.getScore() > max_score) {
            max_score = source_vertex.getScore();
            max_vertex = source_vertex;
        }
    }
}

Example 3 with BidiMap

use of org.apache.commons.collections4.BidiMap in project polyGembler by c-zhou.

the class RenjinLOD method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    final BidiMap<Integer, String> scaffs = new TreeBidiMap<Integer, String>();
    final List<Double> boundary_lg = new ArrayList<Double>();
    try {
        BufferedReader br = Utils.getBufferedReader(txt_in);
        String line = br.readLine();
        String[] s;
        while (line != null) {
            if (line.startsWith("$order")) {
                int i = 0;
                while ((line = br.readLine()) != null && line.length() > 0) {
                    s = line.split("\\s+")[1].split("-");
                    for (String scf : s) scaffs.put(i++, scf.replaceAll("^scaffold", ""));
                    boundary_lg.add((double) i);
                }
                break;
            }
            line = br.readLine();
        }
        br.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    int n = scaffs.size();
    double[][] recomfJ = new double[n][n];
    double[][] lodscrJ = new double[n][n];
    final double constr = Math.log10(.5);
    try {
        String line;
        String[] s;
        Integer scf_i1, scf_i2;
        double f, l, NR, R;
        for (String in : ds_in) {
            BufferedReader br = Utils.getBufferedReader(in);
            while ((line = br.readLine()) != null) {
                s = line.split("\\s+");
                scf_i1 = scaffs.getKey(s[6]);
                scf_i2 = scaffs.getKey(s[7]);
                if (scf_i1 == null || scf_i2 == null)
                    continue;
                f = Double.parseDouble(s[1]);
                recomfJ[scf_i1][scf_i2] = f;
                recomfJ[scf_i2][scf_i1] = f;
                if (f == 0) {
                    l = 100.0;
                } else {
                    NR = (1 - f);
                    R = f;
                    l = Math.min(100.0, n_hap * (Math.log10(NR) * NR + Math.log10(R) * R - constr));
                }
                lodscrJ[scf_i1][scf_i2] = l;
                lodscrJ[scf_i2][scf_i1] = l;
            }
            br.close();
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    DoubleMatrixBuilder reccoo = new DoubleMatrixBuilder(n * (n - 1), 5);
    int w = 0;
    for (int i = 1; i < n; i++) {
        for (int j = 0; j < i; j++) {
            reccoo.set(w, 0, j);
            reccoo.set(w, 1, i);
            reccoo.set(w, 2, j + 1);
            reccoo.set(w, 3, i + 1);
            reccoo.set(w, 4, lodscrJ[i][j]);
            w++;
            reccoo.set(w, 0, i);
            reccoo.set(w, 1, j);
            reccoo.set(w, 2, i + 1);
            reccoo.set(w, 3, j + 1);
            reccoo.set(w, 4, recomfJ[i][j]);
            w++;
        }
    }
    DoubleMatrixBuilder recomf = new DoubleMatrixBuilder(n, n);
    DoubleMatrixBuilder lodscr = new DoubleMatrixBuilder(n, n);
    for (int i = 0; i < n; i++) {
        for (int j = 0; j < n; j++) {
            recomf.set(i, j, recomfJ[i][j]);
            lodscr.set(i, j, lodscrJ[i][j]);
        }
    }
    ScriptEngineManager manager = new ScriptEngineManager();
    ScriptEngine engine = manager.getEngineByName("Renjin");
    if (engine == null) {
        throw new RuntimeException("Renjin not found!!!");
    }
    StringVector scf = new StringArrayVector(scaffs.values());
    recomf.setRowNames(scf);
    recomf.setColNames(scf);
    lodscr.setRowNames(scf);
    lodscr.setColNames(scf);
    try {
        Context context = Context.newTopLevelContext();
        FileOutputStream fos = new FileOutputStream(r_out);
        GZIPOutputStream zos = new GZIPOutputStream(fos);
        RDataWriter writer = new RDataWriter(context, zos);
        ListVector.NamedBuilder dat = new ListVector.NamedBuilder();
        dat.add("scaffs", scf);
        dat.add("boundary_lg", new DoubleArrayVector(boundary_lg));
        dat.add("recomf", recomf.build());
        dat.add("lodscr", lodscr.build());
        dat.add("reccoo", reccoo.build());
        writer.save(dat.build());
        writer.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 4 with BidiMap

use of org.apache.commons.collections4.BidiMap in project polyGembler by c-zhou.

the class RenjinLOD method run2.

public void run2() {
    // TODO Auto-generated method stub
    final BidiMap<Integer, String> scaffs = new TreeBidiMap<Integer, String>();
    final List<Double> boundary_lg = new ArrayList<Double>();
    try {
        BufferedReader br = Utils.getBufferedReader(txt_in);
        String line = br.readLine();
        String[] s;
        while (line != null) {
            if (line.startsWith("$order")) {
                int i = 0;
                while ((line = br.readLine()) != null && line.length() > 0) {
                    s = line.split("\\s+")[1].split("-");
                    for (String scf : s) scaffs.put(i++, scf.replaceAll("^scaffold", ""));
                    boundary_lg.add((double) i);
                }
                break;
            }
            line = br.readLine();
        }
        br.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    double[][] recomf = new double[scaffs.size()][scaffs.size()];
    double[][] lodscr = new double[scaffs.size()][scaffs.size()];
    final double constr = Math.log10(.5);
    try {
        String line;
        String[] s;
        Integer scf_i1, scf_i2;
        double f, l, NR, R;
        for (String in : ds_in) {
            BufferedReader br = Utils.getBufferedReader(in);
            while ((line = br.readLine()) != null) {
                s = line.split("\\s+");
                scf_i1 = scaffs.getKey(s[6]);
                scf_i2 = scaffs.getKey(s[7]);
                if (scf_i1 == null || scf_i2 == null)
                    continue;
                f = Double.parseDouble(s[1]);
                recomf[scf_i1][scf_i2] = f;
                recomf[scf_i2][scf_i1] = f;
                if (f == 0) {
                    l = 100.0;
                } else {
                    NR = (1 - f);
                    R = f;
                    l = Math.min(100.0, n_hap * (Math.log10(NR) * NR + Math.log10(R) * R - constr));
                }
                lodscr[scf_i1][scf_i2] = l;
                lodscr[scf_i2][scf_i1] = l;
            }
            br.close();
        }
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    StringVector scf = new StringArrayVector(scaffs.values());
}

Example 5 with BidiMap

use of org.apache.commons.collections4.BidiMap in project polyGembler by c-zhou.

the class DataRetrievor method main.

public static void main(String[] args) {
    String in_vcf = "C:\\Users\\chenxi.zhou\\Desktop\\new_alg\\____2.vcf";
    String ncsu_sample = "C:\\Users\\chenxi.zhou\\Desktop\\new_alg\\ncsu_samples.txt";
    String out_txt = "C:\\Users\\chenxi.zhou\\Desktop\\new_alg\\gbs_nsp306_02.txt";
    String[] parent_sample = new String[] { "440132", "440166" };
    int M = 10;
    BidiMap<String, Integer> target_sample = new TreeBidiMap<String, Integer>();
    target_sample.put(parent_sample[0], 0);
    target_sample.put(parent_sample[1], 1);
    int idx = 2;
    String line;
    try {
        BufferedReader br_s = Utils.getBufferedReader(ncsu_sample);
        while ((line = br_s.readLine()) != null) {
            if (!target_sample.containsKey(line))
                target_sample.put(line, idx++);
        }
        br_s.close();
        // C:\\Users\\chenxi.zhou\\Desktop\\new_alg\\gbs_nsp306_01.txt
        // int[] retrieve_line = new int[]{
        // 134, 160, 184, 186, 189, 191, 192, 201, 214, 215,
        // 217, 219, 221, 222, 227, 229, 230, 233, 256, 273
        // };
        int[] retrieve_line = new int[] { 160, 200, 213, 215, 216, 227, 229, 304, 348, 462 };
        int N = target_sample.size();
        BufferedReader br_v = Utils.getBufferedReader(in_vcf);
        int skip = 0;
        final Map<Integer, Integer> sample_index = new HashMap<Integer, Integer>();
        String[] s;
        while ((line = br_v.readLine()) != null) {
            skip++;
            if (line.startsWith("#") && !line.startsWith("##")) {
                s = line.split("\\s+");
                for (int i = 0; i != s.length; i++) if (target_sample.containsKey(s[i]))
                    sample_index.put(target_sample.get(s[i]), i);
                break;
            }
        }
        BufferedWriter bw_txt = Utils.getBufferedWriter(out_txt);
        bw_txt.write(N + "\n");
        bw_txt.write(M + "\n");
        bw_txt.write(parent_sample[0]);
        for (int i = 1; i != N; i++) bw_txt.write("\t" + target_sample.getKey(i));
        bw_txt.write("\n");
        bw_txt.write(parent_sample[0] + "\t" + parent_sample[0] + "\n");
        bw_txt.write("M1");
        for (int i = 1; i != M; i++) bw_txt.write("\tM" + (i + 1));
        bw_txt.write("\n");
        for (int i = 0; i != M; i++) {
            if (i == 0)
                skip = retrieve_line[0] - skip - 1;
            else
                skip = retrieve_line[i] - retrieve_line[i - 1] - 1;
            for (int j = 0; j != skip; j++) br_v.readLine();
            line = br_v.readLine();
            s = line.split("\\s+");
            bw_txt.write("M" + (i + 1) + "\t" + s[1] + "\tA");
            int m = s[3].split(";").length;
            for (int j = 1; j != m; j++) bw_txt.write("," + (char) ('A' + j));
            for (int j = 0; j != N; j++) {
                idx = sample_index.get(j);
                if (s[idx].equals(".")) {
                    bw_txt.write("\t0");
                    for (int k = 1; k != m; k++) bw_txt.write(",0");
                } else
                    bw_txt.write("\t" + s[idx].replaceAll(";", ","));
            }
            bw_txt.write("\n");
        }
        br_v.close();
        bw_txt.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}