Examples with Coverage algorithms.utils.Coverage used on opensource projects

Example 6 with Coverage

use of algorithms.utils.Coverage in project Smiles2Monomers by yoann-dufresne.

the class ProcessPolymers method main.

public static void main(String[] args) {
    // ----------------- Parameters ---------------------------
    String monoDBname = "data/monomers.json";
    String pepDBname = "data/polymers.json";
    String rulesDBname = "data/rules.json";
    String residuesDBname = "data/residues.json";
    String chainsDBFile = "data/chains.json";
    String outfile = "results/coverages.json";
    String outfolderName = "results/";
    String imgsFoldername = "images/";
    boolean html = false;
    boolean zip = false;
    String serialFolder = "data/serials/";
    boolean lightMatch = true;
    boolean verbose = false;
    int removeDistance = 2;
    int retryCount = 2;
    int modulationDepth = 2;
    // Parsing
    loop: for (int idx = 0; idx < args.length; idx++) {
        if (args[idx].startsWith("-")) {
            switch(args[idx]) {
                case "-rul":
                    rulesDBname = args[idx + 1];
                    break;
                case "-mono":
                    monoDBname = args[idx + 1];
                    break;
                case "-poly":
                    pepDBname = args[idx + 1];
                    break;
                case "-res":
                    residuesDBname = args[idx + 1];
                    break;
                case "-cha":
                    chainsDBFile = args[idx + 1];
                    break;
                case "-serial":
                    serialFolder = args[idx + 1];
                    break;
                case "-outfile":
                    outfile = args[idx + 1];
                    break;
                case "-outfolder":
                    outfolderName = args[idx + 1];
                    break;
                case "-imgs":
                    imgsFoldername = args[idx + 1];
                    break;
                case "-strict":
                    lightMatch = false;
                    continue loop;
                case "-v":
                    verbose = true;
                    continue loop;
                case "-html":
                    html = true;
                    continue loop;
                case "-zip":
                    zip = true;
                    continue loop;
                default:
                    System.err.println("Wrong option " + args[idx]);
                    System.exit(1);
                    break;
            }
            idx++;
        } else {
            System.err.println("Wrong parameter " + args[idx]);
            System.exit(1);
        }
    }
    // ------------------- Loadings ------------------------
    System.out.println("--- Loading ---");
    // Maybe loading can be faster for the learning base, using serialized molecules instead of CDK SMILES parsing method.
    long loadingTime = System.currentTimeMillis();
    MonomersDB monoDB = new MonomersJsonLoader(false).loadFile(monoDBname);
    MonomersSerialization ms = new MonomersSerialization();
    ms.deserialize(monoDB, serialFolder + "monos.serial");
    boolean d2 = html || zip;
    PolymersJsonLoader pjl = new PolymersJsonLoader(monoDB, d2);
    PolymersDB polDB = pjl.loadFile(pepDBname);
    RulesDB rulesDB = RulesJsonLoader.loader.loadFile(rulesDBname);
    ResidueJsonLoader rjl = new ResidueJsonLoader(rulesDB, monoDB);
    // Need optimizations
    FamilyDB families = rjl.loadFile(residuesDBname);
    FamilyChainIO fcio = new FamilyChainIO(families);
    ChainsDB chains = fcio.loadFile(chainsDBFile);
    loadingTime = System.currentTimeMillis() - loadingTime;
    System.out.println("Loading time : " + (loadingTime / 1000) + "s");
    // ------------------- Spliting ------------------------
    System.out.println("--- Monomers search ---");
    long searchTime = System.currentTimeMillis();
    MonomericSpliting.setVerbose(verbose);
    MonomericSpliting split = new MonomericSpliting(families, chains, removeDistance, retryCount, modulationDepth);
    split.setAllowLightMatchs(lightMatch);
    Coverage[] covs = split.computeCoverages(polDB);
    searchTime = System.currentTimeMillis() - searchTime;
    System.out.println("Search time : " + (searchTime / 1000) + "s");
    // ------------------- Output ------------------------
    System.out.println("--- Output creations ---");
    long outputTime = System.currentTimeMillis();
    // Creation of the out directory
    File outfolder = new File(outfolderName);
    if (!outfolder.exists())
        outfolder.mkdir();
    CoveragesJsonLoader cjl = new CoveragesJsonLoader(polDB, families);
    cjl.saveFile(covs, outfile);
    // Images generation
    if (html || zip) {
        File imgsFolder = new File(imgsFoldername);
        if (!imgsFolder.exists())
            imgsFolder.mkdir();
        ImagesGeneration ig = new ImagesGeneration();
        ig.generateMonomerImages(imgsFolder, monoDB);
        Map<Coverage, ColorsMap> colors = ig.generatePeptidesImages(imgsFolder, covs);
        if (html) {
            // HTML
            Coverages2HTML c2h = new Coverages2HTML(covs, monoDB, families);
            File htmlFile = new File(outfolderName + "/s2m.html");
            c2h.createResults(htmlFile, imgsFolder, colors);
        }
        if (zip) {
            // Zip File
            OutputZiper oz = new OutputZiper(outfolderName + "/s2m.zip");
            oz.createZip(imgsFolder.getPath(), outfile, pepDBname, monoDBname, residuesDBname, colors);
        }
    }
    outputTime = System.currentTimeMillis() - outputTime;
    System.out.println("Ouputing time : " + (outputTime / 1000) + "s");
    System.out.println("--- Ended ---");
}

Example 7 with Coverage

use of algorithms.utils.Coverage in project Smiles2Monomers by yoann-dufresne.

the class OutputZiper method createSupplementaries.

@SuppressWarnings("unchecked")
private void createSupplementaries(String path, Map<Coverage, ColorsMap> allColors) {
    File sup = new File(path);
    if (sup.exists())
        sup.delete();
    JSONArray array = new JSONArray();
    for (Coverage cov : allColors.keySet()) {
        JSONObject jso = new JSONObject();
        jso.put("id", cov.getId());
        jso.put("ratio", cov.getCoverageRatio());
        ColorsMap cm = allColors.get(cov);
        JSONArray colorsArray = new JSONArray();
        jso.put("colors", colorsArray);
        for (Residue res : cm.keySet()) {
            JSONObject resObj = new JSONObject();
            JSONArray resColors = new JSONArray();
            for (Color col : cm.get(res)) {
                resColors.add(Integer.toHexString(col.getRGB()));
            }
            resObj.put(res.getId(), resColors);
            colorsArray.add(resObj);
        }
        array.add(jso);
    }
    try {
        FileWriter fw = new FileWriter(sup);
        fw.write(array.toJSONString());
        fw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 8 with Coverage

use of algorithms.utils.Coverage in project Smiles2Monomers by yoann-dufresne.

the class ImagesGeneration method generatePeptidesImages.

public Map<Coverage, ColorsMap> generatePeptidesImages(File imgsFolder, Coverage[] covs) {
    // Coverage images directory
    File coverageDir = new File(imgsFolder.getPath() + "/peptides");
    if (!coverageDir.exists())
        coverageDir.mkdir();
    for (File f : coverageDir.listFiles()) f.delete();
    Map<Coverage, ColorsMap> covsColors = new HashMap<>();
    for (Coverage cov : covs) {
        // File png = new File(coverageDir.getPath() + "/" + cov.getChemicalObject().getId() + ".png");
        String name = cov.getChemicalObject().getName().replaceAll("\\s", "_");
        File png = new File(coverageDir.getPath() + "/" + cov.getChemicalObject().getId() + "_" + name + ".png");
        ColorsMap colors = pg.createPNG(cov, png);
        covsColors.put(cov, colors);
    }
    return covsColors;
}

Example 9 with Coverage

use of algorithms.utils.Coverage in project Smiles2Monomers by yoann-dufresne.

the class CoveragesJsonLoader method objectFromJson.

@Override
protected Coverage objectFromJson(JSONObject obj) {
    // TODO : Create new parser with the files created by the new output functions
    System.err.println("From classe '" + CoveragesJsonLoader.class.getName() + "' method 'objectFromJson':");
    System.err.println("This is deprecated ! You will have some problems with recent json files !");
    ChemicalObject co = null;
    try {
        co = this.db.getObject("" + ((Number) obj.get("peptide")).intValue());
    } catch (NullPointerException e) {
        System.err.println(e.getMessage());
        System.err.println("Maybe coverage json and molecule json don't match");
        System.exit(2);
    }
    Coverage cov = new Coverage(co);
    JSONArray array = (JSONArray) obj.get("matches");
    for (Object o : array) {
        JSONObject jso = (JSONObject) o;
        Residue res = null;
        try {
            res = this.residues.getObject("" + ((Number) jso.get("residue")).intValue());
        } catch (NullPointerException e) {
            e.printStackTrace();
        }
        JSONObject jMatch = (JSONObject) jso.get("match");
        Match match = new Match(res);
        JSONArray atoms = (JSONArray) jMatch.get("atoms");
        for (Object atObj : atoms) {
            JSONObject atom = (JSONObject) atObj;
            int idx = ((Number) atom.get("a")).intValue();
            match.addAtom(idx);
            match.addHydrogens(idx, ((Number) atom.get("h")).intValue());
        }
        JSONArray bonds = (JSONArray) jMatch.get("bonds");
        for (Object boObj : bonds) {
            int bond = ((Number) boObj).intValue();
            match.addBond(bond);
        }
        cov.addMatch(match);
    }
    cov.calculateGreedyCoverage();
    return cov;
}

Example 10 with Coverage

use of algorithms.utils.Coverage in project Smiles2Monomers by yoann-dufresne.

the class CoveragesDB method addObject.

@Override
public void addObject(String id, Coverage o) {
    if (!this.database.containsKey(id))
        super.addObject(id, o);
    else {
        Coverage prev = this.database.get(id);
        prev.addMatches(o);
    }
}