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

Example 1 with Coverage

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

the class ImagesGeneration method generatePeptidesImages.

public Map<Coverage, ColorsMap> generatePeptidesImages(File imgsDirectory, Iterable<Coverage> coverages) {
    // Coverage images directory
    File coverageDir = new File(imgsDirectory.getPath() + "/peptides");
    if (!coverageDir.exists())
        coverageDir.mkdir();
    for (File f : coverageDir.listFiles()) f.delete();
    Map<Coverage, ColorsMap> covsColors = new HashMap<>();
    for (Coverage cov : coverages) {
        // 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 2 with Coverage

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

the class ChainsFamilyMatching method matchFamilly.

@Override
public Coverage matchFamilly(Family family) {
    if (this.co == null)
        return null;
    this.coverage = new Coverage(co);
    FamilyChainsDB fc = this.chains.getObject(family.getJsonName());
    this.toMatch.addAll(family.getRoots());
    while (!toMatch.isEmpty()) {
        Residue res = toMatch.remove();
        List<MappedChain> mcs = null;
        List<ChainAdd> adds = fc.getAdds(res);
        // If the residue is a root
        if (adds.size() == 0) {
            Chain rootChain = fc.getRootChains().get(res);
            mcs = Isomorphism.searchAChain(rootChain, this.co, this.matchingType);
        } else // From previous mapping
        {
            mcs = new ArrayList<>();
            Residue from = adds.get(0).getFrom();
            for (MappedChain mc : mappings.get(from)) {
                try {
                    MappedChain clone = mc;
                    for (ChainAdd add : adds) clone = add.applyAndClone(mc, this.matchingType);
                    mcs.add(clone);
                } catch (Exception e) {
                }
            }
        }
        // Save results and recursive add
        if (mcs.size() > 0) {
            this.mappings.put(res, mcs);
            this.addToCoverage(family, mcs, res);
            for (Residue child : fc.getFamily().getChildrenOf(res)) {
                if (fc.getAdds(child).get(0).getFrom().equals(res)) {
                    this.toMatch.add(child);
                }
            }
        }
    }
    this.mappings.clear();
    return this.coverage;
}

Example 3 with Coverage

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

the class MonomericSpliting method computeCoverage.

/**
 * Calculate an object Coverage with all matches from families.
 * @param pep Peptide to match
 */
public void computeCoverage(Polymer pep) {
    this.coverage = new Coverage(pep);
    this.matcher.setChemicalObject(pep);
    Isomorphism.setMappingStorage(true);
    // Step 1 : Strict Matching
    if (verbose) {
        System.out.println("+Strict matching");
        System.out.println("++Search residues");
    }
    this.matchAllFamilies(MatchingType.STRONG);
    double ratio = this.coverage.getCoverageRatio();
    if (ratio < 1.0) {
        if (verbose)
            System.out.println("++Modulation");
        this.coverage = this.modulation.modulate(this.coverage);
    }
    Coverage save = this.coverage.clone();
    // conditions to go to light matching
    if (!this.allowLightMatchs || ratio == 1.0) {
        Isomorphism.setMappingStorage(false);
        return;
    }
    // TODO : Why if/else ?
    if (this.condition == null)
        this.condition = new ExtendsNTimes(this.retry);
    else
        this.condition.init();
    this.remover.init();
    // Successive matchings
    int depth = 0;
    while (this.coverage.getCoverageRatio() < 1.0 && this.condition.toContinue(this.coverage)) {
        depth++;
        // Contract the atomic graph to monomeric graph
        ContractedGraph contracted = new ContractedGraph(this.coverage);
        // Remove monomers from the current solution to try with other matching strategy
        this.remover.remove(this.coverage, contracted);
        // Create a masked molecule to only search on free polymer areas
        Molecule mol = DeepenMatcher.mask(this.coverage);
        this.coverage.setCurrentMaskedMol(mol);
        OtherChemicalObject tmp = new OtherChemicalObject(mol);
        this.matcher.setChemicalObject(tmp);
        if (verbose) {
            System.out.println("+Light matching, depth " + depth);
            System.out.println("++Search residues");
        }
        // Compute for all families with ligth matching
        this.matchAllFamilies(MatchingType.LIGHT);
        // Re-compute coverage
        this.coverage.calculateGreedyCoverage();
        if (this.coverage.getCoverageRatio() < 1.0) {
            if (verbose)
                System.out.println("++Modulation");
            this.coverage = this.modulation.modulate(this.coverage);
        }
        if (this.coverage.getCoverageRatio() > save.getCoverageRatio())
            save = this.coverage.clone();
        this.remover.nextLevel();
    }
    Isomorphism.setMappingStorage(false);
    if (save.getCoverageRatio() > this.coverage.getCoverageRatio())
        this.coverage = save;
}

Example 4 with Coverage

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

the class MonomericSpliting method computeCoverages.

public Coverage[] computeCoverages(PolymersDB polDB) {
    Coverage[] covs = new Coverage[polDB.size()];
    int idx = 0;
    for (Polymer pol : polDB.getObjects()) {
        this.computeCoverage(pol);
        covs[idx] = this.getCoverage();
        idx += 1;
    }
    return covs;
}

Example 5 with Coverage

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

the class Json2HTML method main.

public static void main(String[] args) {
    if (args.length < 6) {
        System.err.println("Command line :\n\tjava main.AtomicToMonomeric <monomersFile> <peptidesFile> <rulesFile> <residuesFile> <coveragesFile> <outType> [outFile]  [-v]");
        System.err.println("  outType can be \"-zip\" or \"-html\"");
        System.exit(42);
    }
    String monoDBname = args[0];
    String pepDBname = args[1];
    String rulesDBname = args[2];
    String residuesDBname = args[3];
    String covsFile = args[4];
    boolean zip = args[5].equals("-zip") ? true : false;
    String outFile = null;
    if (zip && args.length < 7) {
        System.err.println("Command line :\n\tjava main.AtomicToMonomeric <monomersFile> <peptidesFile> <rulesFile> <residuesFile> <coveragesFile> <outType> [outFile]  [-v]");
        System.err.println("  outType can be \"-zip\" or \"-html\"");
        System.exit(42);
    } else if (zip && args.length >= 7)
        outFile = args[6];
    // Loading databases
    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, "data/serials/monos.serial");
    PolymersJsonLoader pcl = new PolymersJsonLoader(monoDB, true);
    PolymersDB pepDB = pcl.loadFile(pepDBname);
    RulesDB rules = RulesJsonLoader.loader.loadFile(rulesDBname);
    ResidueJsonLoader rjl = new ResidueJsonLoader(rules, monoDB);
    FamilyDB families = rjl.loadFile(residuesDBname);
    loadingTime = (System.currentTimeMillis() - loadingTime) / 1000;
    System.out.println("--- Json to HTML ---");
    long creationTime = System.currentTimeMillis();
    CoveragesJsonLoader cl = new CoveragesJsonLoader(pepDB, families);
    CoveragesDB covs = cl.loadFile(covsFile);
    List<Coverage> covsList = covs.getObjects();
    Collections.sort(covsList);
    // Common generations
    File imgs = new File("tmp_imgs_" + covsFile.substring(covsFile.lastIndexOf("/") + 1, covsFile.lastIndexOf(".")));
    if (!imgs.exists())
        imgs.mkdir();
    ImagesGeneration ig = new ImagesGeneration();
    Map<Coverage, ColorsMap> allColors = ig.generate(imgs, monoDB, covsList);
    if (!zip) {
        // HTML
        File resultDir = null;
        if (covsFile.contains("/"))
            resultDir = new File(covsFile.substring(0, covsFile.lastIndexOf("/")));
        else
            resultDir = new File(".");
        if (!resultDir.exists())
            resultDir.mkdir();
        Coverages2HTML c2h = new Coverages2HTML(covsList, monoDB, families);
        File htmlFile = new File(resultDir.getPath() + "/test.html");
        c2h.createResults(htmlFile, imgs, allColors);
    } else {
        // Zip File
        OutputZiper oz = new OutputZiper(outFile);
        oz.createZip(imgs.getPath(), covsFile, pepDBname, monoDBname, residuesDBname, allColors);
    }
    ig.cleanTmp(imgs);
    creationTime = (System.currentTimeMillis() - creationTime) / 1000;
    System.out.println();
    System.out.println("Total time to load datas : " + loadingTime + "s");
    System.out.println("Total time to create HTML : " + creationTime + "s");
    System.out.println();
    System.out.println("--- Program ended ---");
}