Examples with Start2FoldResidueAnnotation de.bioforscher.jstructure.efr.model.Start2FoldResidueAnnotation used on opensource projects

Example 1 with Start2FoldResidueAnnotation

use of de.bioforscher.jstructure.efr.model.Start2FoldResidueAnnotation in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parse.

public static void parse(Chain chain, InputStream inputStream) {
    try {
        // assign baseline resp. entry container for each residue
        chain.aminoAcids().forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
        Document document = Jsoup.parse(inputStream, "UTF-8", "/");
        Elements experimentElements = document.getElementsByTag("experiment");
        logger.debug("found {} experiments", experimentElements.size());
        List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).collect(Collectors.toList());
        for (Experiment experiment : experiments) {
            assignValues(experiment, chain);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}

Example 2 with Start2FoldResidueAnnotation

use of de.bioforscher.jstructure.efr.model.Start2FoldResidueAnnotation in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parseSpecificExperiment.

public static void parseSpecificExperiment(Chain chain, InputStream inputStream, List<Integer> experimentIds) {
    logger.debug("ids: {}", experimentIds);
    try {
        // assign baseline resp. entry container for each residue if not already happened
        chain.aminoAcids().filter(aminoAcid -> !aminoAcid.getFeatureContainer().getFeatureOptional(Start2FoldResidueAnnotation.class).isPresent()).forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
        Document document = Jsoup.parse(inputStream, "UTF-8", "/");
        Elements experimentElements = document.getElementsByTag("experiment");
        List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).filter(experiment -> experimentIds.contains(experiment.getExperimentId())).collect(Collectors.toList());
        logger.debug("processing {} experiments", experiments.size());
        if (experimentIds.size() != experiments.size()) {
            throw new IllegalArgumentException("did not find all referenced experiments");
        }
        for (Experiment experiment : experiments) {
            assignValuesForEarly(experiment, chain);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}

Example 3 with Start2FoldResidueAnnotation

use of de.bioforscher.jstructure.efr.model.Start2FoldResidueAnnotation in project jstructure by JonStargaryen.

the class Start2FoldXmlParser method parseStability.

public static void parseStability(Chain chain, InputStream inputStream) {
    try {
        // assign baseline resp. entry container for each residue if not already happened
        chain.aminoAcids().filter(aminoAcid -> !aminoAcid.getFeatureContainer().getFeatureOptional(Start2FoldResidueAnnotation.class).isPresent()).forEach(aminoAcid -> aminoAcid.getFeatureContainer().addFeature(new Start2FoldResidueAnnotation()));
        Document document = Jsoup.parse(inputStream, "UTF-8", "/");
        Elements experimentElements = document.getElementsByTag("experiment");
        List<Experiment> experiments = experimentElements.stream().map(Experiment::parse).filter(experiment -> experiment.getMethod() == Method.STABILITY).collect(Collectors.toList());
        for (Experiment experiment : experiments) {
            assignValuesForStrong(experiment, chain);
        }
    } catch (IOException e) {
        throw new UncheckedIOException(e);
    }
}