Examples with AlignmentException de.bioforscher.jstructure.align.AlignmentException used on opensource projects

Example 6 with AlignmentException

use of de.bioforscher.jstructure.align.AlignmentException in project jstructure by JonStargaryen.

the class TMAlignService method process.

private synchronized TMAlignAlignmentResult process(String[] arguments, int run) throws AlignmentException {
    try {
        logger.debug("spawning tmalign process with arguments:{}{}", System.lineSeparator(), arguments);
        ProcessBuilder processBuilder = new ProcessBuilder(arguments);
        Process process = processBuilder.start();
        List<String> outputLines;
        try (BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()))) {
            outputLines = br.lines().collect(Collectors.toList());
        }
        List<String> errorLines;
        try (BufferedReader br = new BufferedReader(new InputStreamReader(process.getErrorStream()))) {
            errorLines = br.lines().collect(Collectors.toList());
        }
        process.waitFor();
        if (outputLines.stream().anyMatch(line -> line.startsWith("Can not open file:"))) {
            throw new ComputationException("error during tmalign execution:" + System.lineSeparator() + outputLines.stream().collect(Collectors.joining(System.lineSeparator())));
        }
        // errors are not reported in error stream
        if (!errorLines.isEmpty()) {
            throw new ComputationException("error during tmalign execution:" + System.lineSeparator() + errorLines.stream().collect(Collectors.joining(System.lineSeparator())));
        }
        int length1 = 0;
        int length2 = 0;
        int alignedLength = 0;
        RootMeanSquareDeviation rootMeanSquareDeviation = null;
        double seqId = 0;
        TemplateModelingScore templateModelingScore1 = null;
        TemplateModelingScore templateModelingScore2 = null;
        for (String outputLine : outputLines) {
            if (outputLine.startsWith("Length of Chain_1")) {
                length1 = Integer.valueOf(outputLine.split(":")[1].trim().split("\\s+")[0]);
            } else if (outputLine.startsWith("Length of Chain_2")) {
                length2 = Integer.valueOf(outputLine.split(":")[1].trim().split("\\s+")[0]);
            } else if (outputLine.startsWith("Aligned length")) {
                String[] split = outputLine.split("=");
                alignedLength = Integer.valueOf(split[1].split(",")[0].trim());
                rootMeanSquareDeviation = new RootMeanSquareDeviation(Double.valueOf(split[2].split(",")[0].trim()));
                seqId = Double.valueOf(split[4].trim());
            } else if (outputLine.startsWith("TM-score")) {
                double tmscore = Double.valueOf(outputLine.split("=")[1].split("\\(")[0].trim());
                TemplateModelingScore templateModelingScore = new TemplateModelingScore(tmscore);
                if (outputLine.contains("Chain_1")) {
                    templateModelingScore1 = templateModelingScore;
                } else {
                    templateModelingScore2 = templateModelingScore;
                }
            }
        }
        return new TMAlignAlignmentResult(length1, length2, alignedLength, rootMeanSquareDeviation, seqId, templateModelingScore1, templateModelingScore2);
    } catch (Exception e) {
        if (run > 3) {
            logger.warn("tmalign computation finally failed:{}{}", System.lineSeparator(), Arrays.toString(arguments), e);
            throw new AlignmentException("could not run tmalign", e);
        }
        return process(arguments, run + 1);
    }
}