com.act.lcms.db.io.parser.ConstructAnalysisFileParser.java Source code

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Here is the source code for com.act.lcms.db.io.parser.ConstructAnalysisFileParser.java

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/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program is free software: you can redistribute it and/or modify  *
*  it under the terms of the GNU General Public License as published by  *
*  the Free Software Foundation, either version 3 of the License, or     *
*  (at your option) any later version.                                   *
*                                                                        *
*  This program is distributed in the hope that it will be useful,       *
*  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
*  GNU General Public License for more details.                          *
*                                                                        *
*  You should have received a copy of the GNU General Public License     *
*  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
*                                                                        *
*************************************************************************/

package com.act.lcms.db.io.parser;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.tuple.Pair;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

public class ConstructAnalysisFileParser {
    public static final String PRODUCT_KIND_SEPARATOR = "\t";
    public static final Pattern CONSTRUCT_DESIGNATOR_PATTERN = Pattern.compile("^>(.*)$");
    public static final String INTERMEDIATE_PRODUCT_DESIGNATOR = "INTERMEDIATE";

    private List<Pair<String, List<ConstructAssociatedChemical>>> constructProducts = new ArrayList<>();

    public void parse(File inFile) throws IOException {
        try (BufferedReader reader = new BufferedReader(new FileReader(inFile))) {

            String line;
            String constructId = null;
            List<ConstructAssociatedChemical> products = null;
            while ((line = reader.readLine()) != null) {
                Matcher matcher = CONSTRUCT_DESIGNATOR_PATTERN.matcher(line);
                if (matcher.matches()) {
                    if (constructId != null) {
                        handleConstructProductsList(constructId, products);
                    }
                    constructId = matcher.group(1).trim();
                    products = new ArrayList<>();
                } else {
                    if (constructId == null || products == null) {
                        throw new RuntimeException(
                                "Found construct product step line without a pre-defined construct");
                    }
                    String[] fields = StringUtils.splitByWholeSeparatorPreserveAllTokens(line,
                            PRODUCT_KIND_SEPARATOR);
                    if (fields.length != 2) {
                        System.err.format("Skipping line with unexpected number of fields (%d): %s\n",
                                fields.length, line);
                        continue;
                    }
                    String chemical = fields[0];
                    String kind = fields[1];
                    products.add(new ConstructAssociatedChemical(chemical, kind));
                }
            }
            // Finish processing anything that's left over.
            if (constructId != null) {
                handleConstructProductsList(constructId, products);
            }
        }
    }

    private void handleConstructProductsList(String construct, List<ConstructAssociatedChemical> products) {
        int step = 0;
        for (int i = products.size() - 1; i >= 0; i--) {
            products.get(i).setIndex(step);
            step++;
        }
        constructProducts.add(Pair.of(construct, products));
    }

    public List<Pair<String, List<ConstructAssociatedChemical>>> getConstructProducts() {
        return constructProducts;
    }

    public static class ConstructAssociatedChemical {
        Integer index;
        String chemical;
        String kind;

        public ConstructAssociatedChemical(String chemical, String kind) {
            this.chemical = chemical;
            this.kind = kind;
        }

        public ConstructAssociatedChemical(Integer index, String chemical, String kind) {
            this.index = index;
            this.chemical = chemical;
            this.kind = kind;
        }

        public Integer getIndex() {
            return index;
        }

        protected void setIndex(Integer index) {
            this.index = index;
        }

        public String getChemical() {
            return chemical;
        }

        public String getKind() {
            return kind;
        }
    }

}