content: /*************************************************************************
  *                                                                        *
  *  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;
      }
    }
  
  }
  