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 org.twentyn.proteintodna;
  
  import java.util.ArrayList;
  import java.util.HashMap;
  import java.util.HashSet;
  import java.util.List;
  import java.util.Map;
  import java.util.Set;
  
  /**
   * This class checks a sequence for passing Gen9 and Beersheba constraints
   */
  public class SequenceChecker {
      
      private boolean verbose = false;
      
      public void setVerbose(boolean isVerbose) {
          verbose = isVerbose;
      }
      
      private void printIfVerbose(String msg) {
          if(verbose) {
              System.out.println(msg);
          }
      }
      
      public boolean check(String dnaseq) {
          String revcomp = SequenceUtils.reverseComplement(dnaseq);
          String combined = dnaseq + "x" + revcomp;
          combined = combined.toUpperCase();
          if(combined.contains("AAAAAAAA")) {
              printIfVerbose("Sequence has poly(A)");
              return false;
          }
          if(combined.contains("TTTTTTTT")) {
              printIfVerbose("Sequence has poly(T)");
              return false;
          }
          if(combined.contains("CCCCCCCC")) {
              printIfVerbose("Sequence has poly(C)");
              return false;
          }
          if(combined.contains("GGGGGGGG")) {
              printIfVerbose("Sequence has poly(G)");
              return false;
          }
          if(combined.contains("CAATTG")) {
              printIfVerbose("Sequence has MfeI");
              return false;
          }
          if(combined.contains("GAATTC")) {
              printIfVerbose("Sequence has EcoRI");
              return false;
          }
          if(combined.contains("GGATCC")) {
              printIfVerbose("Sequence has BamHI");
              return false;
          }
          if(combined.contains("AGATCT")) {
              printIfVerbose("Sequence has BglII");
              return false;
          }
          if(combined.contains("ACTAGT")) {
              printIfVerbose("Sequence has SpeI");
              return false;
          }
          if(combined.contains("TCTAGA")) {
              printIfVerbose("Sequence has XbaI");
              return false;
          }
          if(combined.contains("GGTCTC")) {
              printIfVerbose("Sequence has BsaI");
              return false;
          }
          if(combined.contains("GAGGAG")) {
              printIfVerbose("Sequence has BseRI");
              return false;
          }
          if(combined.contains("CGTCTC")) {
              printIfVerbose("Sequence has BsmBI");
              return false;
          }
          if(combined.contains("CACCTGC")) {
              printIfVerbose("Sequence has AarI");
              return false;
          }
          if(combined.contains("CTGCAG")) {
              printIfVerbose("Sequence has PstI");
              return false;
          }
          if(combined.contains("CTCGAG")) {
              printIfVerbose("Sequence has XhoI");
              return false;
          }
          if(combined.contains("GCATGC")) {
              printIfVerbose("Sequence has SphI");
              return false;
          }
          if(combined.contains("GTCGAC")) {
              printIfVerbose("Sequence has SalI");
              return false;
          }
          if(combined.contains("GCGGCCGC")) {
              printIfVerbose("Sequence has NotI");
              return false;
          }
          if(combined.contains("AAGCTT")) {
              printIfVerbose("Sequence has HindIII");
              return false;
          }
          
          return true;
      }
      
      public static void main(String[] args) {
          SequenceChecker checker = new SequenceChecker();
          boolean result = checker.check("GGGGGGGG");  //returns false due to poly(G)
          System.out.println(result);
      }
  }
  