libsequence: ComplementBase.cc Source File

00001 /*
00002 
00003 Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu
00004 
00005 Remove the brackets to email me.
00006 
00007 This file is part of libsequence.
00008 
00009 libsequence is free software: you can redistribute it and/or modify
00010 it under the terms of the GNU General Public License as published by
00011 the Free Software Foundation, either version 3 of the License, or
00012 (at your option) any later version.
00013 
00014 libsequence is distributed in the hope that it will be useful,
00015 but WITHOUT ANY WARRANTY; without even the implied warranty of
00016 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00017 GNU General Public License for more details.
00018 
00019 You should have received a copy of the GNU General Public License
00020 long with libsequence.  If not, see <http://www.gnu.org/licenses/>.
00021 
00022 */
00023 
00024 #include <Sequence/ComplementBase.hpp>
00025 #include <cctype>
00026 
00027 
00028 namespace Sequence
00029   {
00030   void ComplementBase::operator()(char &ch) const
00034     {
00035       //      char uch = std::toupper(ch);
00036       switch(ch)
00037         {
00038         case 'A':
00039           ch = 'T';
00040           break;
00041         case 'a':
00042           ch = 't';
00043           break;
00044         case 'T':
00045           ch = 'A';
00046           break;
00047         case 't':
00048           ch = 'a';
00049           break;
00050         case 'G':
00051           ch = 'C';
00052           break;
00053         case 'g':
00054           ch = 'c';
00055           break;
00056         case 'C':
00057           ch = 'G';
00058           break;
00059         case 'c':
00060           ch = 'g';
00061           break;
00062         case 'M':
00063           ch = 'K';
00064           break;
00065         case 'm':
00066           ch ='k';
00067           break;
00068         case 'K':
00069           ch = 'M';
00070           break;
00071         case 'k':
00072           ch = 'm';
00073         case 'R':
00074           ch = 'Y';
00075           break;
00076         case 'r':
00077           ch = 'y';
00078           break;
00079         case 'Y':
00080           ch = 'R';
00081           break;
00082         case 'y':
00083           ch = 'r';
00084           break;
00085         case 'W':
00086           ch = 'W';
00087           break;
00088         case 'w':
00089           ch = 'w';
00090           break;
00091         case 'S':
00092           ch = 'S';
00093           break;
00094         case 's':
00095           ch = 's';
00096           break;
00097         case 'B':
00098           ch = 'V';
00099           break;
00100         case 'b':
00101           ch = 'v';
00102           break;
00103         case 'V':
00104           ch = 'B';
00105           break;
00106         case 'v':
00107           ch = 'b';
00108           break;
00109         case 'D':
00110           ch = 'H';
00111           break;
00112         case 'd':
00113           ch = 'h';
00114           break;
00115         case 'H':
00116           ch = 'D';
00117           break;
00118         case 'h':
00119           ch = 'd';
00120           break;
00121         case 'X':
00122           ch = 'X';
00123           break;
00124         case 'x':
00125           ch = 'x';
00126           break;
00127         case 'N':
00128           ch = 'N';
00129           break;
00130         case 'n':
00131           ch = 'n';
00132         case '-':
00133           ch = '-';
00134           break;
00135         default:
00136           ch = '?';
00137           break;
00138         }
00139     }
00140 
00141 }
00142