4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
10 #include "alignment/Alignment.h"
11 #include "alignment/Sequence.h"
12 #include "general/clustalw.h"
13 #include "general/UserParameters.h"
14 #include "substitutionMatrix/SubMatrix.h"
15 #include "general/Utility.h"
16 #include "fileInput/FileReader.h"
17 #include "interface/InteractiveMenu.h"
18 #include "interface/CommandLineParser.h"
19 #include "general/DebugLog.h"
20 #include "general/ClustalWResources.h"
21 #include "general/Stats.h"
25 UserParameters* userParameters;
26 Utility* utilityObject;
32 using namespace clustalw;
34 int main(int argc, char **argv)
36 userParameters = new UserParameters(false);
37 utilityObject = new Utility();
38 subMatrix = new SubMatrix();
39 statsObject = new Stats();
40 ClustalWResources *resources = ClustalWResources::Instance();
41 resources->setPathToExecutable(string(argv[0]));
42 userParameters->setDisplayInfo(true);
46 //userParameters->setDebug(5);
50 cout << "debugging is on\n\n\n";
51 logObject = new DebugLog("logfile.txt");
52 logObject->logMsg("Loggin is on!");
60 //start = time (NULL);
61 //userParameters->setDisplayInfo(false);
63 for (int i = 1; i < argc; ++i)
65 args.push_back(argv[i]);
67 CommandLineParser cmdLineParser(&args, false);
69 if (statsObject->isEnabled())
70 statsObject->logCmdLine(argc,argv);
73 //dif = difftime(end, start);
74 //cout << "It took " << dif << " seconds\n";
76 if (argc<=1 || userParameters->getInteractive())
78 // FIXME: additional parameters like infile are ignored!
80 userParameters->setMenuFlag(true);
81 userParameters->setInteractive(true);
84 delete userParameters;