Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / main.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/main.cpp b/website/archive/binaries/mac/src/clustalw/src/main.cpp
new file mode 100644 (file)
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+++ b/website/archive/binaries/mac/src/clustalw/src/main.cpp
@@ -0,0 +1,94 @@
+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+#ifdef HAVE_CONFIG_H
+    #include "config.h"
+#endif
+#include <iostream>
+#include "alignment/Alignment.h"
+#include "alignment/Sequence.h"
+#include "general/clustalw.h"
+#include "general/UserParameters.h"
+#include "substitutionMatrix/SubMatrix.h"
+#include "general/Utility.h"
+#include "fileInput/FileReader.h"
+#include "interface/InteractiveMenu.h"
+#include "interface/CommandLineParser.h"
+#include "general/DebugLog.h"
+#include "general/ClustalWResources.h"
+#include "general/Stats.h"
+#include <ctime>
+namespace clustalw
+{ 
+    UserParameters* userParameters;
+    Utility* utilityObject;
+    SubMatrix *subMatrix; 
+    DebugLog* logObject;
+    Stats* statsObject;
+}
+using namespace std;
+using namespace clustalw;
+
+int main(int argc, char **argv)
+{      
+    userParameters = new UserParameters(false);
+    utilityObject = new Utility();   
+    subMatrix = new SubMatrix();
+    statsObject = new Stats();
+    ClustalWResources *resources = ClustalWResources::Instance();
+    resources->setPathToExecutable(string(argv[0]));
+    userParameters->setDisplayInfo(true);
+
+
+    
+    //userParameters->setDebug(5);       
+    #if DEBUGFULL    
+        if(DEBUGLOG)
+        {
+            cout << "debugging is on\n\n\n";
+            logObject = new DebugLog("logfile.txt");
+            logObject->logMsg("Loggin is on!");
+        }
+    #endif
+
+    if (argc > 1)
+    {    
+        //time_t start, end;
+        //double dif;
+        //start = time (NULL);
+        //userParameters->setDisplayInfo(false);        
+        vector<string> args;
+        for (int i = 1; i < argc; ++i)
+        {
+            args.push_back(argv[i]);
+        }
+        CommandLineParser cmdLineParser(&args, false);
+        
+        if (statsObject->isEnabled())
+            statsObject->logCmdLine(argc,argv);
+        
+        //end = time (NULL);
+        //dif = difftime(end, start);
+        //cout << "It took " << dif << " seconds\n";
+    }
+    if (argc<=1 || userParameters->getInteractive())
+    {
+        // FIXME: additional parameters like infile are ignored!
+        InteractiveMenu menu;
+        userParameters->setMenuFlag(true);
+        userParameters->setInteractive(true);
+        menu.mainMenu();
+    }
+    delete userParameters;
+    delete utilityObject;
+    delete subMatrix;
+    
+    if(logObject)
+    {
+        delete logObject;
+    }
+    return 0;
+}
+