added get.otus and remove.otus commands

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 4f91c2e90a0b52aa8c3f51140e857660e8ba038f..9ed0dfc5d1645c5c2b65cabdb04063e300634d04 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -12,7 +12,6 @@
 #include "globaldata.hpp"
 #include "mothurout.h"
 
-
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
@@ -36,8 +35,7 @@ void ctrlc_handler ( int sig ) {
 /***********************************************************************/
 int main(int argc, char *argv[]){
        MothurOut* m = MothurOut::getInstance();
-       try {
-               
+       try {   
                signal(SIGINT, ctrlc_handler );
                                
                time_t ltime = time(NULL); /* calendar time */  
@@ -58,7 +56,7 @@ int main(int argc, char *argv[]){
                                m->mothurOutEndLine(); m->mothurOutEndLine();
                        #else
                                m->mothurOutJustToLog("Linux version");
-                               >m->mothurOutEndLine(); m->mothurOutEndLine();
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
                        #endif
 
                #else
@@ -72,10 +70,42 @@ int main(int argc, char *argv[]){
                        m->mothurOutEndLine(); m->mothurOutEndLine();
                #endif
                
+               #ifdef MOTHUR_FILES
+                       string temp = MOTHUR_FILES; 
+                       
+                       //add / to name if needed
+                       string lastChar = temp.substr(temp.length()-1);
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               if (lastChar != "/") { temp += "/"; }
+                       #else
+                               if (lastChar != "\\") { temp += "\\"; } 
+                       #endif
+                       
+                       temp = m->getFullPathName(temp);
+                       m->setDefaultPath(temp);
+                       
+                       m->mothurOutJustToLog("Using default file location " + temp);
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif
+               
+               #ifdef BIT_VERSION
+                       m->mothurOutJustToLog("Running 64Bit Version");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #else
+                       m->mothurOutJustToLog("Running 32Bit Version");
+                       m->mothurOutEndLine(); m->mothurOutEndLine();
+               #endif
+               
+               //get releaseDate from Make
+               string releaseDate = RELEASE_DATE; 
+               string mothurVersion = VERSION; 
+               m->setReleaseDate(releaseDate);
+               m->setVersion(mothurVersion);
+               
                //header
-               m->mothurOut("mothur v.1.9");
+               m->mothurOut("mothur v." + mothurVersion);
                m->mothurOutEndLine();          
-               m->mothurOut("Last updated: 4/16/2010");
+               m->mothurOut("Last updated: " + releaseDate);
                m->mothurOutEndLine();  
                m->mothurOutEndLine();          
                m->mothurOut("by");
@@ -119,7 +149,7 @@ int main(int argc, char *argv[]){
                Engine* mothur;
                bool bail = 0;
                string input;
-
+ 
                if(argc>1){
                        input = argv[1];
 
@@ -161,11 +191,11 @@ int main(int argc, char *argv[]){
 
                        }else {
                                ofstream outNewLog;
-                               openOutputFileAppend(newlogFileName, outNewLog);
+                               m->openOutputFileAppend(newlogFileName, outNewLog);
                                outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
                                outNewLog.close();
                                
-                               appendFiles(logFileName, newlogFileName);
+                               m->appendFiles(logFileName, newlogFileName);
                                remove(logFileName.c_str());
                        }
                }else{