fixes while testing 1.12.0

[mothur.git] / mothur.cpp

diff --git a/mothur.cpp b/mothur.cpp
index 623601207afe90ae92a691646110eac2e9a18f79..a95c381658009f988e6caff879181a9412851c3d 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -12,7 +12,6 @@
 #include "globaldata.hpp"
 #include "mothurout.h"
 
-
 /**************************************************************************************************/
 
 GlobalData* GlobalData::_uniqueInstance = 0;
@@ -58,7 +57,7 @@ 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 +71,36 @@ 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 = 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
+               
                //header
-               m->mothurOut("mothur v.1.8");
+               m->mothurOut("mothur v.1.12.0");
                m->mothurOutEndLine();          
-               m->mothurOut("Last updated: 2/02/2010");
+               m->mothurOut("Last updated: 7/23/2010");
                m->mothurOutEndLine();  
                m->mothurOutEndLine();          
                m->mothurOut("by");
@@ -144,12 +169,37 @@ int main(int argc, char *argv[]){
                
                while(bail == 0)        {       bail = mothur->getInput();      }
                
+               //closes logfile so we can rename
+               m->closeLog();
+               
                string outputDir = mothur->getOutputDir();
-               string newlogFileName = outputDir + logFileName;
-       
-               //need this because m->mothurOut makes the logfile, but doesn't know where to put it
-               rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+               string tempLog = mothur->getLogFileName();
+               bool append = mothur->getAppend();
+               
+               string newlogFileName;
+               if (tempLog != "") {
+                       newlogFileName = outputDir + tempLog;
+                       
+                       if (!append) {  
+                               //need this because m->mothurOut makes the logfile, but doesn't know where to put it
+                               rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+
+                       }else {
+                               ofstream outNewLog;
+                               openOutputFileAppend(newlogFileName, outNewLog);
+                               outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+                               outNewLog.close();
+                               
+                               appendFiles(logFileName, newlogFileName);
+                               remove(logFileName.c_str());
+                       }
+               }else{  
+                       newlogFileName = outputDir + logFileName;
+                       //need this because m->mothurOut makes the logfile, but doesn't know where to put it
+                       rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
+               }
                
+                               
                delete mothur;
                
                #ifdef USE_MPI