fixed sub.sample groups bug

diff --git a/catchallcommand.h b/catchallcommand.h
index 583191db8d547996bef24378fb2dfd50b7ac0a13..a1c9d0e2e8b1d6806a7c84c45419f297110f5320 100644 (file)
--- a/catchallcommand.h
+++ b/catchallcommand.h
@@ -30,7 +30,7 @@ public:
        
        vector<string> setParameters();
        string getCommandName()                 { return "catchall";                    }
-       string getCommandCategory()             { return "Hypothesis Testing";  }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
        string getHelpString(); 
        
        int execute(); 

diff --git a/engine.cpp b/engine.cpp
index dbdcc36300f2fd5d3f5ea6135dbc8666f328bba0..f128c4684040346110d519c56f45c9506e953866 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -179,6 +179,13 @@ bool InteractEngine::getInput(){
                                        //cout << pid << " is in execute " << commandName << endl;
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->Groups.clear();
+                                       mout->namesOfGroups.clear();
+                                       mout->Treenames.clear();
+                                       mout->names.clear();
+                                       mout->saveNextLabel = "";
+                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                                        
@@ -353,6 +360,13 @@ bool BatchEngine::getInput(){
                                                if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->Groups.clear();
+                                       mout->namesOfGroups.clear();
+                                       mout->Treenames.clear();
+                                       mout->names.clear();
+                                       mout->saveNextLabel = "";
+                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                                        
@@ -455,9 +469,11 @@ bool ScriptEngine::getInput(){
                        
                        if (input == "") { input = "quit()"; }
                        
-                       mout->mothurOutEndLine();
-                       mout->mothurOut("mothur > " + input);
-                       mout->mothurOutEndLine();
+                       if ((!mout->gui) || (input != "quit()")) {
+                               mout->mothurOutEndLine();
+                               mout->mothurOut("mothur > " + input);
+                               mout->mothurOutEndLine();
+                       }
                        
                        #ifdef USE_MPI
                                //send commandName
@@ -505,6 +521,13 @@ bool ScriptEngine::getInput(){
                                                        //cout << pid << " is in execute" << endl;      
                                        #endif
                                        //executes valid command
+                                       mout->runParse = true;
+                                       mout->Groups.clear();
+                                       mout->namesOfGroups.clear();
+                                       mout->Treenames.clear();
+                                       mout->names.clear();
+                                       mout->saveNextLabel = "";
+                                                       
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
                                        

diff --git a/mothur.cpp b/mothur.cpp
index 74e7e731cc391441280d202bb6913019e0fd0538..3e2a4397dd155f6969af09406d7f34d2999efebd 100644 (file)
--- a/mothur.cpp
+++ b/mothur.cpp
@@ -46,32 +46,15 @@ int main(int argc, char *argv[]){
 
                m->setFileName(logFileName);
                
-                               
-               //version
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        system("clear");
-                       #if defined (__APPLE__) || (__MACH__)
-                               m->mothurOutJustToLog("Mac version");
-                               m->mothurOutEndLine(); m->mothurOutEndLine();
-                       #else
-                               m->mothurOutJustToLog("Linux version");
-                               m->mothurOutEndLine(); m->mothurOutEndLine();
-                       #endif
-
                #else
                        system("CLS");
-                       m->mothurOutJustToLog("Windows version");
-                       m->mothurOutEndLine(); m->mothurOutEndLine();
-               #endif          
-               
-               #ifdef USE_READLINE
-                       m->mothurOutJustToLog("Using ReadLine");
-                       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)
@@ -79,20 +62,14 @@ int main(int argc, char *argv[]){
                        #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();
+               #ifdef USE_MPI
+                       int version, subversion;
+                       MPI_Get_version(&version, &subversion);
                #endif
                
                //get releaseDate from Make
@@ -101,46 +78,86 @@ int main(int argc, char *argv[]){
                m->setReleaseDate(releaseDate);
                m->setVersion(mothurVersion);
                
-               //header
-               m->mothurOut("mothur v." + mothurVersion);
-               m->mothurOutEndLine();          
-               m->mothurOut("Last updated: " + releaseDate);
-               m->mothurOutEndLine();  
-               m->mothurOutEndLine();          
-               m->mothurOut("by");
-               m->mothurOutEndLine();          
-               m->mothurOut("Patrick D. Schloss");
-               m->mothurOutEndLine();
-               m->mothurOutEndLine();                  
-               m->mothurOut("Department of Microbiology & Immunology");
-               m->mothurOutEndLine();  
-               m->mothurOut("University of Michigan");
-               m->mothurOutEndLine();                  
-               m->mothurOut("pschloss@umich.edu");
-               m->mothurOutEndLine();          
-               m->mothurOut("http://www.mothur.org");
-               m->mothurOutEndLine();
-               m->mothurOutEndLine();
-               m->mothurOut("When using, please cite:");
-               m->mothurOutEndLine();
-               m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
-               m->mothurOutEndLine();  
-               m->mothurOutEndLine();          
-               m->mothurOut("Distributed under the GNU General Public License");
-               m->mothurOutEndLine();
-               m->mothurOutEndLine();                  
-               m->mothurOut("Type 'help()' for information on the commands that are available");
-               m->mothurOutEndLine();
-               m->mothurOutEndLine();                  
-               m->mothurOut("Type 'quit()' to exit program");
-               m->mothurOutEndLine();  
+               //will make the gui output "pretty"
+               bool guiMode = false;
+               if (argc>1) {
+                       string guiInput = argv[1];
+                       if (guiInput[0] == '+') { guiMode = true; }
+               }
                
-               #ifdef USE_MPI
-                       m->mothurOutJustToLog("Using MPI\tversion ");
-                       int version, subversion;
-                       MPI_Get_version(&version, &subversion);
-                       m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
-               #endif
+               if (!guiMode) {
+                       //version
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               #if defined (__APPLE__) || (__MACH__)
+                                       m->mothurOutJustToLog("Mac version");
+                                       m->mothurOutEndLine(); m->mothurOutEndLine();
+                               #else
+                                       m->mothurOutJustToLog("Linux version");
+                                       m->mothurOutEndLine(); m->mothurOutEndLine();
+                               #endif
+
+                       #else
+                               m->mothurOutJustToLog("Windows version");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
+                       #endif          
+                       
+                       #ifdef USE_READLINE
+                               m->mothurOutJustToLog("Using ReadLine");
+                               m->mothurOutEndLine(); m->mothurOutEndLine();
+                       #endif
+                       
+                       #ifdef MOTHUR_FILES
+                               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." + mothurVersion);
+                       m->mothurOutEndLine();          
+                       m->mothurOut("Last updated: " + releaseDate);
+                       m->mothurOutEndLine();  
+                       m->mothurOutEndLine();          
+                       m->mothurOut("by");
+                       m->mothurOutEndLine();          
+                       m->mothurOut("Patrick D. Schloss");
+                       m->mothurOutEndLine();
+                       m->mothurOutEndLine();                  
+                       m->mothurOut("Department of Microbiology & Immunology");
+                       m->mothurOutEndLine();  
+                       m->mothurOut("University of Michigan");
+                       m->mothurOutEndLine();                  
+                       m->mothurOut("pschloss@umich.edu");
+                       m->mothurOutEndLine();          
+                       m->mothurOut("http://www.mothur.org");
+                       m->mothurOutEndLine();
+                       m->mothurOutEndLine();
+                       m->mothurOut("When using, please cite:");
+                       m->mothurOutEndLine();
+                       m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
+                       m->mothurOutEndLine();  
+                       m->mothurOutEndLine();          
+                       m->mothurOut("Distributed under the GNU General Public License");
+                       m->mothurOutEndLine();
+                       m->mothurOutEndLine();                  
+                       m->mothurOut("Type 'help()' for information on the commands that are available");
+                       m->mothurOutEndLine();
+                       m->mothurOutEndLine();                  
+                       m->mothurOut("Type 'quit()' to exit program");
+                       m->mothurOutEndLine();  
+                       
+                       #ifdef USE_MPI
+                               m->mothurOutJustToLog("Using MPI\tversion ");
+                               m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
+                       #endif
+               }
                
                //srand(54321);
                srand( (unsigned)time( NULL ) );
@@ -151,12 +168,16 @@ int main(int argc, char *argv[]){
  
                if(argc>1){
                        input = argv[1];
+                       //m->mothurOut("input = " + input); m->mothurOutEndLine();
 
                        if (input[0] == '#') {
                                m->mothurOutJustToLog("Script Mode");
                                m->mothurOutEndLine(); m->mothurOutEndLine();
 
                                mothur = new ScriptEngine(argv[0], argv[1]);
+                       }else if (input[0] == '+') {
+                                       mothur = new ScriptEngine(argv[0], argv[1]);
+                                       m->gui = true;
                        }else{
                                m->mothurOutJustToLog("Batch Mode");
                                m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -191,7 +212,10 @@ int main(int argc, char *argv[]){
                        }else {
                                ofstream outNewLog;
                                m->openOutputFileAppend(newlogFileName, outNewLog);
-                               outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+                               
+                               if (!m->gui) {
+                                       outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
+                               }
                                outNewLog.close();
                                
                                m->appendFiles(logFileName, newlogFileName);

diff --git a/mothurout.h b/mothurout.h
index f20d5c197df59b06c3f5069709aa4e036436a768..57d3f7647dabf43dd30f2caeefa9ae2bd09a0d30 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -95,7 +95,7 @@ class MothurOut {
                unsigned int fromBase36(string);
 
                int control_pressed;
-               bool executing, runParse, jumble;
+               bool executing, runParse, jumble, gui;
                
                //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles.
                string getPhylipFile()          { return phylipfile;            }
@@ -169,6 +169,7 @@ class MothurOut {
                        accnosfile = "";
                        taxonomyfile = "";
                        processors = "1";
+                       gui = false;
                };
                ~MothurOut();