X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.cpp;h=ace1b00dc0b45e9500d6ba9aa8657fc44b854042;hb=264c8a3c759d9a999c485236e98dac98d4f0db5f;hp=b0e5eff6652a9defaa887eb7d21bb9bfe9e372a6;hpb=995238e9aa4455e3b59053e3dfe497b89caed79e;p=mothur.git

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index b0e5eff..ace1b00 100644
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -25,6 +25,7 @@ vector<string> CatchAllCommand::getValidParameters(){
 //**********************************************************************************************************************
 CatchAllCommand::CatchAllCommand(){	
 	try {
+		abort = true; calledHelp = true;
 		//initialize outputTypes
 		vector<string> tempOutNames;
 		outputTypes["csv"] = tempOutNames;
@@ -62,11 +63,11 @@ vector<string> CatchAllCommand::getRequiredFiles(){
 CatchAllCommand::CatchAllCommand(string option)  {	
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -173,24 +174,27 @@ void CatchAllCommand::help(){
 int CatchAllCommand::execute() {	
 	try {
 		
-		if (abort == true) { return 0; }
-		
-		//prepare full output directory
-		outputDir = m->getFullPathName(outputDir);
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//get location of catchall
 		GlobalData* globaldata = GlobalData::getInstance();
 		path = globaldata->argv;
-		path = path.substr(0, (path.find_last_of('m')));
+		path = path.substr(0, (path.find_last_of("othur")-5));
 		path = m->getFullPathName(path);
-
+		
+		savedOutputDir = outputDir;
 		string catchAllCommandExe = ""; 
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			catchAllCommandExe += "mono " + path + "CatchAllcmdL.exe ";
+			if (outputDir == "") { outputDir = "./"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
 		#else
 			catchAllCommandExe += "\"" + path + "CatchAllcmdW.exe\"" + " ";
+			if (outputDir == "") { outputDir = ".\\"; } //force full pathname to be created for catchall, this is necessary because if catchall is in the path it will look for input file whereever the exe is and not the cwd.
 		#endif
 		
+		//prepare full output directory
+		outputDir = m->getFullPathName(outputDir);
+		
 		vector<string> inputFileNames;
 		if (sharedfile != "") { inputFileNames = parseSharedFile(sharedfile);  globaldata->setFormat("sabund");  }
 		else {  inputFileNames.push_back(sabundfile);  }		
@@ -236,12 +240,14 @@ int CatchAllCommand::execute() {
 							//wrap entire string in ""
 							catchAllCommand = "\"" + catchAllCommand + "\"";
 						#endif
-										//run catchall
+					
+						//run catchall
 						system(catchAllCommand.c_str());
 					
 						remove(filename.c_str());
 					
 						filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+						if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 					
 						outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 						outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -285,6 +291,7 @@ int CatchAllCommand::execute() {
 						remove(filename.c_str());
 					
 						filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+						if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 					
 						outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 						outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -349,6 +356,7 @@ int CatchAllCommand::execute() {
 				remove(filename.c_str());
 				
 				filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
+				if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
 				
 				outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 				outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
@@ -368,7 +376,7 @@ int CatchAllCommand::execute() {
 		}
 		
 		if (sharedfile == "") {  
-			string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
+			string summaryfilename = savedOutputDir + m->getRootName(m->getSimpleName(inputFileNames[0])) + "catchall.summary";
 			summaryfilename = m->getFullPathName(summaryfilename);
 			outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
 		}else { //combine summaries
@@ -378,6 +386,8 @@ int CatchAllCommand::execute() {
 			}
 			string summaryfilename = combineSummmary(sumNames);
 			outputNames.push_back(summaryfilename); outputTypes["summary"].push_back(summaryfilename);
+			
+			globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");
 		}
 		
 		m->mothurOutEndLine();
@@ -424,7 +434,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
 	try {
 		
 		ofstream out;
-		string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
+		string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "catchall.summary";
 		
 		//open combined file
 		m->openOutputFile(combineFileName, out);