X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=83ea8c9b4b5ab077283454089b35d9de13908003;hb=72e0be6b9c80009d4dbee24e8d690ad9514dc6fb;hp=6f4bb454ba57c8fba0c4b501038679d5e48e6a61;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 6f4bb45..83ea8c9 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -42,7 +42,7 @@ vector<string> SummaryCommand::setParameters(){
 		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
 		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
 		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
 		CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
 		CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
 		CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
@@ -102,6 +102,7 @@ SummaryCommand::SummaryCommand(string option)  {
 				
 		//allow user to run help
 		if(option == "help") {  help();  abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -163,22 +164,22 @@ SummaryCommand::SummaryCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
 			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
-			else {  format = "sabund"; inputfile = sabundfile; }
+			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  format = "sharedfile"; inputfile = sharedfile; }
+			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
 				//is there are current file available for any of these?
@@ -222,13 +223,18 @@ SummaryCommand::SummaryCommand(string option)  {
 				 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
 			}
 			m->splitAtDash(calc, Estimators);
+			if (m->inUsersGroups("citation", Estimators)) { 
+				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+				//remove citation from list of calcs
+				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+			}
 
 			string temp;
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, size); 
+			m->mothurConvert(temp, size); 
 			
 			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "T"; }
 			groupMode = m->isTrue(temp);
@@ -331,7 +337,7 @@ int SummaryCommand::execute(){
 			}
 			
 			//if the users entered no valid calculators don't execute command
-			if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+			if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 			
 			ofstream outputFileHandle;
 			m->openOutputFile(fileNameRoot, outputFileHandle);
@@ -357,11 +363,11 @@ int SummaryCommand::execute(){
 			set<string> processedLabels;
 			set<string> userLabels = labels;
 			
-			if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+			if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 			
 			while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 				
-				if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+				if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 				
 				if(allLines == 1 || labels.count(sabund->getLabel()) == 1){			
 					
@@ -373,7 +379,7 @@ int SummaryCommand::execute(){
 					for(int i=0;i<sumCalculators.size();i++){
 						vector<double> data = sumCalculators[i]->getValues(sabund);
 						
-						if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+						if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 
 						outputFileHandle << '\t';
 						sumCalculators[i]->print(outputFileHandle);
@@ -396,7 +402,7 @@ int SummaryCommand::execute(){
 					for(int i=0;i<sumCalculators.size();i++){
 						vector<double> data = sumCalculators[i]->getValues(sabund);
 						
-						if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
+						if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	 m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
 						
 						outputFileHandle << '\t';
 						sumCalculators[i]->print(outputFileHandle);
@@ -414,7 +420,7 @@ int SummaryCommand::execute(){
 				sabund = input->getSAbundVector();
 			}
 			
-			if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+			if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 
 			//output error messages about any remaining user labels
 			set<string>::iterator it;
@@ -439,7 +445,7 @@ int SummaryCommand::execute(){
 				for(int i=0;i<sumCalculators.size();i++){
 					vector<double> data = sumCalculators[i]->getValues(sabund);
 					
-					if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
+					if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
 
 					outputFileHandle << '\t';
 					sumCalculators[i]->print(outputFileHandle);
@@ -451,19 +457,19 @@ int SummaryCommand::execute(){
 			
 			outputFileHandle.close();
 			
-			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 
 			
 			delete input;  
 			for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
 		}
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }  return 0;  }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }  return 0;  }
 		
 		//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
 		if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }  return 0;  }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }  return 0;  }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -492,7 +498,7 @@ vector<string> SummaryCommand::parseSharedFile(string filename) {
 		
 		//clears file before we start to write to it below
 		for (int i=0; i<lookup.size(); i++) {
-			remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+			m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 			filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 		}
 		
@@ -586,7 +592,7 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
 			files[outputNames[i]] = thisFilesLines;
 			
 			temp.close();
-			remove(outputNames[i].c_str());
+			m->mothurRemove(outputNames[i]);
 		}
 		
 		//output label line to new file