X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=64bdbb4ceebd18f5abeff63b26fbb4d4ac3dc924;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=746b09e8df8f4719f7ded9504e4f732b49fb559b;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 746b09e..64bdbb4 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -49,7 +49,7 @@ string RareFactSharedCommand::getHelpString(){
 		helpString += validCalculator.printCalc("sharedrarefaction");
 		helpString += "The label parameter is used to analyze specific labels in your input.\n";
 		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -81,6 +81,7 @@ RareFactSharedCommand::RareFactSharedCommand(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();
@@ -123,7 +124,7 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 				sharedfile = m->getSharedFile(); 
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -146,20 +147,25 @@ RareFactSharedCommand::RareFactSharedCommand(string option)  {
 				 if (calc == "default")  {  calc = "sharedobserved";  }
 			}
 			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; } }
+			}
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
 			}
-			m->Groups = Groups;
+			m->setGroups(Groups);
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
-			convert(temp, nIters); 
+			m->mothurConvert(temp, nIters); 
 			
 			temp = validParameter.validFile(parameters, "jumble", false);			if (temp == "not found") { temp = "T"; }
 			if (m->isTrue(temp)) { jumble = true; }
@@ -205,10 +211,10 @@ int RareFactSharedCommand::execute(){
 		string lastLabel = lookup[0]->getLabel();
 		
 		if (m->control_pressed) { 
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			delete input;
 			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 			return 0;
 		}
@@ -227,10 +233,10 @@ int RareFactSharedCommand::execute(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			if (m->control_pressed) { 
-				m->Groups.clear(); 
+				m->clearGroups(); 
 				delete input;
 				for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 				for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 				return 0;
 			}
@@ -272,10 +278,10 @@ int RareFactSharedCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			delete input;
 			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 			return 0;
 		}
 		
@@ -293,10 +299,10 @@ int RareFactSharedCommand::execute(){
 		}
 		
 		if (m->control_pressed) { 
-			m->Groups.clear(); 
+			m->clearGroups(); 
 			delete input; 
 			for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}
 			return 0;
 		}
 		
@@ -313,10 +319,10 @@ int RareFactSharedCommand::execute(){
 		}
 		
 		for(int i=0;i<rDisplays.size();i++){	delete rDisplays[i];	}	
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		delete input;
 		
-		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();