X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=ff1209287b4e17b2fcc58678703123aae2cadbc1;hb=c651c46022761aef61644f78462365d8f767ff0b;hp=a8c2d156be775455c729d9341386ecfb952323e4;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index a8c2d15..ff12092 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -43,7 +43,7 @@ string ParsimonyCommand::getHelpString(){
 		helpString += "Example parsimony(random=out, iters=500).\n";
 		helpString += "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n";
 		helpString += "and iters is 1000.  The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. random), '=' and parameters (i.e.yourOutputFilename).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -74,6 +74,7 @@ ParsimonyCommand::ParsimonyCommand(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();
@@ -125,6 +126,10 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 			}
 			
 			m->runParse = true;
+			m->Groups.clear();
+			m->namesOfGroups.clear();
+			m->Treenames.clear();
+			m->names.clear();
 			
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";	}
 			
@@ -139,16 +144,18 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
 					treefile = m->getTreeFile(); 
 					if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 					else { 	m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }								
-				}	
+				}else { m->setTreeFile(treefile); }	
 				
 				//check for required parameters
 				groupfile = validParameter.validFile(parameters, "group", true);
 				if (groupfile == "not open") { abort = true; }
 				else if (groupfile == "not found") { groupfile = ""; }
+				else { m->setGroupFile(groupfile); }
 				
 				namefile = validParameter.validFile(parameters, "name", true);
 				if (namefile == "not open") { abort = true; }
 				else if (namefile == "not found") { namefile = ""; }
+				else { m->setNameFile(namefile); }
 			}
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -188,6 +195,9 @@ int ParsimonyCommand::execute() {
 		//randomtree will tell us if user had their own treefile or if they just want the random distribution
 		//user has entered their own tree
 		if (randomtree == "") { 
+			
+			m->setTreeFile(treefile);
+			
 			if (groupfile != "") {
 				//read in group map info.
 				tmap = new TreeMap(groupfile);
@@ -231,7 +241,7 @@ int ParsimonyCommand::execute() {
 					
 					if (m->control_pressed) { 
 						delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-						for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+						for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 						m->Groups.clear();
 						return 0;
 					}
@@ -286,7 +296,7 @@ int ParsimonyCommand::execute() {
 			delete reading; delete pars; delete output;
 			delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 			if (randomtree == "") {  outSum.close();  }
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 			m->Groups.clear();
 			return 0;
 		}
@@ -311,7 +321,7 @@ int ParsimonyCommand::execute() {
 					delete reading; delete pars; delete output;
 					delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 					if (randomtree == "") {  outSum.close();  }
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 					m->Groups.clear();
 					return 0;
 				}
@@ -349,7 +359,7 @@ int ParsimonyCommand::execute() {
 				if (m->control_pressed) { 
 					delete reading; delete pars; delete output; delete randT;
 					if (randomtree == "") {  outSum.close();  }
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 					delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 					m->Groups.clear();
 					return 0;
@@ -387,7 +397,7 @@ int ParsimonyCommand::execute() {
 				if (m->control_pressed) { 
 					delete reading; delete pars; delete output; delete randT;
 					delete tmap; 
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 					m->Groups.clear();
 					return 0;
 				}
@@ -399,7 +409,7 @@ int ParsimonyCommand::execute() {
 				if (m->control_pressed) { 
 					delete reading; delete pars;  delete output; delete randT;
 					delete tmap; 
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 					m->Groups.clear();
 					return 0;
 				}
@@ -456,7 +466,7 @@ int ParsimonyCommand::execute() {
 				delete reading; delete pars; delete output;
 				delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 				if (randomtree == "") {  outSum.close();  }
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
 				m->Groups.clear();
 				return 0;
 		}
@@ -475,7 +485,7 @@ int ParsimonyCommand::execute() {
 		delete pars; delete output; 
 		delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();