X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylodiversitycommand.cpp;h=2b15d11d29580d1455ffea983788ab0715fe194b;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=8e8c7b67715ae9fb262fe4a41f7c9ef121dc2bff;hpb=d154abda2a21879424002f28c50c6e0965865acf;p=mothur.git

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 8e8c7b6..2b15d11 100644
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -137,38 +137,40 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 			}
 			
 			m->runParse = true;
-			m->Groups.clear();
-			m->namesOfGroups.clear();
+			m->clearGroups();
+			m->clearAllGroups();
 			m->Treenames.clear();
 			m->names.clear();
 			
 			//check for required parameters
 			treefile = validParameter.validFile(parameters, "tree", true);
-			if (treefile == "not open") { abort = true; }
+			if (treefile == "not open") { treefile = ""; abort = true; }
 			else if (treefile == "not found") { 				
 				//if there is a current design file, use it
 				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") { groupfile = ""; abort = true; }
 			else if (groupfile == "not found") { groupfile = ""; }
+			else { m->setGroupFile(groupfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { abort = true; }
+			if (namefile == "not open") { namefile = ""; abort = true; }
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(treefile);	}
 			
 			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, iters); 
+			m->mothurConvert(temp, iters); 
 			
 			temp = validParameter.validFile(parameters, "rarefy", false);			if (temp == "not found") { temp = "F"; }
 			rarefy = m->isTrue(temp);
@@ -185,16 +187,21 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = "";  }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+			
+			if (namefile == "") {
+				vector<string> files; files.push_back(treefile);
+				parser.getNameFile(files);
+			}
 		}
 		
 	}
@@ -255,8 +262,8 @@ int PhyloDiversityCommand::execute(){
 				
 				if (m->control_pressed) { 
 					delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[i]; }
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } outputTypes.clear();
-					m->Groups.clear();
+					for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } outputTypes.clear();
+					m->clearGroups();
 					return 0;
 				}
 				
@@ -275,18 +282,21 @@ int PhyloDiversityCommand::execute(){
 		}
 		
 		SharedUtil* util = new SharedUtil();
-		util->setGroups(m->Groups, tmap->namesOfGroups, "phylo.diversity");	//sets the groups the user wants to analyze
+		vector<string> mGroups = m->getGroups();
+		vector<string> tGroups = tmap->getNamesOfGroups();
+		util->setGroups(mGroups, tGroups, "phylo.diversity");	//sets the groups the user wants to analyze
 		delete util;
 		
 		//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
-		for (int i = 0; i < m->Groups.size(); i++) { if (m->Groups[i] == "xxx") { m->Groups.erase(m->Groups.begin()+i);  break; }  }
+		for (int i = 0; i < mGroups.size(); i++) { if (mGroups[i] == "xxx") { mGroups.erase(mGroups.begin()+i);  break; }  }
+		m->setGroups(mGroups);
 		 
 		vector<string> outputNames;
 		
 		//for each of the users trees
 		for(int i = 0; i < trees.size(); i++) {
 		
-			if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) {	remove(outputNames[j].c_str()); 	} return 0; }
+			if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]); 	} return 0; }
 			
 			ofstream outSum, outRare, outCollect;
 			string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + ".phylodiv.summary";
@@ -302,7 +312,7 @@ int PhyloDiversityCommand::execute(){
 			//create a vector containing indexes of leaf nodes, randomize it, select nodes to send to calculator
 			vector<int> randomLeaf;
 			for (int j = 0; j < numLeafNodes; j++) {  
-				if (m->inUsersGroups(trees[i]->tree[j].getGroup(), m->Groups) == true) { //is this a node from the group the user selected.
+				if (m->inUsersGroups(trees[i]->tree[j].getGroup(), mGroups) == true) { //is this a node from the group the user selected.
 					randomLeaf.push_back(j); 
 				}
 			}
@@ -317,15 +327,15 @@ int PhyloDiversityCommand::execute(){
 			
 			//find largest group total 
 			int largestGroup = 0;
-			for (int j = 0; j < m->Groups.size(); j++) {  
-				if (tmap->seqsPerGroup[m->Groups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[m->Groups[j]]; }
+			for (int j = 0; j < mGroups.size(); j++) {  
+				if (tmap->seqsPerGroup[mGroups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[mGroups[j]]; }
 				
 				//initialize diversity
-				diversity[m->Groups[j]].resize(tmap->seqsPerGroup[m->Groups[j]]+1, 0.0);		//numSampled
+				diversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);		//numSampled
 																											//groupA		0.0			0.0
 																											
 				//initialize sumDiversity
-				sumDiversity[m->Groups[j]].resize(tmap->seqsPerGroup[m->Groups[j]]+1, 0.0);
+				sumDiversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);
 			}	
 
 			//convert freq percentage to number
@@ -339,8 +349,8 @@ int PhyloDiversityCommand::execute(){
 			if(largestGroup % increment != 0){	numSampledList.insert(largestGroup);   }
 			
 			//add other groups ending points
-			for (int j = 0; j < m->Groups.size(); j++) {  
-				if (numSampledList.count(diversity[m->Groups[j]].size()-1) == 0) {  numSampledList.insert(diversity[m->Groups[j]].size()-1); }
+			for (int j = 0; j < mGroups.size(); j++) {  
+				if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) {  numSampledList.insert(diversity[mGroups[j]].size()-1); }
 			}
 			
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -375,7 +385,7 @@ int PhyloDiversityCommand::execute(){
 		}
 		
 	
-		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();
@@ -465,7 +475,7 @@ int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map<
 			}
 				
 			in.close();
-			remove(inTemp.c_str());
+			m->mothurRemove(inTemp);
 		}
 		
 #endif
@@ -482,6 +492,7 @@ int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map<
 int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum, bool doSumCollect){
 	try {
 		int numLeafNodes = randomLeaf.size();
+		vector<string> mGroups = m->getGroups();
 	
 		for (int l = 0; l < numIters; l++) {
 				random_shuffle(randomLeaf.begin(), randomLeaf.end());
@@ -489,7 +500,7 @@ int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, ma
 				//initialize counts
 				map<string, int> counts;
 				map< string, set<int> > countedBranch;  
-				for (int j = 0; j < m->Groups.size(); j++) {  counts[m->Groups[j]] = 0; countedBranch[m->Groups[j]].insert(-2);  }  //add dummy index to initialize countedBranch sets
+				for (int j = 0; j < mGroups.size(); j++) {  counts[mGroups[j]] = 0; countedBranch[mGroups[j]].insert(-2);  }  //add dummy index to initialize countedBranch sets
 				
 				for(int k = 0; k < numLeafNodes; k++){
 						
@@ -520,9 +531,9 @@ int PhyloDiversityCommand::driver(Tree* t, map< string, vector<float> >& div, ma
 				
 				if (rarefy) {
 					//add this diversity to the sum
-					for (int j = 0; j < m->Groups.size(); j++) {  
-						for (int g = 0; g < div[m->Groups[j]].size(); g++) {
-							sumDiv[m->Groups[j]][g] += div[m->Groups[j]][g];
+					for (int j = 0; j < mGroups.size(); j++) {  
+						for (int g = 0; g < div[mGroups[j]].size(); g++) {
+							sumDiv[mGroups[j]][g] += div[mGroups[j]][g];
 						}
 					}
 				}
@@ -548,15 +559,16 @@ void PhyloDiversityCommand::printSumData(map< string, vector<float> >& div, ofst
 		out << "Groups\tnumSampled\tphyloDiversity" << endl;
 		
 		out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-			
-		for (int j = 0; j < m->Groups.size(); j++) {
-			int numSampled = (div[m->Groups[j]].size()-1);
-			out << m->Groups[j] << '\t' << numSampled << '\t';
+		
+		vector<string> mGroups = m->getGroups();
+		for (int j = 0; j < mGroups.size(); j++) {
+			int numSampled = (div[mGroups[j]].size()-1);
+			out << mGroups[j] << '\t' << numSampled << '\t';
 		
 			 
 			float score;
-			if (scale)	{  score = (div[m->Groups[j]][numSampled] / (float)numIters) / (float)numSampled;	}
-			else		{	score = div[m->Groups[j]][numSampled] / (float)numIters;	}
+			if (scale)	{  score = (div[mGroups[j]][numSampled] / (float)numIters) / (float)numSampled;	}
+			else		{	score = div[mGroups[j]][numSampled] / (float)numIters;	}
 				
 			out << setprecision(4) << score << endl;
 		}
@@ -575,7 +587,8 @@ void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float>
 	try {
 		
 		out << "numSampled\t";
-		for (int i = 0; i < m->Groups.size(); i++) { out << m->Groups[i] << '\t';  }
+		vector<string> mGroups = m->getGroups();
+		for (int i = 0; i < mGroups.size(); i++) { out << mGroups[i] << '\t';  }
 		out << endl;
 		
 		out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -584,12 +597,12 @@ void PhyloDiversityCommand::printData(set<int>& num, map< string, vector<float>
 			int numSampled = *it;
 			
 			out << numSampled << '\t';  
-			
-			for (int j = 0; j < m->Groups.size(); j++) {
-				if (numSampled < div[m->Groups[j]].size()) { 
+		
+			for (int j = 0; j < mGroups.size(); j++) {
+				if (numSampled < div[mGroups[j]].size()) { 
 					float score;
-					if (scale)	{  score = (div[m->Groups[j]][numSampled] / (float)numIters) / (float)numSampled;	}
-					else		{	score = div[m->Groups[j]][numSampled] / (float)numIters;	}
+					if (scale)	{  score = (div[mGroups[j]][numSampled] / (float)numIters) / (float)numSampled;	}
+					else		{	score = div[mGroups[j]][numSampled] / (float)numIters;	}
 
 					out << setprecision(4) << score << '\t';
 				}else { out << "NA" << '\t'; }