X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=unifracweightedcommand.cpp;h=cf54e6420e6b1e4e2c54c87672142b0fb89dc655;hp=a7a41f37b820cb8af77ede45cf31d0b0f4885d84;hb=cd37904452dc95b183ff313ff05720c562902487;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index a7a41f3..cf54e64 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,14 +24,14 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			string Array[] =  {"groups","iters"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
-			parser = new OptionParser();
-			parser->parse(option, parameters);  delete parser;
+			OptionParser parser(option);
+			map<string,string> parameters=parser.getParameters();
 			
-			ValidParameters* validParameter = new ValidParameters();
+			ValidParameters validParameter;
 		
 			//check to make sure all parameters are valid for command
-			for (it4 = parameters.begin(); it4 != parameters.end(); it4++) { 
-				if (validParameter->isValidParameter(it4->first, myArray, it4->second) != true) {  abort = true;  }
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
 			if (globaldata->gTree.size() == 0) {//no trees were read
@@ -39,17 +39,16 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 										
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
-			groups = validParameter->validFile(parameters, "groups", false);			
+			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
 				splitAtDash(groups, Groups);
 				globaldata->Groups = Groups;
 			}
 				
-			itersString = validParameter->validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
+			itersString = validParameter.validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
 			convert(itersString, iters); 
-			
-			delete validParameter;
+		
 			
 			if (abort == false) {
 				T = globaldata->gTree;
@@ -222,7 +221,7 @@ void UnifracWeightedCommand::printWeightedFile() {
 		for(int a = 0; a < numComp; a++) {
 			output->initFile(groupComb[a], tags);
 			//print each line
-			for (it = validScores.begin(); it != validScores.end(); it++) { 
+			for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
 				data.push_back(it->first);  data.push_back(rScoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); 
 				output->output(data);
 				data.clear();
@@ -310,7 +309,7 @@ void UnifracWeightedCommand::calculateFreqsCumuls() {
 		for (int f = 0; f < numComp; f++) {
 			for (int i = 0; i < rScores[f].size(); i++) { //looks like 0,0,1,1,1,2,4,7...  you want to make a map that say rScoreFreq[0] = 2, rScoreFreq[1] = 3...
 				validScores[rScores[f][i]] = rScores[f][i];
-				it = rScoreFreq[f].find(rScores[f][i]);
+				map<float,float>::iterator it = rScoreFreq[f].find(rScores[f][i]);
 				if (it != rScoreFreq[f].end()) {
 					rScoreFreq[f][rScores[f][i]]++;
 				}else{
@@ -323,9 +322,9 @@ void UnifracWeightedCommand::calculateFreqsCumuls() {
 		for(int a = 0; a < numComp; a++) {
 			float rcumul = 1.0000;
 			//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
-			for (it = validScores.begin(); it != validScores.end(); it++) {
+			for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 				//make rscoreFreq map and rCumul
-				it2 = rScoreFreq[a].find(it->first);
+				map<float,float>::iterator it2 = rScoreFreq[a].find(it->first);
 				rCumul[a][it->first] = rcumul;
 				//get percentage of random trees with that info
 				if (it2 != rScoreFreq[a].end()) {  rScoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }