merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index bc8eb477f088ade4a8e8e0cb4c1c94930d78dc9b..154c528a851eb297a0783e26bb206aae80fc278c 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -24,14 +24,14 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(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 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(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;
@@ -146,8 +145,8 @@ int UnifracUnweightedCommand::execute() {
                                
                                for(int k = 0; k < numComp; k++) {      
                                        //add trees unweighted score to map of scores
-                                       it2 = rscoreFreq[k].find(randomData[k]);
-                                       if (it2 != rscoreFreq[k].end()) {//already have that score
+                                       map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
+                                       if (it != rscoreFreq[k].end()) {//already have that score
                                                rscoreFreq[k][randomData[k]]++;
                                        }else{//first time we have seen this score
                                                rscoreFreq[k][randomData[k]] = 1;
@@ -162,9 +161,9 @@ int UnifracUnweightedCommand::execute() {
                        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;  }
@@ -212,7 +211,7 @@ void UnifracUnweightedCommand::printUnweightedFile() {
                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();