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

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index a7a41f37b820cb8af77ede45cf31d0b0f4885d84..cf54e6420e6b1e4e2c54c87672142b0fb89dc655 100644 (file)
--- 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;  }