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

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index e081279489deb949427f30c5208cec0f8bb50290..266dd3b9a2ad5c3e7730ac6950e7077164b12bb2 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -24,17 +24,17 @@ ParsimonyCommand::ParsimonyCommand(string option) {
                        string Array[] =  {"random","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;  }
                        }
                        
-                       randomtree = validParameter->validFile(parameters, "random", false);            if (randomtree == "not found") { randomtree = ""; }
+                       randomtree = validParameter.validFile(parameters, "random", false);             if (randomtree == "not found") { randomtree = ""; }
                        
                        //are you trying to use parsimony without reading a tree or saying you want random distribution
                        if (randomtree == "")  {
@@ -44,18 +44,16 @@ ParsimonyCommand::ParsimonyCommand(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) {
                                //randomtree will tell us if user had their own treefile or if they just want the random distribution
                                //user has entered their own tree
@@ -149,7 +147,7 @@ int ParsimonyCommand::execute() {
                                for(int k = 0; k < numComp; k++) {
 
                                        //update uscoreFreq
-                                       it = uscoreFreq[k].find(userData[k]);
+                                       map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
                                        if (it == uscoreFreq[k].end()) {//new score
                                                uscoreFreq[k][userData[k]] = 1;
                                        }else{ uscoreFreq[k][userData[k]]++; }
@@ -175,8 +173,8 @@ int ParsimonyCommand::execute() {
                                        
                                for(int r = 0; r < numComp; r++) {
                                        //add trees pscore to map of scores
-                                       it2 = rscoreFreq[r].find(randomData[r]);
-                                       if (it2 != rscoreFreq[r].end()) {//already have that score
+                                       map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+                                       if (it != rscoreFreq[r].end()) {//already have that score
                                                rscoreFreq[r][randomData[r]]++;
                                        }else{//first time we have seen this score
                                                rscoreFreq[r][randomData[r]] = 1;
@@ -206,8 +204,8 @@ int ParsimonyCommand::execute() {
                        
                                for(int r = 0; r < numComp; r++) {
                                        //add trees pscore to map of scores
-                                       it2 = rscoreFreq[r].find(randomData[r]);
-                                       if (it2 != rscoreFreq[r].end()) {//already have that score
+                                       map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
+                                       if (it != rscoreFreq[r].end()) {//already have that score
                                                rscoreFreq[r][randomData[r]]++;
                                        }else{//first time we have seen this score
                                                rscoreFreq[r][randomData[r]] = 1;
@@ -228,9 +226,9 @@ int ParsimonyCommand::execute() {
                        float rcumul = 0.0000;
                        float ucumul = 0.0000;
                        //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<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
                                if (randomtree == "") {
-                                       it2 = uscoreFreq[a].find(it->first);
+                                       map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
                                        //user data has that score 
                                        if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second;  }
                                        else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
@@ -239,7 +237,7 @@ int ParsimonyCommand::execute() {
                                }
                        
                                //make rscoreFreq map and rCumul
-                               it2 = rscoreFreq[a].find(it->first);
+                               map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
                                //get percentage of random trees with that info
                                if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul+= it2->second;  }
                                else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
@@ -298,7 +296,7 @@ void ParsimonyCommand::printParsimonyFile() {
                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<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) { 
                                if (randomtree == "") {
                                        data.push_back(it->first);  data.push_back(uscoreFreq[a][it->first]); data.push_back(uCumul[a][it->first]); data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]); 
                                }else{