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

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 92aab92af537dbb8cbd9cb294e058a5e88115a63..791889996a0ec1d7c726885d22eb7277388d7f14 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -26,14 +26,14 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        string Array[] =  {"fasta","list","line","label","name", "group"};
                        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;  }
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -43,30 +43,24 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        }
                        
                        //check for required parameters
-                       fastafile = validParameter->validFile(parameters, "fasta", true);
+                       fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { cout << "fasta is a required parameter for the get.oturep command." << endl; abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
-                       else { 
-                               globaldata->setFastaFile(fastafile);
-                       }
                
-                       listfile = validParameter->validFile(parameters, "list", true);
+                       listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") { cout << "list is a required parameter for the get.oturep command." << endl; abort = true; }
                        else if (listfile == "not open") { abort = true; }      
-                       else { 
-                               globaldata->setListFile(listfile);
-                       }
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter->validFile(parameters, "line", false);                            
+                       line = validParameter.validFile(parameters, "line", false);                             
                        if (line == "not found") { line = "";  }
                        else { 
                                if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
-                       label = validParameter->validFile(parameters, "label", false);                  
+                       label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
                                if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
@@ -82,11 +76,11 @@ GetOTURepCommand::GetOTURepCommand(string option){
                                lines = globaldata->lines;
                        }
                        
-                       namesfile = validParameter->validFile(parameters, "name", true);
+                       namesfile = validParameter.validFile(parameters, "name", true);
                        if (namesfile == "not open") { abort = true; }  
                        else if (namesfile == "not found") { namesfile = ""; }
 
-                       groupfile = validParameter->validFile(parameters, "group", true);
+                       groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
                        else {
@@ -94,9 +88,7 @@ GetOTURepCommand::GetOTURepCommand(string option){
                                groupMap = new GroupMap(groupfile);
                                groupMap->readMap();
                        }
-       
-                       delete validParameter;
-       
+               
                        if (abort == false) {
                        
                                if(globaldata->gSparseMatrix != NULL)   {       matrix = new SparseMatrix(*globaldata->gSparseMatrix);          }       
@@ -186,7 +178,7 @@ int GetOTURepCommand::execute(){
                fasta->readFastaFile(in);
                
                //set format to list so input can get listvector
-               globaldata->setFormat("list");
+//             globaldata->setFormat("list");
                
                //if user gave a namesfile then use it
                if (namesfile != "") {
@@ -236,9 +228,8 @@ int GetOTURepCommand::execute(){
                }
                
                //output error messages about any remaining user labels
-               set<string>::iterator it;
                bool needToRun = false;
-               for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+               for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {  
                        cout << "Your file does not include the label "<< *it; 
                        if (processedLabels.count(lastList->getLabel()) != 1) {
                                cout << ". I will use " << lastList->getLabel() << "." << endl;
@@ -316,7 +307,6 @@ string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
        try{
                vector<string> names;
                map<string, float> sums;
-               map<string, float>::iterator it4;
                map<int, string> binMap; //subset of namesToIndex - just member of this bin
                string binnames;
                float min = 10000;
@@ -354,13 +344,13 @@ string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
                else {
                        //fill binMap
                        for (int i = 0; i < names.size(); i++) {
-                               for (it3 = nameToIndex.begin(); it3 != nameToIndex.end(); it3++) {
+                               for (map<string, int>::iterator it = nameToIndex.begin(); it != nameToIndex.end(); it++) {
 
-                                       if (it3->first == names[i]) {  
-                                               binMap[it3->second] = it3->first;
+                                       if (it->first == names[i]) {  
+                                               binMap[it->second] = it->first;
 
                                                //initialize sums map
-                                               sums[it3->first] = 0.0;
+                                               sums[it->first] = 0.0;
                                                break;
                                        }
                                }
@@ -369,8 +359,8 @@ string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
                        //go through each cell in the sparsematrix
                        for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
                                //is this a distance between 2 members of this bin
-                               it = binMap.find(currentCell->row);
-                               it2 = binMap.find(currentCell->column);
+                               map<int, string>::iterator it = binMap.find(currentCell->row);
+                               map<int, string>::iterator it2 = binMap.find(currentCell->column);
                                
                                //sum the distance of the sequences in the bin to eachother
                                if ((it != binMap.end()) && (it2 != binMap.end())) {
@@ -381,7 +371,7 @@ string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
                        }
                        
                        //smallest sum is the representative
-                       for (it4 = sums.begin(); it4 != sums.end(); it4++) {
+                       for (map<string, float>::iterator it4 = sums.begin(); it4 != sums.end(); it4++) {
                                if (it4->second < min) {
                                        min = it4->second;
                                        minName = it4->first;