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

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 31b6bb7137579796c3a6652b283858bff435731a..5789fd0665f849822ec8d8c365de3a26e65b77ef 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -14,7 +14,6 @@
 
 ScreenSeqsCommand::ScreenSeqsCommand(string option){
        try {
-               globaldata = GlobalData::getInstance();
                abort = false;
                
                //allow user to run help
@@ -25,59 +24,50 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
                        string AlignArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
-                       parser = new OptionParser();
-                       parser->parse(option, parameters);      delete parser; 
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
                        
-                       ValidParameters* validParameter = new ValidParameters();
-               
                        //check to make sure all parameters are valid for command
-                       for (it = parameters.begin(); it != parameters.end(); it++) { 
-                               if (validParameter->isValidParameter(it->first, myArray, it->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;  }
                        }
                        
                        //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 screen.seqs command." << endl; abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
-                       else { globaldata->setFastaFile(fastafile); }
                
-                       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 { 
-                               globaldata->setGroupFile(groupfile);
-                       }
                        
-                       namefile = validParameter->validFile(parameters, "name", true);
+                       namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-                       else { 
-                               globaldata->setNameFile(namefile);
-                       }
 
                
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        string temp;
-                       temp = validParameter->validFile(parameters, "start", false);                   if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "start", false);                    if (temp == "not found") { temp = "-1"; }
                        convert(temp, startPos); 
                
-                       temp = validParameter->validFile(parameters, "end", false);                             if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "end", false);                              if (temp == "not found") { temp = "-1"; }
                        convert(temp, endPos);  
 
-                       temp = validParameter->validFile(parameters, "maxambig", false);                if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
                        convert(temp, maxAmbig);  
 
-                       temp = validParameter->validFile(parameters, "maxhomop", false);                if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
                        convert(temp, maxHomoP);  
 
-                       temp = validParameter->validFile(parameters, "minlength", false);               if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "minlength", false);                if (temp == "not found") { temp = "-1"; }
                        convert(temp, minLength); 
                        
-                       temp = validParameter->validFile(parameters, "maxlength", false);               if (temp == "not found") { temp = "-1"; }
+                       temp = validParameter.validFile(parameters, "maxlength", false);                if (temp == "not found") { temp = "-1"; }
                        convert(temp, maxLength); 
-               
-                       delete validParameter;
                }
 
        }
@@ -187,13 +177,13 @@ int ScreenSeqsCommand::execute(){
 void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 
        ifstream inputNames;
-       openInputFile(globaldata->getNameFile(), inputNames);
+       openInputFile(namefile, inputNames);
        set<string> badSeqGroups;
        string seqName, seqList, group;
        set<string>::iterator it;
 
-       string goodNameFile = getRootName(globaldata->getNameFile()) + "good" + getExtension(globaldata->getNameFile());
-       string badNameFile = getRootName(globaldata->getNameFile()) + "bad" + getExtension(globaldata->getNameFile());
+       string goodNameFile = getRootName(namefile) + "good" + getExtension(namefile);
+       string badNameFile = getRootName(namefile) + "bad" + getExtension(namefile);
        
        ofstream goodNameOut;   openOutputFile(goodNameFile, goodNameOut);
        ofstream badNameOut;    openOutputFile(badNameFile, badNameOut);                
@@ -205,7 +195,7 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                if(it != badSeqNames.end()){
                        badSeqNames.erase(it);
                        badNameOut << seqName << '\t' << seqList << endl;
-                       if(globaldata->getNameFile() != ""){
+                       if(namefile != ""){
                                int start = 0;
                                for(int i=0;i<seqList.length();i++){
                                        if(seqList[i] == ','){
@@ -225,13 +215,13 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
        goodNameOut.close();
        badNameOut.close();
        
-       if(globaldata->getGroupFile() != ""){
+       if(groupfile != ""){
                
                ifstream inputGroups;
-               openInputFile(globaldata->getGroupFile(), inputGroups);
+               openInputFile(groupfile, inputGroups);
 
-               string goodGroupFile = getRootName(globaldata->getGroupFile()) + "good" + getExtension(globaldata->getGroupFile());
-               string badGroupFile = getRootName(globaldata->getGroupFile()) + "bad" + getExtension(globaldata->getGroupFile());
+               string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
+               string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
                
                ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
                ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);              
@@ -261,12 +251,12 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 
        ifstream inputGroups;
-       openInputFile(globaldata->getGroupFile(), inputGroups);
+       openInputFile(groupfile, inputGroups);
        string seqName, group;
        set<string>::iterator it;
        
-       string goodGroupFile = getRootName(globaldata->getGroupFile()) + "good" + getExtension(globaldata->getGroupFile());
-       string badGroupFile = getRootName(globaldata->getGroupFile()) + "bad" + getExtension(globaldata->getGroupFile());
+       string goodGroupFile = getRootName(groupfile) + "good" + getExtension(groupfile);
+       string badGroupFile = getRootName(groupfile) + "bad" + getExtension(groupfile);
        
        ofstream goodGroupOut;  openOutputFile(goodGroupFile, goodGroupOut);
        ofstream badGroupOut;   openOutputFile(badGroupFile, badGroupOut);