added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / sensspeccommand.cpp

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 82922ededbff38fd76909d1694742c6adac7666b..b62bb00548f3e1ee66f0c1cf2b4bee117c5416cf 100644 (file)
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -14,12 +14,11 @@ vector<string> SensSpecCommand::setParameters(){
        try {
                CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
                CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-               //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
                CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
                CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+               CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -45,6 +44,26 @@ string SensSpecCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string SensSpecCommand::getOutputFileNameTag(string type, string inputName=""){        
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "sensspec")            {   outputFileName =  "sensspec";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SensSpecCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -116,16 +135,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                                        path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["column"] = inputDir + it->second;           }
-                               }
-                               
-                               //it = parameters.find("name");
-                               //user has given a template file
-                               //if(it != parameters.end()){ 
-                                       //path = m->hasPath(it->second);
-                                       //if the user has not given a path then, add inputdir. else leave path alone.
-                                       //if (path == "") {     parameters["name"] = inputDir + it->second;             }
-                               //}
-                               
+                               }                               
                        }
                        //check for required parameters
                        listFile = validParameter.validFile(parameters, "list", true);
@@ -176,12 +186,6 @@ SensSpecCommand::SensSpecCommand(string option)  {
                        else if(!m->isTrue(temp))       {       hard = 0;       }
                        else if(m->isTrue(temp))        {       hard = 1;       }
                        
-//                     temp = validParameter.validFile(parameters, "name", true);
-//                     if (temp == "not found")        {       nameFile = "";          }
-//                     else if(temp == "not open")     {       abort = true;           }
-//                     else                                            {       nameFile = temp;        }
-//                     cout << "name:\t" << nameFile << endl;
-
                        temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found") { temp = "-1.00"; }
                        m->mothurConvert(temp, cutoff);  
 //                     cout << cutoff << endl;
@@ -197,7 +201,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
                                else { allLines = 1;  }
                        }
                        
-                       sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + "sensspec";
+                       sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + getOutputFileNameTag("sensspec");
                }
        }
        catch(exception& e) {
@@ -256,7 +260,9 @@ int SensSpecCommand::processPhylip(){
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
+                       if(m->control_pressed){
+                for (int i = 0; i < outputNames.size(); i++){  m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
+            }
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
                                
@@ -324,7 +330,9 @@ int SensSpecCommand::processPhylip(){
                exit(1);
        }
 }
+
 //***************************************************************************************************************
+
 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
        try {
                //for each otu
@@ -387,7 +395,7 @@ int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
                return numSeqs;
        }
        catch(exception& e) {
-               m->errorOut(e, "SensSpecCommand", "fillSeqMap");
+               m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
                exit(1);
        }
 }
@@ -401,7 +409,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
                ifstream phylipFile;
                m->openInputFile(distFile, phylipFile);
                phylipFile >> pNumSeqs;
-               if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); m->control_pressed = true; }
+               if(pNumSeqs != lNumSeqs){       m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
                
                string seqName;
                double distance;
@@ -426,7 +434,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
                
                m->mothurOut(label); m->mothurOutEndLine();
                
-               for(int i=0;i<lNumSeqs;i++){
+               for(int i=0;i<pNumSeqs;i++){
                        
                        if (m->control_pressed) { return 0; }