working on testing

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 8bf93ce68db55f9b380307feb73d83ecf3700c5d..1926ae0b017abc926c2256e2c3b0396de1dbae40 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -22,7 +22,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir"};
+                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -47,7 +47,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("alignreport");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
                                }
@@ -55,7 +55,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("fasta");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
                                }
@@ -63,7 +63,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("accnos");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
                                }
@@ -71,7 +71,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("list");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["list"] = inputDir + it->second;             }
                                }
@@ -79,7 +79,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("name");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       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;             }
                                }
@@ -87,7 +87,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("group");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
@@ -95,7 +95,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                                it = parameters.find("taxonomy");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
                                }
@@ -133,7 +133,7 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
                        
                        string usedDups = "true";
                        string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
-                       dups = isTrue(temp);
+                       dups = m->isTrue(temp);
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
                
@@ -206,14 +206,15 @@ int GetSeqsCommand::execute(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readFasta(){
        try {
-               if (outputDir == "") { outputDir += hasPath(fastafile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" +  getExtension(fastafile);
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
                
                ifstream in;
-               openInputFile(fastafile, in);
+               m->openInputFile(fastafile, in);
                string name;
                
                bool wroteSomething = false;
@@ -233,15 +234,13 @@ int GetSeqsCommand::readFasta(){
                                        currSeq.printSequence(out);
                                }
                        }
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();     
                out.close();
                
-               if (wroteSomething == false) {
-                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
-                       remove(outputFileName.c_str()); 
-               }else {  outputNames.push_back(outputFileName); }
+               if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
+               outputNames.push_back(outputFileName); 
                
                return 0;
 
@@ -254,13 +253,14 @@ int GetSeqsCommand::readFasta(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readList(){
        try {
-               if (outputDir == "") { outputDir += hasPath(listfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" +  getExtension(listfile);
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
                ifstream in;
-               openInputFile(listfile, in);
+               m->openInputFile(listfile, in);
                
                bool wroteSomething = false;
                
@@ -306,15 +306,13 @@ int GetSeqsCommand::readList(){
                                newList.print(out);
                        }
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();     
                out.close();
                
-               if (wroteSomething == false) {
-                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
-                       remove(outputFileName.c_str()); 
-               }else {  outputNames.push_back(outputFileName); }
+               if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
+               outputNames.push_back(outputFileName); 
                
                return 0;
 
@@ -327,14 +325,15 @@ int GetSeqsCommand::readList(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readName(){
        try {
-               if (outputDir == "") { outputDir += hasPath(namefile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" +  getExtension(namefile);
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
 
                ifstream in;
-               openInputFile(namefile, in);
+               m->openInputFile(namefile, in);
                string name, firstCol, secondCol;
                
                bool wroteSomething = false;
@@ -400,15 +399,13 @@ int GetSeqsCommand::readName(){
                                        }
                                }
                        }
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
                
-               if (wroteSomething == false) {
-                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
-                       remove(outputFileName.c_str()); 
-               }else {  outputNames.push_back(outputFileName); }
+               if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
+               outputNames.push_back(outputFileName); 
                
                return 0;
                
@@ -422,14 +419,15 @@ int GetSeqsCommand::readName(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readGroup(){
        try {
-               if (outputDir == "") { outputDir += hasPath(groupfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
 
                ifstream in;
-               openInputFile(groupfile, in);
+               m->openInputFile(groupfile, in);
                string name, group;
                
                bool wroteSomething = false;
@@ -449,15 +447,13 @@ int GetSeqsCommand::readGroup(){
                                out << name << '\t' << group << endl;
                        }
                                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
                
-               if (wroteSomething == false) {
-                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
-                       remove(outputFileName.c_str()); 
-               }else {  outputNames.push_back(outputFileName); }
+               if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
+               outputNames.push_back(outputFileName); 
                
                return 0;
 
@@ -470,13 +466,14 @@ int GetSeqsCommand::readGroup(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readTax(){
        try {
-               if (outputDir == "") { outputDir += hasPath(taxfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(taxfile)) + "pick" + getExtension(taxfile);
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
                ifstream in;
-               openInputFile(taxfile, in);
+               m->openInputFile(taxfile, in);
                string name, tax;
                
                bool wroteSomething = false;
@@ -495,16 +492,14 @@ int GetSeqsCommand::readTax(){
                                out << name << '\t' << tax << endl;
                        }
                                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
                
-               if (wroteSomething == false) {
-                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
-                       remove(outputFileName.c_str()); 
-               }else {  outputNames.push_back(outputFileName); }
-               
+               if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
+               outputNames.push_back(outputFileName); 
+                       
                return 0;
 
        }
@@ -517,14 +512,15 @@ int GetSeqsCommand::readTax(){
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 int GetSeqsCommand::readAlign(){
        try {
-               if (outputDir == "") { outputDir += hasPath(alignfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
+               string thisOutputDir = outputDir;
+               if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
 
                ifstream in;
-               openInputFile(alignfile, in);
+               m->openInputFile(alignfile, in);
                string name, junk;
                
                bool wroteSomething = false;
@@ -564,15 +560,13 @@ int GetSeqsCommand::readAlign(){
                                }
                        }
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
                
-               if (wroteSomething == false) {
-                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
-                       remove(outputFileName.c_str()); 
-               }else {  outputNames.push_back(outputFileName); }
+               if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
+               outputNames.push_back(outputFileName); 
                
                return 0;
                
@@ -588,7 +582,7 @@ int GetSeqsCommand::readAccnos(){
        try {
                
                ifstream in;
-               openInputFile(accnosfile, in);
+               m->openInputFile(accnosfile, in);
                string name;
                
                while(!in.eof()){
@@ -596,7 +590,7 @@ int GetSeqsCommand::readAccnos(){
                                                
                        names.insert(name);
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();