moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index ef0a1ac36de925af45e66c1c9420272272b32f2e..e7226ceca0b1e959040fbea6d78818ba23731a6e 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -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 +206,14 @@ int GetSeqsCommand::execute(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readFasta(){
        try {
-               if (outputDir == "") { outputDir += hasPath(fastafile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" +  getExtension(fastafile);
+               if (outputDir == "") { outputDir += m->hasPath(fastafile); }
+               string outputFileName = outputDir + 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;
@@ -233,7 +233,7 @@ int GetSeqsCommand::readFasta(){
                                        currSeq.printSequence(out);
                                }
                        }
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();     
                out.close();
@@ -252,13 +252,13 @@ int GetSeqsCommand::readFasta(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readList(){
        try {
-               if (outputDir == "") { outputDir += hasPath(listfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" +  getExtension(listfile);
+               if (outputDir == "") { outputDir += m->hasPath(listfile); }
+               string outputFileName = outputDir + 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;
                
@@ -304,7 +304,7 @@ int GetSeqsCommand::readList(){
                                newList.print(out);
                        }
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();     
                out.close();
@@ -323,14 +323,14 @@ int GetSeqsCommand::readList(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readName(){
        try {
-               if (outputDir == "") { outputDir += hasPath(namefile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" +  getExtension(namefile);
+               if (outputDir == "") { outputDir += m->hasPath(namefile); }
+               string outputFileName = outputDir + 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;
@@ -396,7 +396,7 @@ int GetSeqsCommand::readName(){
                                        }
                                }
                        }
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
@@ -416,14 +416,14 @@ int GetSeqsCommand::readName(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readGroup(){
        try {
-               if (outputDir == "") { outputDir += hasPath(groupfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
+               if (outputDir == "") { outputDir += m->hasPath(groupfile); }
+               string outputFileName = outputDir + 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;
@@ -443,7 +443,7 @@ int GetSeqsCommand::readGroup(){
                                out << name << '\t' << group << endl;
                        }
                                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
@@ -462,13 +462,13 @@ int GetSeqsCommand::readGroup(){
 //**********************************************************************************************************************
 int GetSeqsCommand::readTax(){
        try {
-               if (outputDir == "") { outputDir += hasPath(taxfile); }
-               string outputFileName = outputDir + getRootName(getSimpleName(taxfile)) + "pick" + getExtension(taxfile);
+               if (outputDir == "") { outputDir += m->hasPath(taxfile); }
+               string outputFileName = outputDir + 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;
@@ -487,7 +487,7 @@ int GetSeqsCommand::readTax(){
                                out << name << '\t' << tax << endl;
                        }
                                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
@@ -507,14 +507,14 @@ 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";
+               if (outputDir == "") { outputDir += m->hasPath(alignfile); }
+               string outputFileName = outputDir + 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;
@@ -554,7 +554,7 @@ int GetSeqsCommand::readAlign(){
                                }
                        }
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                out.close();
@@ -576,7 +576,7 @@ int GetSeqsCommand::readAccnos(){
        try {
                
                ifstream in;
-               openInputFile(accnosfile, in);
+               m->openInputFile(accnosfile, in);
                string name;
                
                while(!in.eof()){
@@ -584,7 +584,7 @@ int GetSeqsCommand::readAccnos(){
                                                
                        names.insert(name);
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();