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

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 3200137343e8691e2e8df3f70fcd1940f933b88c..a3f88cf74d2c1eaa5c88fd792f678a7e5a7b4bf3 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -47,7 +47,7 @@ ListSeqsCommand::ListSeqsCommand(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 @@ ListSeqsCommand::ListSeqsCommand(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 @@ ListSeqsCommand::ListSeqsCommand(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;             }
                                }
@@ -71,7 +71,7 @@ ListSeqsCommand::ListSeqsCommand(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;             }
                                }
@@ -79,7 +79,7 @@ ListSeqsCommand::ListSeqsCommand(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;            }
                                }
@@ -87,7 +87,7 @@ ListSeqsCommand::ListSeqsCommand(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;         }
                                }
@@ -169,12 +169,12 @@ int ListSeqsCommand::execute(){
                //sort in alphabetical order
                sort(names.begin(), names.end());
                
-               if (outputDir == "") {  outputDir += hasPath(inputFileName);  }
+               if (outputDir == "") {  outputDir += m->hasPath(inputFileName);  }
                
-               string outputFileName = outputDir + getRootName(getSimpleName(inputFileName)) + "accnos";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "accnos";
 
                ofstream out;
-               openOutputFile(outputFileName, out);
+               m->openOutputFile(outputFileName, out);
                
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
@@ -206,7 +206,7 @@ int ListSeqsCommand::readFasta(){
        try {
                
                ifstream in;
-               openInputFile(fastafile, in);
+               m->openInputFile(fastafile, in);
                string name;
                
                while(!in.eof()){
@@ -218,7 +218,7 @@ int ListSeqsCommand::readFasta(){
                        
                        if (name != "") {  names.push_back(name);  }
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();     
                
@@ -234,7 +234,7 @@ int ListSeqsCommand::readFasta(){
 int ListSeqsCommand::readList(){
        try {
                ifstream in;
-               openInputFile(listfile, in);
+               m->openInputFile(listfile, in);
                
                if(!in.eof()){
                        //read in list vector
@@ -271,7 +271,7 @@ int ListSeqsCommand::readName(){
        try {
                
                ifstream in;
-               openInputFile(namefile, in);
+               m->openInputFile(namefile, in);
                string name, firstCol, secondCol;
                
                while(!in.eof()){
@@ -291,7 +291,7 @@ int ListSeqsCommand::readName(){
                        //get name after last ,
                        names.push_back(secondCol);
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                return 0;
@@ -308,7 +308,7 @@ int ListSeqsCommand::readGroup(){
        try {
        
                ifstream in;
-               openInputFile(groupfile, in);
+               m->openInputFile(groupfile, in);
                string name, group;
                
                while(!in.eof()){
@@ -320,7 +320,7 @@ int ListSeqsCommand::readGroup(){
                        
                        names.push_back(name);
                                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                return 0;
@@ -338,7 +338,7 @@ int ListSeqsCommand::readAlign(){
        try {
        
                ifstream in;
-               openInputFile(alignfile, in);
+               m->openInputFile(alignfile, in);
                string name, junk;
                
                //read column headers
@@ -362,7 +362,7 @@ int ListSeqsCommand::readAlign(){
                        
                        names.push_back(name);
                                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();
                
@@ -380,7 +380,7 @@ int ListSeqsCommand::readTax(){
        try {
                
                ifstream in;
-               openInputFile(taxfile, in);
+               m->openInputFile(taxfile, in);
                string name, firstCol, secondCol;
                
                while(!in.eof()){
@@ -392,7 +392,7 @@ int ListSeqsCommand::readTax(){
                        
                        names.push_back(firstCol);
                        
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();