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

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index d2e40887851e046fe4ab23f0985c5a76b4903478..492195d702286af6cc82d919311aae7a59260596 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -50,7 +50,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(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;            }
                                }
@@ -58,7 +58,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(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;             }
                                }
@@ -66,7 +66,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(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;            }
                                }
@@ -90,7 +90,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -101,7 +101,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else { 
                                userGroups = "unique." + groups;
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                                
                        }
@@ -110,7 +110,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                        if (groups == "not found") { groups = "";  }
                        else { 
                                userGroups = groups;
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                                unique = false;
                        }
@@ -188,12 +188,12 @@ int GetSharedOTUCommand::execute(){
                
                if (fastafile != "") {
                        ifstream inFasta;
-                       openInputFile(fastafile, inFasta);
+                       m->openInputFile(fastafile, inFasta);
                        
                        while(!inFasta.eof()) {
                                if (m->control_pressed) { inFasta.close(); delete groupMap; return 0; }
                                
-                               Sequence seq(inFasta); gobble(inFasta);
+                               Sequence seq(inFasta); m->gobble(inFasta);
                                if (seq.getName() != "") {  seqs.push_back(seq);   }
                        }
                        inFasta.close();
@@ -207,7 +207,7 @@ int GetSharedOTUCommand::execute(){
                set<string> userLabels = labels;
                
                ifstream in;
-               openInputFile(listfile, in);
+               m->openInputFile(listfile, in);
                
                //as long as you are not at the end of the file or done wih the lines you want
                while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -228,7 +228,7 @@ int GetSharedOTUCommand::execute(){
                                userLabels.erase(list->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = list->getLabel();
                                        
                                        m->mothurOut(lastlist->getLabel()); 
@@ -302,13 +302,13 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                ofstream outNames;
                string outputFileNames;
                
-               if (outputDir == "") { outputDir += hasPath(listfile); }
+               if (outputDir == "") { outputDir += m->hasPath(listfile); }
                if (output != "accnos") {
-                       outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
+                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
                }else {
-                       outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
+                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
                }
-               openOutputFile(outputFileNames, outNames);
+               m->openOutputFile(outputFileNames, outNames);
                
                bool wroteSomething = false;
                int num = 0;
@@ -410,10 +410,10 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                
                //if fasta file provided output new fasta file
                if ((fastafile != "") && wroteSomething) {
-                       if (outputDir == "") { outputDir += hasPath(fastafile); }
-                       string outputFileFasta = outputDir + getRootName(getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+                       if (outputDir == "") { outputDir += m->hasPath(fastafile); }
+                       string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
                        ofstream outFasta;
-                       openOutputFile(outputFileFasta, outFasta);
+                       m->openOutputFile(outputFileFasta, outFasta);
                        outputNames.push_back(outputFileFasta);
                        
                        for (int k = 0; k < seqs.size(); k++) {