added shared file type to get.groups and remove.groups

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index ba59dfe66e1b333f88317542e3a17844ac6d558e..29ffdb44c16862994993566583393c0de9f6644a 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -152,12 +152,12 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else{ inputFile = listfile; }   
+                       else{ inputFile = listfile; m->setListFile(listfile); } 
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-                       else{ inputFile = namefile; }   
+                       else{ inputFile = namefile; m->setNameFile(namefile); } 
                
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
@@ -165,7 +165,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") {  groupfile = ""; abort = true; } 
@@ -175,7 +175,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                
                                int error = groupMap->readMap();
                                if (error == 1) { abort = true; }
-       
+                               m->setGroupFile(groupfile);
                        }
                        
                        groups = validParameter.validFile(parameters, "groups", false);         
@@ -250,11 +250,11 @@ int SplitAbundCommand::execute(){
                        if (namefile != "") {  readNamesFile();         }
                        else                            { createNameMap(list);  }
                        
-                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
                        
                        while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
                                
                                if(allLines == 1 || labels.count(list->getLabel()) == 1){
                                                
@@ -288,7 +288,7 @@ int SplitAbundCommand::execute(){
                                list = input->getListVector(); //get new list vector to process
                        }
                        
-                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -304,7 +304,7 @@ int SplitAbundCommand::execute(){
 
                        }
                        
-                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) { delete input;  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
                        
                        //run last label if you need to
                        if (needToRun == true)  {
@@ -319,7 +319,7 @@ int SplitAbundCommand::execute(){
                        
                        delete input;
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); }       return 0;       }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }      return 0;       }
                                                                        
                }else { //you are using the namefile to determine abundance
                        if (outputDir == "") { outputDir = m->hasPath(namefile); }