fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index f7490f73b3411e9335ba21fa329e6a9b0fc63c0c..8131fa9195f6b8d939b27891605dd862d618964b 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -82,11 +82,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
-               
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
@@ -154,12 +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; }
@@ -167,7 +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; } 
@@ -177,13 +175,13 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                
                                int error = groupMap->readMap();
                                if (error == 1) { abort = true; }
-       
+                               m->setGroupFile(groupfile);
                        }
                        
                        groups = validParameter.validFile(parameters, "groups", false);         
                        if (groups == "not found") { groups = ""; }
                        else if (groups == "all") { 
-                               if (groupfile != "") {  Groups = groupMap->namesOfGroups;  } 
+                               if (groupfile != "") {  Groups = groupMap->getNamesOfGroups();  } 
                                else {  m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = "";   }
                        }else { 
                                m->splitAtDash(groups, Groups);
@@ -215,10 +213,9 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        accnos = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);                           if (temp == "not found") { temp = "0"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
 
                        if (cutoff == 0) {  m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true;  }
-
                }
 
        }
@@ -252,11 +249,11 @@ 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){
                                                
@@ -290,7 +287,7 @@ 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;
@@ -306,7 +303,7 @@ 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)  {
@@ -321,7 +318,7 @@ 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); }