added count.groups command and paralellized align.seqs for windows

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 3effaf4eaafe09659252e6f93fa81f31dcc4e1db..39cc44f86e2cbe70efba4cb2700ad3154eb91945 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "catchallcommand.h"
-#include "globaldata.hpp"
 
 //**********************************************************************************************************************
 vector<string> CatchAllCommand::setParameters(){       
@@ -73,6 +72,7 @@ CatchAllCommand::CatchAllCommand(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 {
                        vector<string> myArray = setParameters();
@@ -119,10 +119,12 @@ CatchAllCommand::CatchAllCommand(string option)  {
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }
                        else if (sabundfile == "not found") { sabundfile = "";  }
+                       else { m->setSabundFile(sabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }
                        else if (sharedfile == "not found") { sharedfile = "";   }
+                       else { m->setSharedFile(sharedfile); }
                        
                        string label = validParameter.validFile(parameters, "label", false);                    
                        if (label == "not found") { label = ""; }
@@ -234,7 +236,7 @@ int CatchAllCommand::execute() {
                                                //run catchall
                                                system(catchAllCommand.c_str());
                                        
-                                               remove(filename.c_str());
+                                               m->mothurRemove(filename);
                                        
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
@@ -246,7 +248,7 @@ int CatchAllCommand::execute() {
                                        
                                                createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
                                                                                        
-                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str());    }  delete input;  delete sabund;  return 0; }
+                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }  delete input;  delete sabund;  return 0; }
 
                                                processedLabels.insert(sabund->getLabel());
                                                userLabels.erase(sabund->getLabel());
@@ -278,7 +280,7 @@ int CatchAllCommand::execute() {
                                                //run catchall
                                                system(catchAllCommand.c_str());
                                        
-                                               remove(filename.c_str());
+                                               m->mothurRemove(filename);
                                        
                                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
@@ -290,7 +292,7 @@ int CatchAllCommand::execute() {
                                        
                                                createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out);
                                        
-                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str());    }  delete input;  delete sabund;  return 0; }
+                                               if (m->control_pressed) { out.close(); for (int i = 0; i < outputNames.size(); i++) {m->mothurRemove(outputNames[i]);   }  delete input;  delete sabund;  return 0; }
 
                                                processedLabels.insert(sabund->getLabel());
                                                userLabels.erase(sabund->getLabel());
@@ -343,7 +345,7 @@ int CatchAllCommand::execute() {
                                //run catchall
                                system(catchAllCommand.c_str());
                                
-                               remove(filename.c_str());
+                               m->mothurRemove(filename);
                                
                                filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                if (savedOutputDir == "") { filename = m->getSimpleName(filename); }
@@ -361,7 +363,7 @@ int CatchAllCommand::execute() {
                        out.close();
                        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; }
                                
                }
                
@@ -469,7 +471,7 @@ string CatchAllCommand::combineSummmary(vector<string>& outputNames) {
                        numLines = thisFilesLines.size();
                        
                        temp.close();
-                       remove(outputNames[i].c_str());
+                       m->mothurRemove(outputNames[i]);
                }
                
                //for each label
@@ -577,7 +579,7 @@ vector<string> CatchAllCommand::parseSharedFile(string filename) {
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
-                       remove((sharedFileRoot + lookup[i]->getGroup() + ".sabund").c_str());
+                       m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
                        filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
                        groups.push_back(lookup[i]->getGroup());
                }