X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.cpp;h=39cc44f86e2cbe70efba4cb2700ad3154eb91945;hb=74dc92cf53df65fd8b14d8eaf35489bbecbccac6;hp=3effaf4eaafe09659252e6f93fa81f31dcc4e1db;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 3effaf4..39cc44f 100644
--- 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());
 		}