X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.cpp;h=d1cf54ba03216996b3335e030e6db7d80efd7222;hb=793f4d2406a7f6b56d174c13959244234ab30628;hp=adb145aecfd388a9eee5941e30d7bc31a8404358;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index adb145a..d1cf54b 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -157,6 +157,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+			else { m->setSharedFile(sharedfile); }
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -180,12 +181,12 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 			}
 			
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 				
 			calc = validParameter.validFile(parameters, "calc", false);			
 			if (calc == "not found") { calc = "jclass-thetayc";  }
@@ -329,12 +330,12 @@ int MatrixOutputCommand::execute(){
 			lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 		}	
 		
-		if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0;  }
+		if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0;  }
 				
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 		
-			if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
+			if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 		
 			if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){			
 				m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
@@ -367,7 +368,7 @@ int MatrixOutputCommand::execute(){
 			lookup = input->getSharedRAbundVectors();
 		}
 		
-		if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
+		if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -382,7 +383,7 @@ int MatrixOutputCommand::execute(){
 			}
 		}
 		
-		if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
+		if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 
 		//run last label if you need to
 		if (needToRun == true)  {
@@ -394,10 +395,10 @@ int MatrixOutputCommand::execute(){
 			for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
 		}
 		
-		if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
+		if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 		
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		
 		//set phylip file as new current phylipfile
 		string current = "";
@@ -526,7 +527,7 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 					}
 				}
 				intemp.close();
-				remove(tempdistFileName.c_str());
+				m->mothurRemove(tempdistFileName);
 			}
 			
 		}
@@ -597,7 +598,7 @@ int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int star
 						
 						if (m->control_pressed) { return 1; }
 						
-						seqDist temp(l, k, (1.0 - tempdata[0]));
+						seqDist temp(l, k, tempdata[0]);
 						calcDists[i].push_back(temp);
 					}
 				}