created mothurOut class to handle logfiles

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 4cc0ea73b6a4a561ce0a511ca5cbb5da4b9d581c..f03152bcfa84047813da249e0fedb3673139861c 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -53,7 +53,7 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
 
        }
        catch(exception& e) {
-               errorOut(e, "SharedCommand", "SharedCommand");
+               m->errorOut(e, "SharedCommand", "SharedCommand");
                exit(1);
        }
 }
@@ -77,7 +77,7 @@ int SharedCommand::execute(){
                vector<SharedRAbundVector*> lookup; 
                
                if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
-                       mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine(); 
+                       m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); 
                        
                        out.close();
                        remove(filename.c_str()); //remove blank shared file you made
@@ -128,7 +128,7 @@ int SharedCommand::execute(){
                                        if (pickedGroups) { //check for otus with no seqs in them
                                                eliminateZeroOTUS(lookup);
                                        }
-                                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                        
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -147,7 +147,7 @@ int SharedCommand::execute(){
                                        if (pickedGroups) { //check for otus with no seqs in them
                                                eliminateZeroOTUS(lookup);
                                        }
-                                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                        
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -184,7 +184,7 @@ int SharedCommand::execute(){
                        if (pickedGroups) { //check for otus with no seqs in them
                                eliminateZeroOTUS(lookup);
                        }
-                       mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        
                        printSharedData(lookup); //prints info to the .shared file
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -210,7 +210,7 @@ int SharedCommand::execute(){
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "SharedCommand", "execute");
+               m->errorOut(e, "SharedCommand", "execute");
                exit(1);
        }
 }
@@ -232,7 +232,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
  
        }
        catch(exception& e) {
-               errorOut(e, "SharedCommand", "printSharedData");
+               m->errorOut(e, "SharedCommand", "printSharedData");
                exit(1);
        }
 }
@@ -272,7 +272,7 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
  
        }
        catch(exception& e) {
-               errorOut(e, "SharedCommand", "eliminateZeroOTUS");
+               m->errorOut(e, "SharedCommand", "eliminateZeroOTUS");
                exit(1);
        }
 }
@@ -285,7 +285,7 @@ void SharedCommand::createMisMatchFile() {
                //you have sequences in your list file that are not in your group file
                if (SharedList->getNumSeqs() > groupMap->getNumSeqs()) { 
                        outputMisMatchName += "missing.group";
-                       mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+                       m->mothurOut("For a list of names that are in your list file and not in your group file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
                        
                        openOutputFile(outputMisMatchName, outMisMatch);
                        
@@ -305,7 +305,7 @@ void SharedCommand::createMisMatchFile() {
                                        if(group == "not found") {      outMisMatch << name << endl;  }
                                        
                                        itList = listNames.find(name);
-                                       if (itList != listNames.end()) {  mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+                                       if (itList != listNames.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
                                        else { listNames[name] = name; }
                                }
                        
@@ -314,7 +314,7 @@ void SharedCommand::createMisMatchFile() {
                                if(group == "not found") {      outMisMatch << names << endl;  }        
                                
                                itList = listNames.find(names);
-                               if (itList != listNames.end()) {  mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+                               if (itList != listNames.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
                                else { listNames[names] = names; }
 
                        }
@@ -325,7 +325,7 @@ void SharedCommand::createMisMatchFile() {
                }else {//you have sequences in your group file that are not in you list file
                        
                        outputMisMatchName += "missing.name";
-                       mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); mothurOutEndLine();
+                       m->mothurOut("For a list of names that are in your group file and not in your list file, please refer to " + outputMisMatchName + "."); m->mothurOutEndLine();
                        
                        map<string, string> namesInList;
                        map<string, string>::iterator itList;
@@ -340,14 +340,14 @@ void SharedCommand::createMisMatchFile() {
                                        names = names.substr(names.find_first_of(',')+1, names.length());
                                        
                                        itList = namesInList.find(name);
-                                       if (itList != namesInList.end()) {  mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+                                       if (itList != namesInList.end()) {  m->mothurOut(name + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 
                                        namesInList[name] = name;
                                        
                                }
                                
                                itList = namesInList.find(names);
-                               if (itList != namesInList.end()) {  mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); mothurOutEndLine(); }
+                               if (itList != namesInList.end()) {  m->mothurOut(names + " is in your list file more than once.  Sequence names must be unique. please correct."); m->mothurOutEndLine(); }
 
                                //get last name
                                namesInList[names] = names;                             
@@ -375,7 +375,7 @@ void SharedCommand::createMisMatchFile() {
  
        }
        catch(exception& e) {
-               errorOut(e, "SharedCommand", "createMisMatchFile");
+               m->errorOut(e, "SharedCommand", "createMisMatchFile");
                exit(1);
        }
 }
@@ -399,7 +399,7 @@ bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {
                return false;
        }
        catch(exception& e) {
-               errorOut(e, "SharedCommand", "isValidGroup");
+               m->errorOut(e, "SharedCommand", "isValidGroup");
                exit(1);
        }
 }