created mothurOut class to handle logfiles

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index ce014fcaf439d2d838cd630cbb5b012f2c8b8efe..4838988346bb962d7ef91d32c483cf2e379f5895 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -14,7 +14,7 @@ ParseListCommand::ParseListCommand(string option)  {
        try {
                abort = false;
                allLines = 1;
-               
+                       
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
@@ -76,7 +76,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        }
                        
                        //do you have all files needed
-                       if ((listfile == "") || (groupfile == "")) { mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); mothurOutEndLine(); abort = true;  }
+                       if ((listfile == "") || (groupfile == "")) { m->mothurOut("You must enter both a listfile and groupfile for the parse.list command. "); m->mothurOutEndLine(); abort = true;  }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -90,24 +90,24 @@ ParseListCommand::ParseListCommand(string option)  {
 
        }
        catch(exception& e) {
-               errorOut(e, "ParseListCommand", "ParseListCommand");
+               m->errorOut(e, "ParseListCommand", "ParseListCommand");
                exit(1);
        }
 }
 //**********************************************************************************************************************
 void ParseListCommand::help(){
        try {
-               mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile \n");
-               mothurOut("The parse.list command parameters are list, group and label.\n");
-               mothurOut("The list and group parameters are required.\n");
-               mothurOut("The label parameter is used to read specific labels in your input you want to use.\n");
-               mothurOut("The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n");
-               mothurOut("Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
+               m->mothurOut("The parse.list command reads a list and group file and generates a list file for each group in the groupfile \n");
+               m->mothurOut("The parse.list command parameters are list, group and label.\n");
+               m->mothurOut("The list and group parameters are required.\n");
+               m->mothurOut("The label parameter is used to read specific labels in your input you want to use.\n");
+               m->mothurOut("The parse.list command should be used in the following format: parse.list(list=yourListFile, group=yourGroupFile, label=yourLabels).\n");
+               m->mothurOut("Example: parse.list(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 
        }
        catch(exception& e) {
-               errorOut(e, "ParseListCommand", "help");
+               m->errorOut(e, "ParseListCommand", "help");
                exit(1);
        }
 }
@@ -121,6 +121,7 @@ int ParseListCommand::execute(){
                
                //set fileroot
                string fileroot = outputDir + getRootName(getSimpleName(listfile));
+               vector<string> outputNames;
                
                //fill filehandles with neccessary ofstreams
                int i;
@@ -130,6 +131,7 @@ int ParseListCommand::execute(){
                        filehandles[groupMap->namesOfGroups[i]] = temp;
                        
                        string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
+                       outputNames.push_back(filename);
                        openOutputFile(filename, *temp);
                }
                
@@ -146,7 +148,7 @@ int ParseListCommand::execute(){
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){
                                        
                                        parse(list);
-                                       mothurOut(list->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                                        
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
@@ -159,7 +161,7 @@ int ParseListCommand::execute(){
                                        list = input->getListVector(lastLabel); //get new list vector to process
                                        
                                        parse(list);
-                                       mothurOut(list->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                                        
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
@@ -179,12 +181,12 @@ int ParseListCommand::execute(){
                set<string>::iterator it;
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       mothurOut("Your file does not include the label " + *it); 
+                       m->mothurOut("Your file does not include the label " + *it); 
                        if (processedLabels.count(lastLabel) != 1) {
-                               mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+                               m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
                                needToRun = true;
                        }else {
-                               mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+                               m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
                        }
 
                }
@@ -195,7 +197,7 @@ int ParseListCommand::execute(){
                        list = input->getListVector(lastLabel); //get new list vector to process
                        
                        parse(list);            
-                       mothurOut(list->getLabel()); mothurOutEndLine();
+                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                        
                        delete list;
                }
@@ -207,10 +209,15 @@ int ParseListCommand::execute(){
                
                delete groupMap;
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOutEndLine();
+               
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ParseListCommand", "execute");
+               m->errorOut(e, "ParseListCommand", "execute");
                exit(1);
        }
 }
@@ -241,7 +248,7 @@ void ParseListCommand::parse(ListVector* thisList) {
                        for (int j = 0; j < names.size(); j++) {
                                string group = groupMap->getGroup(names[j]);
                                
-                               if (group == "not found") { mothurOut(names[j] + " is not in your groupfile. please correct."); mothurOutEndLine(); exit(1); }
+                               if (group == "not found") { m->mothurOut(names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); exit(1); }
                                
                                itGroup = groupBins.find(group);
                                if(itGroup == groupBins.end()) {
@@ -267,7 +274,7 @@ void ParseListCommand::parse(ListVector* thisList) {
 
        }
        catch(exception& e) {
-               errorOut(e, "ParseListCommand", "parse");
+               m->errorOut(e, "ParseListCommand", "parse");
                exit(1);
        }
 }