created mothurOut class to handle logfiles

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 032282411f60905990f59dc0275259266e86d7e7..12382a48864a87363f5faae62425de574cb5d0e7 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -31,7 +31,7 @@
 
 //**********************************************************************************************************************
 
-SummaryCommand::SummaryCommand(string option){
+SummaryCommand::SummaryCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
@@ -58,7 +58,7 @@ SummaryCommand::SummaryCommand(string option){
                        }
                        
                        //make sure the user has already run the read.otu command
-                       if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); mothurOutEndLine(); abort = true; }
+                       if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the summary.single command."); m->mothurOutEndLine(); abort = true; }
                        
                        //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"){  
@@ -98,7 +98,7 @@ SummaryCommand::SummaryCommand(string option){
                }
        }
        catch(exception& e) {
-               errorOut(e, "SummaryCommand", "SummaryCommand");
+               m->errorOut(e, "SummaryCommand", "SummaryCommand");
                exit(1);
        }
 }
@@ -106,19 +106,19 @@ SummaryCommand::SummaryCommand(string option){
 
 void SummaryCommand::help(){
        try {
-               mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
-               mothurOut("The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
-               mothurOut("The summary.single command parameters are label, calc, abund.  No parameters are required.\n");
-               mothurOut("The summary.single command should be in the following format: \n");
-               mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
-               mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
+               m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
+               m->mothurOut("The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
+               m->mothurOut("The summary.single command parameters are label, calc, abund.  No parameters are required.\n");
+               m->mothurOut("The summary.single command should be in the following format: \n");
+               m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
+               m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
                validCalculator->printCalc("summary", cout);
-               mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
-               mothurOut("The label parameter is used to analyze specific labels in your input.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
+               m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
+               m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "SummaryCommand", "help");
+               m->errorOut(e, "SummaryCommand", "help");
                exit(1);
        }
 }
@@ -134,6 +134,8 @@ int SummaryCommand::execute(){
        
                if (abort == true) { return 0; }
                
+               vector<string> outputNames;
+               
                if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }
                else {  inputFileNames = parseSharedFile(globaldata->getSharedFile());  globaldata->setFormat("rabund");  }
                
@@ -141,9 +143,10 @@ int SummaryCommand::execute(){
                        
                        string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary";
                        globaldata->inputFileName = inputFileNames[p];
+                       outputNames.push_back(fileNameRoot);
                        
                        if (inputFileNames.size() > 1) {
-                               mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
+                               m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
                        }
                        
                        sumCalculators.clear();
@@ -230,7 +233,7 @@ int SummaryCommand::execute(){
                                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){                     
                                        
-                                       mothurOut(sabund->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
                                        
@@ -249,7 +252,7 @@ int SummaryCommand::execute(){
                                        delete sabund;
                                        sabund = input->getSAbundVector(lastLabel);
                                        
-                                       mothurOut(sabund->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
                                        
@@ -275,12 +278,12 @@ int SummaryCommand::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();
                                }
                        }
                        
@@ -289,7 +292,7 @@ int SummaryCommand::execute(){
                                if (sabund != NULL) {   delete sabund;  }
                                sabund = input->getSAbundVector(lastLabel);
                                
-                               mothurOut(sabund->getLabel()); mothurOutEndLine();
+                               m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
                                outputFileHandle << sabund->getLabel();
                                for(int i=0;i<sumCalculators.size();i++){
                                        vector<double> data = sumCalculators[i]->getValues(sabund);
@@ -308,10 +311,15 @@ int SummaryCommand::execute(){
                        globaldata->sabund = NULL;
                }
                
+               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, "SummaryCommand", "execute");
+               m->errorOut(e, "SummaryCommand", "execute");
                exit(1);
        }
 }
@@ -370,7 +378,7 @@ vector<string> SummaryCommand::parseSharedFile(string filename) {
                return filenames;
        }
        catch(exception& e) {
-               errorOut(e, "SummaryCommand", "parseSharedFile");
+               m->errorOut(e, "SummaryCommand", "parseSharedFile");
                exit(1);
        }
 }