created mothurOut class to handle logfiles

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index fcc42ced634b80790d6aa3f5977ea6ef3121f77a..6053f474224368a5b7f786f24237b2c8645ea1e0 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -10,13 +10,13 @@
 #include "getlistcountcommand.h"
 
 //**********************************************************************************************************************
-GetListCountCommand::GetListCountCommand(string option){
+GetListCountCommand::GetListCountCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
                allLines = 1;
                labels.clear();
-               
+                               
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
@@ -57,7 +57,7 @@ GetListCountCommand::GetListCountCommand(string option){
                        
                        //check for required parameters
                        listfile = validParameter.validFile(parameters, "list", true);
-                       if ((listfile == "not found") && (globaldata->getListFile() == ""))  { mothurOut("You must read a listfile before running the get.listcount command.");  mothurOutEndLine(); abort = true; }
+                       if ((listfile == "not found") && (globaldata->getListFile() == ""))  { m->mothurOut("You must read a listfile before running the get.listcount command.");  m->mothurOutEndLine(); abort = true; }
                        else if ((listfile == "not found") && (globaldata->getListFile() != "")) { listfile = globaldata->getListFile(); }
                        else if (listfile == "not open") { abort = true; }      
                        else { globaldata->setListFile(listfile); }
@@ -80,7 +80,7 @@ GetListCountCommand::GetListCountCommand(string option){
                }
        }
        catch(exception& e) {
-               errorOut(e, "GetListCountCommand", "GetListCountCommand");
+               m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
                exit(1);
        }
 }
@@ -88,17 +88,17 @@ GetListCountCommand::GetListCountCommand(string option){
 
 void GetListCountCommand::help(){
        try {
-               mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n");
-               mothurOut("The get.listcount command parameters are list and label.  No parameters are required.\n");
-               mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
-               mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
-               mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
-               mothurOut("The default value for label is all lines in your inputfile.\n");
-               mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
+               m->mothurOut("The get.listcount command can only be executed after a successful read.otu command of a listfile or providing a list file using the list parameter.\n");
+               m->mothurOut("The get.listcount command parameters are list and label.  No parameters are required.\n");
+               m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
+               m->mothurOut("The get.listcount command should be in the following format: get.listcount(list=yourlistFile, label=yourLabels).\n");
+               m->mothurOut("Example get.listcount(list=amazon.fn.list, label=0.10).\n");
+               m->mothurOut("The default value for label is all lines in your inputfile.\n");
+               m->mothurOut("The get.listcount command outputs a .otu file for each distance you specify listing the bin number and the names of the sequences in that bin.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "GetListCountCommand", "help");
+               m->errorOut(e, "GetListCountCommand", "help");
                exit(1);
        }
 }
@@ -163,12 +163,12 @@ int GetListCountCommand::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();
                        }
                }
                
@@ -184,10 +184,15 @@ int GetListCountCommand::execute(){
                delete read;
                globaldata->gListVector = 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, "GetListCountCommand", "execute");
+               m->errorOut(e, "GetListCountCommand", "execute");
                exit(1);
        }
 }
@@ -200,8 +205,9 @@ void GetListCountCommand::process(ListVector* list) {
                if (outputDir == "") { outputDir += hasPath(listfile); }
                string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + list->getLabel() + ".otu";
                openOutputFile(outputFileName, out);
+               outputNames.push_back(outputFileName);
                
-               mothurOut(list->getLabel()); mothurOutEndLine();
+               m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                
                //for each bin in the list vector
                for (int i = 0; i < list->getNumBins(); i++) {
@@ -212,7 +218,7 @@ void GetListCountCommand::process(ListVector* list) {
                out.close();
        }
        catch(exception& e) {
-               errorOut(e, "GetListCountCommand", "process");
+               m->errorOut(e, "GetListCountCommand", "process");
                exit(1);
        }
 }