created mothurOut class to handle logfiles

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 274240158068655fcbbc501d81e335238966edfa..4efcbcce17e7daeb102a3c3c98d4baedbc185093 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -13,7 +13,7 @@
 
 //***************************************************************************************************************
 
-ReverseSeqsCommand::ReverseSeqsCommand(string option){
+ReverseSeqsCommand::ReverseSeqsCommand(string option)  {
        try {
                abort = false;
                
@@ -53,7 +53,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                        //check for required parameters
                        fasta = validParameter.validFile(parameters, "fasta", true);
                        if (fasta == "not open") { abort = true; }
-                       else if (fasta == "not found") { fasta = ""; mothurOut("fasta is a required parameter for the reverse.seqs command."); mothurOutEndLine(); abort = true;  }     
+                       else if (fasta == "not found") { fasta = ""; m->mothurOut("fasta is a required parameter for the reverse.seqs 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"){  
@@ -64,7 +64,7 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                }
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+               m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
                exit(1);
        }
 }
@@ -72,13 +72,13 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
 
 void ReverseSeqsCommand::help(){
        try {
-               mothurOut("The reverse.seqs command reads a fastafile and ....\n");
-               mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
-               mothurOut("The reverse.seqs command should be in the following format: \n");
-               mothurOut("reverse.seqs(fasta=yourFastaFile) \n");      
+               m->mothurOut("The reverse.seqs command reads a fastafile and ....\n");
+               m->mothurOut("The reverse.seqs command parameter is fasta and it is required.\n");
+               m->mothurOut("The reverse.seqs command should be in the following format: \n");
+               m->mothurOut("reverse.seqs(fasta=yourFastaFile) \n");   
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "help");
+               m->errorOut(e, "ReverseSeqsCommand", "help");
                exit(1);
        }
 }
@@ -112,11 +112,17 @@ int ReverseSeqsCommand::execute(){
                inFASTA.close();
                outFASTA.close();
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(reverseFile); m->mothurOutEndLine();       
+               m->mothurOutEndLine();
+
+               
                return 0;
                
        }
        catch(exception& e) {
-               errorOut(e, "ReverseSeqsCommand", "execute");
+               m->errorOut(e, "ReverseSeqsCommand", "execute");
                exit(1);
        }
 }