created mothurOut class to handle logfiles

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 00c40845484e9ba4eba4e62f7c645135f703e9d2..fcfd320e0b6be3aa3572b661a579311c9dead5bf 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -10,7 +10,7 @@
 #include "deconvolutecommand.h"
 
 /**************************************************************************************/
-DeconvoluteCommand::DeconvoluteCommand(string option) {        
+DeconvoluteCommand::DeconvoluteCommand(string option)  {       
        try {
                abort = false;
                
@@ -59,7 +59,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
                        //check for required parameters
                        inFastaName = validParameter.validFile(parameters, "fasta", true);
                        if (inFastaName == "not open") { abort = true; }
-                       else if (inFastaName == "not found") { inFastaName = ""; mothurOut("fasta is a required parameter for the unique.seqs command."); mothurOutEndLine(); abort = true;  }  
+                       else if (inFastaName == "not found") { inFastaName = ""; m->mothurOut("fasta is a required parameter for the unique.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"){  
@@ -74,7 +74,7 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
 
        }
        catch(exception& e) {
-               errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+               m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
                exit(1);
        }
 }
@@ -82,15 +82,15 @@ DeconvoluteCommand::DeconvoluteCommand(string option) {
 
 void DeconvoluteCommand::help(){
        try {
-               mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
-               mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
-               mothurOut("If the sequence is unique the second column will just contain its name. \n");
-               mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
-               mothurOut("The unique.seqs command should be in the following format: \n");
-               mothurOut("unique.seqs(fasta=yourFastaFile) \n");       
+               m->mothurOut("The unique.seqs command reads a fastafile and creates a namesfile.\n");
+               m->mothurOut("It creates a file where the first column is the groupname and the second column is a list of sequence names who have the same sequence. \n");
+               m->mothurOut("If the sequence is unique the second column will just contain its name. \n");
+               m->mothurOut("The unique.seqs command parameter is fasta and it is required.\n");
+               m->mothurOut("The unique.seqs command should be in the following format: \n");
+               m->mothurOut("unique.seqs(fasta=yourFastaFile) \n");    
        }
        catch(exception& e) {
-               errorOut(e, "DeconvoluteCommand", "help");
+               m->errorOut(e, "DeconvoluteCommand", "help");
                exit(1);
        }
 }
@@ -113,10 +113,18 @@ int DeconvoluteCommand::execute() {
                fastamap.printCondensedFasta(outFastaFile);
                fastamap.printNamesFile(outNameFile);
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               m->mothurOut(outFastaFile); m->mothurOutEndLine();      
+               m->mothurOut(outNameFile); m->mothurOutEndLine();
+               m->mothurOutEndLine();
+
+
+               
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "DeconvoluteCommand", "execute");
+               m->errorOut(e, "DeconvoluteCommand", "execute");
                exit(1);
        }
 }