created mothurOut class to handle logfiles

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index d0b00bd3061d2a14365ee43ef96db1bc04ac1cb0..f3710c9e4d0aabd728c0714d0f8b7d41c0b73c24 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -13,7 +13,7 @@
 
 //**********************************************************************************************************************
 
-ListSeqsCommand::ListSeqsCommand(string option){
+ListSeqsCommand::ListSeqsCommand(string option)  {
        try {
                abort = false;
                
@@ -107,17 +107,17 @@ ListSeqsCommand::ListSeqsCommand(string option){
                        else if (listfile == "not found") {  listfile = "";  }
 
                        
-                       if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == ""))  { mothurOut("You must provide a file."); mothurOutEndLine(); abort = true; }
+                       if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        
                        int okay = 1;
                        if (outputDir != "") { okay++; }
                        
-                       if (parameters.size() > okay) { mothurOut("You may only enter one file."); mothurOutEndLine(); abort = true;  }
+                       if (parameters.size() > okay) { m->mothurOut("You may only enter one file."); m->mothurOutEndLine(); abort = true;  }
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+               m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
                exit(1);
        }
 }
@@ -125,14 +125,14 @@ ListSeqsCommand::ListSeqsCommand(string option){
 
 void ListSeqsCommand::help(){
        try {
-               mothurOut("The list.seqs command reads a fasta, name, group, list or alignreport file and outputs a .accnos file containing sequence names.\n");
-               mothurOut("The list.seqs command parameters are fasta, name, group and alignreport.  You must provide one of these parameters.\n");
-               mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
-               mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+               m->mothurOut("The list.seqs command reads a fasta, name, group, list or alignreport file and outputs a .accnos file containing sequence names.\n");
+               m->mothurOut("The list.seqs command parameters are fasta, name, group and alignreport.  You must provide one of these parameters.\n");
+               m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
+               m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "help");
+               m->errorOut(e, "ListSeqsCommand", "help");
                exit(1);
        }
 }
@@ -167,11 +167,16 @@ int ListSeqsCommand::execute(){
                }
                out.close();
                
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               m->mothurOutEndLine();
+               
                return 0;               
        }
 
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "execute");
+               m->errorOut(e, "ListSeqsCommand", "execute");
                exit(1);
        }
 }
@@ -196,7 +201,7 @@ void ListSeqsCommand::readFasta(){
 
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "readFasta");
+               m->errorOut(e, "ListSeqsCommand", "readFasta");
                exit(1);
        }
 }
@@ -227,7 +232,7 @@ void ListSeqsCommand::readList(){
                
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "readList");
+               m->errorOut(e, "ListSeqsCommand", "readList");
                exit(1);
        }
 }
@@ -261,7 +266,7 @@ void ListSeqsCommand::readName(){
                
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "readName");
+               m->errorOut(e, "ListSeqsCommand", "readName");
                exit(1);
        }
 }
@@ -287,7 +292,7 @@ void ListSeqsCommand::readGroup(){
 
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "readGroup");
+               m->errorOut(e, "ListSeqsCommand", "readGroup");
                exit(1);
        }
 }
@@ -327,7 +332,7 @@ void ListSeqsCommand::readAlign(){
                
        }
        catch(exception& e) {
-               errorOut(e, "ListSeqsCommand", "readAlign");
+               m->errorOut(e, "ListSeqsCommand", "readAlign");
                exit(1);
        }
 }