created mothurOut class to handle logfiles

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 48bf17119c98d832b0176dcab78675a94ecf80e8..bb8d1f53714e3d953eb0f6c9c7bd4a829b3cb833 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -12,7 +12,7 @@
 
 //***************************************************************************************************************
 
-ScreenSeqsCommand::ScreenSeqsCommand(string option){
+ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
        try {
                abort = false;
                
@@ -76,7 +76,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
 
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not found") { mothurOut("fasta is a required parameter for the screen.seqs command."); mothurOutEndLine(); abort = true; }
+                       if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
        
                        groupfile = validParameter.validFile(parameters, "group", true);
@@ -121,7 +121,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
 
        }
        catch(exception& e) {
-               errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
+               m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
                exit(1);
        }
 }
@@ -129,25 +129,25 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option){
 
 void ScreenSeqsCommand::help(){
        try {
-               mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
-               mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group.\n");
-               mothurOut("The fasta parameter is required.\n");
-               mothurOut("The start parameter .... The default is -1.\n");
-               mothurOut("The end parameter .... The default is -1.\n");
-               mothurOut("The maxambig parameter .... The default is -1.\n");
-               mothurOut("The maxhomop parameter .... The default is -1.\n");
-               mothurOut("The minlength parameter .... The default is -1.\n");
-               mothurOut("The maxlength parameter .... The default is -1.\n");
-               mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
-               mothurOut("The screen.seqs command should be in the following format: \n");
-               mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n");
-               mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");       
-               mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+               m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
+               m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, and group.\n");
+               m->mothurOut("The fasta parameter is required.\n");
+               m->mothurOut("The start parameter .... The default is -1.\n");
+               m->mothurOut("The end parameter .... The default is -1.\n");
+               m->mothurOut("The maxambig parameter .... The default is -1.\n");
+               m->mothurOut("The maxhomop parameter .... The default is -1.\n");
+               m->mothurOut("The minlength parameter .... The default is -1.\n");
+               m->mothurOut("The maxlength parameter .... The default is -1.\n");
+               m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
+               m->mothurOut("The screen.seqs command should be in the following format: \n");
+               m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n");
+               m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");    
+               m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 
        }
        catch(exception& e) {
-               errorOut(e, "ScreenSeqsCommand", "help");
+               m->errorOut(e, "ScreenSeqsCommand", "help");
                exit(1);
        }
 }
@@ -203,10 +203,18 @@ int ScreenSeqsCommand::execute(){
                goodSeqOut.close();
                badSeqOut.close();
                inFASTA.close();
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               m->mothurOut(goodSeqFile); m->mothurOutEndLine();       
+               m->mothurOut(badSeqFile); m->mothurOutEndLine();        
+               m->mothurOutEndLine();
+
+               
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ScreenSeqsCommand", "execute");
+               m->errorOut(e, "ScreenSeqsCommand", "execute");
                exit(1);
        }
 }
@@ -257,8 +265,8 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
        //we were unable to remove some of the bad sequences
        if (badSeqNames.size() != 0) {
                for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
-                       mothurOut("Your namefile does not include the sequence " + *it + " please correct."); 
-                       mothurOutEndLine();
+                       m->mothurOut("Your namefile does not include the sequence " + *it + " please correct."); 
+                       m->mothurOutEndLine();
                }
        }
 
@@ -294,8 +302,8 @@ void ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
                //we were unable to remove some of the bad sequences
                if (badSeqGroups.size() != 0) {
                        for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {  
-                               mothurOut("Your namefile does not include the sequence " + *it + " please correct."); 
-                               mothurOutEndLine();
+                               m->mothurOut("Your namefile does not include the sequence " + *it + " please correct."); 
+                               m->mothurOutEndLine();
                        }
                }
        }
@@ -333,8 +341,8 @@ void ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
        //we were unable to remove some of the bad sequences
        if (badSeqNames.size() != 0) {
                for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
-                       mothurOut("Your groupfile does not include the sequence " + *it + " please correct."); 
-                       mothurOutEndLine();
+                       m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct."); 
+                       m->mothurOutEndLine();
                }
        }
        
@@ -389,8 +397,8 @@ void ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
        //we were unable to remove some of the bad sequences
        if (badSeqNames.size() != 0) {
                for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {  
-                       mothurOut("Your file does not include the sequence " + *it + " please correct."); 
-                       mothurOutEndLine();
+                       m->mothurOut("Your file does not include the sequence " + *it + " please correct."); 
+                       m->mothurOutEndLine();
                }
        }