created mothurOut class to handle logfiles

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 19a4bc032abbcd1a5a7c9f53cdeac1b1be2c5715..c76c7113f237c45df86a91faa523f93163fc6ff8 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -13,7 +13,7 @@
 
 //**********************************************************************************************************************
 
-RemoveSeqsCommand::RemoveSeqsCommand(string option){
+RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
        try {
                abort = false;
                
@@ -97,7 +97,7 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
                        //check for required parameters
                        accnosfile = validParameter.validFile(parameters, "accnos", true);
                        if (accnosfile == "not open") { abort = true; }
-                       else if (accnosfile == "not found") {  accnosfile = "";  mothurOut("You must provide an accnos file."); mothurOutEndLine(); abort = true; }     
+                       else if (accnosfile == "not found") {  accnosfile = "";  m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }       
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
@@ -123,20 +123,20 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
                        string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
                        dups = isTrue(temp);
                        
-                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); mothurOutEndLine(); abort = true; }
+                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); m->mothurOutEndLine(); abort = true; }
                        
                        int okay = 2;
                        if (outputDir != "") { okay++; }
                        if (usedDups != "") { okay++;  }
                        
-                       if ((usedDups != "") && (namefile == "")) {  mothurOut("You may only use dups with the name option."); mothurOutEndLine();  abort = true; }
+                       if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
                        
-                       if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); mothurOutEndLine(); abort = true;  }
+                       if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true;  }
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
+               m->errorOut(e, "RemoveSeqsCommand", "RemoveSeqsCommand");
                exit(1);
        }
 }
@@ -144,16 +144,16 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
 
 void RemoveSeqsCommand::help(){
        try {
-               mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
-               mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
-               mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, alignreport and dups.  You must provide accnos and one of the file parameters.\n");
-               mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new .accnos file containing all the sequences removed. \n");
-               mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
-               mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+               m->mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
+               m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
+               m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, alignreport and dups.  You must provide accnos and one of the file parameters.\n");
+               m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new .accnos file containing all the sequences removed. \n");
+               m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
+               m->mothurOut("Example remove.seqs(accnos=amazon.accnos, 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, "RemoveSeqsCommand", "help");
+               m->errorOut(e, "RemoveSeqsCommand", "help");
                exit(1);
        }
 }
@@ -175,11 +175,18 @@ int RemoveSeqsCommand::execute(){
                else if (alignfile != "")       {               readAlign();    }
                else if (listfile != "")        {               readList();             }
                
+               if (outputNames.size() != 0) {
+                       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, "RemoveSeqsCommand", "execute");
+               m->errorOut(e, "RemoveSeqsCommand", "execute");
                exit(1);
        }
 }
@@ -216,13 +223,13 @@ void RemoveSeqsCommand::readFasta(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else { outputNames.push_back(outputFileName); }
 
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "readFasta");
+               m->errorOut(e, "RemoveSeqsCommand", "readFasta");
                exit(1);
        }
 }
@@ -281,13 +288,13 @@ void RemoveSeqsCommand::readList(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else { outputNames.push_back(outputFileName); }
 
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "readList");
+               m->errorOut(e, "RemoveSeqsCommand", "readList");
                exit(1);
        }
 }
@@ -374,16 +381,16 @@ void RemoveSeqsCommand::readName(){
                if (dups) { out2.close();  }
                if (wroteDups == false) {
                        remove(outputFileName2.c_str()); 
-               }
+               }else { outputNames.push_back(outputFileName2); }
                
                if (wroteSomething == false) {
-                       mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else { outputNames.push_back(outputFileName); }
                
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "readName");
+               m->errorOut(e, "RemoveSeqsCommand", "readName");
                exit(1);
        }
 }
@@ -419,13 +426,13 @@ void RemoveSeqsCommand::readGroup(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else { outputNames.push_back(outputFileName); }
 
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "readGroup");
+               m->errorOut(e, "RemoveSeqsCommand", "readGroup");
                exit(1);
        }
 }
@@ -485,13 +492,13 @@ void RemoveSeqsCommand::readAlign(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else { outputNames.push_back(outputFileName); }
                
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "readAlign");
+               m->errorOut(e, "RemoveSeqsCommand", "readAlign");
                exit(1);
        }
 }
@@ -514,7 +521,7 @@ void RemoveSeqsCommand::readAccnos(){
 
        }
        catch(exception& e) {
-               errorOut(e, "RemoveSeqsCommand", "readAccnos");
+               m->errorOut(e, "RemoveSeqsCommand", "readAccnos");
                exit(1);
        }
 }