created mothurOut class to handle logfiles

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index d63dc79974ac007f504f7f1928ed8d0f031dcfe3..ec0539093be68f0581b12f24170f07f726b1ee29 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -13,10 +13,10 @@
 
 //**********************************************************************************************************************
 
-GetSeqsCommand::GetSeqsCommand(string option){
+GetSeqsCommand::GetSeqsCommand(string option)  {
        try {
                abort = false;
-               
+                               
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
@@ -97,7 +97,7 @@ GetSeqsCommand::GetSeqsCommand(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; }
@@ -119,17 +119,17 @@ GetSeqsCommand::GetSeqsCommand(string option){
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
                        
-                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true; }
+                       if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or listfile."); m->mothurOutEndLine(); abort = true; }
                        
                        int okay = 2;
                        if (outputDir != "") { okay++; }
                        
-                       if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); mothurOutEndLine(); abort = true;  }
+                       if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport or listfile."); m->mothurOutEndLine(); abort = true;  }
                }
 
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
+               m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
                exit(1);
        }
 }
@@ -137,15 +137,15 @@ GetSeqsCommand::GetSeqsCommand(string option){
 
 void GetSeqsCommand::help(){
        try {
-               mothurOut("The get.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 only the sequences in the .accnos file.\n");
-               mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list and alignreport.  You must provide accnos and one of the other parameters.\n");
-               mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
-               mothurOut("Example get.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 get.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 only the sequences in the .accnos file.\n");
+               m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list and alignreport.  You must provide accnos and one of the other parameters.\n");
+               m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
+               m->mothurOut("Example get.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, "GetSeqsCommand", "help");
+               m->errorOut(e, "GetSeqsCommand", "help");
                exit(1);
        }
 }
@@ -167,11 +167,18 @@ int GetSeqsCommand::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, "GetSeqsCommand", "execute");
+               m->errorOut(e, "GetSeqsCommand", "execute");
                exit(1);
        }
 }
@@ -184,6 +191,7 @@ void GetSeqsCommand::readFasta(){
                ofstream out;
                openOutputFile(outputFileName, out);
                
+               
                ifstream in;
                openInputFile(fastafile, in);
                string name;
@@ -210,13 +218,13 @@ void GetSeqsCommand::readFasta(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else {  outputNames.push_back(outputFileName); }
 
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "readFasta");
+               m->errorOut(e, "GetSeqsCommand", "readFasta");
                exit(1);
        }
 }
@@ -275,13 +283,13 @@ void GetSeqsCommand::readList(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else {  outputNames.push_back(outputFileName); }
 
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "readList");
+               m->errorOut(e, "GetSeqsCommand", "readList");
                exit(1);
        }
 }
@@ -292,6 +300,7 @@ void GetSeqsCommand::readName(){
                string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" +  getExtension(namefile);
                ofstream out;
                openOutputFile(outputFileName, out);
+               
 
                ifstream in;
                openInputFile(namefile, in);
@@ -357,13 +366,13 @@ void GetSeqsCommand::readName(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else {  outputNames.push_back(outputFileName); }
                
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "readName");
+               m->errorOut(e, "GetSeqsCommand", "readName");
                exit(1);
        }
 }
@@ -375,6 +384,7 @@ void GetSeqsCommand::readGroup(){
                string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
                ofstream out;
                openOutputFile(outputFileName, out);
+               
 
                ifstream in;
                openInputFile(groupfile, in);
@@ -402,13 +412,13 @@ void GetSeqsCommand::readGroup(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else {  outputNames.push_back(outputFileName); }
 
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "readGroup");
+               m->errorOut(e, "GetSeqsCommand", "readGroup");
                exit(1);
        }
 }
@@ -421,6 +431,7 @@ void GetSeqsCommand::readAlign(){
                string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);
+               
 
                ifstream in;
                openInputFile(alignfile, in);
@@ -468,13 +479,13 @@ void GetSeqsCommand::readAlign(){
                out.close();
                
                if (wroteSomething == false) {
-                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
-               }
+               }else {  outputNames.push_back(outputFileName); }
                
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "readAlign");
+               m->errorOut(e, "GetSeqsCommand", "readAlign");
                exit(1);
        }
 }
@@ -498,7 +509,7 @@ void GetSeqsCommand::readAccnos(){
 
        }
        catch(exception& e) {
-               errorOut(e, "GetSeqsCommand", "readAccnos");
+               m->errorOut(e, "GetSeqsCommand", "readAccnos");
                exit(1);
        }
 }