finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime...

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index d60470cdebcc70114afcb79cc08edbb333816292..ef1515863dbca8b0f930d1b26f3c9f2936c7eec4 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -71,7 +71,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
-               
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        
@@ -150,15 +150,18 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -167,10 +170,12 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
-
+                       else { m->setListFile(listfile); }
+                       
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        
@@ -218,13 +223,13 @@ int ListSeqsCommand::execute(){
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
                        
-                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
                        
                        out << names[i] << endl;
                }
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0; }
                
                m->setAccnosFile(outputFileName);