1.20.0

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index ebfd07565bcca4458d7ce51b4911d5cc659e711e..3fe8360e3241477b869c26f5b1892541e28d84a4 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; }
                        
@@ -257,18 +262,32 @@ int ListSeqsCommand::readFasta(){
                m->openInputFile(fastafile, in);
                string name;
                
+               //ofstream out;
+               //string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+               //m->openOutputFile(newFastaName, out);
+               //int count = 1;
+               //string lastName = "";
+               
                while(!in.eof()){
                        
                        if (m->control_pressed) { in.close(); return 0; }
                        
                        Sequence currSeq(in);
                        name = currSeq.getName();
+                       //if (lastName == "") { lastName = name; }
+                       //if (name != lastName) { count = 1; }
+               //      lastName = name;
+                       
+                       //Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+                       //newSeq.printSequence(out);
                        
                        if (name != "") {  names.push_back(name);  }
                        
                        m->gobble(in);
+                       //count++;
                }
                in.close();     
+               //out.close();
                
                return 0;