added get.repseqs command, started matrix output command

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index c3c68abacffd43efaf5768796655e8816da87bd6..7810ea9f793255e31e44c854a5a4c21639019c60 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -57,7 +57,7 @@ int BinSeqCommand::execute(){
                }
                
                //read list file
-               read = new ReadPhilFile(globaldata->getListFile());     
+               read = new ReadOTUFile(globaldata->getListFile());      
                read->read(&*globaldata); 
                
                input = globaldata->ginput;
@@ -67,10 +67,6 @@ int BinSeqCommand::execute(){
                        
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
                                
-                               //make new folder for bin info
-                               //string foldername = "/" + getRootName(globaldata->getListFile()) + list->getLabel() + ".bins/";
-                       //      mkdir(foldername.c_str()); 
-                       
                                string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
                                openOutputFile(outputFileName, out);
 
@@ -78,10 +74,6 @@ int BinSeqCommand::execute(){
                                
                                //for each bin in the list vector
                                for (int i = 0; i < list->size(); i++) {
-                               
-                                       //create output file
-                                       //string outputFileName = foldername + getRootName(globaldata->getListFile()) + "bin" + toString(i+1) + ".fasta";
-                                       //openOutputFile(outputFileName, out);
 
                                        binnames = list->get(i);
                                        while (binnames.find_first_of(',') != -1) { 
@@ -105,7 +97,7 @@ int BinSeqCommand::execute(){
                                        //get last name
                                        sequence = fasta->getSequence(binnames);
                                        if (sequence != "not found") {
-                                               name = binnames + "bin" + toString(i+1);
+                                               name = binnames + '|' + toString(i+1);
                                                out << ">" << name << endl;
                                                out << sequence << endl;
                                        }else { 
@@ -113,11 +105,12 @@ int BinSeqCommand::execute(){
                                                remove(outputFileName.c_str());
                                                return 0;
                                        }
-                                       //out.close();
+                                       
                                }
                                out.close();
                        }
                        
+                       delete list;
                        list = input->getListVector();
                        count++;
                }