fixed some bugs

[mothur.git] / binsequencecommand.cpp

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index abe000fbe4ed191b13389420899389e17bcc7cd4..1627b42d7bec5090a708c77d7491b93fa3bc7cdd 100644 (file)
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -44,11 +44,6 @@ BinSeqCommand::BinSeqCommand(string option){
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { cout << "fasta is a required parameter for the bin.seqs command." << endl; abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
-                       else { 
-                               openInputFile(fastafile, in);
-                               fasta = new FastaMap();
-                       }
-               
                
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -82,10 +77,14 @@ BinSeqCommand::BinSeqCommand(string option){
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") { groupfile = ""; }
-                       else {
-                               //read in group map info.
-                               groupMap = new GroupMap(groupfile);
-                               groupMap->readMap();
+                       
+                       if (abort == false) { 
+                               openInputFile(fastafile, in);
+                               fasta = new FastaMap();
+                               if (groupfile != "") {
+                                       groupMap = new GroupMap(groupfile);
+                                       groupMap->readMap();
+                               }
                        }
        
                }
@@ -130,17 +129,12 @@ void BinSeqCommand::help(){
 BinSeqCommand::~BinSeqCommand(){
        //made new in execute
        if (abort == false) {
-               delete input;
+               delete input;  globaldata->ginput = NULL;
                delete read;
-               delete list;
-       }
-       
-       //made new in constructor
-       delete fasta;
-       if (groupfile != "") {
-                       delete groupMap;
+               globaldata->gListVector = NULL;
+               delete fasta;
+               if (groupfile != "") {  delete groupMap;  globaldata->gGroupmap = NULL; }
        }
-
 }
 
 //**********************************************************************************************************************
@@ -155,6 +149,8 @@ int BinSeqCommand::execute(){
                //read fastafile
                fasta->readFastaFile(in);
                
+               in.close();
+               
                //set format to list so input can get listvector
 //             globaldata->setFormat("list");