fixed some bugs

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index ccfd9bbec751e3000afd318d063a094c9745ec4a..064189b1423434f24e88fb05df3ad67a7ea4967f 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -104,9 +104,13 @@ AlignCommand::AlignCommand(string option){
 
 //**********************************************************************************************************************
 
-AlignCommand::~AlignCommand(){                 
-       delete templateDB;
-       delete alignment;
+AlignCommand::~AlignCommand(){ 
+
+       if (abort == false) {
+               for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+               delete templateDB;
+               delete alignment;
+       }
 }
 
 //**********************************************************************************************************************
@@ -178,6 +182,7 @@ int AlignCommand::execute(){
                        lines.push_back(new linePair(0, numFastaSeqs));
                        
                        driver(lines[0], alignFileName, reportFileName);
+                       
                }
                else{
                        vector<int> positions;
@@ -216,6 +221,7 @@ int AlignCommand::execute(){
                                appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
                                remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
                        }
+                       
                }
 #else
                ifstream inFASTA;
@@ -262,7 +268,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
                        Sequence* candidateSeq = new Sequence(inFASTA);
                        report.setCandidate(candidateSeq);
                        
-                       Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq);
+                       Sequence temp = templateDB->findClosestSequence(candidateSeq);
+                       Sequence* templateSeq = &temp;
+                       
                        report.setTemplate(templateSeq);
                        report.setSearchParameters(search, templateDB->getSearchScore());