added stricter compilation requirements and fixed resulting errors

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 6f4ebcc1fa84028113e150c39e028e340ae86c26..0cba83323db70f0748e4e6a5ec0d902ee8294945 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -19,7 +19,7 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        
        globaldata = GlobalData::getInstance();
        
-       cout << "Generating the temporary BLAST database...\t"; cout.flush();
+       mothurOut("Generating the temporary BLAST database...\t");      cout.flush();
 
        int randNumber = rand();
        dbFileName = toString(randNumber) + ".template.unaligned.fasta";
@@ -32,7 +32,7 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        
        for(int i=0;i<numSeqs;i++){                                                                     //      generating a fasta file with unaligned template
                unalignedFastaFile << '>' << i << endl;                                 //      sequences, which will be input to formatdb
-               unalignedFastaFile << templateSequences[i]->getUnaligned() << endl;
+               unalignedFastaFile << templateSequences[i].getUnaligned() << endl;
        }
        unalignedFastaFile.close();
        
@@ -42,11 +42,11 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability
        system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
                                                                                                                                        //      option tells formatdb that seqs are DNA, not prot
-       cout << "DONE." << endl << endl;        cout.flush();
-       emptySequence = new Sequence();
-       emptySequence->setName("no_match");
-       emptySequence->setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
-       emptySequence->setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+       mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
+       emptySequence = Sequence();
+       emptySequence.setName("no_match");
+       emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+       emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
 
 
 }
@@ -54,6 +54,10 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 /**************************************************************************************************/
 
 BlastDB::~BlastDB(){
+       //for (int i = 0; i < templateSequences.size(); i++) {  delete templateSequences[i];   }
+       //templateSequences.clear();
+       //delete emptySequence;
+       
        remove(queryFileName.c_str());                          //      let's clean stuff up and remove the temp files
        remove(dbFileName.c_str());                                     //      let's clean stuff up and remove the temp files
        remove(blastFileName.c_str());                          //      let's clean stuff up and remove the temp files
@@ -61,7 +65,7 @@ BlastDB::~BlastDB(){
 
 /**************************************************************************************************/
 
-Sequence* BlastDB::findClosestSequence(Sequence* candidate){
+Sequence BlastDB::findClosestSequence(Sequence* candidate){
 
        ofstream queryFile;
        openOutputFile(queryFileName, queryFile);
@@ -93,6 +97,7 @@ Sequence* BlastDB::findClosestSequence(Sequence* candidate){
                searchScore = 0.00;
                return emptySequence;
        }
+       m8FileHandle.close();
 }
 
 /**************************************************************************************************/