created mothurOut class to handle logfiles

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index b139f3eb7a47bcc86f0920bdc0fc22bad368816a..17db069cdedb8a019d980c32fc4b6e7767fab27b 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -72,10 +72,27 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                }
                m8FileHandle.close();
                
+               string root = dbFileName;
+               string temp = dbFileName + ".nsq";
+               remove(temp.c_str());   
+               temp = dbFileName + ".nsi";
+               remove(temp.c_str());
+               
+               temp = dbFileName + ".nsd";
+               remove(temp.c_str());   
+
+               temp = dbFileName + ".nin";
+               remove(temp.c_str());   
+
+               temp = dbFileName + ".nhr";
+               remove(temp.c_str());   
+       
+
+               
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosestSequences");
+               m->errorOut(e, "BlastDB", "findClosestSequences");
                exit(1);
        }
 
@@ -101,7 +118,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
-               openInputFile(blastFileName, m8FileHandle);
+               openInputFile(blastFileName, m8FileHandle, "no error");
        
                string dummy;
                int templateAccession;
@@ -115,13 +132,14 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                        
                        gobble(m8FileHandle);
                        topMatches.push_back(templateAccession);
+//cout << templateAccession << endl;
                }
                m8FileHandle.close();
-               
+//cout << "\n\n" ;             
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosest");
+               m->errorOut(e, "BlastDB", "findClosest");
                exit(1);
        }
 }
@@ -140,7 +158,7 @@ void BlastDB::addSequence(Sequence seq) {
                count++;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "addSequence");
+               m->errorOut(e, "BlastDB", "addSequence");
                exit(1);
        }
 }
@@ -148,7 +166,7 @@ void BlastDB::addSequence(Sequence seq) {
 void BlastDB::generateDB() {
        try {
        
-               //mothurOut("Generating the temporary BLAST database...\t");    cout.flush();
+               //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
                
                path = globaldata->argv;
                path = path.substr(0, (path.find_last_of('m')));
@@ -156,10 +174,10 @@ void BlastDB::generateDB() {
                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
-               //mothurOut("DONE."); mothurOutEndLine();       mothurOutEndLine(); cout.flush();
+               //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "generateDB");
+               m->errorOut(e, "BlastDB", "generateDB");
                exit(1);
        }
 }