added checks for ^C to quit command instead of program

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 50a0401b2cb8780765ba56a3ba2c025380c4e212..17db069cdedb8a019d980c32fc4b6e7767fab27b 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -50,7 +50,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
                
-               string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28 -v " + toString(n);
+               string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
                blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
                system(blastCommand.c_str());
                
@@ -72,19 +72,36 @@ 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);
        }
 
 }
 /**************************************************************************************************/
 //assumes you have added all the template sequences using the addSequence function and run generateDB.
-map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
        try{
-               map<int, float> topMatches;
+               vector<int> topMatches;
                
                ofstream queryFile;
                openOutputFile(queryFileName, queryFile);
@@ -96,36 +113,33 @@ map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
                //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
        
-               string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -b " + toString(n) + " -v " + toString(n);
+               string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
                blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
-               openInputFile(blastFileName, m8FileHandle);
+               openInputFile(blastFileName, m8FileHandle, "no error");
        
                string dummy;
                int templateAccession;
                gobble(m8FileHandle);
-//string name = seq->getName();
-//ofstream out;
-//openOutputFileAppend(name, out);     
+               
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
-//out << dummy << '\t' <<  templateAccession   << '\t' << searchScore << endl;
+                       
                        //get rest of junk in line
-                       while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); 
-                       //out << c; 
-                       if (c == 10 || c == 13){        break;  }       } 
+                       while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
                        
                        gobble(m8FileHandle);
-                       topMatches[templateAccession] = searchScore;
+                       topMatches.push_back(templateAccession);
+//cout << templateAccession << endl;
                }
                m8FileHandle.close();
-//out.close();         
+//cout << "\n\n" ;             
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosest");
+               m->errorOut(e, "BlastDB", "findClosest");
                exit(1);
        }
 }
@@ -144,7 +158,7 @@ void BlastDB::addSequence(Sequence seq) {
                count++;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "addSequence");
+               m->errorOut(e, "BlastDB", "addSequence");
                exit(1);
        }
 }
@@ -152,7 +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')));
@@ -160,10 +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);
        }
 }