pat's changes to seq.error command

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 760824dbb23f9b2a9d680ace769ccc1c6ffab96c..979d507c23d61b4537d62a1a4736721624616fb2 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -29,23 +29,38 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 /**************************************************************************************************/
 
 BlastDB::BlastDB() : Database() {
-       
-       globaldata = GlobalData::getInstance();
-       count = 0;
-
-       int randNumber = rand();
-       dbFileName = toString(randNumber) + ".template.unaligned.fasta";
-       queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
-       blastFileName = toString(randNumber) + ".blast";
+       try {
+               globaldata = GlobalData::getInstance();
+               count = 0;
 
+               int randNumber = rand();
+               dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+               queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+               blastFileName = toString(randNumber) + ".blast";
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BlastDB", "BlastDB");
+               exit(1);
+       }
 }
 
 /**************************************************************************************************/
 
 BlastDB::~BlastDB(){
-       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
+       try{
+               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((dbFileName+".nsq").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nsi").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nsd").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nin").c_str());                                    //      let's clean stuff up and remove the temp files
+               remove((dbFileName+".nhr").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
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BlastDB", "~BlastDB");
+               exit(1);
+       }
 }
 /**************************************************************************************************/
 //assumes you have added all the template sequences using the addSequence function and run generateDB.
@@ -54,7 +69,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               openOutputFile((queryFileName+seq->getName()), queryFile);
+               m->openOutputFile((queryFileName+seq->getName()), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -69,11 +84,11 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
-               openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+               m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
                
                string dummy;
                int templateAccession;
-               gobble(m8FileHandle);
+               m->gobble(m8FileHandle);
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
@@ -81,7 +96,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                        //get rest of junk in line
                        while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
                        
-                       gobble(m8FileHandle);
+                       m->gobble(m8FileHandle);
                        topMatches.push_back(templateAccession);
                }
                m8FileHandle.close();
@@ -103,7 +118,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               openOutputFile((queryFileName+seq->getName()), queryFile);
+               m->openOutputFile((queryFileName+seq->getName()), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -117,11 +132,11 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                system(blastCommand.c_str());
 
                ifstream m8FileHandle;
-               openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+               m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
        
                string dummy;
                int templateAccession;
-               gobble(m8FileHandle);
+               m->gobble(m8FileHandle);
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
@@ -129,7 +144,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                        //get rest of junk in line
                        while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
                        
-                       gobble(m8FileHandle);
+                       m->gobble(m8FileHandle);
                        topMatches.push_back(templateAccession);
 //cout << templateAccession << endl;
                }
@@ -149,7 +164,7 @@ void BlastDB::addSequence(Sequence seq) {
        try {
        
                ofstream unalignedFastaFile;
-               openOutputFileAppend(dbFileName, unalignedFastaFile);                           
+               m->openOutputFileAppend(dbFileName, unalignedFastaFile);                                
        
                //      generating a fasta file with unaligned template
                unalignedFastaFile << '>' << count << endl;                                     //      sequences, which will be input to formatdb