added multiple processors option for Windows users to align.seqs, dist.seqs, summary...

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index af157203630c68bc8e8cfd0e09a2bcf846e4d33c..bc646dfaa498750448ba741f5649450a185415dd 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -14,19 +14,23 @@
 
 /**************************************************************************************************/
 
-BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b) : Database(), 
+BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b, int tid) : Database(), 
 gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
        try {
                count = 0;
                path = b;
+               threadID = tid;
 
                int randNumber = rand();
                //int randNumber = 12345;
                string pid = "";
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               pid +=  toString(getpid());
+               pid += getpid();        
+#else
+               pid += toString(threadID);      
 #endif
                
+               
                dbFileName = tag + pid + toString(randNumber) + ".template.unaligned.fasta";
                queryFileName = tag + pid + toString(randNumber) + ".candidate.unaligned.fasta";
                blastFileName = tag + pid + toString(randNumber) + ".blast";
@@ -96,11 +100,12 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 }
 /**************************************************************************************************/
 
-BlastDB::BlastDB(string b) : Database() {
+BlastDB::BlastDB(string b, int tid) : Database() {
        try {
                count = 0;
                
                path = b;
+               threadID = tid;
                
                //make sure blast exists in the write place
                if (path == "") {
@@ -119,7 +124,9 @@ BlastDB::BlastDB(string b) : Database() {
                int randNumber = rand();
                string pid = "";
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               pid +=  toString(getpid());
+               pid += getpid();        
+#else
+               pid += toString(threadID);      
 #endif
                
                dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
@@ -206,10 +213,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                
                ofstream queryFile;
                int randNumber = rand();
-               string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               pid +=  toString(getpid());
-#endif
+               string pid = scrubName(seq->getName());
                
                m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
                queryFile << '>' << seq->getName() << endl;
@@ -273,10 +277,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                
                ofstream queryFile;
                int randNumber = rand();
-               string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-               pid += toString(getpid());
-#endif
+               string pid = scrubName(seq->getName());
                
                m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
                queryFile << '>' << seq->getName() << endl;
@@ -382,6 +383,24 @@ void BlastDB::generateDB() {
        }
 }
 /**************************************************************************************************/
+string BlastDB::scrubName(string seqName) {
+       try {
+               
+               string cleanName = "";
+               
+               for (int i = 0; i < seqName.length(); i++) {
+                       if (isalnum(seqName[i])) { cleanName += seqName[i]; }
+                       else { cleanName += "_";  }
+               }
+               
+               return cleanName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "BlastDB", "scrubName");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
 
 /**************************************************************************************************/