added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index c7003f4489232b347d6927d718c5d7497d050ae8..48b09fba5fad87eca53d089ec369ee0149b19ade 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -35,9 +35,9 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                formatdbCommand = path + "blast/bin/formatdb";  //      format the database, -o option gives us the ability
 #else
-               formatdbCommand = path + "blast\\bin\\formatdb";
+               formatdbCommand = path + "blast\\bin\\formatdb.exe";
                //wrap entire string in ""
-               formatdbCommand = "\"" + formatdbCommand + "\"";
+               //formatdbCommand = "\"" + formatdbCommand + "\"";
 #endif
                
                //test to make sure formatdb exists
@@ -50,9 +50,9 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                blastCommand = path + "blast/bin/blastall";     //      format the database, -o option gives us the ability
 #else
-               blastCommand = path + "blast\\bin\\blastall";
+               blastCommand = path + "blast\\bin\\blastall.exe";
                //wrap entire string in ""
-               blastCommand = "\"" + blastCommand + "\"";
+               //blastCommand = "\"" + blastCommand + "\"";
 #endif
                
                //test to make sure formatdb exists
@@ -66,9 +66,9 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                megablastCommand = path + "blast/bin/megablast";        //      format the database, -o option gives us the ability
 #else
-               megablastCommand = path + "blast\\bin\\megablast";
+               megablastCommand = path + "blast\\bin\\megablast.exe";
                //wrap entire string in ""
-               megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+               //megablastCommand = "\"" + megablastCommand + "\"";
 #endif
                
                //test to make sure formatdb exists
@@ -105,9 +105,9 @@ BlastDB::BlastDB() : Database() {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                formatdbCommand = path + "blast/bin/formatdb";  //      format the database, -o option gives us the ability
 #else
-               formatdbCommand = path + "blast\\bin\\formatdb";
+               formatdbCommand = path + "blast\\bin\\formatdb.exe";
                //wrap entire string in ""
-               formatdbCommand = "\"" + formatdbCommand + "\"";
+               //formatdbCommand = "\"" + formatdbCommand + "\"";
 #endif
                
                //test to make sure formatdb exists
@@ -120,9 +120,9 @@ BlastDB::BlastDB() : Database() {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                blastCommand = path + "blast/bin/blastall";     //      format the database, -o option gives us the ability
 #else
-               blastCommand = path + "blast\\bin\\blastall";
+               blastCommand = path + "blast\\bin\\blastall.exe";
                //wrap entire string in ""
-               blastCommand = "\"" + blastCommand + "\"";
+               //blastCommand = "\"" + blastCommand + "\"";
 #endif
                
                //test to make sure formatdb exists
@@ -136,9 +136,9 @@ BlastDB::BlastDB() : Database() {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                megablastCommand = path + "blast/bin/megablast";        //      format the database, -o option gives us the ability
 #else
-               megablastCommand = path + "blast\\bin\\megablast";
+               megablastCommand = path + "blast\\bin\\megablast.exe";
                //wrap entire string in ""
-               megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+               //megablastCommand = "\"" + megablastCommand + "\"";
 #endif
                
                //test to make sure formatdb exists