changing command name classify.shared to classifyrf.shared

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index bc646dfaa498750448ba741f5649450a185415dd..2eced7e14dc6fa42e0147747fc622bfa088250f7 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -24,7 +24,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
                int randNumber = rand();
                //int randNumber = 12345;
                string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                pid += getpid();        
 #else
                pid += toString(threadID);      
@@ -42,7 +42,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
                        for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
                        path = path.substr(0, (tempPath.find_last_of('m')));
                        
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        path += "blast/bin/";   
 #else
                        path += "blast\\bin\\";
@@ -51,7 +51,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
                
                
                string formatdbCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                formatdbCommand = path + "formatdb";    //      format the database, -o option gives us the ability
 #else
                formatdbCommand = path + "formatdb.exe";
@@ -64,7 +64,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
                if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
                
                string blastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                blastCommand = path + "blastall";       //      format the database, -o option gives us the ability
 #else
                blastCommand = path + "blastall.exe";
@@ -80,7 +80,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
                
                
                string megablastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                megablastCommand = path + "megablast";  //      format the database, -o option gives us the ability
 #else
                megablastCommand = path + "megablast.exe";
@@ -114,7 +114,7 @@ BlastDB::BlastDB(string b, int tid) : Database() {
                        for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
                        path = path.substr(0, (tempPath.find_last_of('m')));
                        
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        path += "blast/bin/";   
 #else
                        path += "blast\\bin\\";
@@ -123,7 +123,7 @@ BlastDB::BlastDB(string b, int tid) : Database() {
                
                int randNumber = rand();
                string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                pid += getpid();        
 #else
                pid += toString(threadID);      
@@ -134,7 +134,7 @@ BlastDB::BlastDB(string b, int tid) : Database() {
                blastFileName = pid + toString(randNumber) + ".blast";
                
                string formatdbCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                formatdbCommand = path + "formatdb";    //      format the database, -o option gives us the ability
 #else
                formatdbCommand = path + "formatdb.exe";
@@ -149,7 +149,7 @@ BlastDB::BlastDB(string b, int tid) : Database() {
                if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " +  formatdbCommand + " file does not exist. mothur requires formatdb.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
                
                string blastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                blastCommand = path + "blastall";       //      format the database, -o option gives us the ability
 #else
                blastCommand = path + "blastall.exe";
@@ -165,7 +165,7 @@ BlastDB::BlastDB(string b, int tid) : Database() {
                
                
                string megablastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                megablastCommand = path + "megablast";  //      format the database, -o option gives us the ability
 #else
                megablastCommand = path + "megablast.exe";
@@ -226,7 +226,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
                
                string blastCommand;
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                
                        blastCommand = path + "blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
                        blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
@@ -289,7 +289,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
 //7000004128189528left 0       100             66      0       0       1       66      61      126     1e-31    131    
                string blastCommand;
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        blastCommand = path + "megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
                        blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
                #else
@@ -363,7 +363,7 @@ void BlastDB::generateDB() {
                        
                string formatdbCommand;
                
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        formatdbCommand = path + "formatdb -p F -o T -i " + dbFileName; //      format the database, -o option gives us the ability
                #else
                        //formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName;   //      format the database, -o option gives us the ability