Wrap codebase in namespace

src/Bifrost.cpp

@@ -2,6 +2,7 @@
 #include "ColoredCDBG.hpp"
 
 using namespace std;
+using namespace Bifrost;
 
 void PrintVersion() {
 

src/BitContainer.cpp

@@ -1,5 +1,9 @@
 #include "BitContainer.hpp"
 
+using namespace Bifrost;
+
+namespace Bifrost {
+
 BitContainer::BitContainer() : setBits(localBitVector) {}
 
 BitContainer::BitContainer(const BitContainer& o) {
@@ -1043,3 +1047,5 @@ const size_t BitContainer::shiftMaskBits = 3;
 
 const uintptr_t BitContainer::flagMask = 0x7;
 const uintptr_t BitContainer::pointerMask = 0xFFFFFFFFFFFFFFF8;
+
+}

src/BitContainer.hpp

@@ -4,6 +4,7 @@
 #include "roaring.hh"
 #include "TinyBitmap.hpp"
 
+namespace Bifrost {
 
 class BitContainer {
 
@@ -200,4 +201,6 @@ class BitContainer {
         uintptr_t setBits;
 };
 
+}
+
 #endif

src/BlockedBloomFilter.cpp

@@ -1,5 +1,9 @@
 #include "BlockedBloomFilter.hpp"
 
+using namespace Bifrost;
+
+namespace Bifrost {
+
 #if defined(__AVX2__)
 
 BlockedBloomFilter::BlockedBloomFilter() : table_(nullptr), blocks_(0), k_(0) {
@@ -1152,3 +1156,5 @@ bool BlockedBloomFilter::insert_unpar(uint64_t kmer_hash, const uint64_t min_has
 }
 
 #endif
+
+}

src/BlockedBloomFilter.hpp

@@ -24,6 +24,8 @@
 #include <x86intrin.h>
 #endif
 
+namespace Bifrost {
+
 class BlockedBloomFilter {
 
     public:
@@ -120,4 +122,6 @@ class BlockedBloomFilter {
         bool insert_unpar(const uint64_t kmer_hash, const uint64_t min_hash);
 };
 
+}
+
 #endif // BFG_BLOCKEDBLOOMFILTER_HPP

src/ColorSet.cpp

@@ -1,5 +1,7 @@
 #include "ColorSet.hpp"
 
+using namespace Bifrost;
+
 UnitigColors::UnitigColors() : setBits(localBitVector) {}
 
 UnitigColors::UnitigColors(const UnitigColors& o) {

src/ColorSet.hpp

@@ -6,6 +6,8 @@
 #include "CompactedDBG.hpp"
 #include "TinyBitmap.hpp"
 
+namespace Bifrost {
+
 /** @file src/ColorSet.hpp
 * Interface for UnitigColors, the unitig container of k-mer color sets used in ColoredCDBG.
 * Code snippets using this interface are provided in snippets/test.cpp.
@@ -473,4 +475,6 @@ struct UnitigColorsHash {
     }
 };
 
+}
+
 #endif

src/ColoredCDBG.hpp

@@ -11,6 +11,8 @@
 
 #include "getRSS.h"
 
+namespace Bifrost {
+
 /** @file src/ColoredCDBG.hpp
 * Interface for the Colored and Compacted de Bruijn graph API.
 * Code snippets using this interface are provided in test/snippets.hpp.
@@ -356,6 +358,8 @@ class ColoredCDBG : public CompactedDBG<DataAccessor<Unitig_data_t>, DataStorage
         bool invalid;
 };
 
+}
+
 #include "ColoredCDBG.tcc"
 
 #endif