Fixed namespace.

bbuchfink · Jun 7, 2020 · b357cd9 · b357cd9
1 parent e7bb7e9
commit b357cd9
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Showing 8 changed files with 39 additions and 85 deletions.
diff --git a/src/basic/basic.cpp b/src/basic/basic.cpp
@@ -28,7 +28,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "sequence.h"
 #include "masking.h"
 
-const char* Const::version_string = "0.9.33";
+const char* Const::version_string = "0.9.34";
 const char* Const::program_name = "diamond";
 const char* Const::id_delimiters = " \a\b\f\n\r\t\v\1";
 
@@ -254,71 +254,7 @@ vector<vector<string>> shape_codes = {
 "1110000001000001011",
 "1100100000100001011",
 "1100100000001000111" // 13 64x7
-},
-	{ "1111111",
-"11110111",
-"11101111",
-"11110111",
-"110111011",
-"111011011",
-"110110111",
-"111001111",
-"1110100111",
-"1110101011",
-"1101010111",
-"11100011011",
-"11100100111",
-"11101001011",
-"11010011011",
-"11100101011",
-"11011000111",
-"110010100111",
-"110110001101",
-"110100010111",
-"111000101011",
-"111001001011",
-"110011001011",
-"110101000111",
-"1101010000111",
-"1101010010011",
-"1100101000111",
-"1101001010011",
-"1110000101011",
-"11100000101011",
-"11010100010011",
-"11100100001011",
-"11001010001011",
-"11010010010011",
-"11010001001011",
-"11001001000111",
-"110100001010011",
-"110010010010101",
-"101010000100111",
-"101010001010011",
-"110100010001011",
-"110001001001011",
-"110010000101011",
-"110100100010011",
-"110010001000111",
-"111000100001011",
-"1101000010001011",
-"1100100010010101",
-"1100010100001011",
-"1101000100010011",
-"1010100100100011",
-"11100010000100011",
-"11000100010001011",
-"11001010000000111",
-"11100001000010101",
-"11010010000010101",
-"11010000010000111",
-"11001000001001011",
-"11010000001010011",
-"10101001000001011",
-"11001000010010011",
-"11010001000001011",
-"11100001000100011",
-"11010000100001011" } // 14 64x7
+}
 
 };
 

diff --git a/src/basic/const.h b/src/basic/const.h
@@ -1,6 +1,10 @@
 /****
 DIAMOND protein aligner
-Copyright (C) 2013-2017 Benjamin Buchfink <[email protected]>
+Copyright (C) 2013-2020 Max Planck Society for the Advancement of Science e.V.
+                        Benjamin Buchfink
+                        Eberhard Karls Universitaet Tuebingen
+						
+Code developed by Benjamin Buchfink <[email protected]>
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -16,14 +20,12 @@ You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ****/
 
-#ifndef CONST_H_
-#define CONST_H_
-
+#pragma once
 struct Const
 {
 
 	enum {
-		build_version = 134,
+		build_version = 135,
 		seedp_bits = 10,
 		seedp = 1<<seedp_bits,
 		max_seed_weight = 32,
@@ -41,5 +43,3 @@ static constexpr int MAX_CONTEXT = 6;
 // #define FREQUENCY_MASKING
 // #define ST_JOIN
 // #define NO_COLLISION_FILTER
-
-#endif /* CONST_H_ */
diff --git a/src/dp/swipe/banded_swipe.cpp b/src/dp/swipe/banded_swipe.cpp
@@ -369,7 +369,7 @@ struct CBSBuffer<_sv, const int8_t*> {
 	_sv operator()(int i) const {
 		return data[i];
 	}
-	vector<_sv, AlignmentAllocator<_sv, 32>> data;
+	vector<_sv, Util::Memory::AlignmentAllocator<_sv, 32>> data;
 };
 
 template<typename _sv, typename _traceback, typename _cbs>

diff --git a/src/run/workflow.h b/src/run/workflow.h
@@ -49,5 +49,3 @@ void run(const Options &options);
 
 }
 }
-
-#endif
diff --git a/src/search/stage1.cpp b/src/search/stage1.cpp
@@ -33,7 +33,7 @@ namespace DISPATCH_ARCH {
 const unsigned tile_size[] = { 1024, 128 };
 
 constexpr ptrdiff_t INNER_LOOP_QUERIES = 6;
-typedef vector<Finger_print, AlignmentAllocator<Finger_print, 16>> Container;
+typedef vector<Finger_print, Util::Memory::AlignmentAllocator<Finger_print, 16>> Container;
 typedef Container::const_iterator Ptr;
 
 struct Range_ref

diff --git a/src/test/test_cases.cpp b/src/test/test_cases.cpp
@@ -46,7 +46,7 @@ const uint64_t ref_hashes[] = {
 0xa2ea51fd070b9485,
 0x7c90bb1c62c71cfb,
 0xc40f9bffc00c4f97,
-0x494651aafd055246,
+0xda437ed1f7ddb589,
 0xdf32d46bc18e400a,
 };
 

diff --git a/src/util/data_structures/mem_buffer.h b/src/util/data_structures/mem_buffer.h
@@ -33,20 +33,20 @@ struct MemBuffer {
 	{}
 
 	MemBuffer(size_t n):
-		data_((_t*)aligned_malloc(n * sizeof(_t), ALIGN)),
+		data_((_t*)Util::Memory::aligned_malloc(n * sizeof(_t), ALIGN)),
 		size_(n),
 		alloc_size_(n)
 	{
 	}
 
 	~MemBuffer() {
-		aligned_free(data_);
+		Util::Memory::aligned_free(data_);
 	}
 
 	void resize(size_t n) {
 		if (alloc_size_ < n) {
-			aligned_free(data_);
-			data_ = (_t*)aligned_malloc(n * sizeof(_t), ALIGN);
+			Util::Memory::aligned_free(data_);
+			data_ = (_t*)Util::Memory::aligned_malloc(n * sizeof(_t), ALIGN);
 			alloc_size_ = n;
 		}
 		size_ = n;

diff --git a/src/util/memory/alignment.h b/src/util/memory/alignment.h
@@ -1,10 +1,30 @@
-#ifndef ALIGNMENT_H_
-#define ALIGNMENT_H_
+/****
+DIAMOND protein aligner
+Copyright (C) 2020 Max Planck Society for the Advancement of Science e.V.
 
+Code developed by Benjamin Buchfink <[email protected]>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+****/
+
+#pragma once
 #include <stdlib.h>
 #include <cstddef>
 #include <exception>
 
+namespace Util { namespace Memory {
+
 static inline void* aligned_malloc(size_t n, size_t align) {
 #ifdef WIN32
     void* p = _aligned_malloc(n, align);
@@ -93,4 +113,4 @@ class AlignmentAllocator {
     }
 };
 
-#endif
+}}