BLAST

gromdimon · Nov 17, 2024 · d75bef9 · d75bef9
1 parent c9dc2d8
commit d75bef9
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diff --git a/algo/BLAST/BLAST_Neighborhood.hpp b/algo/BLAST/BLAST_Neighborhood.hpp
@@ -2,12 +2,10 @@
 
 #include <string>
 #include <vector>
-//#include <omp.h> // not needed here, but in .cpp
 
 
-#include "a4_util.h"
+#include "blst_util.h"
 
-// ... more includes here...
 #include <iostream> // DEBUG
 #include <stdexcept>
 
@@ -36,7 +34,6 @@ struct NHResult
 
 class BLAST_Neighborhood
 {
-  // do NOT change the public interface
   public:
     /**
      Berechnet die BLAST Nachbarschaft fuer eine Query.
@@ -59,8 +56,6 @@ class BLAST_Neighborhood
 
 
   private:
-    // your private member _functions_ go here <> (if needed)
-    // hint: private member _variables_ are probably not required 
     std::vector<char> amino_acids = {'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'};
 
     void generateWords(const std::string& query, int word_size, std::vector<std::string>& output);

diff --git a/algo/BLAST/Makefile b/algo/BLAST/Makefile
@@ -5,13 +5,13 @@ INC =
 CXXFLAGS = -std=c++17 -Wall -pedantic -O2 -D_GLIBCXX_ASSERTIONS -g -fsanitize=address -fopenmp
 # -D_GLIBCXX_DEBUG // bad for openmp performance
 
-%.o: %.cpp a4_util.h BLAST_Neighborhood.hpp
+%.o: %.cpp blst_util.h BLAST_Neighborhood.hpp
 	${CXX} ${CXXFLAGS} -I . -c $*.cpp
 
 
-aufgabe4_main: BLAST_Neighborhood.o aufgabe4_main.o a4_util.o
-	${CXX} ${CXXFLAGS} -I . $^ -o aufgabe4_main
+blst_main: BLAST_Neighborhood.o blst_main.o blst_util.o
+	${CXX} ${CXXFLAGS} -I . $^ -o blst_main
 
-aufgabe4_test: BLAST_Neighborhood.o aufgabe4_test.o a4_util.o
-	${CXX} ${CXXFLAGS} -I . $^ -o aufgabe4_test
-
+blst_test: BLAST_Neighborhood.o blst_test.o blst_util.o
+	${CXX} ${CXXFLAGS} -I . $^ -o blst_test
+
diff --git a/algo/BLAST/README.md b/algo/BLAST/README.md
@@ -0,0 +1,19 @@
+# BLAST
+
+To compile and run the program:
+
+```bash
+make blst_main
+./blst_main <SEQ> <SCORE_MATRIX> <WORD_SIZE> <THRESHOLD> <THREADS>
+```
+
+To test the program:
+
+```bash
+make blst_test
+./blst_test
+```
+
+> [!NOTE]
+> The compilation uses `-fopenmp` to enable parallelization.
+> This is not supported by all compilers, e.g. by Mac's GCC.
diff --git a/algo/BLAST/aufgabe4_main.cpp → algo/BLAST/blst_main.cpp b/algo/BLAST/aufgabe4_main.cpp → algo/BLAST/blst_main.cpp
@@ -9,7 +9,7 @@ int main(int argc, char** argv) {
     int threads;
 
     if (argc != 6) {
-        std::cout << "Usage: ./aufgabe4_main <SEQ> <SCORE_MATRIX> <WORD_SIZE> <THRESHOLD> <THREADS>\n";
+        std::cout << "Usage: ./blst_main <SEQ> <SCORE_MATRIX> <WORD_SIZE> <THRESHOLD> <THREADS>\n";
         return 1;
     }
     query = argv[1];

diff --git a/algo/BLAST/aufgabe4_test.cpp → algo/BLAST/blst_test.cpp b/algo/BLAST/aufgabe4_test.cpp → algo/BLAST/blst_test.cpp
@@ -6,7 +6,7 @@
 #include <omp.h>
 
 #include "BLAST_Neighborhood.hpp"
-#include "a4_util.h"
+#include "blst_util.h"
 
 using namespace std;
 

diff --git a/algo/BLAST/a4_util.cpp → algo/BLAST/blst_util.cpp b/algo/BLAST/a4_util.cpp → algo/BLAST/blst_util.cpp
@@ -1,4 +1,4 @@
-#include "a4_util.h"
+#include "blst_util.h"
 
 IOException::IOException() : std::exception(), message("Failed!"), errorState(8)
 {}
@@ -30,48 +30,48 @@ unsigned IOException::getErrorState() const
 	return errorState;
 }
 
-
-/*
-* @var TranslationTableAminoAcids::CHAR_TO_INT
-* @brief Mapping from residue to index.
-* @signature const unsigned TranslationTableAminoAcids::CHAR_TO_INT[256];
-* @note Defintion of static array must be outside of class. Use the functions toId and toAminoAcid respectively.
-* @see toId();
-* @see toAminoAcid();
-*/
-const unsigned TranslationTableAminoAcids::CHAR_TO_INT[256] =
-  { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 0, 8, 9, 10, 11, 0,
-    // A, B, C, D, E, F, G, H, I, J, K, L,  M,  N, O
-    12, 13, 14, 15, 16, 0, 17, 18, 0, 19, 0, 0, 0, 0, 0, 0,
-    // P,  Q,  R,  S,  T, U,  V,  W, X,  Y, Z
-    0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 0, 8, 9, 10, 11, 0,
-    //   a, b, c, d, e, f, g, h, i, j, k, l,  m, n, o
-    12, 13, 14, 15, 16, 0, 17, 18, 0, 19, 0, 0, 0, 0, 0, 0,
-    // p,  q,  r,  s,  t, u,  v,  w, x,  y, z
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
-
-
-/*
-* @var TranslationTableAminoAcids::INT_TO_CHAR
-* @brief Mapping from index to residue.
-* @signature const char TranslationTableAminoAcids::INT_TO_CHAR[TranslationTableAminoAcids::ALPHABET_SIZE];
-* @note Defintion of static array must be outside of class. Use the functions toId and toAminoAcid respectively.
-* @see toId();
-* @see toAminoAcid();
-*/
-const char TranslationTableAminoAcids::INT_TO_CHAR[TranslationTableAminoAcids::ALPHABET_SIZE] =
-{ 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y' };
+
+/*
+* @var TranslationTableAminoAcids::CHAR_TO_INT
+* @brief Mapping from residue to index.
+* @signature const unsigned TranslationTableAminoAcids::CHAR_TO_INT[256];
+* @note Defintion of static array must be outside of class. Use the functions toId and toAminoAcid respectively.
+* @see toId();
+* @see toAminoAcid();
+*/
+const unsigned TranslationTableAminoAcids::CHAR_TO_INT[256] =
+  { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 0, 8, 9, 10, 11, 0,
+    // A, B, C, D, E, F, G, H, I, J, K, L,  M,  N, O
+    12, 13, 14, 15, 16, 0, 17, 18, 0, 19, 0, 0, 0, 0, 0, 0,
+    // P,  Q,  R,  S,  T, U,  V,  W, X,  Y, Z
+    0, 0, 0, 1, 2, 3, 4, 5, 6, 7, 0, 8, 9, 10, 11, 0,
+    //   a, b, c, d, e, f, g, h, i, j, k, l,  m, n, o
+    12, 13, 14, 15, 16, 0, 17, 18, 0, 19, 0, 0, 0, 0, 0, 0,
+    // p,  q,  r,  s,  t, u,  v,  w, x,  y, z
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+    0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+
+
+/*
+* @var TranslationTableAminoAcids::INT_TO_CHAR
+* @brief Mapping from index to residue.
+* @signature const char TranslationTableAminoAcids::INT_TO_CHAR[TranslationTableAminoAcids::ALPHABET_SIZE];
+* @note Defintion of static array must be outside of class. Use the functions toId and toAminoAcid respectively.
+* @see toId();
+* @see toAminoAcid();
+*/
+const char TranslationTableAminoAcids::INT_TO_CHAR[TranslationTableAminoAcids::ALPHABET_SIZE] =
+{ 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y' };
 
 //==================================================================
 // Member functions.

diff --git a/algo/BLAST/a4_util.h → algo/BLAST/blst_util.h b/algo/BLAST/a4_util.h → algo/BLAST/blst_util.h
diff --git a/algo/README.md b/algo/README.md
@@ -12,6 +12,7 @@ organization. Look at Readme's and comments in the code for more details.
 - [Horspool Algorithm](./horspool)
 - [Suffix Array](./suftab)
 - [Alignment Challenge](./align)
+- [BLAST](./BLAST)
 
 ## Languages
 - Python