Updated API

bench/include/file_benchmark.h

@@ -265,42 +265,41 @@ class FileBenchmark : public Benchmark {
   void BenchmarkCore() {
     fprintf(stderr, "Benchmarking Core Functions...\n\n");
     fprintf(stderr, "Benchmarking lookupNPA...\n");
-    BenchmarkLookupFunction(&SuccinctFile::LookupNPA,
-                            succinct_file_->Name() + ".npa");
+    BenchmarkLookupFunction(&SuccinctFile::LookupNPA, "result.npa");
     fprintf(stderr, "Done!\n\n");
     fprintf(stderr, "Benchmarking lookupSA...\n");
     BenchmarkLookupFunction(&SuccinctFile::LookupSA,
-                            succinct_file_->Name() + ".sa");
+                            "result.sa");
     fprintf(stderr, "Done!\n\n");
     fprintf(stderr, "Benchmarking lookupISA...\n");
     BenchmarkLookupFunction(&SuccinctFile::LookupISA,
-                            succinct_file_->Name() + ".isa");
+                            "result.isa");
     fprintf(stderr, "Done!\n\n");
   }
 
   void BenchmarkFile() {
     fprintf(stderr, "Benchmarking File Functions...\n\n");
     fprintf(stderr, "Benchmarking extract ticks...\n");
-    BenchmarkExtractTicks(succinct_file_->Name() + ".extract.ticks");
+    BenchmarkExtractTicks("result.extract.ticks");
     fprintf(stderr, "Done!\n\n");
     fprintf(stderr, "Benchmarking extract...\n");
-    BenchmarkExtract(succinct_file_->Name() + ".extract");
+    BenchmarkExtract("result.extract");
     fprintf(stderr, "Done!\n\n");
     if (queries_.size() == 0) {
       fprintf(stderr, "[WARNING]: No queries have been loaded.\n");
       fprintf(stderr, "[WARNING]: Skipping count and search benchmarks.\n");
     } else {
       fprintf(stderr, "Benchmarking count ticks...\n");
-      BenchmarkCountTicks(succinct_file_->Name() + ".count.ticks");
+      BenchmarkCountTicks("result.count.ticks");
       fprintf(stderr, "Done!\n\n");
       fprintf(stderr, "Benchmarking search ticks...\n");
-      BenchmarkSearchTicks(succinct_file_->Name() + ".search.ticks");
+      BenchmarkSearchTicks("result.search.ticks");
       fprintf(stderr, "Done!\n\n");
       fprintf(stderr, "Benchmarking count...\n");
-      BenchmarkCount(succinct_file_->Name() + ".count");
+      BenchmarkCount("result.count");
       fprintf(stderr, "Done!\n\n");
       fprintf(stderr, "Benchmarking search...\n");
-      BenchmarkSearch(succinct_file_->Name() + ".search");
+      BenchmarkSearch("result.search");
       fprintf(stderr, "Done!\n\n");
     }
   }

bench/src/file_benchmark.cc

@@ -103,9 +103,7 @@ int main(int argc, char **argv) {
                                         npa_scheme);
 
     // Serialize and save to file
-    std::ofstream s_out(inputpath + ".succinct");
-    fd->Serialize();
-    s_out.close();
+    fd->Serialize(inputpath + ".succinct");
 
     // Create benchmark
     file_bench = new FileBenchmark(fd, querypath);

bench/src/regex_benchmark.cc

@@ -111,9 +111,7 @@ int main(int argc, char **argv) {
     s_file = new SuccinctFile(filename);
 
     std::cout << "Serializing Succinct data structures...\n";
-    std::ofstream s_out(filename + ".succinct");
-    s_file->Serialize();
-    s_out.close();
+    s_file->Serialize(filename + ".succinct");
   } else {
     std::cout << "De-serializing Succinct data structures...\n";
     s_file = new SuccinctFile(filename, SuccinctMode::LOAD_IN_MEMORY);

bench/src/shard_benchmark.cc

@@ -152,7 +152,7 @@ int main(int argc, char **argv) {
                            sa_sampling_rate, isa_sampling_rate,
                            npa_sampling_rate, scheme, scheme, npa_scheme);
     // Serialize
-    fd->Serialize();
+    fd->Serialize(inputpath + ".succinct");
   } else if (mode == 1) {
     fprintf(stderr, "SuccinctMode = Load in memory.\n");
     fd = new SuccinctShard(0, inputpath, SuccinctMode::LOAD_IN_MEMORY,

core/include/succinct_core.h

@@ -37,7 +37,7 @@ class SuccinctCore : public SuccinctBase {
   typedef std::pair<int64_t, int64_t> Range;
 
   /* Constructors */
-  SuccinctCore(const char *filename, SuccinctMode s_mode =
+  SuccinctCore(const std::string& filename, SuccinctMode s_mode =
                    SuccinctMode::CONSTRUCT_IN_MEMORY,
                uint32_t sa_sampling_rate = 32, uint32_t isa_sampling_rate = 32,
                uint32_t npa_sampling_rate = 128, uint32_t context_len = 3,
@@ -49,6 +49,15 @@ class SuccinctCore : public SuccinctBase {
                    NPA::NPAEncodingScheme::ELIAS_GAMMA_ENCODED,
                uint32_t sampling_range = 1024);
 
+  SuccinctCore() {
+    this->alphabet_ = NULL;
+    this->sa_ = NULL;
+    this->isa_ = NULL;
+    this->npa_ = NULL;
+    this->alphabet_size_ = 0;
+    this->input_size_ = 0;
+  }
+
   virtual ~SuccinctCore() {
   }
 
@@ -69,13 +78,13 @@ class SuccinctCore : public SuccinctBase {
   char CharAt(uint64_t i);
 
   // Serialize succinct data structures
-  virtual size_t Serialize();
+  virtual size_t Serialize(const std::string& filename);
 
   // Deserialize succinct data structures
-  virtual size_t Deserialize();
+  virtual size_t Deserialize(const std::string& filename);
 
   // Memory map succinct data structures
-  virtual size_t MemoryMap();
+  virtual size_t MemoryMap(const std::string& filename);
 
   // Get size of original input
   uint64_t GetOriginalSize();
@@ -108,9 +117,31 @@ class SuccinctCore : public SuccinctBase {
 
  protected:
 
+  // Allocates high level containers
+  void Allocate(uint32_t sa_sampling_rate, uint32_t isa_sampling_rate,
+                uint32_t npa_sampling_rate, uint32_t context_len,
+                SamplingScheme sa_sampling_scheme,
+                SamplingScheme isa_sampling_scheme,
+                NPA::NPAEncodingScheme npa_encoding_scheme,
+                uint32_t sampling_range);
+
+  // Constructs the core data structures
+  void Construct(const std::string& filename, uint32_t sa_sampling_rate,
+                 uint32_t isa_sampling_rate, uint32_t npa_sampling_rate,
+                 uint32_t context_len, SamplingScheme sa_sampling_scheme,
+                 SamplingScheme isa_sampling_scheme,
+                 NPA::NPAEncodingScheme npa_encoding_scheme,
+                 uint32_t sampling_range);
+
+  // Constructs the core data structures
+  void Construct(uint8_t* input, size_t input_size, uint32_t sa_sampling_rate,
+                 uint32_t isa_sampling_rate, uint32_t npa_sampling_rate,
+                 uint32_t context_len, SamplingScheme sa_sampling_scheme,
+                 SamplingScheme isa_sampling_scheme,
+                 NPA::NPAEncodingScheme npa_encoding_scheme,
+                 uint32_t sampling_range);
+
   /* Metadata */
-  std::string filename_;               // Name of input file
-  std::string succinct_path_;          // Name of succinct path
   uint64_t input_size_;                // Size of input
 
   /* Primary data structures */
@@ -124,13 +155,6 @@ class SuccinctCore : public SuccinctBase {
   uint32_t alphabet_size_;             // Size of the input alphabet_
 
  private:
-  // Constructs the core data structures
-  void Construct(const char* filename, uint32_t sa_sampling_rate,
-                 uint32_t isa_sampling_rate, uint32_t npa_sampling_rate,
-                 uint32_t context_len, SamplingScheme sa_sampling_scheme,
-                 SamplingScheme isa_sampling_scheme,
-                 NPA::NPAEncodingScheme npa_encoding_scheme,
-                 uint32_t sampling_range);
 
   uint64_t ComputeContextValue(char* data, uint32_t i, uint32_t context_len) {
     uint64_t val = 0;

core/include/succinct_file.h

@@ -24,11 +24,6 @@ class SuccinctFile : public SuccinctCore {
                    NPA::NPAEncodingScheme::ELIAS_GAMMA_ENCODED,
                uint32_t context_len = 3, uint32_t sampling_range = 1024);
 
-  /*
-   * Get the name of the SuccinctFile
-   */
-  std::string Name();
-
   /*
    * Random access into the Succinct file with the specified offset
    * and length
@@ -56,9 +51,6 @@ class SuccinctFile : public SuccinctCore {
   std::pair<int64_t, int64_t> GetRange(const char *str, uint64_t len);
   uint64_t ComputeContextValue(const char *str, uint64_t pos);
 
-  std::string input_filename_;
-  std::string succinct_filename_;
-
 };
 
 #endif

core/include/succinct_shard.h

@@ -36,6 +36,12 @@ class SuccinctShard : public SuccinctCore {
                     NPA::NPAEncodingScheme::ELIAS_GAMMA_ENCODED,
                 uint32_t context_len = 3, uint32_t sampling_range = 1024);
 
+  SuccinctShard()
+      : SuccinctCore() {
+    id_ = 0;
+    invalid_offsets_ = NULL;
+  }
+
   virtual ~SuccinctShard() {
   }
 
@@ -45,11 +51,9 @@ class SuccinctShard : public SuccinctCore {
 
   uint32_t GetNPASamplingRate();
 
-  std::string Name();
-
   size_t GetNumKeys();
 
-  void Get(std::string& result, int64_t key);
+  virtual void Get(std::string& result, int64_t key);
 
   void Access(std::string& result, int64_t key, int32_t offset, int32_t len);
 
@@ -69,13 +73,13 @@ class SuccinctShard : public SuccinctCore {
   void RegexCount(std::vector<size_t>& result, const std::string& str);
 
   // Serialize succinct data structures
-  virtual size_t Serialize();
+  virtual size_t Serialize(const std::string& path);
 
   // Deserialize succinct data structures
-  virtual size_t Deserialize();
+  virtual size_t Deserialize(const std::string& path);
 
   // Memory map succinct data structures
-  virtual size_t MemoryMap();
+  virtual size_t MemoryMap(const std::string& path);
 
   // Get succinct shard size
   virtual size_t StorageSize();