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-rw-r--r--CMakeLists.txt1
-rw-r--r--example.cc8
-rw-r--r--src/istream/buffer.cc2
-rw-r--r--src/util/query.cc57
-rw-r--r--src/util/query.h12
5 files changed, 77 insertions, 3 deletions
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f67bc42..45d4b67 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,6 +14,7 @@ add_library(
DictzipQuery
SHARED
src/util/base64.cc
+ src/util/query.cc
src/istream/stream.cc
src/istream/buffer.cc
)
diff --git a/example.cc b/example.cc
index f2a091d..f1fbc8c 100644
--- a/example.cc
+++ b/example.cc
@@ -1,5 +1,6 @@
#include "istream/stream.h"
#include "util/base64.h"
+#include "util/query.h"
#include <string>
#include <iostream>
@@ -17,10 +18,13 @@ std::string get(const std::string& path, std::size_t offset, std::size_t length)
}
int main() {
+ // Get location of _Accession_
+ const std::string line = dictzip::get_line_starting_with("gcide.index", "Accession");
+
// Decode location of _Accession_
// `gcide.index[1089]: "Accession 8Aw Wt"
- const std::size_t offset = dictzip::base64_decode("8Aw");
- const std::size_t length = dictzip::base64_decode("Wt");
+ const std::size_t offset = dictzip::base64_decode(dictzip::get_encoded_offset(line));
+ const std::size_t length = dictzip::base64_decode(dictzip::get_encoded_length(line));
// Print the GCIDE definition of _Accession_
std::cout << get("gcide.dict.dz", offset, length) << std::endl;
diff --git a/src/istream/buffer.cc b/src/istream/buffer.cc
index 26697f4..2a195e0 100644
--- a/src/istream/buffer.cc
+++ b/src/istream/buffer.cc
@@ -20,7 +20,7 @@ void IstreamBuf::readChunk(long n) {
std::fseek(dictzip_file_, data_offset_ + chunkN.offset, SEEK_SET);
- if ( fread(zBuf, 1, chunkN.size, dictzip_file_) != chunkN.size ) {
+ if ( std::fread(zBuf, 1, chunkN.size, dictzip_file_) != chunkN.size ) {
throw std::runtime_error("Could not read dictzip chunk.");
}
diff --git a/src/util/query.cc b/src/util/query.cc
new file mode 100644
index 0000000..a6fdcd3
--- /dev/null
+++ b/src/util/query.cc
@@ -0,0 +1,57 @@
+#include "query.h"
+
+#include <fcntl.h>
+
+#include <cstdio>
+#include <cstring>
+
+#include <stdexcept>
+
+namespace dictzip {
+
+std::string get_line_starting_with(
+ const std::string& path, const std::string& substring) {
+ static const auto BUFFER_SIZE = 16*1024;
+
+ FILE* file = std::fopen(path.c_str(), "r");
+
+ posix_fadvise(fileno(file), 0, 0, 1); // FDADVICE_SEQUENTIAL
+
+ char buffer[BUFFER_SIZE + 1];
+ char* start_of_match = nullptr;
+
+ while( std::size_t bytes_read = std::fread(buffer, sizeof(char), BUFFER_SIZE, file) ) {
+ if ( bytes_read ) {
+ for ( char* p = buffer;
+ (p = static_cast<char*>(std::memchr(p, '\n', (buffer + bytes_read) - p)));
+ ++p ) {
+ if ( start_of_match == nullptr ) {
+ if ( std::strncmp(substring.c_str(), p+1, substring.size()) == 0 ) {
+ start_of_match = p+1;
+ }
+ } else {
+ return std::string(start_of_match, p-start_of_match);
+ }
+ }
+ } else {
+ break;
+ }
+ }
+
+ throw std::runtime_error("No match found");
+}
+
+std::string get_encoded_offset(const std::string& line) {
+ const std::size_t start = line.find_first_of('\t');
+ const std::size_t end = line.find_last_of('\t');
+
+ return line.substr(start + 1, end - (start + 1));
+}
+
+std::string get_encoded_length(const std::string& line) {
+ const std::size_t start = line.find_last_of('\t');
+
+ return line.substr(start + 1);
+}
+
+}
diff --git a/src/util/query.h b/src/util/query.h
new file mode 100644
index 0000000..3a25206
--- /dev/null
+++ b/src/util/query.h
@@ -0,0 +1,12 @@
+#pragma once
+
+#include <string>
+
+namespace dictzip {
+
+std::string get_line_starting_with(const std::string& path, const std::string& substring);
+
+std::string get_encoded_offset(const std::string& line);
+std::string get_encoded_length(const std::string& line);
+
+}