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test_critbit_tree.cpp
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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "test_critbit_tree.h"
void test_critbit_tree::test_01(){
char str[] = "mississipi";
uint64_t sa[] = {0, 1, 2, 3};
critbit_tree cbt;
cbt.set_text((uint8_t*)str, 10);
for(int i = 0; i < 4; i++)
cbt.insert_suffix(sa[i]); /* insert a suffix in critbit tree */
fprintf(stdout, "g = %lu\n", cbt.m_g);
fprintf(stdout, "%lu.\n", cbt.contains((uint8_t*)str, 10));
fprintf(stdout, "%lu.\n", cbt.contains((uint8_t*)&(str[1]),9));
fprintf(stdout, "%lu.\n", cbt.contains((uint8_t*)"ssis", 4));
fprintf(stdout, "%lu.\n", cbt.contains((uint8_t*)"sissipi", 7));
fprintf(stdout, "%lu.\n", cbt.contains((uint8_t*)"issipi", 6));
uint8_t sym1 = 'a'; /* 97 : 01100001 */
uint8_t sym2 = 't'; /* 116 : 01110100 */
uint8_t sym3 = 'z'; /* 122 : 01111010 */
uint8_t sym4 = ','; /* 44 : 00101100 */
uint8_t sym5 = 212; /* 212 : 11010100 */
uint8_t sym6 = 'u'; /* 117 : 01110101 */
uint64_t critbit_bit_pos12 = 3; /*从左向右数(begin with 0)，找到首个不同的地方 */
uint64_t critbit_bit_pos13 = 3;
uint64_t critbit_bit_pos14 = 1;
uint64_t critbit_bit_pos23 = 4;
uint64_t critbit_bit_pos24 = 1;
uint64_t critbit_bit_pos34 = 1;
uint64_t critbit_bit_pos45 = 0;
uint64_t critbit_bit_pos26 = 7;
/* 因为critbit_tree是string-B-tree的关键性组成部分，所以需要保证critbit_tree的正确性 */
fprintf(stdout, "---------------------------------------------------------\n");
fprintf(stdout, "%d.\n", cbt.get_critbit_pos(sym1, sym2) == critbit_bit_pos12);
fprintf(stdout, "%d.\n", cbt.get_critbit_pos(sym1, sym3) == critbit_bit_pos13);
fprintf(stdout, "%d.\n", cbt.get_critbit_pos(sym1, sym4) == critbit_bit_pos14);
fprintf(stdout, "%d.\n", cbt.get_critbit_pos(sym2, sym3) == critbit_bit_pos23);
fprintf(stdout, "%d.\n", cbt.get_critbit_pos(sym2, sym4) == critbit_bit_pos24);
fprintf(stdout, "---------------------------------------------------------\n");
}
void test_critbit_tree::test_02(){
char str[] = "mississipi"; // length = 10
uint64_t sa[] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
critbit_tree cbt;
cbt.set_text((uint8_t*)str, 10);
for(int i = 0; i < 10; i++)
cbt.insert_suffix(sa[i]);
/* test critbit_tree's insert and delete operation */
/* ------test delete_suffix------ */
fprintf(stdout, "g = %lu\n", cbt.m_g);
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issis", 5));
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issi", 4));
cbt.delete_suffix(1); // delete suffix T[1..n]
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issis", 5)); /* doesn't exist*/
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issi", 4)); /* still exist */
cbt.insert_suffix(1);
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issis", 5)); /* exist! */
}
void test_critbit_tree::test_03(){
char str[] = "mississipi";
uint64_t sa[] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
critbit_tree cbt;
cbt.set_text((uint8_t*)str, 10);
// cbt.create_from_suffixes(sa, 4);
for(int i = 0; i < 10; i++)
cbt.insert_suffix(sa[i]);
/*--------------- test collecting all the suffix ------------------------*/
fprintf(stdout, "g = %lu\n", cbt.m_g);
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issi", 4));
uint64_t* results;
uint64_t count;
uint8_t* P = (uint8_t*)"issi";
uint64_t m = 4;
count = cbt.suffixes(P, m, &results);
fprintf(stdout, "'%s' has %lu suffixes.\n", P, count);
for(uint64_t i = 0; i < count; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
/*---------------------------------------------------------------------------*/
P = (uint8_t*)"s";
m = 1;
fprintf(stdout, "-----------------------------------------------\n");
count = cbt.suffixes(P, m, &results);
fprintf(stdout, "'%s' has %lu suffixes.\n", P, count);
for(uint64_t i = 0; i < count; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
/*-----------------------------------------------------------------*/
P = (uint8_t*)"i";
m = 1;
fprintf(stdout,"---------------------------------------------\n");
count = cbt.suffixes(P, m, &results);
fprintf(stdout, "'%s' has %lu suffixes.\n", P, count);
for(uint64_t i = 0; i < count; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
/*****************************************************************/
P = (uint8_t*)"$";
m = 1;
fprintf(stdout,"---------------------------------------------\n");
count = cbt.suffixes(P, m, &results);
fprintf(stdout, "'%s' has %lu suffixes.\n", P, count);
for(uint64_t i = 0; i < count; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
/********************************************************************/
P = (uint8_t*)"mississipi$";
m = 11;
fprintf(stdout,"---------------------------------------------\n");
count = cbt.suffixes(P, m, &results);
fprintf(stdout, "'%s' has %lu suffixes.\n", P, count);
for(uint64_t i = 0; i < count; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
/********************************************************************/
P = (uint8_t*)"";
m = 0;
fprintf(stdout,"---------------------------------------------\n");
count = cbt.suffixes(P, m, &results);
fprintf(stdout, "'%s' has %lu suffixes.\n", P, count);
for(uint64_t i = 0; i < count; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
/****** It looks right! Maybe need more test! ******************/
}
void test_critbit_tree::test_help_contains(critbit_tree& cbt, uint8_t* P, uint64_t m){
fprintf(stdout,"\n----------------contains-----------------------------\n");
if(cbt.contains(P, m))
fprintf(stdout, "'%s' : yes.\n", P);
else
fprintf(stdout, "'%s' : no.\n", P);
}
void test_critbit_tree::test_help_suffixes(critbit_tree& cbt, uint8_t* P, uint64_t m, uint64_t** results){
fprintf(stdout, "\n--------------suffixes-------------------------------\n");
uint64_t count = cbt.suffixes(P, m, results);
fprintf(stdout, " '%s' occurs %lu times.\n", P, count);
free(*results);
}
void test_critbit_tree::test_bible(){
uint8_t* filename = (uint8_t*)"./bible";
uint8_t* T;
fprintf(stdout, "\n------ begin reading file '%s' ------\n", filename);
uint64_t bytes = sb_read_file(filename, &T);
fprintf(stdout, "'\n------file size is %lu bytees.-------------\n", bytes);
critbit_tree cbt;
cbt.set_text(T, bytes);
fprintf(stdout, "\n--------------start inserting suffixes --------------\n");
for(uint64_t i = 0; i < bytes; i++)
cbt.insert_suffix(i);
fprintf(stdout, "\n--------------end inserting %lu suffixes-------------\n", bytes);
uint8_t* P = (uint8_t*)"god"; /*should be 347 times*/
uint64_t m = 3;
uint64_t* results = NULL;
test_help_contains(cbt, P, m);
test_help_suffixes(cbt, P, m, &results);
P = (uint8_t*)"and"; /* should be 43878 times */
m = 3;
results = NULL;
test_help_suffixes(cbt, P, m, &results);
P = (uint8_t*)"Mehujael begat Methusael:"; /*should be 1 times */
m = strlen((char*)P);
results = NULL;
test_help_suffixes(cbt, P, m, &results);
P = (uint8_t*)"Mehujael begat Methusael:a"; /*should be 0 times */
m = strlen((char*)P);
results = NULL;
test_help_suffixes(cbt, P, m, &results);
}
void test_critbit_tree::test_kernel() {
uint8_t* filename = (uint8_t*)"./sources.100MB";
uint8_t* T;
fprintf(stdout, "\n------ begin reading file '%s' ------\n", filename);
uint64_t bytes = sb_read_file(filename, &T);
fprintf(stdout, "\n------ file size is %lu bytes--------.\n", bytes);
critbit_tree cbt;
cbt.set_text(T, bytes);
fprintf(stdout, "\n------ start inserting suffixes.-----\n");
for(uint64_t i = 0; i < bytes; i++)
cbt.insert_suffix(i);
fprintf(stdout, "\n------ end inserting suffixes. ------\n");
uint8_t* P = (uint8_t*)"int";
uint64_t m = 3;
uint64_t* results = NULL;
test_help_suffixes(cbt, P, m, &results);
P = (uint8_t*) "set";
m = 3;
results = NULL;
test_help_suffixes(cbt, P, m, &results);
}
void test_critbit_tree::test_04(){
/* test file I/O, write critbit_tree into file*/
uint8_t* T = (uint8_t*)"mississipi";
uint64_t n = 10;
critbit_tree cbt;
cbt.set_text(T, n);
uint64_t SA[] = {0, 1, 3, 4, 2, 5, 9, 6, 8, 7};
uint64_t nsa = 10;
cbt.create_from_suffixes(SA, nsa);
FILE* out = fopen("./raw_data/missi.cbt", "w");
if(out == NULL){
fprintf(stderr, "write critbit_tree error.\n");
exit(EXIT_FAILURE);
}
uint64_t size = cbt.write(out);
fprintf(stdout, "-----------write %ld bytes datas-------------\n", size);
fclose(out);
}
void test_critbit_tree::test_05(){
/* test file I/O: read critbit tree from file .cbt */
critbit_tree cbt;
uint8_t* T = (uint8_t*)"mississipi";
uint64_t n = 10;
cbt.set_text(T, n);
uint8_t* filename = (uint8_t*)"./raw_data/missi.cbt";
uint64_t fsize = sb_file_size(filename); /*in bytes*/
fsize = fsize >> 3; /* in 64 bits */
FILE* in = fopen((char*)filename, "r");
if(!in){
fprintf(stderr, "read critbit_tree error: open file.\n");
exit(EXIT_FAILURE);
}
uint64_t* mem = (uint64_t*)malloc(sizeof(uint64_t)*fsize);
uint64_t x = fread(mem, sizeof(uint64_t), fsize, in);
if( x!= fsize){
fprintf(stderr, "read critbit_tree error: read men.\n");
exit(EXIT_FAILURE);
}
fprintf(stdout, "%ld elements read from '%s'\n ", x, filename);
cbt.load_from_mem(mem, fsize);
/* test critbit tree */
/* ------------------ test contains and delete ---------------------------------------- */
fprintf(stdout, "g = %lu\n", cbt.m_g);
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issis", 5));
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issi", 4));
cbt.delete_suffix(1);
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issis", 5));
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issi", 4));
cbt.insert_suffix(1);
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"issis", 5));
fprintf(stdout, "%lu\n", cbt.contains((uint8_t*)"i", 1));
/*-------- It looks correct ----------*/
uint64_t* results;
uint64_t sufcount = cbt.suffixes((uint8_t*)"i", 1, &results);
for(uint64_t i = 0; i < sufcount; i++)
fprintf(stdout, "%lu ", results[i]);
fprintf(stdout, "\n");
free(results);
}
void test_critbit_tree::test_cbt_write(){
uint8_t* filename = (uint8_t*)"sources.100MB";
uint8_t* outfilename = (uint8_t*)"./raw_data/sources.100MB.cbt";
uint8_t* T;
fprintf(stdout, "\n==============begin reading file %s=================\n", filename);
uint64_t bytes = sb_read_file(filename, &T);
fprintf(stdout, "\n--------------file size is %lu bytes-----------------.\n", bytes);
critbit_tree cbt;
cbt.set_text(T, bytes);
fprintf(stdout, "\n------ start inserting suffixes.-----\n");
for(uint64_t i = 0; i < bytes; i++)
cbt.insert_suffix(i);
fprintf(stdout, "\n------ end inserting suffixes. ------\n");
fprintf(stdout, "\n------ begin to write ---------\n");
FILE* out = fopen((char*)outfilename, "w");
if(!out){
fprintf(stdout, "error test_kernel_write: open file error.\n");
exit(EXIT_FAILURE);
}
uint64_t written = cbt.write(out);
fprintf(stdout, "\n------- end written %lu bytes ------\n",written);
fclose(out);
}
void test_critbit_tree::test_cbt_read() {
uint8_t* filename = (uint8_t*)"sources.100MB";
uint8_t* infilename = (uint8_t*)"./raw_data/sources.100MB.cbt";
uint8_t* T;
fprintf(stdout, "\n------ begin reading file '%s' ------\n", filename);
uint64_t bytes = sb_read_file(filename, &T);
fprintf(stdout, "\n------ file size is %lu bytes--------.\n", bytes);
critbit_tree cbt;
cbt.set_text(T, bytes);
fprintf(stdout, "\n------ start reading raw_data.-----\n");
uint64_t fsize = sb_file_size(infilename);
fsize = fsize >> 3;
uint64_t* mem = (uint64_t*)malloc(fsize * 8);
FILE* in = fopen((char*)infilename, "r");
if(!in){
fprintf(stderr, "%s\n", "error open file error");
exit(EXIT_FAILURE);
}
uint64_t readcount = fread(mem, sizeof(uint64_t), fsize, in);
if(readcount != fsize) {
fprintf(stdout, " reading file error.(%lu, %lu)\n", readcount, fsize);
exit(EXIT_FAILURE);
}
fclose(in);
cbt.load_from_mem(mem, fsize);
fprintf(stdout, "\n------ end loading raw_data. ------\n");
uint8_t* P = (uint8_t*)"int"; /*258350 times*/
// uint8_t* P = (uint8_t*)"god"; /*347 times*/
uint64_t m = 3;
uint64_t* results = NULL;
test_help_suffixes(cbt, P, m, &results);
P = (uint8_t*) "set"; m = 3; /**87438 times, right/
// P = (uint8_t*)"help"; m = 4; /*181 times*/
results = NULL;
test_help_suffixes(cbt, P, m, &results);
}