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FindEditDistanceMod.c
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FindEditDistanceMod.c
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/*
* Copyright (C) 2010 University of Tartu
* Authors: Reina Käärik, Siim Orasmaa, Kristo Tammeoja, Jaak Vilo
* Contact: siim . orasmaa {at} ut . ee
*
* This file is part of Generalized Edit Distance Tool.
*
* Generalized Edit Distance Tool 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.
*
* Generalized Edit Distance Tool 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 Generalized Edit Distance Tool.
* If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "FindEditDistanceMod.h"
// Insert value into table[row][col]
int addValueToTable(int cols, double table[][cols], int row, int col, double value){
if(value < table[row][col])
table[row][col] = value;
return 0;
}
// Search 'remove' operations from trie and apply if possible
int searchFromRemTrie(int cols, double table[][cols], wchar_t *string, int i , int j){
ARTNode *tmp;
double value;
int r = 1;
tmp = remT->firstNode;
value = table[i][j] + getPenaltOfChangingPosWithGenEd(i);
while(tmp != NULL && string != L'\0'){
if(tmp->label == *string){
/* If given node in trie is an end node: */
if(tmp->value != DBL_MAX){
// Operation: at position i. in the search string, remove following r characters
addValueToTable(cols, table, (i+r), j, (value + tmp->value));
}
string = string + 1;
tmp = tmp->nextNode;
value += getPenaltOfChangingPosWithGenEd(i+r);
r++;
}
else tmp = tmp->rightNode;
}
return 0;
}
// Search 'add' operations from trie and apply if possible
int searchFromAddTrie(int cols, double table[][cols], wchar_t *string, int i , int j){
ARTNode *tmp;
double value;
int c = 1;
tmp = addT->firstNode;
value = table[i][j] + getPenaltOfChangingPosWithGenEd(i);
while(tmp != NULL && string != L'\0'){
if(tmp->label == *string){
/* If given node in trie is an end node: */
if(tmp->value != DBL_MAX){
// Operation: at position i. in the search string, insert c characters
addValueToTable(cols, table, i, (j+c), (value + tmp->value));
}
string = string + 1;
tmp = tmp->nextNode;
c++;
}
else tmp = tmp->rightNode;
}
return 0;
}
// Checks from EndNode list, whether there are replacements corresponding to string, and tries to apply them
int findReplacement(int cols, EndNode *n, double table[][cols], wchar_t *string, int i, int j, double value){
wchar_t *repl;
int c;
while(n != NULL){
repl = n->edit;
c = 0;
// Check, whether given replacement can be made
while(1){
if(string[c] == repl[c] || repl[c] == L'\0'){
if(repl[c] == '\0'){
// End of replacement string
addValueToTable(cols, table, i, (j + c), (value + n->value));
goto nextRepl;
}
c++;
}
else break;
}
nextRepl: n = n->nextEN;
}
return 0;
}
// Search 'replace' operations from trie and apply if possible
int searchFromRepTrie(int cols, double table[][cols], wchar_t *string1, wchar_t *string2, int i, int j){
TrieNode *tmp;
EndNode *repl;
double value;
int r;
tmp = t->firstNode;
value = table[i][j] + getPenaltOfChangingPosWithGenEd(i);
r = 1;
while(tmp != NULL){
if(tmp->label == *string1){
/* If given node in trie is an end node: */
if(tmp->replacement != NULL){
// Operation: from position i. in the search string, replace next r characters (including i.)
repl = tmp->replacement;
findReplacement(cols, repl, table, string2, (i+r), j, value);
}
string1 = string1 + 1;
tmp = tmp->nextNode;
value += getPenaltOfChangingPosWithGenEd(i+r);
r++;
}
else tmp = tmp->rightNode;
}
return 0;
}
// Gets a penalty which applies for changing i-th char in the search string via edit distance
double getPenaltOfChangingPos(int i){
if (changeSearchStringWithEd_pen != NULL){
return changeSearchStringWithEd_pen[ i + 1 ];
}
return 0.0;
}
// Gets a penalty which applies for changing i-th char in the search string via generalized edit distance
double getPenaltOfChangingPosWithGenEd(int i){
if (changeSearchStringWithGenEd_pen != NULL){
return changeSearchStringWithGenEd_pen[ i + 1 ];
}
return 0.0;
}
// Finds regular edit distance between strings a and b.
int editDistance(wchar_t* a, wchar_t* b, int aLen, int bLen){
int i, j;
int rows = aLen + 1;
int cols = bLen +1;
int table[rows][cols];
// fill the first row
for(i = 0; i < rows; i++){
table[i][0] = i;
}
for(j = 1; j < cols; j++){
table[0][j] = j;
for(i = 1; i < rows; i++){
if(*(a+(i-1)) == *(b+(j-1))){
table[i][j] = min(table[i-1][j-1],
min(table[i][j-1]+1, table[i-1][j]+1));
} else
table[i][j] = min(table[i-1][j-1]+1,
min(table[i][j-1]+1, table[i-1][j]+1));
}
}
return table[rows-1][cols-1];
}
// Finds generalized edit distance between strings a and b, without applying any penalties
double genEditDistance(wchar_t *a, wchar_t *b, int aLen, int bLen, Transformations *transF){
int i, j;
int rows = aLen +1; // search string
int cols = bLen +1; // text
double table[rows][cols];
double value;
/* Fill table with initial values (so we can check applicability of generalized
* edit distance transformations even if we haven't reached to the particular
* cell yet )
*/
for(i = 0; i < rows; i++){
for(j = 0; j < cols; j++){
table[i][j] = DBL_MAX;
}
}
table[0][0] = 0;
// fill the first column
for(i = 1; i < rows; i++){
if(remT->firstNode != NULL)
searchFromRemTrie(cols, table, (a + i-1), i-1 ,0);
value = table[i-1][0] + rem;
if(value < table[i][0]) table[i][0] = value;
}
for(j = 1; j < cols; j++){
if(addT->firstNode != NULL)
searchFromAddTrie(cols, table, (b + j - 1), 0, j-1);
value = table[0][j-1] + add;
if(value < table[0][j]) table[0][j] = value;
for(i = 1; i < rows; i++){
if(remT->firstNode != NULL)
searchFromRemTrie(cols, table, (a + i-1), i-1 ,j);
if(addT->firstNode != NULL)
searchFromAddTrie(cols, table, (b + j - 1), i, j-1);
if(t->firstNode != NULL)
searchFromRepTrie(cols, table, (a + i-1 ), b + j-1 , i-1, j-1);
if(a[i-1] == b[j-1]){
value = min(table[i-1][j-1],
min(table[i][j-1]+ add,
table[i-1][j] + rem ));
if(value < table[i][j]) table[i][j] = value;
} else {
value = min(table[i-1][j-1] + rep,
min(table[i][j-1]+ add,
table[i-1][j] + rem ));
if(value < table[i][j]) table[i][j] = value;
}
}
}
/* Print table for debug */
/*
puts("\n");
printf("%ls",b);
puts("\n");
for(i = 0; i < rows; i++){
for(j = 0; j < cols; j++){
printf("%f ",table[i][j]);
}
puts("\n");
}
puts("\n");
*/
if (transF != NULL){
// if required, backtrace the transformations
findBestPaths(cols, table, a, b, aLen, bLen, transF, traceRemT, traceAddT, traceT);
}
return table[rows-1][cols-1];
}
// Finds generalized edit distance between strings a and b, also applies penalties if possible
double genEditDistance_pens(wchar_t *a, wchar_t *b, int aLen, int bLen, double* start_pen, double* end_pen){
int i, j;
int rows = aLen +1; // search string
int cols = bLen +1; // text
double table[rows][cols];
double value;
/* Fill table with initial values (so we can check applicability of generalized
* edit distance transformations even if we haven't reached to the particular
* cell yet )
*/
for(i = 0; i < rows; i++){
for(j = 0; j < cols; j++){
table[i][j] = DBL_MAX;
}
}
table[0][0] = 0;
// Fill the first row with start penalties (penalty of starting match at given pos in text)
if (start_pen != NULL){
for(j = 0; j < bLen; j++){
table[0][j] = start_pen[j];
}
}
// fill the first column
for(i = 1; i < rows; i++){
if(remT->firstNode != NULL)
searchFromRemTrie(cols, table, (a + i-1), i-1 ,0);
value = table[i-1][0] + rem + getPenaltOfChangingPos(i-1); // regular deletion at the search string pos i.
if(value < table[i][0]) table[i][0] = value;
}
for(j = 1; j < cols; j++){
if(addT->firstNode != NULL)
searchFromAddTrie(cols, table, (b + j - 1), 0, j-1);
value = table[0][j-1] + add + getPenaltOfChangingPos(-1); // adding at the beginning of the search string
if(value < table[0][j]) table[0][j] = value;
for(i = 1; i < rows; i++){
if(remT->firstNode != NULL)
searchFromRemTrie(cols, table, (a + i-1), i-1 ,j);
if(addT->firstNode != NULL)
searchFromAddTrie(cols, table, (b + j - 1), i, j-1);
if(t->firstNode != NULL)
searchFromRepTrie(cols, table, (a + i-1 ), b + j-1 , i-1, j-1);
if(a[i-1] == b[j-1]){
value = min(table[i-1][j-1], // identity at search string pos i.
min(table[i][j-1] + add + getPenaltOfChangingPos(i), // insert after search string pos i.
table[i-1][j] + rem + getPenaltOfChangingPos(i-1) )); // delete from search string pos i.
if(value < table[i][j]) table[i][j] = value;
} else {
value = min(table[i-1][j-1] + rep + getPenaltOfChangingPos(i-1), // replace at search string pos i.
min(table[i][j-1] + add + getPenaltOfChangingPos(i), // insert after search string pos i.
table[i-1][j] + rem + getPenaltOfChangingPos(i-1) )); // delete from search string pos i.
if(value < table[i][j]) table[i][j] = value;
}
//
// NB! The 'add penalty' above { table[i][j-1] + add + getPenaltOfChangingPos(i) } is useful
// only when the position i+1 (following position i) is also penalized or if it is the end of word.
// If the position i+1 is free (unpenalized), the blocked adding can be still done by replacements
// at position i+1 and additions after i+1.
//
}
}
double score = DBL_MAX;
if (end_pen == NULL){
score = table[rows-1][cols-1];
} else {
// Fill the last row with end penalties (penalty of ending match at given pos in text)
for(j = 0; j < bLen; j++){
double newScore = table[rows-1][j+1] + end_pen[j];
if (newScore < score){
score = newScore;
}
}
}
return score;
}
// Finds generalized edit distance between strings a and b, allowing only partial matches with b
double genEditDistance_mod(wchar_t *a, wchar_t *b, int aLen, int bLen, short isPrefix, short isSuffix){
double prefix[bLen];
double suffix[bLen];
double* prefix_ptr = NULL;
double* suffix_ptr = NULL;
int i;
if (!isPrefix){
for (i = 0; i < bLen; i++) prefix[i] = 0.0;
prefix_ptr = prefix;
}
if (!isSuffix){
for (i = 0; i < bLen; i++) suffix[i] = 0.0;
suffix_ptr = suffix;
}
return genEditDistance_pens(a, b, aLen, bLen, prefix_ptr, suffix_ptr);
}
// Finds generalized edit distance between strings a and prefix of b, allows penalizing changes in search string
double genEditDistance_prefix(wchar_t *a, wchar_t *b, int aLen, int bLen){
return genEditDistance_mod(a, b, aLen, bLen, 1, 0);
}
// Finds generalized edit distance between strings a and suffix of b, allows penalizing changes in search string
double genEditDistance_suffix(wchar_t *a, wchar_t *b, int aLen, int bLen){
return genEditDistance_mod(a, b, aLen, bLen, 0, 1);
}
// Finds generalized edit distance between strings a and infix of b, allows penalizing changes in search string
double genEditDistance_middle(wchar_t *a, wchar_t *b, int aLen, int bLen){
return genEditDistance_mod(a, b, aLen, bLen, 0, 0);
}
// Finds generalized edit distance between full strings a and b, allows penalizing changes in search string
double genEditDistance_full(wchar_t *a, wchar_t *b, int aLen, int bLen){
return genEditDistance_mod(a, b, aLen, bLen, 1, 1);
}
// Prints a view of debug table
void printTableWithChangingPenalties(
wchar_t *a, wchar_t *b, int aLen, int bLen, int rows, int cols, double table[rows][cols]){
int i, j;
puts("\n");
printf("%ls",b);
puts("\n");
for(i = 0; i < rows; i++){ // in search string
int m = 0;
for(m = 0; m < 3; m++){
for(j = 0; j < cols; j++){ // in text
if (i > 0 && j == 0) {
printf( "%5.1f ", table[i-1][0] + rem + getPenaltOfChangingPos(i-1) );
} else if (i > 0 && j > 0){
if (m==0){
if(a[i-1] == b[j-1]){
printf( "Sme: %5.1f ",table[i-1][j-1] );
} else {
printf( "Rep: %5.1f ",table[i-1][j-1] + rep + getPenaltOfChangingPos(i-1) );
}
}
else if (m==1){
printf( "Add: %5.1f ",table[i][j-1]+ add + getPenaltOfChangingPos(i) );
}
else if (m==2){
printf( "Rem: %5.1f ",table[i-1][j] + rem + getPenaltOfChangingPos(i-1) );
}
} else {
printf( "%5.1f ",table[i][j] );
}
}
printf("\n");
}
printf("\n");
}
}