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FastNWModule.c
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FastNWModule.c
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/**********************************************************************
* FastNW: Fast Needleman-Wunsch
* Copyright (C) 2014 Jonathan Richards
*
* This program 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 2 of the License, or
* (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* Written by Jonathan Richards, [email protected]
**********************************************************************/
#include <Python.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <limits.h>
#include <float.h>
__inline int mymax(int a, int b) {
return a > b ? a : b;
}
typedef enum {false, true} bool;
typedef struct {
char *shorter;
char *longer;
int match;
int mismatch;
int gap;
int gap_extend;
bool switched;
} Arguments;
const Arguments FAILED = {
NULL, NULL, 0, 0, 0, 0, false
};
typedef struct {
int score;
char *align1;
char *align2;
} Alignment;
typedef struct {
int score;
size_t index;
} HirschReturn;
const HirschReturn NEED_MEM = {
0, -1
};
typedef struct {
int *cur;
int *cur_right;
int *cur_down;
} ScoreReturn;
const ScoreReturn NO_MEM = {
0, NULL, NULL
};
typedef enum {NONE, DOWN, RIGHT, ANY} Direction;
typedef struct {
int index;
Direction left;
Direction right;
} PartitionReturn;
//for quickly counting a Needleman Wunsch _score_
//returns a ScoreReturn object that must be freed after use
//returning entire bottom row allows use in Partition
ScoreReturn Score(const char *horizontal, size_t hl, size_t hr,
const char *vertical, size_t vl, size_t vr,
int match, int mismatch, int gap, int gap_extend,
Direction start_direction) {
//dimensions of matrix
size_t width = hr-hl+1;
size_t height = vr-vl+1;
//loop variables
size_t i;
size_t j;
//return value
ScoreReturn ret;
//current and previous row given not in a gap, in a down gap, and in a right gap
int *cur = malloc(width*sizeof(int));
int *prev = malloc(width*sizeof(int));
int *cur_right = malloc(width*sizeof(int));
int *prev_right = malloc(width*sizeof(int));
int *cur_down = malloc(width*sizeof(int));
int *prev_down = malloc(width*sizeof(int));
int *temp; //for switching cur and prev
/******************** Check Memory ***********************/
if (cur==NULL || prev==NULL || cur_right==NULL
|| prev_right==NULL || cur_down==NULL || prev_down==NULL) {
free(cur);
free(prev);
free(cur_right);
free(prev_right);
free(cur_down);
free(prev_down);
return NO_MEM;
}
/*************** Initial assignment of cur ***************/
cur[0] = 0;
cur_right[0] = INT_MIN/4;
cur_down[0] = INT_MIN/4;
for (i=1; i<width; i++) {
cur[i] = INT_MIN/4;
cur_right[i] = mymax(cur[i-1] + gap, cur_right[i-1] + gap_extend);
cur_down[i] = INT_MIN/4;
}
/******** Second row depends on start_direction **********/
if (height > 1) {
temp = prev;
prev = cur;
cur = temp;
temp = prev_down;
prev_down = cur_down;
cur_down = temp;
temp = prev_right;
prev_right = cur_right;
cur_right = temp;
cur[0] = INT_MIN/4;
cur_right[0] = INT_MIN/4;
switch (start_direction) {
case NONE : //cant use prev_right or cur_down
cur_down[0] = INT_MIN/4;
for (i=1; i<width; i++) {
if (horizontal[hl+i-1] == vertical[vl])
cur[i] = prev[i-1]+match;
else
cur[i] = prev[i-1]+mismatch;
cur_right[i] = mymax(cur[i-1] + gap, cur_right[i-1] + gap_extend);
cur_down[i] = INT_MIN/4;
}
break;
case DOWN : //can only use cur_down
cur_down[0] = gap;
for (i=1; i<width; i++) {
cur[i] = INT_MIN/4;
cur_right[i] = INT_MIN/4;
cur_down[i] = INT_MIN/4;
}
break;
case RIGHT : //cant use prev or cur_down
cur_down[0] = INT_MIN/4;
for (i=1; i<width; i++) {
if (horizontal[hl+i-1] == vertical[vl])
cur[i] = prev_right[i-1]+match;
else
cur[i] = prev_right[i-1]+mismatch;
cur_right[i] = mymax(cur[i-1] + gap, cur_right[i-1] + gap_extend);
cur_down[i] = INT_MIN/4;
}
break;
case ANY : //can use arrays as normal
cur_down[0] = gap;
for (i=1; i<width; i++) {
if (horizontal[hl+i-1] == vertical[vl])
cur[i] = mymax(prev[i-1], prev_right[i-1])+match;
else
cur[i] = mymax(prev[i-1], prev_right[i-1])+mismatch;
cur_right[i] = mymax(cur[i-1] + gap, cur_right[i-1] + gap_extend);
cur_down[i] = INT_MIN/4;
}
break;
default :
printf("ERROR: Initial direction error\n");
break;
}
}
/***************** Assign rest of matrix *****************/
for (j=2; j<height; j++) {
//current becomes previous
temp = prev;
prev = cur;
cur = temp;
temp = prev_down;
prev_down = cur_down;
cur_down = temp;
temp = prev_right;
prev_right = cur_right;
cur_right = temp;
cur[0] = INT_MIN/4;
cur_right[0] = INT_MIN/4;
cur_down[0] = mymax(prev[0]+gap, prev_down[0]+gap_extend);
//calculate current row
for (i=1; i<width; i++) {
//calculate score after diagonal path
if (horizontal[hl+i-1] == vertical[vl+j-1]) {
cur[i] = mymax(prev[i-1], mymax(prev_right[i-1], prev_down[i-1])) + match;
} else {
cur[i] = mymax(prev[i-1], mymax(prev_right[i-1], prev_down[i-1])) + mismatch;
}
//calculate score after downward path
cur_down[i] = mymax(prev[i] + gap, prev_down[i] + gap_extend);
//calculate score after rightward path
cur_right[i] = mymax(cur[i-1] + gap, cur_right[i-1] + gap_extend);
}
}
free(prev);
free(prev_right);
free(prev_down);
ret.cur = cur;
ret.cur_right = cur_right;
ret.cur_down = cur_down;
return ret;
}
//Full Needleman Wunsch algorithm, with added capability
//for starting and ending requirements (allowing it to be used with Hirsch)
HirschReturn NeedlemanWunsch(char *Z, char *W, size_t Z_spot,
const char *horizontal, size_t hl, size_t hr,
const char *vertical, size_t vl, size_t vr,
int match, int mismatch, int gap, int gap_extend,
Direction start_direction, Direction end_direction) {
//for indexing
size_t i;
size_t j;
//matrix dimensions
size_t width = hr-hl+1;
size_t height = vr-vl+1;
//temporary calculations
int from;
int from_right;
int from_down;
//score matrix
int *mat = malloc(width*height*sizeof(int));
int *mat_right = malloc(width*height*sizeof(int));
int *mat_down = malloc(width*height*sizeof(int));
//0=none, 1=right, 2=down
int trace;
int *mat_dir = malloc(width*height*sizeof(int));
int *mat_right_dir = malloc(width*height*sizeof(int));
int *mat_down_dir = malloc(width*height*sizeof(int));
//backwards alignments
size_t rev_spot;
char *rev_Z = malloc((width+height)*sizeof(char));
char *rev_W = malloc((width+height)*sizeof(char));
HirschReturn ret;
if (mat==NULL || mat_right==NULL || mat_down==NULL
|| mat_dir==NULL || mat_right_dir==NULL || mat_down_dir==NULL
|| rev_Z==NULL || rev_W==NULL) {
free(mat);
free(mat_right);
free(mat_down);
free(mat_dir);
free(mat_right_dir);
free(mat_down_dir);
free(rev_Z);
free(rev_W);
return NEED_MEM;
}
/*
printf(horizontal);
printf("\n");
printf(vertical);
printf("\n");
printf("width = %d\n", width);
printf("height = %d\n", height);
*/
/********************** First row ************************/
mat[0] = 0;
mat_dir[0] = -1;
mat_right[0] = INT_MIN/4;
mat_right_dir[0] = -1;
mat_down[0] = INT_MIN/4;
mat_down_dir[0] = -1;
for (i=1; i<width; i++) {
mat[i] = INT_MIN/4;
mat_dir[i] = -1;
from = mat[i-1] + gap;
from_right = mat_right[i-1] + gap_extend;
if (from > from_right) {
mat_right[i] = from;
mat_right_dir[i] = 0;
} else {
mat_right[i] = from_right;
mat_right_dir[i] = 1;
}
mat_down[i] = INT_MIN/4;
mat_down_dir[i] = -1; //added down
}
/******** Second row depends on start_direction **********/
if (height > 1) {
j = width;
mat[j] = INT_MIN/4;
mat_dir[j] = -1;
mat_right[j] = INT_MIN/4;
mat_right_dir[j] = -1;
switch (start_direction) {
case NONE : //cant use prev_right or cur_down
mat_down[j] = INT_MIN/4;
mat_down_dir[j] = -1;
for (i=1; i<width; i++) {
if (horizontal[hl+i-1] == vertical[vl])
mat[j+i] = mat[i-1]+match;
else
mat[j+i] = mat[i-1]+mismatch;
mat_dir[j+i] = 0;
from = mat[j+i-1] + gap;
from_right = mat_right[j+i-1] + gap_extend;
if (from > from_right) {
mat_right[j+i] = from;
mat_right_dir[j+i] = 0;
} else {
mat_right[j+i] = from_right;
mat_right_dir[j+i] = 1;
}
mat_down[j+i] = INT_MIN/4;
mat_down_dir[j+i] = -1;
}
break;
case DOWN : //can only use cur_down
//printf("Starting down\n");
mat_down[j] = gap;
mat_down_dir[j] = 0;
for (i=1; i<width; i++) {
mat[j+i] = INT_MIN/4;
mat_dir[j+i] = -1;
mat_right[j+i] = INT_MIN/4;
mat_right_dir[j+i] = -1;
mat_down[j+i] = INT_MIN/4;
mat_down_dir[j+i] = -1;
}
break;
case RIGHT : //cant use prev or cur_down
mat_down[j] = INT_MIN/4;
mat_down_dir[j] = -1;
for (i=1; i<width; i++) {
if (horizontal[hl+i-1] == vertical[vl])
mat[j+i] = mat_right[i-1]+match;
else
mat[j+i] = mat_right[i-1]+mismatch;
mat_dir[j+i] = 0;
from = mat[j+i-1] + gap;
from_right = mat_right[j+i-1] + gap_extend;
if (from > from_right) {
mat_right[j+i] = from;
mat_right_dir[j+i] = 0;
} else {
mat_right[j+i] = from_right;
mat_right_dir[j+i] = 1;
}
mat_down[j+i] = INT_MIN/4;
mat_down_dir[j+i] = -1;
}
break;
case ANY : //can use arrays as normal
mat_down[j] = gap;
mat_down_dir[j] = 0;
for (i=1; i<width; i++) {
from = mat[i-1];
from_right = mat_right[i-1];
if (from > from_right) {
mat[j+i] = from;
mat_dir[j+i] = 0;
} else {
mat[j+i] = from_right;
mat_dir[j+i] = 1;
}
if (horizontal[hl+i-1] == vertical[vl])
mat[j+i] += match;
else
mat[j+i] += mismatch;
from = mat[j+i-1] + gap; //added j
from_right = mat_right[j+i-1] + gap_extend; //added j
if (from > from_right) {
mat_right[j+i] = from;
mat_right_dir[j+i] = 0;
} else {
mat_right[j+i] = from_right;
mat_right_dir[j+i] = 1;
}
mat_down[j+i] = INT_MIN/4;
mat_down_dir[j+i] = -1;
}
break;
default :
printf("ERROR: Initial direction error\n");
break;
}
}
/***************** Assign rest of matrix *****************/
for (j=2*width; j<width*height; j+=width) {
mat[j] = INT_MIN/4;
mat_dir[j] = -1;
mat_right[j] = INT_MIN/4;
mat_right_dir[j] = -1;
from = mat[j-width]+gap;
from_down = mat_down[j-width]+gap_extend;
if (from > from_down) {
mat_down[j] = from;
mat_down_dir[j] = 0;
} else {
mat_down[j] = from_down;
mat_down_dir[j] = 2;
}
//calculate current row
for (i=1; i<width; i++) {
//calculate score after diagonal path
from = mat[j-width+i-1];
from_right = mat_right[j-width+i-1];
from_down = mat_down[j-width+i-1];
if (from > from_right && from > from_down) {
mat[j+i] = from;
mat_dir[j+i] = 0;
} else if (from_right > from_down) {
mat[j+i] = from_right;
mat_dir[j+i] = 1;
} else {
mat[j+i] = from_down;
mat_dir[j+i] = 2;
}
if (horizontal[hl+i-1] == vertical[vl+j/width-1]) {
mat[j+i] += match;
} else {
mat[j+i] += mismatch;
}
//calculate score after rightward path
from = mat[j+i-1] + gap; //removed -width
from_right = mat_right[j+i-1] + gap_extend; //removed -width
if (from > from_right) {
mat_right[j+i] = from;
mat_right_dir[j+i] = 0;
} else {
mat_right[j+i] = from_right;
mat_right_dir[j+i] = 1;
}
//calculate score after downward path
from = mat[j-width+i] + gap;
from_down = mat_down[j-width+i] + gap_extend;
if (from > from_down) {
mat_down[j+i] = from;
mat_down_dir[j+i] = 0;
} else {
mat_down[j+i] = from_down;
mat_down_dir[j+i] = 2;
}
}
}
/*
for (j=0; j<width*height; j+=width) {
for (i=0; i<width; i++) {
printf("%d, ", mat[j+i]);
}
printf("\n");
}
for (j=0; j<width*height; j+=width) {
for (i=0; i<width; i++) {
printf("%d, ", mat_dir[j+i]);
}
printf("\n");
}
for (j=0; j<width*height; j+=width) {
for (i=0; i<width; i++) {
printf("%d, ", mat_right[j+i]);
}
printf("\n");
}
for (j=0; j<width*height; j+=width) {
for (i=0; i<width; i++) {
printf("%d, ", mat_right_dir[j+i]);
}
printf("\n");
}
for (j=0; j<width*height; j+=width) {
for (i=0; i<width; i++) {
printf("%d, ", mat_down[j+i]);
}
printf("\n");
}
for (j=0; j<width*height; j+=width) {
for (i=0; i<width; i++) {
printf("%d, ", mat_down_dir[j+i]);
}
printf("\n");
}
*/
/*********** Matrix completed, begin backtrace **************/
//calculate backtrace starting position
i = width*height-1;
switch (end_direction) {
case NONE :
ret.score = mat[i];
trace = 0;
//rev_Z[0] = horizontal[hr-1];
//rev_W[0] = vertical[vr-1];
break;
case RIGHT :
ret.score = mat_right[i];
trace = 1;
//rev_Z[0] = horizontal[hr-1];
//rev_W[0] = '-';
break;
case DOWN :
//printf("start trace down\n");
ret.score = mat_down[i];
trace = 2;
//rev_Z[0] = '-';
//rev_W[0] = vertical[vr-1];
break;
case ANY :
if (mat[i] > mat_right[i] && mat[i] > mat_down[i]) {
ret.score = mat[i];
trace = 0;
//rev_Z[0] = horizontal[hr-1];
//rev_W[0] = vertical[vr-1];
} else if (mat_right[i] > mat_down[i]) {
ret.score = mat_right[i];
trace = 1;
//rev_Z[0] = horizontal[hr-1];
//rev_W[0] = '-';
} else {
//printf("hi\n");
ret.score = mat_down[i];
trace = 2;
//rev_Z[0] = '-';
//rev_W[0] = vertical[vr-1];
//printf("Trace = %d\n", trace);
}
break;
default :
printf("ERROR: end direction error\n");
break;
}
//printf("Populating\n");
//populate rev alignments
j = height-1;
i = width-1;
rev_spot = 0;
while (j > 0 || i > 0) {
//printf("i=%d, j=%d, t=%d\n", i, j, trace);
switch (trace) {
case 0 :
trace = mat_dir[j*width+i];
i--;
j--;
rev_Z[rev_spot] = horizontal[hl+i];
rev_W[rev_spot] = vertical[vl+j];
break;
case 1 :
trace = mat_right_dir[j*width+i];
i--;
rev_Z[rev_spot] = horizontal[hl+i];
rev_W[rev_spot] = '-';
break;
case 2 :
trace = mat_down_dir[j*width+i];
j--;
rev_Z[rev_spot] = '-';
rev_W[rev_spot] = vertical[vl+j];
break;
default :
printf("ERROR: traceback error\n");
exit(0);
break;
}
rev_spot++;
}
ret.index = Z_spot + rev_spot;
/************ Put rev alignments into Z and W ************/
rev_Z[rev_spot] = '\0';
rev_W[rev_spot] = '\0';
/*
printf("Aligning ");
printf(rev_Z);
printf(" and ");
printf(rev_W);
printf("\n");
*/
for (rev_spot; rev_spot > 0; rev_spot--, Z_spot++) {
//printf("%d, %d\n", rev_spot, Z_spot);
Z[Z_spot] = rev_Z[rev_spot-1];
W[Z_spot] = rev_W[rev_spot-1];
}
if (Z_spot != ret.index) {
printf("ERROR: indexing problem\n");
}
free(mat);
free(mat_right);
free(mat_down);
free(mat_dir);
free(mat_right_dir);
free(mat_down_dir);
free(rev_Z);
free(rev_W);
//printf("Done\n");
return ret;
}
PartitionReturn Partition(ScoreReturn ScoreL, ScoreReturn ScoreR, size_t width,
int gap, int gap_extend) {
size_t i;
size_t j=width;
int best = INT_MIN;
int score;
PartitionReturn ret;
/*
for (i=0; i<=width; i++,j--) {
printf("%d, ", ScoreL.cur[i]);
}
j=width;
printf("\n");
for (i=0; i<=width; i++,j--) {
printf("%d, ", ScoreL.cur_down[i]);
}
j=width;
printf("\n");
for (i=0; i<=width; i++,j--) {
printf("%d, ", ScoreL.cur_right[i]);
}
j=width;
printf("\n");
for (i=0; i<=width; i++,j--) {
printf("%d, ", ScoreR.cur[i]);
}
j=width;
printf("\n");
for (i=0; i<=width; i++,j--) {
printf("%d, ", ScoreR.cur_down[i]);
}
j=width;
printf("\n");
for (i=0; i<=width; i++,j--) {
printf("%d, ", ScoreR.cur_right[i]);
}
j=width;
printf("\n");
*/
//need some way to force other partitions into ending in gap or not
for (i=0; i<=width; i++, j--) {
//neither gap
score = ScoreL.cur[i] + ScoreR.cur[j];
if (score > best) {
best = score;
ret.index = i;
ret.left = NONE;
ret.right = NONE;
}
//both down gaps. Have to correct scores
score = ScoreL.cur_down[i] + ScoreR.cur_down[j] - gap + gap_extend;
if (score > best) {
best = score;
ret.index = i;
ret.left = DOWN;
ret.right = DOWN;
}
//one is down, other is not
score = ScoreL.cur[i] + ScoreR.cur_down[j];
if (score > best) {
best = score;
ret.index = i;
ret.left = NONE;
ret.right = DOWN;
}
//one is down, other is not
score = ScoreL.cur_down[i] + ScoreR.cur[j];
if (score > best) {
best = score;
ret.index = i;
ret.left = DOWN;
ret.right = NONE;
}
//any combination of right and cur can be represented here
score = ScoreL.cur_right[i] + ScoreR.cur[j];
if (score > best) {
best = score;
ret.index = i;
ret.left = RIGHT;
ret.right = NONE;
}
/*
score = ScoreL.cur_right[i] + ScoreR.cur_right[j];
if (score > best) {
best = score;
ret.index = i;
ret.left = RIGHT;
ret.right = RIGHT;
}
score = ScoreL.cur[i] + ScoreR.cur_right[j];
if (score > best) {
best = score;
ret.index = i;
ret.left = NONE;
ret.right = RIGHT;
}
*/
}
//printf("score = %d, %d\n", best, ret.index);
free(ScoreL.cur);
free(ScoreL.cur_right);
free(ScoreL.cur_down);
free(ScoreR.cur);
free(ScoreR.cur_right);
free(ScoreR.cur_down);
return ret;
}
//recursive function for hirshberg algorithm
HirschReturn Hirsch(char *Z, char *W, size_t Z_spot,
const char *horizontal, const char *rev_hor, size_t hl, size_t hr,
const char *vertical, const char *rev_vert, size_t vl, size_t vr,
int match, int mismatch, int gap, int gap_extend,
Direction start_direction, Direction end_direction) {
//get input string lengths
size_t width = hr-hl;
size_t height = vr-vl;
//for indexing
//size_t i;
//size_t j;
size_t h_mid;
size_t v_mid;
//alignment scores fo partitioning
ScoreReturn ScoreL;
ScoreReturn ScoreR;
PartitionReturn pres;
HirschReturn ret; //return value
HirschReturn res; //result from NeedlemanWunsch
ret.score = 0; //the relative score of this recursion call
ret.index = Z_spot; //the absolute position in aligned strings
//printf("hor: %d, %d\n", hl, hr);
//printf("vert: %d, %d\n", vl, vr);
//printf("width: %d\n", width);
//printf("height: %d\n", height);
if (width*height <= 1000000 || width==1 || height==1) {
//printf("Args: %d, %d, %d, %d, %d\n", hl, hr, vl, vr, Z_spot);
/*
printf("start = %d\n", start_direction);
printf("end = %d\n", end_direction);
for (i=hl; i<hr; i++) {
printf("%c", horizontal[i]);
}
printf("\n");
for (j=vl; j<vr; j++) {
printf("%c", vertical[j]);
}
printf("\n");
*/
res = NeedlemanWunsch(Z, W, Z_spot, horizontal, hl, hr,
vertical, vl, vr,
match, mismatch, gap, gap_extend,
start_direction, end_direction);
ret.score = res.score;
ret.index = res.index;
} else {
v_mid = (vl+vr)/2; //split vertical in half
ScoreL = Score(horizontal, hl, hr,
vertical, vl, v_mid,
match, mismatch, gap, gap_extend, start_direction);
ScoreR = Score(rev_hor, strlen(rev_hor)-hr, strlen(rev_hor)-hl,
rev_vert, strlen(rev_vert)-vr, strlen(rev_vert)-v_mid,
match, mismatch, gap, gap_extend, end_direction);
//partition horizontal
pres = Partition(ScoreL, ScoreR, width, gap, gap_extend);
h_mid = hl+pres.index;
//printf("pres.left = %d\n", pres.left);
//printf("pres.right = %d\n", pres.right);
/*
for (i=hl; i<hr; i++) {
printf("%c", horizontal[i]);
}
printf("\n");
printf("%d\n", h_mid);
for (j=vl; j<vr; j++) {
printf("%c", vertical[j]);
}
printf("\n");
*/
/*
printf("hor: %d, %d, %d\n", hl, h_mid, hr);
printf("vert: %d, %d, %d\n", vl, v_mid, vr);
printf(rev_hor);
printf("\n");
printf(rev_vert);
printf("\n");
*/
res = Hirsch(Z, W, Z_spot,
horizontal, rev_hor, hl, h_mid,
vertical, rev_vert, vl, v_mid,
match, mismatch, gap, gap_extend,
start_direction, pres.left);
ret.score = res.score;
Z_spot = res.index;
res = Hirsch(Z, W, Z_spot,
horizontal, rev_hor, h_mid, hr,
vertical, rev_vert, v_mid, vr,
match, mismatch, gap, gap_extend,
pres.right, end_direction);
ret.score += res.score;
ret.index = res.index;
//have to remember that this is actually 1 gap, not 2
if (pres.left == DOWN && pres.right == DOWN)
ret.score += gap_extend-gap;
}
return ret;
}
//interprets python arguments
Arguments GetArguments(PyObject *args) {
char *temp; //for switching longer and shorter
Arguments arguments; //return value
arguments.gap_extend = INT_MIN;
//parse python args
if (!PyArg_ParseTuple(args, "ssiii|i",
&arguments.shorter, &arguments.longer, &arguments.match,
&arguments.mismatch, &arguments.gap, &arguments.gap_extend))
return FAILED;
//find shorter and longer inputs
if (arguments.switched = (strlen(arguments.shorter) > strlen(arguments.longer))) {
temp = arguments.shorter;
arguments.shorter = arguments.longer;
arguments.longer = temp;
}
//if gap_extend isn't specified, must be equal to gap
if (arguments.gap_extend == INT_MIN) {
arguments.gap_extend = arguments.gap;
}
return arguments;
}
//handler for score method from python
static PyObject * NWScore(PyObject *self, PyObject *args) {
ScoreReturn res; //return value
int width;
int ret;
Arguments arguments = GetArguments(args);
if (!arguments.shorter)
return NULL;
width = strlen(arguments.shorter);
res = Score(arguments.shorter, 0, strlen(arguments.shorter),
arguments.longer, 0, strlen(arguments.longer),
arguments.match, arguments.mismatch, arguments.gap, arguments.gap_extend,
ANY);
ret = mymax(res.cur[width], mymax(res.cur_right[width], res.cur_down[width]));
free(res.cur);
free(res.cur_right);
free(res.cur_down);
return Py_BuildValue("i", ret);
}
//handler for align method from python
static PyObject * Align(PyObject *self, PyObject *args) {
HirschReturn res; //result from hirschberg algorithm
PyObject *ret; //return value
char *Z; //short alignment
char *W; //long alignment
char *rev_hor; //reverse of input strings
char *rev_vert;
//input string sizes
size_t width;
size_t height;
size_t i;
Arguments arguments = GetArguments(args);
if (!arguments.shorter)
return NULL;
width = strlen(arguments.shorter);
height = strlen(arguments.longer);
rev_hor = malloc((width+1)*sizeof(char));
rev_vert = malloc((height+1)*sizeof(char)); // extra +1 for \0 to use strlen
Z = malloc((width+height)*sizeof(char));
W = malloc((width+height)*sizeof(char));