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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: WaveFront penalties handling module
*/
#include "utils/commons.h"
#include "system/mm_allocator.h"
#include "wavefront_penalties.h"
/*
* Penalties adjustment
*/
void wavefront_penalties_set_indel(
wavefront_penalties_t* const wf_penalties) {
// Set distance model
wf_penalties->distance_metric = indel;
// Set penalties
wf_penalties->match = 0;
wf_penalties->mismatch = -1;
wf_penalties->gap_opening1 = 1;
wf_penalties->gap_extension1 = -1;
wf_penalties->gap_opening2 = -1;
wf_penalties->gap_extension2 = -1;
}
void wavefront_penalties_set_edit(
wavefront_penalties_t* const wf_penalties) {
// Set distance model
wf_penalties->distance_metric = edit;
// Set penalties
wf_penalties->match = 0;
wf_penalties->mismatch = 1;
wf_penalties->gap_opening1 = 1;
wf_penalties->gap_extension1 = -1;
wf_penalties->gap_opening2 = -1;
wf_penalties->gap_extension2 = -1;
}
void wavefront_penalties_set_linear(
wavefront_penalties_t* const wf_penalties,
linear_penalties_t* const linear_penalties) {
// Set distance model
wf_penalties->distance_metric = gap_linear;
// Check base penalties
if (linear_penalties->match > 0) {
fprintf(stderr,"[WFA::Penalties] Match score must be negative or zero (M=%d)\n",linear_penalties->match);
exit(1);
} else if (linear_penalties->mismatch <= 0 || linear_penalties->indel <= 0) {
fprintf(stderr,"[WFA::Penalties] Penalties (X=%d,D=%d,I=%d) must be (X>0,D>0,I>0)\n",
linear_penalties->mismatch,linear_penalties->indel,linear_penalties->indel);
exit(1);
}
// Set penalties (if needed, adjust using Eizenga's formula)
if (linear_penalties->match < 0) {
wf_penalties->match = linear_penalties->match;
wf_penalties->mismatch = 2*linear_penalties->mismatch - 2*linear_penalties->match;
wf_penalties->gap_opening1 = 2*linear_penalties->indel - linear_penalties->match;
} else {
wf_penalties->match = 0;
wf_penalties->mismatch = linear_penalties->mismatch;
wf_penalties->gap_opening1 = linear_penalties->indel;
}
// Set unused
wf_penalties->gap_extension1 = -1;
wf_penalties->gap_opening2 = -1;
wf_penalties->gap_extension2 = -1;
}
void wavefront_penalties_set_affine(
wavefront_penalties_t* const wf_penalties,
affine_penalties_t* const affine_penalties) {
// Set distance model
wf_penalties->distance_metric = gap_affine;
// Check base penalties
if (affine_penalties->match > 0) {
fprintf(stderr,"[WFA::Penalties] Match score must be negative or zero (M=%d)\n",affine_penalties->match);
exit(1);
} else if (affine_penalties->mismatch <= 0 ||
affine_penalties->gap_opening < 0 ||
affine_penalties->gap_extension <= 0) {
fprintf(stderr,"[WFA::Penalties] Penalties (X=%d,O=%d,E=%d) must be (X>0,O>=0,E>0)\n",
affine_penalties->mismatch,
affine_penalties->gap_opening,
affine_penalties->gap_extension);
exit(1);
}
// Set penalties (if needed, adjust using Eizenga's formula)
if (affine_penalties->match < 0) {
wf_penalties->match = affine_penalties->match;
wf_penalties->mismatch = 2*affine_penalties->mismatch - 2*affine_penalties->match;
wf_penalties->gap_opening1 = 2*affine_penalties->gap_opening;
wf_penalties->gap_extension1 = 2*affine_penalties->gap_extension - affine_penalties->match;
} else {
wf_penalties->match = 0;
wf_penalties->mismatch = affine_penalties->mismatch;
wf_penalties->gap_opening1 = affine_penalties->gap_opening;
wf_penalties->gap_extension1 = affine_penalties->gap_extension;
}
// Set unused
wf_penalties->gap_opening2 = -1;
wf_penalties->gap_extension2 = -1;
}
void wavefront_penalties_set_affine2p(
wavefront_penalties_t* const wf_penalties,
affine2p_penalties_t* const affine2p_penalties) {
// Set distance model
wf_penalties->distance_metric = gap_affine_2p;
// Check base penalties
if (affine2p_penalties->match > 0) {
fprintf(stderr,"[WFA::Penalties] Match score must be negative or zero (M=%d)\n",affine2p_penalties->match);
exit(1);
} else if (affine2p_penalties->mismatch <= 0 ||
affine2p_penalties->gap_opening1 <= 0 ||
affine2p_penalties->gap_extension1 <= 0 ||
affine2p_penalties->gap_opening2 <= 0 ||
affine2p_penalties->gap_extension2 <= 0) {
fprintf(stderr,"[WFA::Penalties] Penalties (X=%d,O1=%d,E1=%d,O2=%d,E2=%d) must be (X>0,O1>=0,E1>0,O1>=0,E1>0)\n",
affine2p_penalties->mismatch,
affine2p_penalties->gap_opening1,
affine2p_penalties->gap_extension1,
affine2p_penalties->gap_opening2,
affine2p_penalties->gap_extension2);
exit(1);
}
// Set penalties (if needed, adjust using Eizenga's formula)
if (affine2p_penalties->match < 0) {
wf_penalties->match = affine2p_penalties->match;
wf_penalties->mismatch = 2*affine2p_penalties->mismatch - 2*wf_penalties->match;
wf_penalties->gap_opening1 = 2*affine2p_penalties->gap_opening1;
wf_penalties->gap_extension1 = 2*affine2p_penalties->gap_extension1 - affine2p_penalties->match;
wf_penalties->gap_opening2 = 2*affine2p_penalties->gap_opening2;
wf_penalties->gap_extension2 = 2*affine2p_penalties->gap_extension2 - affine2p_penalties->match;
} else {
wf_penalties->match = 0;
wf_penalties->mismatch = affine2p_penalties->mismatch;
wf_penalties->gap_opening1 = affine2p_penalties->gap_opening1;
wf_penalties->gap_extension1 = affine2p_penalties->gap_extension1;
wf_penalties->gap_opening2 = affine2p_penalties->gap_opening2;
wf_penalties->gap_extension2 = affine2p_penalties->gap_extension2;
}
}
/*
* Display
*/
void wavefront_penalties_print(
FILE* const stream,
wavefront_penalties_t* const wf_penalties) {
// Select penalties mode
switch (wf_penalties->distance_metric) {
case indel:
fprintf(stream,"(Indel)");
break;
case edit:
fprintf(stream,"(Edit)");
break;
case gap_linear:
fprintf(stream,"(GapLinear,%d,%d)",
wf_penalties->mismatch,
wf_penalties->gap_opening1);
break;
case gap_affine:
fprintf(stream,"(GapAffine,%d,%d,%d)",
wf_penalties->mismatch,
wf_penalties->gap_opening1,
wf_penalties->gap_extension1);
break;
case gap_affine_2p:
fprintf(stream,"(GapAffine2p,%d,%d,%d,%d,%d)",
wf_penalties->mismatch,
wf_penalties->gap_opening1,
wf_penalties->gap_extension1,
wf_penalties->gap_opening2,
wf_penalties->gap_extension2);
break;
default:
break;
}
}
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