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kalignP_misc.c
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kalignP_misc.c
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/*
kalignP_misc.c
Copyright (C) 2010 Nanjiang Shu <[email protected]>
Department of Biochemistry and Biophysics
Stockholm University
Description: multiple sequence alignment supporting external supplied
position specific gap penalties
This software is derived from
Kalign version 2.03, Copyright (C) 2006 Timo Lassmann
http://msa.cgb.ki.se/
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
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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
A copy of this license is in the COPYING file.
*/
#include <string.h>
#include <ctype.h>
#include "kalignP.h"
#include "assert.h"
#ifndef WHITE_SPACE
#define WHITE_SPACE " \t\r\n"
#endif
void print_tree(struct aln_tree_node* p,struct alignment* aln,char* outfile)
{
FILE *fout = NULL;
if ((fout = fopen(outfile, "w")) == NULL){
fprintf(stderr,"can't open output\n");
exit(0);
}
//fprintf(stderr,"\n\n%s\n",outfile);
/*if(byg_start("xml",outfile) != -1){
fprintf(fout,"<?xml version=\"1.0\" encoding=\"UTF-8\"?> <phyloxml xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.phyloxml.org/schema/phyloxml.xsd\"><phylogeny>\n");
print_phyloxml_tree(p,aln,fout);
fprintf(fout,"</phylogeny></phyloxml>\n");
}else{*/
print_newick_tree(p,aln,fout);
fprintf(fout,";");
//}
fclose(fout);
}
void print_newick_tree(struct aln_tree_node* p,struct alignment* aln,FILE *fout)
{
int j;
if(p->links[0]){
fprintf(fout,"(");
print_newick_tree(p->links[0],aln,fout);
}
if(p->num < numseq){
//If you want to print the actual names of the sequences
for (j = 0; j < aln->lsn[p->num];j++){
if(isspace((int)aln->sn[p->num][j])){
fprintf(fout,"_");
}else{
fprintf(fout,"%c",aln->sn[p->num][j]);
}
}
//If you want to print the just the number of the sequence
//fprintf(stdout,"%d",p->num);
}else{
fprintf(fout,",");
}
if(p->links[1]){
print_newick_tree(p->links[1],aln,fout);
fprintf(fout,")");
}
}
void print_phyloxml_tree(struct aln_tree_node* p,struct alignment* aln,FILE *fout)
{
int j;
if(p->links[0]){
fprintf(fout,"<clade>\n");
print_phyloxml_tree(p->links[0],aln,fout);
}
if(p->num < numseq){
//If you want to print the actual names of the sequences
fprintf(fout,"<clade>\n<name>");
for (j = 0; j < aln->lsn[p->num];j++){
fprintf(fout,"%c",aln->sn[p->num][j]);
}
fprintf(fout,"</name>\n</clade>\n");
//If you want to print the just the number of the sequence
//fprintf(stdout,"%d",p->num);
}else{
//fprintf(fout,",");
}
if(p->links[1]){
print_phyloxml_tree(p->links[1],aln,fout);
fprintf(fout,"</clade>\n");
}
}
struct alignment* sort_sequences(struct alignment* aln,int* tree,char* sort)
{
int i,j,a,b,c;
int choice = 0;
if(sort){
if (byg_start("input",sort) != -1){
choice = 0;
}else if (byg_start("tree",sort) != -1){
choice = 1;
}else if (byg_start("gaps",sort) != -1){
choice = 2;
}else{
choice = 3;
}
}
//fprintf(stderr,"COICE:%d\n",choice);
switch(choice){
case 0:
for (i = 0; i < numseq;i++){
aln->nsip[i] = i;
}
break;
case 1:
c = 0;
for (i = 0; i < (numseq-1)*3;i +=3){
//fprintf(stderr,"TREE %d %d %d\n",tree[i],tree[i+1],tree[i+2]);
if(tree[i] < numseq){
aln->nsip[c] = tree[i];
c++;
}
if(tree[i+1] < numseq){
aln->nsip[c] = tree[i+1];
c++;
}
}
break;
case 2:
for (i = 0; i < numseq;i++){
a = 1000000;
b = -1;
for (j =0; j<numseq;j++){
if(aln->nsip[j] < a){
a = aln->nsip[j];
b = j;
}
}
tree[i] = b;
aln->nsip[b] = 1000000;
}
for (i = 0; i < numseq;i++){
aln->nsip[i] = tree[i];
}
break;
case 3:
aln = sort_in_relation(aln,sort);
break;
default:
for (i = 0; i < numseq;i++){
aln->nsip[i] = i;
}
break;
}
/*for (i = 0; i < numseq;i++){
fprintf(stderr,"%d\n",aln->nsip[i]);
}*/
return aln;
}
struct alignment* sort_in_relation(struct alignment* aln,char* sort)
{
int i,j,c;
int target = -1;
int id = 0;
int positions = 0;
int posa = 0;
int posb = 0;
for (i = 0; i < numseq;i++){
if (byg_start(sort,aln->sn[i]) != -1){
target = i;
aln->sip[i][0] = 1000;
break;
}
}
if(target == -1){
target = 0;
aln->sip[0][0] = 1000;
}
for (i = 0; i < numseq;i++){
if(i != target){
posa = 0;
posb =0;
c = 0;
id = 0;
positions = 0;
for (j = 0; j < aln->sl[i];j++){
posa += aln->s[i][j]+1;
while(posa > posb){
posb += aln->s[target][c]+1;
c++;
}
if(posa == posb){
if((int) aln->seq[i][j] == (int) aln->seq[target][c-1]){
id += 1000;
}
positions += 1;
}
}
if(positions){
aln->sip[i][0] = id/positions;
}else{
aln->sip[i][0] = 0;
}
}
}
for (i = 0; i < numseq;i++){
aln->nsip[i] = i;
}
quickSort(aln, numseq);
return aln;
}
void quickSort(struct alignment* aln, int array_size)
{
q_sort(aln, 0, array_size - 1);
}
void q_sort(struct alignment* aln, int left, int right)
{
int pivot, l_hold, r_hold;
int pivot2;
l_hold = left;
r_hold = right;
pivot2 = aln->nsip[left];
pivot = aln->sip[left][0];// numbers[left];
while (left < right){
while ((aln->sip[right][0] <= pivot) && (left < right)){
right--;
}
if (left != right){
aln->sip[left][0] = aln->sip[right][0];
aln->nsip[left] = aln->nsip[right];
left++;
}
while ((aln->sip[left][0] >= pivot) && (left < right)){
left++;
}
if (left != right){
aln->sip[right][0] = aln->sip[left][0];
aln->nsip[right] = aln->nsip[left];
right--;
}
}
aln->sip[left][0] = pivot;
aln->nsip[left] = pivot2;
pivot = left;
left = l_hold;
right = r_hold;
if (left < pivot){
q_sort(aln, left, pivot-1);
}
if (right > pivot){
q_sort(aln, pivot+1, right);
}
}
int* readtree(struct aln_tree_node* p,int* tree)
{
if(p->links[0]){
tree = readtree(p->links[0],tree);
}
if(p->links[1]){
tree = readtree(p->links[1],tree);
}
if(p->links[0]){
if(p->links[1]){
tree[tree[0]] = p->links[0]->num;
tree[tree[0]+1] = p->links[1]->num;
tree[tree[0]+2] = p->num;
tree[0] +=3;
free(p->links[0]->internal_lables);
free(p->links[0]->links);
free(p->links[0]);
free(p->links[1]->internal_lables);
free(p->links[1]->links);
free(p->links[1]);
}
}
return tree;
}
struct alignment* make_dna(struct alignment* aln)
{
//int aacode[26] = {0,1,2,3,4,5,6,7,8,-1,9,10,11,12,23,13,14,15,16,17,17,18,19,20,21,22};
int i,j;
int* p;
for(i = 0;i < numseq;i++){
p = aln->s[i];
for (j = 0; j < aln->sl[i];j++){
switch(p[j]){
case 2: //C
p[j] = 1;
break;
case 6: //G
p[j] = 2;
break;
case 17: //T or U
p[j] = 3;
break;
case 12: // N
p[j] = 4;
break;
case 20: // X
p[j] = 4;
break;
case 23://O whatever that is...
p[j] = 4;
break;
}
// printf("%d\n",p[j]);
}
}
return aln;
}
int IsInCharSet(const char ch, const char *charSet, int n /*= 0 */)/*{{{*/
/*****************************************************************************
* check if the character "ch" is in charSet,
****************************************************************************/
{
if(n == 0)
n = strlen(charSet);
int i;
for(i = 0 ;i < n ; i ++)
{
if(ch == charSet[i])
return 1;
}
return 0;
}/*}}}*/
char *SpanExcluding(const char* strForSpan,char* strAfterSpan, const char charSet[]/*=WHITE_SPACE*/)/*{{{*/
//**********************************************************************
// SpanExcluding()
// compress the string by removing the characters in the charSet
// and store the compressed string into strAfterSpan
// the search is case-sensitive
// default charSet is WHITE_SPACE
//**********************************************************************
{
int l = strlen(strForSpan);
int n = strlen(charSet);
int i,j ;
j = 0 ;
for(i = 0 ; i < l ;i ++)
{
if(!IsInCharSet(strForSpan[i],charSet, n))
{
strAfterSpan[j] = strForSpan[i] ;
j ++ ;
}
}
strAfterSpan[j] = '\0' ;
return strAfterSpan;
}/*}}}*/
int fgetline(FILE* fp, char* line, int max/* = 0x7FFFFFFF*/)/*{{{*/
/*****************************************************************************
* Read one line from fp, copying it to line array (but no more than max
* chars). Does not place terminating \n in line array.
* it can be called without "max" flag, but should make sure the allocated
* memory for "line" is larger than the longest line.
*
* Returns: line length, or 0 for empty line, or "EOF" for end-of-file.
*
* since fgetc(), getc(), getchar(), returns int value,always use an int
* variable to store the result of the fgetc(), getc() and getchar().
* getc() is faster than fgetc()
* LOG: 2006-04-26 16:31:29 Wednesday Week 17 <nanjiang@shu>
* bug fixed for '\n' return keys,
* now it is valid for both dos and unix
****************************************************************************/
{
int nch = 0; /* record number of characters actually read */
int c;
max = max - 1; /* leave room for '\0' */
while((c = getc(fp)) != EOF)
{
if(c == 0x0d ) continue; /* in unix, '\n'= 0x0a, thus 0x0d will be cheated as another character*/
if(c == '\n') break; /* in dos, '\n' is also equal to 0x0a, but the preceding 0x0d will not be read*/
if(nch < max)
{
line[nch] = c;
nch = nch + 1;
}
}
line[nch] = '\0';
if(c == EOF && nch == 0) return EOF;
else return nch;
}/*}}}*/
int checkfilestream(FILE *fp, const char* filename, const char *mode, int isAssert /*=false*/)/*{{{*/
{
if( fp == 0)
{
fprintf(stderr,"Can not open file '%s' with mode '%s'\n", filename,mode);
if(isAssert)
{
assert(fp != 0);
}
return -1;
}
else
return 0;
}
/*}}}*/
int ReadSMatrix(const char *filename, short **S, char *alphabet)/*{{{*/
/*****************************************************************************
* read in substitution matrix for protein sequence alignment,
* e.g., BLOSUM62
****************************************************************************/
{
int linesize;
int maxline = 300;
char *line = malloc(sizeof(char)*maxline+1);
char *pch;
int i,j;
FILE* fpout = NULL;
fpout = fopen(filename,"r");
checkfilestream(fpout,filename, "r", 1);
while(fgetline(fpout, line,maxline) != EOF)
{
if(line[0] != '#') break ;
}
SpanExcluding(line,alphabet," ");
int n = strlen(alphabet);
char delim[] = WHITE_SPACE;
i = 0;
while((linesize = fgetline(fpout, line,maxline))!= EOF)
{
pch = strtok(line, delim);
j = 0;
while(pch != NULL)
{
if(j >= 1 && j < n+1) {
S[i][j-1] = atoi(pch);
}
j ++;
pch = strtok(NULL,delim);
}
i ++;
}
if (i != n)
{
fprintf(stderr,"Error! The number of rows and columns in the matrix %s are not equal.\n",filename);
assert(i == n);
}
fclose(fpout);
free(line);
return n;
}
/*}}}*/
float** read_matrix_new(float** subm,struct parameters* param) {/*{{{*/
/*updated 2014-11-27 by Nanjiang, this function also accept user input substitution
* matrix*/
int i,j;
int m_pos = 0;
short *matrix_pointer = 0;
char matrix_alphabet[] = "ABCDEFGHIKLMNPQRSTVWXYZ";
int size_sub_matrix = strlen(matrix_alphabet);
short *user_matrix = 0;
if (param->custom_sub_matrix_file){
short **Mtmp = 0;
Mtmp = malloc(sizeof(short*) * size_sub_matrix+10);
for (i = 0; i < size_sub_matrix; i++){
Mtmp[i] = malloc(sizeof(short)*size_sub_matrix+10);
}
char *user_alphabet = malloc(sizeof(char)*size_sub_matrix+10);
int nvalue = ReadSMatrix(param->custom_sub_matrix_file, Mtmp, user_alphabet);
user_matrix = malloc(sizeof(short)*size_sub_matrix*size_sub_matrix);
m_pos = 0;
for (i = 0; i< size_sub_matrix; i++){
for (j=0 ; j <=i; j++){
user_matrix[m_pos] = Mtmp[i][j]*10;
m_pos ++;
}
}
free(user_alphabet);
for (i=0;i<size_sub_matrix;i++){
free(Mtmp[i]);
}
free(Mtmp);
}
short blosum50mt[]={/*{{{*/
5,
-2, 5,
-1, -3, 13,
-2, 5, -4, 8,
-1, 1, -3, 2, 6,
-3, -4, -2, -5, -3, 8,
0, -1, -3, -1, -3, -4, 8,
-2, 0, -3, -1, 0, -1, -2, 10,
-1, -4, -2, -4, -4, 0, -4, -4, 5,
-1, 0, -3, -1, 1, -4, -2, 0, -3, 6,
-2, -4, -2, -4, -3, 1, -4, -3, 2, -3, 5,
-1, -3, -2, -4, -2, 0, -3, -1, 2, -2, 3, 7,
-1, 4, -2, 2, 0, -4, 0, 1, -3, 0, -4, -2, 7,
-1, -2, -4, -1, -1, -4, -2, -2, -3, -1, -4, -3, -2, 10,
-1, 0, -3, 0, 2, -4, -2, 1, -3, 2, -2, 0, 0, -1, 7,
-2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 7,
1, 0, -1, 0, -1, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5,
0, 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5,
0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -3, -3, -3, -3, -2, 0, 5,
-3, -5, -5, -5, -3, 1, -3, -3, -3, -3, -2, -1, -4, -4, -1, -3, -4, -3, -3, 15,
-1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, 0, -1, -3, -1,
-2, -3, -3, -3, -2, 4, -3, 2, -1, -2, -1, 0, -2, -3, -1, -1, -2, -2, -1, 2, -1, 8,
-1, 2, -3, 1, 5, -4, -2, 0, -3, 1, -3, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 5
};/*}}}*/
short blosum62mt[]={/*{{{*/
/*A*/ 40,
/*B*/ -20, 40,
/*C*/ 0, -30, 90,
/*D*/ -20, 40, -30, 60,
/*E*/ -10, 10, -40, 20, 50,
/*F*/ -20, -30, -20, -30, -30, 60,
/*G*/ 0, -10, -30, -10, -20, -30, 60,
/*H*/ -20, 0, -30, -10, 0, -10, -20, 80,
/*I*/ -10, -30, -10, -30, -30, 0, -40, -30, 40,
/*K*/ -10, 0, -30, -10, 10, -30, -20, -10, -30, 50,
/*L*/ -10, -40, -10, -40, -30, 0, -40, -30, 20, -20, 40,
/*M*/ -10, -30, -10, -30, -20, 0, -30, -20, 10, -10, 20, 50,
/*N*/ -20, 30, -30, 10, 0, -30, 0, 10, -30, 0, -30, -20, 60,
/*P*/ -10, -20, -30, -10, -10, -40, -20, -20, -30, -10, -30, -20, -20, 70,
/*Q*/ -10, 0, -30, 0, 20, -30, -20, 0, -30, 10, -20, 0, 0, -10, 50,
/*R*/ -10, -10, -30, -20, 0, -30, -20, 0, -30, 20, -20, -10, 0, -20, 10, 50,
/*S*/ 10, 0, -10, 0, 0, -20, 0, -10, -20, 0, -20, -10, 10, -10, 0, -10, 40,
/*T*/ 0, -10, -10, -10, -10, -20, -20, -20, -10, -10, -10, -10, 0, -10, -10, -10, 10, 50,
/*V*/ 0, -30, -10, -30, -20, -10, -30, -30, 30, -20, 10, 10, -30, -20, -20, -30, -20, 0, 40,
/*W*/ -30, -40, -20, -40, -30, 10, -20, -20, -30, -30, -20, -10, -40, -40, -20, -30, -30, -20, -30, 110,
/*X*/ 0, -10, -20, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -20, -10, -10, 0, 0, -10, -20, -10,
/*Y*/ -20, -30, -20, -30, -20, 30, -30, 20, -10, -20, -10, -10, -20, -30, -10, -20, -20, -20, -10, 20, -10, 70,
/*Z*/ -10, 10, -30, 10, 40, -30, -20, 0, -30, 10, -30, -10, 0, -10, 30, 0, 0, -10, -20, -30, -10, -20, 40
/* A B C D E F G H I K L M N P Q R S T V W X Y Z */
};/*}}}*/
short gon250mt[]={/*{{{*/
24,
0, 0,
5, 0, 115,
-3, 0, -32, 47,
0, 0, -30, 27, 36,
-23, 0, -8, -45, -39, 70,
5, 0, -20, 1, -8, -52, 66,
-8, 0, -13, 4, 4, -1, -14, 60,
-8, 0, -11, -38, -27, 10, -45, -22, 40,
-4, 0, -28, 5, 12, -33, -11, 6, -21, 32,
-12, 0, -15, -40, -28, 20, -44, -19, 28, -21, 40,
-7, 0, -9, -30, -20, 16, -35, -13, 25, -14, 28, 43,
-3, 0, -18, 22, 9, -31, 4, 12, -28, 8, -30, -22, 38,
3, 0, -31, -7, -5, -38, -16, -11, -26, -6, -23, -24, -9, 76,
-2, 0, -24, 9, 17, -26, -10, 12, -19, 15, -16, -10, 7, -2, 27,
-6, 0, -22, -3, 4, -32, -10, 6, -24, 27, -22, -17, 3, -9, 15, 47,
11, 0, 1, 5, 2, -28, 4, -2, -18, 1, -21, -14, 9, 4, 2, -2, 22,
6, 0, -5, 0, -1, -22, -11, -3, -6, 1, -13, -6, 5, 1, 0, -2, 15, 25,
1, 0, 0, -29, -19, 1, -33, -20, 31, -17, 18, 16, -22, -18, -15, -20, -10, 0, 34,
-36, 0, -10, -52, -43, 36, -40, -8, -18, -35, -7, -10, -36, -50, -27, -16, -33, -35, -26, 142,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-22, 0, -5, -28, -27, 51, -40, 22, -7, -21, 0, -2, -14, -31, -17, -18, -19, -19, -11, 41, 0, 78,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};/*}}}*/
if (param->custom_sub_matrix_file){ /*using user defined matrix*/
matrix_pointer = user_matrix;
gpo = (float)55.0;
gpe = (float)8.0;
tgpe = (float)1.0;
}else{
if(param->sub_matrix){
if(byg_start(param->sub_matrix,"blosum62BLOSUM62") != -1){
matrix_pointer = blosum62mt;
//m_pos = 0;
//for (i = 0;i < 23;i++){
// for (j = 0;j <= i;j++){
// matrix_pointer[m_pos] = matrix_pointer[m_pos] * 10;
// m_pos++;
// }
//}
gpo = (float)55.0;
gpe = (float)8.0;
tgpe = (float)1.0;
}
if(byg_start(param->sub_matrix,"blosum50BLOSUM50") != -1){
matrix_pointer = blosum50mt;
m_pos = 0;
for (i = 0;i < 23;i++){
for (j = 0;j <= i;j++){
matrix_pointer[m_pos] = matrix_pointer[m_pos] * 10;
m_pos++;
}
}
gpo = (float)55.0;
gpe = (float)8.0;
tgpe = (float)1.0;
}
//vogt....
}else{
if(!param->dna){
// gpo:5.494941 gpe:0.852492 tgpe:0.442410 bonus: 3.408872 z-cutoff: 58.823309 -> 0.829257 accuracy on bb3
gpo = (float)54.94941;
gpe = (float)8.52492;
tgpe = (float)4.42410;
//gpo = 54;
//gpe = 8;
//tgpe = 4;
//-gpo 10.9898 -gpe 0.852492 -tgpe 0.442410 -bonus 0.2 -zcutoff 58.823309
// param->secret = 0.2;
matrix_pointer = gon250mt;
}else{
//gpo = 400;
// gpe = 30;
//tgpe = 30;
//param->gpo = 43.4;
//param->gpe = 3.94;
//param->tgpe = 29.26;
//gpo = 43.4 *5;
gpo = (float)217.0;
gpe = (float)39.4;
tgpe = (float)292.6;
//param->secret = 28.3;
param->zlevel = (float)61.08;
param->internal_gap_weight = (float)49.14;
}
}
}
if(param->gpo!= -1){
//param->gpo *= 5;
gpo = param->gpo;
}
if(param->gpe != -1){
//param->gpe *= 10;
gpe = param->gpe;
}
if(param->tgpe != -1){
//param->tgpe *= 10;
tgpe = param->tgpe;
}
// if(param->secret != -1){
// //param->secret *= 10;
// }else
if(param->secret == -1){
if(!param->dna){
param->secret = 0.2;
}else{
param->secret = 283.0;
}
}
//fprintf(stderr,"%d %d %d %d\n",gpo,gpe,tgpe, (int)param->secret);
subm = malloc(sizeof (float*) * 32);
for (i = 32;i--;){
subm[i] = malloc(sizeof(float) * 32);
for (j = 32;j--;){
subm[i][j] = param->secret;//0;//gpe << 1;//-5;// better on Balibase
}
}
if(param->dna){
/*subm[0][0] += 10;
subm[0][1] += 6;
subm[1][0] += 6;
subm[1][1] += 10;
subm[2][2] += 10;
subm[2][3] += 6;
subm[3][2] += 6;
subm[3][3] += 10;*/
// A C G T . N
// A 91 -114 -31 -123 0 -43
subm[0][0] += 91;
subm[0][1] += -114;
subm[0][2] += -31;
subm[0][3] += -123;
// C -114 100 -125 -31 0 -43
subm[1][0] += -114;
subm[1][1] += 100;
subm[1][2] += -125;
subm[1][3] += -31;
// G -31 -125 100 -114 0 -43
subm[2][0] += -31;
subm[2][1] += -125;
subm[2][2] += 100;
subm[2][3] += -114;
// T -123 -31 -114 91 0 -43
subm[3][0] += -123;
subm[3][1] += -31;
subm[3][2] += -114;
subm[3][3] += 91;
// . 0 0 0 0 0 0
// N -43 -43 -43 -43 0 -43
/*for (i = 0; i < 4;i++){
for (j = 0;j < 4;j++){
if(i == j){
subm[i][j] += 1;
}else{
subm[i][j] -= 3;
}
}
}*/
}else{
m_pos = 0;
for (i = 0;i < 23;i++){
for (j = 0;j <= i;j++){
if (i == j){
// subm[i][j] += blosum62mt[m_pos]*10;
subm[i][j] += matrix_pointer[m_pos];
}else{
// subm[i][j] += blosum62mt[m_pos]*10;
// subm[j][i] += blosum62mt[m_pos]*10;
subm[i][j] += matrix_pointer[m_pos];
subm[j][i] += matrix_pointer[m_pos];
}
m_pos++;
}
}
/*for (i = 0; i < 23;i++){
for (j = 0; j < 23;j++){
fprintf(stderr,"%d ",subm[i][j]);
}
fprintf(stderr,"\n");
}
fprintf(stderr,"\n");*/
}
if (user_matrix){
free(user_matrix);
}
return subm;
}/*}}}*/
float** read_matrix(float** subm,struct parameters* param)
{
int i,j;
int m_pos = 0;
short *matrix_pointer = 0;
short blosum50mt[]={
5,
-2, 5,
-1, -3, 13,
-2, 5, -4, 8,
-1, 1, -3, 2, 6,
-3, -4, -2, -5, -3, 8,
0, -1, -3, -1, -3, -4, 8,
-2, 0, -3, -1, 0, -1, -2, 10,
-1, -4, -2, -4, -4, 0, -4, -4, 5,
-1, 0, -3, -1, 1, -4, -2, 0, -3, 6,
-2, -4, -2, -4, -3, 1, -4, -3, 2, -3, 5,
-1, -3, -2, -4, -2, 0, -3, -1, 2, -2, 3, 7,
-1, 4, -2, 2, 0, -4, 0, 1, -3, 0, -4, -2, 7,
-1, -2, -4, -1, -1, -4, -2, -2, -3, -1, -4, -3, -2, 10,
-1, 0, -3, 0, 2, -4, -2, 1, -3, 2, -2, 0, 0, -1, 7,
-2, -1, -4, -2, 0, -3, -3, 0, -4, 3, -3, -2, -1, -3, 1, 7,
1, 0, -1, 0, -1, -3, 0, -1, -3, 0, -3, -2, 1, -1, 0, -1, 5,
0, 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 2, 5,
0, -4, -1, -4, -3, -1, -4, -4, 4, -3, 1, 1, -3, -3, -3, -3, -2, 0, 5,
-3, -5, -5, -5, -3, 1, -3, -3, -3, -3, -2, -1, -4, -4, -1, -3, -4, -3, -3, 15,
-1, -1, -2, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, -2, -1, -1, -1, 0, -1, -3, -1,
-2, -3, -3, -3, -2, 4, -3, 2, -1, -2, -1, 0, -2, -3, -1, -1, -2, -2, -1, 2, -1, 8,
-1, 2, -3, 1, 5, -4, -2, 0, -3, 1, -3, -1, 0, -1, 4, 0, 0, -1, -3, -2, -1, -2, 5};
short blosum62mt[]={
40,
-20, 40,
0, -30, 90,
-20, 40, -30, 60,
-10, 10, -40, 20, 50,
-20, -30, -20, -30, -30, 60,
0, -10, -30, -10, -20, -30, 60,
-20, 0, -30, -10, 0, -10, -20, 80,
-10, -30, -10, -30, -30, 0, -40, -30, 40,
-10, 0, -30, -10, 10, -30, -20, -10, -30, 50,
-10, -40, -10, -40, -30, 0, -40, -30, 20, -20, 40,
-10, -30, -10, -30, -20, 0, -30, -20, 10, -10, 20, 50,
-20, 30, -30, 10, 0, -30, 0, 10, -30, 0, -30, -20, 60,
-10, -20, -30, -10, -10, -40, -20, -20, -30, -10, -30, -20, -20, 70,
-10, 0, -30, 0, 20, -30, -20, 0, -30, 10, -20, 0, 0, -10, 50,
-10, -10, -30, -20, 0, -30, -20, 0, -30, 20, -20, -10, 0, -20, 10, 50,
10, 0, -10, 0, 0, -20, 0, -10, -20, 0, -20, -10, 10, -10, 0, -10, 40,
0, -10, -10, -10, -10, -20, -20, -20, -10, -10, -10, -10, 0, -10, -10, -10, 10, 50,
0, -30, -10, -30, -20, -10, -30, -30, 30, -20, 10, 10, -30, -20, -20, -30, -20, 0, 40,
-30, -40, -20, -40, -30, 10, -20, -20, -30, -30, -20, -10, -40, -40, -20, -30, -30, -20, -30, 110,
0, -10, -20, -10, -10, -10, -10, -10, -10, -10, -10, -10, -10, -20, -10, -10, 0, 0, -10, -20, -10,
-20, -30, -20, -30, -20, 30, -30, 20, -10, -20, -10, -10, -20, -30, -10, -20, -20, -20, -10, 20, -10, 70,
-10, 10, -30, 10, 40, -30, -20, 0, -30, 10, -30, -10, 0, -10, 30, 0, 0, -10, -20, -30, -10, -20, 40};
short gon250mt[]={
24,
0, 0,
5, 0, 115,
-3, 0, -32, 47,
0, 0, -30, 27, 36,
-23, 0, -8, -45, -39, 70,
5, 0, -20, 1, -8, -52, 66,
-8, 0, -13, 4, 4, -1, -14, 60,
-8, 0, -11, -38, -27, 10, -45, -22, 40,
-4, 0, -28, 5, 12, -33, -11, 6, -21, 32,
-12, 0, -15, -40, -28, 20, -44, -19, 28, -21, 40,
-7, 0, -9, -30, -20, 16, -35, -13, 25, -14, 28, 43,
-3, 0, -18, 22, 9, -31, 4, 12, -28, 8, -30, -22, 38,
3, 0, -31, -7, -5, -38, -16, -11, -26, -6, -23, -24, -9, 76,
-2, 0, -24, 9, 17, -26, -10, 12, -19, 15, -16, -10, 7, -2, 27,
-6, 0, -22, -3, 4, -32, -10, 6, -24, 27, -22, -17, 3, -9, 15, 47,
11, 0, 1, 5, 2, -28, 4, -2, -18, 1, -21, -14, 9, 4, 2, -2, 22,
6, 0, -5, 0, -1, -22, -11, -3, -6, 1, -13, -6, 5, 1, 0, -2, 15, 25,
1, 0, 0, -29, -19, 1, -33, -20, 31, -17, 18, 16, -22, -18, -15, -20, -10, 0, 34,
-36, 0, -10, -52, -43, 36, -40, -8, -18, -35, -7, -10, -36, -50, -27, -16, -33, -35, -26, 142,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
-22, 0, -5, -28, -27, 51, -40, 22, -7, -21, 0, -2, -14, -31, -17, -18, -19, -19, -11, 41, 0, 78,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
if(param->sub_matrix){
if(byg_start(param->sub_matrix,"blosum62BLOSUM62") != -1){
matrix_pointer = blosum62mt;
//m_pos = 0;
//for (i = 0;i < 23;i++){
// for (j = 0;j <= i;j++){
// matrix_pointer[m_pos] = matrix_pointer[m_pos] * 10;
// m_pos++;
// }
//}
gpo = (float)55.0;
gpe = (float)8.0;
tgpe = (float)1.0;
}
if(byg_start(param->sub_matrix,"blosum50BLOSUM50") != -1){
matrix_pointer = blosum50mt;
m_pos = 0;
for (i = 0;i < 23;i++){
for (j = 0;j <= i;j++){
matrix_pointer[m_pos] = matrix_pointer[m_pos] * 10;
m_pos++;
}
}
gpo = (float)55.0;
gpe = (float)8.0;
tgpe = (float)1.0;
}
//vogt....
}else{
if(!param->dna){
// gpo:5.494941 gpe:0.852492 tgpe:0.442410 bonus: 3.408872 z-cutoff: 58.823309 -> 0.829257 accuracy on bb3
gpo = (float)54.94941;
gpe = (float)8.52492;
tgpe = (float)4.42410;
//gpo = 54;
//gpe = 8;
//tgpe = 4;
//-gpo 10.9898 -gpe 0.852492 -tgpe 0.442410 -bonus 0.2 -zcutoff 58.823309
// param->secret = 0.2;
matrix_pointer = gon250mt;
}else{
//gpo = 400;
// gpe = 30;
//tgpe = 30;
//param->gpo = 43.4;
//param->gpe = 3.94;
//param->tgpe = 29.26;
//gpo = 43.4 *5;
gpo = (float)217.0;
gpe = (float)39.4;
tgpe = (float)292.6;
//param->secret = 28.3;
param->zlevel = (float)61.08;
param->internal_gap_weight = (float)49.14;
}
}
if(param->gpo!= -1){
//param->gpo *= 5;
gpo = param->gpo;
}
if(param->gpe != -1){
//param->gpe *= 10;
gpe = param->gpe;
}
if(param->tgpe != -1){
//param->tgpe *= 10;
tgpe = param->tgpe;
}
// if(param->secret != -1){
// //param->secret *= 10;
// }else{
if(param->secret == -1){
if(!param->dna){
param->secret = 0.2;
}else{
param->secret = 283.0;
}
}
//fprintf(stderr,"%d %d %d %d\n",gpo,gpe,tgpe, (int)param->secret);
subm = malloc(sizeof (float*) * 32);
for (i = 32;i--;){
subm[i] = malloc(sizeof(float) * 32);
for (j = 32;j--;){
subm[i][j] = param->secret;//0;//gpe << 1;//-5;// better on Balibase
}
}
if(param->dna){
/*subm[0][0] += 10;
subm[0][1] += 6;
subm[1][0] += 6;
subm[1][1] += 10;
subm[2][2] += 10;
subm[2][3] += 6;
subm[3][2] += 6;
subm[3][3] += 10;*/
// A C G T . N
// A 91 -114 -31 -123 0 -43
subm[0][0] += 91;
subm[0][1] += -114;
subm[0][2] += -31;
subm[0][3] += -123;
// C -114 100 -125 -31 0 -43
subm[1][0] += -114;
subm[1][1] += 100;
subm[1][2] += -125;
subm[1][3] += -31;
// G -31 -125 100 -114 0 -43
subm[2][0] += -31;
subm[2][1] += -125;
subm[2][2] += 100;
subm[2][3] += -114;
// T -123 -31 -114 91 0 -43
subm[3][0] += -123;
subm[3][1] += -31;
subm[3][2] += -114;
subm[3][3] += 91;
// . 0 0 0 0 0 0
// N -43 -43 -43 -43 0 -43
/*for (i = 0; i < 4;i++){
for (j = 0;j < 4;j++){
if(i == j){
subm[i][j] += 1;
}else{