+++ /dev/null
-#include <stdio.h>
-#include <stdlib.h>
-#include <math.h>
-#include <stdarg.h>
-#include <string.h>
-#include <ctype.h>
-#include "io_lib_header.h"
-#include "util_lib_header.h"
-#include "define_header.h"
-
-
-
-
-//Values as provided in Probcons V1.1
-static float EXP_UNDERFLOW_THRESHOLD = -4.60f;
-static float LOG_UNDERFLOW_THRESHOLD = 7.50f;
-//static float LOG_ZERO = -FLT_MAX;
-static float LOG_ZERO=-200000004008175468544.000000;
-static float LOG_ONE = 0.0f;
-
-//Probabilistic Alignment DNA
-
-
-
-
-static float DNAinitDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
-static float DNAgapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
-static float DNAgapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
-
-static char DNAalphabetDefault[] = "ACGUTN";
-static float DNAemitSingleDefault[6] = {0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f};
-
-static float DNAemitPairsDefault[6][6] = {
- { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f },
- { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f },
- { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f },
- { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
- { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
- { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f }
-};
-
-//Probabilistic ALignment Blosum62mt
-
-
-
-
-static float initDistrib2Default[] = { 0.6814756989f, 8.615339902e-05f, 8.615339902e-05f, 0.1591759622f, 0.1591759622 };
-static float gapOpen2Default[] = { 0.0119511066f, 0.0119511066f, 0.008008334786f, 0.008008334786 };
-static float gapExtend2Default[] = { 0.3965826333f, 0.3965826333f, 0.8988758326f, 0.8988758326 };
-
-static char alphabetDefault[] = "ARNDCQEGHILKMFPSTWYV";
-static float emitSingleDefault[20] = {
- 0.07831005f, 0.05246024f, 0.04433257f, 0.05130349f, 0.02189704f,
- 0.03585766f, 0.05615771f, 0.07783433f, 0.02601093f, 0.06511648f,
- 0.09716489f, 0.05877077f, 0.02438117f, 0.04463228f, 0.03940142f,
- 0.05849916f, 0.05115306f, 0.01203523f, 0.03124726f, 0.07343426f
-};
-
-static float emitPairsDefault[20][20] = {
- {0.02373072f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00244502f, 0.01775118f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00210228f, 0.00207782f, 0.01281864f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00223549f, 0.00161657f, 0.00353540f, 0.01911178f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00145515f, 0.00044701f, 0.00042479f, 0.00036798f, 0.01013470f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00219102f, 0.00253532f, 0.00158223f, 0.00176784f, 0.00032102f, 0.00756604f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00332218f, 0.00268865f, 0.00224738f, 0.00496800f, 0.00037956f, 0.00345128f, 0.01676565f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00597898f, 0.00194865f, 0.00288882f, 0.00235249f, 0.00071206f, 0.00142432f, 0.00214860f, 0.04062876f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00114353f, 0.00132105f, 0.00141205f, 0.00097077f, 0.00026421f, 0.00113901f, 0.00131767f, 0.00103704f, 0.00867996f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00318853f, 0.00138145f, 0.00104273f, 0.00105355f, 0.00094040f, 0.00100883f, 0.00124207f, 0.00142520f, 0.00059716f, 0.01778263f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00449576f, 0.00246811f, 0.00160275f, 0.00161966f, 0.00138494f, 0.00180553f, 0.00222063f, 0.00212853f, 0.00111754f, 0.01071834f, 0.03583921f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00331693f, 0.00595650f, 0.00257310f, 0.00252518f, 0.00046951f, 0.00312308f, 0.00428420f, 0.00259311f, 0.00121376f, 0.00157852f, 0.00259626f, 0.01612228f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00148878f, 0.00076734f, 0.00063401f, 0.00047808f, 0.00037421f, 0.00075546f, 0.00076105f, 0.00066504f, 0.00042237f, 0.00224097f, 0.00461939f, 0.00096120f, 0.00409522f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00165004f, 0.00090768f, 0.00084658f, 0.00069041f, 0.00052274f, 0.00059248f, 0.00078814f, 0.00115204f, 0.00072545f, 0.00279948f, 0.00533369f, 0.00087222f, 0.00116111f, 0.01661038f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00230618f, 0.00106268f, 0.00100282f, 0.00125381f, 0.00034766f, 0.00090111f, 0.00151550f, 0.00155601f, 0.00049078f, 0.00103767f, 0.00157310f, 0.00154836f, 0.00046718f, 0.00060701f, 0.01846071f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00631752f, 0.00224540f, 0.00301397f, 0.00285226f, 0.00094867f, 0.00191155f, 0.00293898f, 0.00381962f, 0.00116422f, 0.00173565f, 0.00250962f, 0.00312633f, 0.00087787f, 0.00119036f, 0.00180037f, 0.01346609f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00389995f, 0.00186053f, 0.00220144f, 0.00180488f, 0.00073798f, 0.00154526f, 0.00216760f, 0.00214841f, 0.00077747f, 0.00248968f, 0.00302273f, 0.00250862f, 0.00093371f, 0.00107595f, 0.00147982f, 0.00487295f, 0.01299436f, 0.0f, 0.0f, 0.0f},
- {0.00039119f, 0.00029139f, 0.00021006f, 0.00016015f, 0.00010666f, 0.00020592f, 0.00023815f, 0.00038786f, 0.00019097f, 0.00039549f, 0.00076736f, 0.00028448f, 0.00016253f, 0.00085751f, 0.00015674f, 0.00026525f, 0.00024961f, 0.00563625f, 0.0f, 0.0f},
- {0.00131840f, 0.00099430f, 0.00074960f, 0.00066005f, 0.00036626f, 0.00070192f, 0.00092548f, 0.00089301f, 0.00131038f, 0.00127857f, 0.00219713f, 0.00100817f, 0.00054105f, 0.00368739f, 0.00047608f, 0.00102648f, 0.00094759f, 0.00069226f, 0.00999315f, 0.0f},
- {0.00533241f, 0.00169359f, 0.00136609f, 0.00127915f, 0.00119152f, 0.00132844f, 0.00178697f, 0.00194579f, 0.00071553f, 0.01117956f, 0.00914460f, 0.00210897f, 0.00197461f, 0.00256159f, 0.00135781f, 0.00241601f, 0.00343452f, 0.00038538f, 0.00148001f, 0.02075171f}
-};
-
-
-static int suboptimal_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL, int mode);
-static int *** forward_so_dp ( Alignment *A, int *ns, int **ls, int **pos,int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL);
-static int *** backward_so_dp ( Alignment *A, int *ns, int **ls,int **pos,int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL);
-static int *** forward_so_dp_biphasic ( Alignment *A, int *ns, int **ls, int **pos,int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL);
-static int *** backward_so_dp_biphasic ( Alignment *A, int *ns, int **ls,int **pos,int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL);
-static int *** forward_so_dp_glocal ( Alignment *A, int *ns, int **ls, int **pos,int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL);
-static int *** backward_so_dp_glocal ( Alignment *A, int *ns, int **ls,int **pos,int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL);
-
-static int match=0;
-static int ins=1;
-static int del=2;
-static int umatch=3;
-static int ins2=3;
-static int del2=4;
-float ** get_emitPairs (char *mat, char *alp, float **p, float *s);
-int subop1_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
-{
- return suboptimal_pair_wise ( A, ns, ls, CL, 1);
-}
-
-int subop2_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
-{
- return suboptimal_pair_wise ( A, ns, ls, CL, 3);
-}
-
-
-
-int suboptimal_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL, int mode)
-{
- int ***F=NULL;
- int ***B=NULL;
- int **pos0;
- int gop, gep,gop2, gep2;
- int i, I, j, J, n, s1, s2;
- char *seqI, *seqJ;
- int id;
- int *entry;
- float opt, min, score, nscore, thres;
- int l1, l2, set;
-
-
- gop=CL->gop*SCORE_K;
- gep=CL->gep*SCORE_K;
-
- /*gop2=CL->gop*10*SCORE_K;*/
- gop2=CL->gop*2*SCORE_K;
- gep2=0;
-
- //Values Adapted from Probcons 1.1
- gop=-132;
- gep=-27;
-
- gop2=-144;
- gep2=-3;
-
- ungap(A->seq_al[ls[0][0]]);
- ungap(A->seq_al[ls[1][0]]);
-
- seqI=A->seq_al[ls[0][0]];
- seqJ=A->seq_al[ls[1][0]];
-
- I=strlen (seqI); J=strlen (seqJ);
- pos0=aln2pos_simple ( A,-1, ns, ls);
- l1=strlen (A->seq_al[ls[0][0]]);
- l2=strlen (A->seq_al[ls[1][0]]);
-
- if ( mode==1)
- {
- F=forward_so_dp (A, ns, ls, pos0,I, J,gop, gep,gop2, gep2,CL);
- B=backward_so_dp (A, ns, ls, pos0,I, J,gop, gep,gop2, gep2, CL);
- }
- else if ( mode ==2)
- {
- F=forward_so_dp_glocal (A, ns, ls, pos0,I, J,gop, gep,gop2, gep2,CL);
- B=backward_so_dp_glocal (A, ns, ls, pos0,I, J,gop, gep,gop2, gep2, CL);
- }
- else if ( mode ==3)
- {
- F=forward_so_dp_biphasic (A, ns, ls, pos0,I, J,gop, gep,gop2, gep2,CL);
- B=backward_so_dp_biphasic (A, ns, ls, pos0,I, J,gop, gep,gop2, gep2, CL);
- }
- if ( MAX5(F[match][l1][l2], F[ins][l1][l2], F[del][l1][l2],F[ins2][l1][l2], F[del2][l1][l2] )!=MAX5( B[match][1][1], B[ins][1][1], B[del][1][1], B[ins2][1][1], B[del2][1][1]))
- {
- HERE ("ERROR in subop_pair");
- fprintf ( stdout, "\nForward: %d", MAX3(F[match][l1][l2], F[ins][l1][l2], F[del][l1][l2]));
- fprintf ( stdout, "\nBackWard: %d \n\n",MAX3( B[match][1][1], B[ins][1][1], B[del][1][1]));
- }
-
-
- for (opt=0,min=0, set=0, i=1; i<=I; i++)
- for (j=1; j<=J; j++)
- {
- if ( F[match][i][j]==UNDEFINED)continue;
- F[match][i][j]+=B[match][i][j]-(CL->get_dp_cost) (A, pos0, ns[0], ls[0], i-1, pos0, ns[1], ls[1],j-1,CL);
- if (set==0)
- {set=1; opt=F[match][i][j];min=F[match][i][j];}
- opt=MAX(F[match][i][j],opt);
- min=MIN(F[match][i][j],min);
- }
-
-
- s1=name_is_in_list (A->name[ls[0][0]], (CL->S)->name, (CL->S)->nseq, 100);
- s2=name_is_in_list (A->name[ls[1][0]], (CL->S)->name, (CL->S)->nseq, 100);
-
- id=idscore_pairseq(seqI,seqJ,-12, -1, CL->M, "idmat");
-
- entry=vcalloc ( CL->entry_len, CL->el_size);
- entry[SEQ1]=s1;entry[SEQ2]=s2;
-
- thres=opt;
- for ( n=0,i=1; i<=I; i++)
- {
- for (j=1; j<=J; j++)
- {
- score=F[0][i][j];
- nscore=((score-min))/(opt-min);
-
- if (score==opt)
- {
- n++;
- entry[R1]=i;entry[R2]=j;
- entry[WE]=id;
- entry[CONS]=1;
- add_entry2list (entry,A->CL);
- }
- }
- }
-
- vfree (entry);
- free_int (pos0, -1);
- free_arrayN (F, 3);
- free_arrayN (B, 3);
-
- return A->score_aln;
-}
-/************************************************************************************************************************/
-/* */
-/* */
-/* GLOCAL */
-/* */
-/* */
-/************************************************************************************************************************/
-int *** forward_so_dp_glocal ( Alignment *A, int *ns, int **ls, int **pos0,int I, int J,int gop, int gep,int gop2, int gep2,Constraint_list *CL)
-{
- int i,j;
- int c;
- int sub;
- int ***M;
- int match=0, del=1, ins=2;
-
- M=declare_arrayN (3, sizeof (int), 5, I+1, J+1);
-
- for ( i=0; i<=I; i++)for (j=0; j<=J; j++)for (c=0; c<5; c++)M[c][i][j]=-999999;
-
- M[match][0][0]=0;
-
- for (i=1; i<=I; i++){M[del] [i][0]=i*gep;M[umatch][i][0]=i*gep2+gop2;}
- for (j=1; j<=J; j++){M[ins] [0][j]=j*gep;M[umatch][0][j]=j*gep2+gop2;}
-
-
- for (i=1; i<=I; i++)
- {
- for ( j=1; j<=J; j++)
- {
- sub=(CL->get_dp_cost) (A, pos0, ns[0], ls[0], i-1, pos0, ns[1], ls[1],j-1,CL);
-
- M[match][i][j] =MAX4 (M[match][i-1][j-1],M[del][i-1][j-1], M[ins][i-1][j-1],M[umatch][i-1][j-1])+sub;
- M[del][i][j] =MAX2 ((M[match][i-1][j]+gop), M[del][i-1][j])+gep;
- M[ins][i][j] =MAX2 ((M[match][i][j-1]+gop), M[ins][i][j-1])+gep;
- M[umatch][i][j]=MAX6 (M[match][i-1][j-1]+gop2, M[match][i][j-1]+gop2, M[match][i-1][j]+gop2,M[umatch][i-1][j-1], M[umatch][i-1][j], M[umatch][i][j-1])+gep2;
- }
- }
- return M;
-}
-int *** backward_so_dp_glocal ( Alignment *A, int *ns, int **ls, int **pos0, int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL)
-{
- int i,j;
- int c;
- int sub;
- int ***M;
-
-
-
- M=declare_arrayN (3, sizeof (int), 5, I+2, J+2);
- for ( i=I+1; i>=0; i--)for (j=J+1; j>=0; j--)for (c=0; c<5; c++)M[c][i][j]=-999999;
- M[match][I+1][J+1]=0;
-
- for (i=I; i>0; i--){M[ins] [i][J+1]=i*gep;M[umatch] [i][J+1]=i*gep2+gop2;}
- for (j=J; j>0; j--){M[del] [I+1][j]=j*gep;M[umatch] [I+1][j]=j*gep2+gop2;}
-
- for (i=I; i>0; i--)
- {
- for ( j=J; j>0; j--)
- {
- sub=(CL->get_dp_cost) (A, pos0, ns[0], ls[0], i-1, pos0, ns[1], ls[1],j-1,CL);
-
- M[match ][i][j] =MAX4 ((M[del][i+1][j+1]+gop), (M[ins][i+1][j+1]+gop), M[match][i+1][j+1], M[umatch][i+1][j+1]+gop2)+sub;
- M[del ][i][j] =MAX2 (M[match][i+1][j], M[del][i+1][j])+gep;
- M[ins ][i][j] =MAX2 (M[match][i][j+1], M[ins][i][j+1])+gep;
- M[umatch][i][j] =MAX6 (M[match][i+1][j+1], M[match][i+1][j],M[match][i][j+1], M[umatch][i+1][j+1], M[umatch][i+1][j], M[umatch][i][j+1])+gep2;
-
- }
- }
- return M;
-}
-
-
-
-
-/************************************************************************************************************************/
-/* */
-/* */
-/* SIMPLE */
-/* */
-/* */
-/************************************************************************************************************************/
-
-int *** forward_so_dp ( Alignment *A, int *ns, int **ls, int **pos0,int I, int J,int gop, int gep,int gop2, int gep2,Constraint_list *CL)
-{
- int i,j;
- int c;
- int sub;
- int ***M;
- int lgop;
-
-
-
- M=declare_arrayN (3, sizeof (int), 5, I+1, J+1);
- for ( i=0; i<=I; i++)for (j=0; j<=J; j++)for (c=0; c<3; c++)M[c][i][j]=-999999;
-
- M[match][0][0]=0;
- for (i=1; i<=I; i++){M[del] [i][0]=i*gep;}
- for (j=1; j<=J; j++){M[ins] [0][j]=j*gep;}
-
-
-
- for (i=1; i<=I; i++)
- {
- for ( j=1; j<=J; j++)
- {
- lgop=(i==I || j==J)?0:gop;
- sub=(CL->get_dp_cost) (A, pos0, ns[0], ls[0], i-1, pos0, ns[1], ls[1],j-1,CL);
-
- M[match][i][j]=MAX3 (M[del][i-1][j-1], M[ins][i-1][j-1], M[match][i-1][j-1])+sub;
- M[del][i][j] =MAX ((M[match][i-1][j]+lgop),M[del][i-1][j])+gep;
- M[ins][i][j] =MAX ((M[match][i][j-1]+lgop), M[ins][i][j-1])+gep;
- }
-
- }
-
- return M;
- }
-int *** backward_so_dp ( Alignment *A, int *ns, int **ls, int **pos0, int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL)
-{
- int i,j, a, b;
-
-
- int ***M, ***T;
-
-
- for (a=0; a<2; a++)
- for (b=0; b<ns[a]; b++)
- {
- invert_string2(A->seq_al[ls[a][b]]);
- invert_string2((CL->S)->seq[A->order[ls[a][b]][0]]);
- }
- T=forward_so_dp(A,ns,ls,pos0, I, J, gop, gep, gop2, gep2, CL);
- for (a=0; a<2; a++)
- for (b=0; b<ns[a]; b++)
- {
- invert_string2(A->seq_al[ls[a][b]]);
- invert_string2((CL->S)->seq[A->order[ls[a][b]][0]]);
- }
-
- M=declare_arrayN (3, sizeof (int), 5, I+2, J+2);
-
-
- for (i=0; i<=I; i++)
- for (j=0; j<=J; j++)
- {
- M[match][i+1][j+1]=T[match][I-i][J-j];
- M[ins][i+1][j+1]=T[ins][I-i][J-j];
- M[del][i+1][j+1]=T[del][I-i][J-j];
- }
- return M;
-}
-
-/************************************************************************************************************************/
-/* */
-/* */
-/* BI-PHASIC */
-/* */
-/* */
-/************************************************************************************************************************/
-int biphasic_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
-{
- int i,j,a,b;
- int c;
- int sub;
- int ***m, ***t;
- int M1, D1, D2, I1, I2, LEN;
- int I, J;
- int n=1;
- char **al, **aln, *char_buf;
- int gop1, gop2, gep1, gep2;
- int **pos0;
- int score, trace, ntrace;
- M1=n++; D1=n++; D2=n++; I1=n++, I2=n++;
-
- I=strlen (A->seq_al[ls[0][0]]);
- J=strlen (A->seq_al[ls[1][0]]);
- m=declare_arrayN (3, sizeof (int),n, I+1, J+1);
- t=declare_arrayN (3, sizeof (int),n, I+1, J+1);
- pos0=aln2pos_simple ( A,-1, ns, ls);
- al=declare_char (2, I+J+1);
- for ( i=0; i<=I; i++)for (j=0; j<=J; j++)for (c=0; c<n; c++)m[c][i][j]=-999999;
-
- gop1=CL->gop*SCORE_K*2;
- gep1=CL->gep*SCORE_K/2;
-
- gop2=CL->gop*SCORE_K/2;
- gep2=CL->gep*SCORE_K*2;
-
- m[M1][0][0]=0;
- for (i=1; i<=I; i++){m[I1][i][0]=gep1*i;}
- for (j=1; j<=J; j++){m[D1][0][j]=gep1*j;}
-
- for (i=1; i<=I; i++){m[I2] [i][0]=gep2*i;}
- for (j=1; j<=J; j++){m[D2] [0][j]=gep2*j;}
-
- for (i=1; i<=I; i++)
- {
- for ( j=1; j<=J; j++)
- {
- sub=(CL->get_dp_cost) (A, pos0, ns[0], ls[0], i-1, pos0, ns[1], ls[1],j-1,CL);
- m[M1][i][j]=max_int (&t[M1][i][j],D1,m[D1][i-1][j-1],I1,m[I1][i-1][j-1], M1, m[M1][i-1][j-1],D2,m[D2][i-1][j-1],I2,m[I2][i-1][j-1], -1)+sub;
-
- m[D1][i][j]=max_int (&t[D1][i][j],M1,(m[M1][i][j-1]+gop1),D1,m[D1][i][j-1], -1)+gep1;
- m[I1][i][j]=max_int (&t[I1][i][j],M1,(m[M1][i-1][j]+gop1),I1,m[I1][i-1][j], -1)+gep1;
-
- m[D2][i][j]=max_int (&t[D2][i][j],M1,(m[M1][i][j-1]+gop2),D2,m[D2][i][j-1], -1)+gep2;
- m[I2][i][j]=max_int (&t[I2][i][j],M1,(m[M1][i-1][j]+gop2),I2,m[I2][i-1][j], -1)+gep2;
- }
- }
-
- score=max_int (&trace,M1,m[M1][I][J],D1,m[D1][I][J],I1, m[I1][I][J],D2,m[D2][I][J],I2,m[I2][I][J], -1);
- LEN=0;i=I;j=J;
-
-
- trace=t[trace][i][j];
- while (!(i==0 &&j==0))
- {
-
- ntrace=t[trace][i][j];
- if (i==0)
- {
- al[0][LEN]=0;
- al[1][LEN]=1;
- j--;
- LEN++;
- }
- else if ( j==0)
- {
- al[0][LEN]=1;
- al[1][LEN]=0;
- i--;
- LEN++;
- }
- else if ( trace==M1)
- {
- al[0][LEN]=1;
- al[1][LEN]=1;
- i--; j--;
- LEN++;
- }
-
- else if ( trace==D1 || trace==D2)
- {
- al[0][LEN]=0;
- al[1][LEN]=1;
- j--;
- LEN++;
- }
- else if ( trace == I1 || trace==I2)
- {
- al[0][LEN]=1;
- al[1][LEN]=0;
- i--;
- LEN++;
- }
- trace=ntrace;
-
- }
-
- invert_list_char ( al[0], LEN);
- invert_list_char ( al[1], LEN);
- if ( A->declared_len<=LEN)A=realloc_aln2 ( A,A->max_n_seq, 2*LEN);
-
- aln=A->seq_al;
- char_buf= vcalloc (LEN+1, sizeof (char));
- for ( c=0; c< 2; c++)
- {
- for ( a=0; a< ns[c]; a++)
- {
- int ch=0;
- for ( b=0; b< LEN; b++)
- {
- if (al[c][b]==1)
- char_buf[b]=aln[ls[c][a]][ch++];
- else
- char_buf[b]='-';
- }
- char_buf[b]='\0';
- sprintf (aln[ls[c][a]],"%s", char_buf);
- }
- }
-
-
- A->len_aln=LEN;
- A->nseq=ns[0]+ns[1];
- free_arrayN((void *)m, 3);
- free_arrayN((void *)t, 3);
- vfree (char_buf);
- free_char (al, -1);
- return score;
- }
-int *** forward_so_dp_biphasic ( Alignment *A, int *ns, int **ls, int **pos0,int I, int J,int gop1, int gep1,int gop2, int gep2,Constraint_list *CL)
-{
- int i,j;
- int c;
- int sub;
- int ***M;
- int match=0, del=1, ins=2;
- int lgop1, lgop2, lgep1, lgep2;
-
- M=declare_arrayN (3, sizeof (int), 5, I+1, J+1);
-
- for ( i=0; i<=I; i++)for (j=0; j<=J; j++)for (c=0; c<5; c++)M[c][i][j]=-999999;
-
- M[match][0][0]=0;
-
- for (i=1; i<=I; i++){M[del] [i][0]=gep1*i+gop1;}
- for (j=1; j<=J; j++){M[ins] [0][j]=gep1*j+gop1;}
-
- for (i=1; i<=I; i++){M[del2] [i][0]=gep2*i+gop2;}
- for (j=1; j<=J; j++){M[ins2] [0][j]=gep2*j+gop2;}
-
- for (i=1; i<=I; i++)
- {
- for ( j=1; j<=J; j++)
- {
- lgop1=(i==I || j==J)?gop1:gop1;
- lgop2=(i==I || j==J)?gop2:gop2;
- lgep1=gep1;
- lgep2=gep2;
-
- sub=(CL->get_dp_cost) (A, pos0, ns[0], ls[0], i-1, pos0, ns[1], ls[1],j-1,CL);
- M[match][i][j]=MAX5 (M[del][i-1][j-1], M[ins][i-1][j-1], M[match][i-1][j-1], M[ins2][i-1][j-1], M[del2][i-1][j-1])+sub;
-
- M[del ][i][j] =MAX2 ((M[match][i-1][j]+lgop1), M[del ][i-1][j])+lgep1;
- M[del2][i][j] =MAX2 ((M[match][i-1][j]+lgop2), M[del2][i-1][j])+lgep2;
-
- M[ins ][i][j] =MAX2 ((M[match][i][j-1]+lgop1), M[ins ][i][j-1] )+lgep1;
- M[ins2][i][j] =MAX2 ((M[match][i][j-1]+lgop2), M[ins2][i][j-1] )+lgep2;
- }
- }
- return M;
- }
-int *** backward_so_dp_biphasic ( Alignment *A, int *ns, int **ls, int **pos0, int I, int J, int gop, int gep,int gop2, int gep2,Constraint_list *CL)
-{
- int i,j, a, b;
-
-
- int ***M, ***T;
-
-
- for (a=0; a<2; a++)
- for (b=0; b<ns[a]; b++)
- {
- invert_string2(A->seq_al[ls[a][b]]);
- invert_string2((CL->S)->seq[A->order[ls[a][b]][0]]);
- }
- T=forward_so_dp_biphasic(A,ns,ls,pos0, I, J, gop, gep, gop2, gep2, CL);
- for (a=0; a<2; a++)
- for (b=0; b<ns[a]; b++)
- {
- invert_string2(A->seq_al[ls[a][b]]);
- invert_string2((CL->S)->seq[A->order[ls[a][b]][0]]);
- }
-
- M=declare_arrayN (3, sizeof (int), 5, I+2, J+2);
-
-
- for (i=0; i<=I; i++)
- for (j=0; j<=J; j++)
- {
- M[match][i+1][j+1]=T[match][I-i][J-j];
- M[ins][i+1][j+1]=T[ins][I-i][J-j];
- M[del][i+1][j+1]=T[del][I-i][J-j];
- M[ins2][i+1][j+1]=T[ins2][I-i][J-j];
- M[del2][i+1][j+1]=T[del2][I-i][J-j];
- }
- free_arrayN(T,3);
- return M;
-}
-
-
-int get_tot_prob (Alignment *A1,Alignment *A2, int *ns, int **ls, int nstates, float **matchProb, float **insProb, float *TmatchProb, float ***TinsProb, Constraint_list *CL);
-
-float * forward_proba_pair_wise ( char *seq1, char *seq2, int NumMatrixTypes, int NumInsertStates, float **transMat, float *initialDistribution,float *TmatchProb, float ***TinsProb, float **transProb);
-float * backward_proba_pair_wise ( char *seq1, char *seq2, int NumMatrixTypes, int NumInsertStates, float **transMat, float *initialDistribution,float *TmatchProb, float ***TinsProb,float **transProb);
-float ComputeTotalProbability (int seq1Length, int seq2Length,int NumMatrixTypes, int NumInsertStates,float *forward, float *backward) ;
-int ProbabilisticModel (int NumMatrixTypes, int NumInsertStates,float *initDistribMat,float *emitSingle, float** emitPairs, float *gapOpen, float *gapExtend, float **transMat, float *initialDistribution, float **matchProb, float **insProb, float **transProb);
-
-Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixTypes, int NumInsertStates, float *forward, float *backward, float thr, Constraint_list *CL);
-
-
-void free_proba_pair_wise ()
-{
- proba_pair_wise (NULL, NULL, NULL, NULL);
-}
-int proba_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
-{
- int NumMatrixTypes=5;
- int NumInsertStates=2;
- static float **transMat, **insProb, **matchProb, *initialDistribution, **transProb, **emitPairs, *emitSingle, ***TinsProb, *TmatchProb;
- static int TinsProb_ml, TmatchProb_ml;
- int i, j,I, J;
- float *F, *B, *P;
- float tot;
- int l, s1, s2;
- float thr=0.01;//ProbCons Default
- char *alphabet;
-
-
-
- //Free all the memory
- if (A==NULL)
- {
- free_float (transMat, -1);transMat=NULL;
- free_float (insProb, -1);insProb=NULL;
- free_float (matchProb, -1);matchProb=NULL;
- vfree (initialDistribution); initialDistribution=NULL;
- free_float (transProb, -1);transProb=NULL;
- free_float (emitPairs, -1);emitPairs=NULL;
- vfree (emitSingle);emitSingle=NULL;
-
-
- free_arrayN((void***)TinsProb, 3);TinsProb=NULL;
- vfree (TmatchProb);TmatchProb=NULL;
- TinsProb_ml=0; TmatchProb_ml=0;
-
- forward_proba_pair_wise (NULL, NULL, 0,0,NULL,NULL,NULL,NULL,NULL);
- backward_proba_pair_wise (NULL, NULL, 0,0,NULL,NULL,NULL,NULL,NULL);
- ProbaMatrix2CL(NULL, NULL, NULL, 0, 0, NULL, NULL, 0, NULL);
- return 0;
- }
-
- if (!transMat && (strm (retrieve_seq_type(), "DNA") ||strm (retrieve_seq_type(), "RNA")) )
- {
- static float **p;
- static float *s;
- if (!p)
- {
- int l,a,b;
- l=strlen (DNAalphabetDefault);
- p=declare_float (l,l);
- s=vcalloc (l, sizeof (float));
- for (a=0; a<l; a++)
- {
- s[a]=DNAemitSingleDefault[a];
- for (b=0; b<l; b++)
- p[a][b]=DNAemitPairsDefault[a][b];
- }
- }
- p=get_emitPairs (CL->method_matrix, DNAalphabetDefault,p,s);
- alphabet=DNAalphabetDefault;
- emitPairs=declare_float (256, 256);
- emitSingle=vcalloc (256, sizeof (float));
- for (i=0; i<256; i++)
- {
- emitSingle[i]=1e-5;
- for (j=0; j<256; j++)
- emitPairs[i][j]=1e-10;
- }
- l=strlen (alphabet);
-
- for (i=0; i<l; i++)
- {
- char C1,c1, C2,c2;
- c1=tolower(alphabet[i]);
- C1=toupper(alphabet[i]);
- emitSingle[c1]=s[i];
- emitSingle[C1]=s[i];
- for (j=0; j<=i; j++)
- {
- c2=tolower(alphabet[j]);
- C2=toupper(alphabet[j]);
-
- emitPairs[c1][c2]=p[i][j];
- emitPairs[C1][c2]=p[i][j];
- emitPairs[C1][C2]=p[i][j];
- emitPairs[c1][C2]=p[i][j];
- emitPairs[c2][c1]=p[i][j];
- emitPairs[C2][c1]=p[i][j];
- emitPairs[C2][C1]=p[i][j];
- emitPairs[c2][C1]=p[i][j];
- }
- }
-
-
- transMat=declare_float (2*NumInsertStates+1, 2*NumInsertStates+1);
- transProb=declare_float (2*NumInsertStates+1,2* NumInsertStates+1);
- insProb=declare_float (256,NumMatrixTypes);
- matchProb=declare_float (256, 256);
- initialDistribution=vcalloc (2*NumMatrixTypes+1, sizeof (float));
-
- ProbabilisticModel (NumMatrixTypes,NumInsertStates,initDistrib2Default, emitSingle,emitPairs,DNAgapOpen2Default,DNAgapExtend2Default, transMat,initialDistribution,matchProb, insProb,transProb);
- }
- else if ( !transMat && strm (retrieve_seq_type(), "PROTEIN"))
- {
- static float **p;
- static float *s;
- if (!p)
- {
- int l,a,b;
- l=strlen (alphabetDefault);
- p=declare_float (l,l);
- s=vcalloc (l, sizeof (float));
- for (a=0; a<l; a++)
- {
- s[a]=emitSingleDefault[a];
- for (b=0; b<l; b++)
- p[a][b]=emitPairsDefault[a][b];
- }
- }
- p=get_emitPairs (CL->method_matrix, alphabetDefault,p,s);
- alphabet=alphabetDefault;
- emitPairs=declare_float (256, 256);
- emitSingle=vcalloc (256, sizeof (float));
- for (i=0; i<256; i++)
- {
- //emitSingle[i]=1e-5;
- emitSingle[i]=1;
- for (j=0; j<256; j++)
- //emitPairs[i][j]=1e-10;
- emitPairs[i][j]=1;
-
- }
- l=strlen (alphabet);
-
- for (i=0; i<l; i++)
- {
- char C1,c1, C2,c2;
- c1=tolower(alphabet[i]);
- C1=toupper(alphabet[i]);
- emitSingle[c1]=s[i];
- emitSingle[C1]=s[i];
- for (j=0; j<=i; j++)
- {
- c2=tolower(alphabet[j]);
- C2=toupper(alphabet[j]);
-
- emitPairs[c1][c2]=p[i][j];
- emitPairs[C1][c2]=p[i][j];
- emitPairs[C1][C2]=p[i][j];
- emitPairs[c1][C2]=p[i][j];
- emitPairs[c2][c1]=p[i][j];
- emitPairs[C2][c1]=p[i][j];
- emitPairs[C2][C1]=p[i][j];
- emitPairs[c2][C1]=p[i][j];
-
- }
- }
-
-
- transMat=declare_float (2*NumInsertStates+1, 2*NumInsertStates+1);
- transProb=declare_float (2*NumInsertStates+1,2* NumInsertStates+1);
- insProb=declare_float (256,NumMatrixTypes);
- matchProb=declare_float (256, 256);
- initialDistribution=vcalloc (2*NumMatrixTypes+1, sizeof (float));
-
- ProbabilisticModel (NumMatrixTypes,NumInsertStates,initDistrib2Default, emitSingle,emitPairs,gapOpen2Default,gapExtend2Default, transMat,initialDistribution,matchProb, insProb,transProb);
- }
-
- I=strlen (A->seq_al[ls[0][0]]);
- J=strlen (A->seq_al[ls[1][0]]);
- //TmatchProb=vcalloc ((I+1)*(J+1), sizeof (float));
- //TinsProb=declare_arrayN (3, sizeof (float),2,NumMatrixTypes,MAX(I,J)+1);
-
- l=(I+1)*(J+1);
- if (l>TmatchProb_ml)
- {
- TmatchProb_ml=l;
- if (TmatchProb)TmatchProb=vrealloc(TmatchProb,TmatchProb_ml*sizeof (float));
- else TmatchProb=vcalloc ( l, sizeof (float));
- }
- l=MAX(I,J)+1;
- if ( l>TinsProb_ml)
- {
- TinsProb_ml=l;
- if (TinsProb)free_arrayN (TinsProb, 3);
- TinsProb=declare_arrayN (3, sizeof (float),2,NumMatrixTypes,TinsProb_ml);
- }
-
- get_tot_prob (A,A, ns,ls,NumMatrixTypes, matchProb, insProb,TmatchProb,TinsProb, CL);
-
- F=forward_proba_pair_wise (A->seq_al[ls[0][0]], A->seq_al[ls[1][0]], NumMatrixTypes,NumInsertStates,transMat, initialDistribution,TmatchProb,TinsProb, transProb);
- B=backward_proba_pair_wise (A->seq_al[ls[0][0]], A->seq_al[ls[1][0]], NumMatrixTypes,NumInsertStates,transMat, initialDistribution,TmatchProb,TinsProb, transProb);
- A->CL=ProbaMatrix2CL(A,ns, ls,NumMatrixTypes,NumInsertStates, F, B, thr,CL);
-
- //free_proba_pair_wise();
- return 1;
- }
-
-int get_tot_prob (Alignment *A1,Alignment *A2, int *ns, int **ls, int nstates, float **matchProb, float **insProb, float *TmatchProb, float ***TinsProb, Constraint_list *CL)
-{
- int i, j, a, b, c,d, k, n,n1,n2, ij;
- char c1, c2;
- int I, J;
- int ***VA1,***VA2, *observed, index;
- //Pre-computation of the pairwise scores in order to use potential profiles
- //The profiles are vectorized AND Compressed so that the actual alphabet size (proteins/DNA) does not need to be considered
-
-
- if (ns[0]==1 && ns[1]==1 )
- {
- int s1, s2;
- int *nns, **nls;
- Alignment *NA1, *NA2;
-
- nns=vcalloc ( 2, sizeof (int));
- nls=vcalloc (2, sizeof (int*));
-
- s1=A1->order[ls[0][0]][0];
- s2=A2->order[ls[1][0]][0];
- NA1=seq2R_template_profile (CL->S,s1);
- NA2=seq2R_template_profile (CL->S,s2);
-
- if (NA1 || NA2)
- {
- if (NA1)
- {
- nns[0]=NA1->nseq;
- nls[0]=vcalloc (NA1->nseq, sizeof (int));
- for (a=0; a<NA1->nseq; a++)
- nls[0][a]=a;
- }
- else
- {
- NA1=A1;
- nns[0]=ns[0];
- nls[0]=vcalloc (ns[0], sizeof (int));
- for (a=0; a<ns[0]; a++)
- nls[0][a]=ls[0][a];
- }
-
- if (NA2)
- {
- nns[1]=NA2->nseq;
- nls[1]=vcalloc (NA2->nseq, sizeof (int));
- for (a=0; a<NA2->nseq; a++)
- nls[1][a]=a;
- }
- else
- {
- NA2=A2;
- nns[1]=ns[1];
- nls[1]=vcalloc (ns[1], sizeof (int));
- for (a=0; a<ns[1]; a++)
- nls[1][a]=ls[1][a];
- }
-
- get_tot_prob (NA1, NA2, nns, nls, nstates, matchProb, insProb, TmatchProb, TinsProb, CL);
- vfree (nns); free_int (nls,-1);
- return 1;
- }
- }
-
- I=strlen (A1->seq_al[ls[0][0]]);
- J=strlen (A2->seq_al[ls[1][0]]);
-
-
-
- //get Ins for I
- for (i=1; i<=I; i++)
- {
- for (k=0; k<nstates; k++)
- {
- TinsProb[0][k][i]=0;
- for (n=0,b=0; b<ns[0]; b++)
- {
- c1=A1->seq_al[ls[0][b]][i-1];
- if (c1!='-')
- {
- TinsProb[0][k][i]+=insProb[c1][k];
-
- n++;
- }
- }
- if (n)TinsProb[0][k][i]/=n;
- }
- }
- //Get Ins for J
- for (j=1; j<=J; j++)
- {
- for (k=0; k<nstates; k++)
- {
- TinsProb[1][k][j]=0;
- for (n=0,b=0; b<ns[1]; b++)
- {
- c2=A2->seq_al[ls[1][b]][j-1];
- if (c2!='-')
- {
- TinsProb[1][k][j]+=insProb[c2][k];
-
- n++;
- }
- }
- if (n)TinsProb[1][k][j]/=n;
- }
- }
-
- observed=vcalloc ( 26, sizeof (int));
- VA1=declare_arrayN (3, sizeof (int),2,26,I);
- for (i=0; i<I; i++)
- {
- for (index=0, b=0; b<ns[0]; b++)
- {
- int in;
- c1=tolower(A1->seq_al[ls[0][b]][i]);
- if ( c1=='-')continue;
- c1-='a';
-
- if (!(in=observed[c1])){in=observed[c1]=++index;}
-
- VA1[0][in-1][i]=c1;
- VA1[1][in-1][i]++;
- }
-
- VA1[0][index][i]=-1;
- for (b=0; b<26; b++)observed[b]=0;
- }
-
- VA2=declare_arrayN (3, sizeof (int),2,26,J);
- for (i=0; i<J; i++)
- {
- for (index=0, b=0; b<ns[1]; b++)
- {
- int in;
-
- c1=tolower(A2->seq_al[ls[1][b]][i]);
- if ( c1=='-')continue;
- c1-='a';
-
- if (!(in=observed[c1])){in=observed[c1]=++index;}
-
- VA2[0][in-1][i]=c1;
- VA2[1][in-1][i]++;
- }
- VA2[0][index][i]=-1;
- for (b=0; b<26; b++)observed[b]=0;
- }
- vfree (observed);
-
- for ( ij=0,i=0; i<=I; i++)
- {
- for ( j=0; j<=J ; j++, ij++)
- {
- n=0;
- TmatchProb[ij]=0;
- if (i==0 || j==0);
- else
- {
- c=0;
- while (VA1[0][c][i-1]!=-1)
- {
- c1=VA1[0][c][i-1]+'a';
- n1=VA1[1][c][i-1];
- d=0;
- while (VA2[0][d][j-1]!=-1)
- {
- c2=VA2[0][d][j-1]+'a';
- n2=VA2[1][d][j-1];
- TmatchProb[ij]+=matchProb[c1][c2]*(double)n1*(double)n2;
- n+=n1*n2;
- d++;
- }
- c++;
- }
- }
- if (n)TmatchProb[ij]/=n;
- }
- }
-
- free_arrayN ((void **)VA1, 3);
- free_arrayN ((void **)VA2, 3);
- return 1;
-}
-
-
-
-
-Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixTypes, int NumInsertStates, float *forward, float *backward, float thr, Constraint_list *CL)
-{
- float totalProb;
- int ij, i, j,k, I, J, s1, s2;
- static int *entry;
- static int **list;
- static int list_max;
- int sim;
- int list_size;
- int list_n;
- int old_n=0;
- double v;
- static float F=4; //potential number of full suboptimal alignmnents incorporated in the library
- static int tot_old, tot_new;
-
- if (!A)
- {
- free_int (list, -1);list=NULL;
- list_max=0;
-
- vfree(entry); entry=NULL;
- return NULL;
- }
-
- I=strlen (A->seq_al[ls[0][0]]);
- J=strlen (A->seq_al[ls[1][0]]);
- s1=name_is_in_list (A->name[ls[0][0]], (CL->S)->name, (CL->S)->nseq, 100);
- s2=name_is_in_list (A->name[ls[1][0]], (CL->S)->name, (CL->S)->nseq, 100);
-
- list_size=I*J;
-
- if ( list_max<list_size)
- {
- free_int (list, -1);
- list_max=list_size;
- list=declare_int (list_max, 3);
- }
-
-
- totalProb = ComputeTotalProbability (I,J,NumMatrixTypes, NumInsertStates,forward, backward);
-
- ij = 0;
- for (list_n=0,ij=0,i =0; i <= I; i++)
- {
- for (j =0; j <= J; j++, ij+=NumMatrixTypes)
- {
- v= EXP (MIN(LOG_ONE,(forward[ij] + backward[ij] - totalProb)));
- if (v>thr)//Conservative reduction of the list size to speed up the sorting
- {
- list[list_n][0]=i;
- list[list_n][1]=j;
- list[list_n][2]=(int)((float)v*(float)NORM_F);
- list_n++;
- }
- if (v>0.01)old_n++;
- }
- }
-
- sort_int_inv (list, 3, 2, 0, list_n-1);
- if (!entry)entry=vcalloc ( CL->entry_len, CL->el_size);
- list_n=MIN(list_n,(F*MIN(I,J)));
- for (i=0; i<list_n; i++)
- {
- entry[SEQ1]=s1;
- entry[SEQ2]=s2;
- entry[R1] =list[i][0];
- entry[R2] =list[i][1];
- entry[WE] =list[i][2];
- entry[CONS]=1;
- add_entry2list (entry,A->CL);
- }
- tot_new+=list_n;
- tot_old+=old_n;
- // HERE ("LIB_SIZE NEW: %d (new) %d (old) [%.2f]", list_n, old_n, (float)tot_new/(float)tot_old);
- return A->CL;
-}
-
-Constraint_list *ProbaMatrix2CL_old (Alignment *A, int *ns, int **ls, int NumMatrixTypes, int NumInsertStates, float *forward, float *backward, float thr, Constraint_list *CL)
-{
- float totalProb;
- int ij, i, j,k, I, J, s1, s2;
- static int *entry;
- int lib_size=0;
- double v;
-
- I=strlen (A->seq_al[ls[0][0]]);
- J=strlen (A->seq_al[ls[1][0]]);
- s1=name_is_in_list (A->name[ls[0][0]], (CL->S)->name, (CL->S)->nseq, 100);
- s2=name_is_in_list (A->name[ls[1][0]], (CL->S)->name, (CL->S)->nseq, 100);
-
- totalProb = ComputeTotalProbability (I,J,NumMatrixTypes, NumInsertStates,forward, backward);
- if (!entry)entry=vcalloc ( CL->entry_len, CL->el_size);
- ij = 0;
- thr=0.01;
-
-
- for (ij=0,i =0; i <= I; i++)
- {
- for (j =0; j <= J; j++)
- {
- v= EXP (MIN(LOG_ONE,(forward[ij] + backward[ij] - totalProb)));
- if (i && j && v>=thr)
-
- {
- entry[SEQ1]=s1;entry[SEQ2]=s2;
- entry[R1]=i;entry[R2]=j;
- entry[WE]=(int)((float)v*(float)NORM_F);
- entry[CONS]=1;
- add_entry2list (entry,A->CL);
- lib_size++;
- }
- ij += NumMatrixTypes;
- }
- }
- HERE ("LIB_SIZE_OLD: %d", lib_size);
- return A->CL;
-}
-
-float ComputeTotalProbability (int seq1Length, int seq2Length,int NumMatrixTypes, int NumInsertStates,float *forward, float *backward)
-{
-
- float totalForwardProb = LOG_ZERO;
- float totalBackwardProb = LOG_ZERO;
- int k;
-
- for (k = 0; k < NumMatrixTypes; k++)
- {
- LOG_PLUS_EQUALS (&totalForwardProb,forward[k + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)] + backward[k + NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1)]);
- }
-
- totalBackwardProb =forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] +backward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)];
-
- for (k = 0; k < NumInsertStates; k++)
- {
- LOG_PLUS_EQUALS (&totalBackwardProb,forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] +backward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)]);
- LOG_PLUS_EQUALS (&totalBackwardProb,forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] +backward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)]);
- }
- return (totalForwardProb + totalBackwardProb) / 2;
- }
-
-
-float * backward_proba_pair_wise ( char *seq1, char *seq2, int NumMatrixTypes, int NumInsertStates, float **transMat, float *initialDistribution,float *matchProb, float ***insProb, float **transProb)
-{
- static float *backward;
- static int max_l;
-
-
- int k, i, j,ij, i1j1, i1j, ij1,a, l, seq1Length, seq2Length, m;
- char c1, c2;
- char *iter1, *iter2;
-
- if (!seq1)
- {
- vfree (backward);
- backward=NULL; max_l=0;
- return NULL;
- }
-
- iter1=seq1-1;
- iter2=seq2-1;
- seq1Length=strlen (seq1);
- seq2Length=strlen (seq2);
- l=(seq1Length+1)*(seq2Length+1)*NumMatrixTypes;
-
- if (!backward)
- {
- backward=vcalloc (l, sizeof (float));
- max_l=l;
- }
- else if (max_l<l)
- {
- backward=vrealloc (backward, l*sizeof(float));
- max_l=l;
- }
-
- for (a=0; a<l; a++)backward[a]=LOG_ZERO;
-
- for (k = 0; k < NumMatrixTypes; k++)
- backward[NumMatrixTypes * ((seq1Length+1) * (seq2Length+1) - 1) + k] = initialDistribution[k];
-
- // remember offset for each index combination
- ij = (seq1Length+1) * (seq2Length+1) - 1;
-
- i1j = ij + seq2Length + 1;
- ij1 = ij + 1;
- i1j1 = ij + seq2Length + 2;
- ij *= NumMatrixTypes;
- i1j *= NumMatrixTypes;
- ij1 *= NumMatrixTypes;
- i1j1 *= NumMatrixTypes;
-
- // compute backward scores
- for (i = seq1Length; i >= 0; i--)
- {
- c1 = (i == seq1Length) ? '~' : (unsigned char) iter1[i+1];
- for (j = seq2Length; j >= 0; j--)
- {
- c2 = (j == seq2Length) ? '~' : (unsigned char) iter2[j+1];
-
- if (i < seq1Length && j < seq2Length)
- {
- m=((i+1)*(seq2Length+1))+j+1;//The backward and the forward are offset by 1
- float ProbXY = backward[0 + i1j1] + matchProb[m];
-
-
- for (k = 0; k < NumMatrixTypes; k++)
- {
- LOG_PLUS_EQUALS (&backward[k + ij], ProbXY + transProb[k][0]);
- }
- }
- if (i < seq1Length)
- {
- for (k = 0; k < NumInsertStates; k++)
- {
- LOG_PLUS_EQUALS (&backward[0 + ij], backward[2*k+1 + i1j] + insProb[0][k][i+1] + transProb[0][2*k+1]);
- LOG_PLUS_EQUALS (&backward[2*k+1 + ij], backward[2*k+1 + i1j] + insProb[0][k][i+1] + transProb[2*k+1][2*k+1]);
- }
- }
- if (j < seq2Length)
- {
- for (k = 0; k < NumInsertStates; k++)
- {
- //+1 because the backward and the forward are offset by 1
- LOG_PLUS_EQUALS (&backward[0 + ij], backward[2*k+2 + ij1] + insProb[1][k][j+1] + transProb[0][2*k+2]);
- LOG_PLUS_EQUALS (&backward[2*k+2 + ij], backward[2*k+2 + ij1] + insProb[1][k][j+1] + transProb[2*k+2][2*k+2]);
- }
- }
-
- ij -= NumMatrixTypes;
- i1j -= NumMatrixTypes;
- ij1 -= NumMatrixTypes;
- i1j1 -= NumMatrixTypes;
- }
- }
-
- return backward;
-}
-float * forward_proba_pair_wise ( char *seq1, char *seq2, int NumMatrixTypes, int NumInsertStates, float **transMat, float *initialDistribution,float *matchProb, float ***insProb, float **transProb)
-{
- static float *forward;
- static int max_l;
- int k, i, j,ij, i1j1, i1j, ij1, seq1Length, seq2Length, m;
- char *iter1, *iter2;
- int l,a;
-
- if (!seq1)
- {
- vfree (forward);
- forward=NULL; max_l=0;
- return NULL;
- }
- iter1=seq1-1;
- iter2=seq2-1;
- seq1Length=strlen (seq1);
- seq2Length=strlen (seq2);
- l=(seq1Length+1)*(seq2Length+1)*NumMatrixTypes;
-
- if (!forward)
- {
- forward=vcalloc (l, sizeof (float));
- max_l=l;
- }
- else if (max_l<l)
- {
- forward=vrealloc (forward, l*sizeof(float));
- max_l=l;
- }
- for (a=0; a<l; a++)forward[a]=LOG_ZERO;
-
-
- forward[0 + NumMatrixTypes * (1 * (seq2Length+1) + 1)] = initialDistribution[0] + matchProb[seq2Length+2];
-
- for (k = 0; k < NumInsertStates; k++)
- {
- forward[2*k+1 + NumMatrixTypes * (1 * (seq2Length+1) + 0)] = initialDistribution[2*k+1] + insProb[0][k][1];
- forward[2*k+2 + NumMatrixTypes * (0 * (seq2Length+1) + 1)] = initialDistribution[2*k+2] + insProb[1][k][1];
- }
-
- // remember offset for each index combination
- ij = 0;
- i1j = -seq2Length - 1;
- ij1 = -1;
- i1j1 = -seq2Length - 2;
-
- ij *= NumMatrixTypes;
- i1j *= NumMatrixTypes;
- ij1 *= NumMatrixTypes;
- i1j1 *= NumMatrixTypes;
-
-
- // compute forward scores
- for (m=0,i = 0; i <= seq1Length; i++)
- {
- for (j = 0; j <= seq2Length; j++, m++)
- {
- if (i > 1 || j > 1)
- {
- if (i > 0 && j > 0)
- {
- //Sum over all possible alignments
- forward[0 + ij] = forward[0 + i1j1] + transProb[0][0];
- for (k = 1; k < NumMatrixTypes; k++)
- {
- LOG_PLUS_EQUALS (&forward[0 + ij], forward[k + i1j1] + transProb[k][0]);
- }
- forward[0 + ij] += matchProb[m];
- }
- if ( i > 0)
- {
- for (k = 0; k < NumInsertStates; k++)
- {
- forward[2*k+1 + ij] = insProb[0][k][i] + LOG_ADD (forward[0 + i1j] + transProb[0][2*k+1],forward[2*k+1 + i1j] + transProb[2*k+1][2*k+1]);
- }
- }
- if (j > 0)
- {
- for (k = 0; k < NumInsertStates; k++)
- {
- forward[2*k+2 + ij] = insProb[1][k][j] +LOG_ADD (forward[0 + ij1] + transProb[0][2*k+2],forward[2*k+2 + ij1] + transProb[2*k+2][2*k+2]);
- }
- }
- }
-
- ij += NumMatrixTypes;
- i1j += NumMatrixTypes;
- ij1 += NumMatrixTypes;
- i1j1 += NumMatrixTypes;
- }
-
- }
- return forward;
- }
-int ProbabilisticModel (int NumMatrixTypes, int NumInsertStates,float *initDistribMat,float *emitSingle, float **emitPairs, float *gapOpen, float *gapExtend, float **transMat, float *initialDistribution, float **matchProb, float **insProb, float **transProb)
-{
-
-
- // build transition matrix
- int i, j;
-
-
- transMat[0][0] = 1;
- for (i = 0; i < NumInsertStates; i++)
- {
- transMat[0][2*i+1] = gapOpen[2*i];
- transMat[0][2*i+2] = gapOpen[2*i+1];
- transMat[0][0] -= (gapOpen[2*i] + gapOpen[2*i+1]);
-
- transMat[2*i+1][2*i+1] = gapExtend[2*i];
- transMat[2*i+2][2*i+2] = gapExtend[2*i+1];
- transMat[2*i+1][2*i+2] = 0;
- transMat[2*i+2][2*i+1] = 0;
- transMat[2*i+1][0] = 1 - gapExtend[2*i];
- transMat[2*i+2][0] = 1 - gapExtend[2*i+1];
- }
-
-
-
- // create initial and transition probability matrices
- for (i = 0; i < NumMatrixTypes; i++){
- initialDistribution[i] = (float)log ((float)initDistribMat[i]);
- for (j = 0; j < NumMatrixTypes; j++)
- transProb[i][j] = (float)log ((float)transMat[i][j]);
- }
-
- // create insertion and match probability matrices
- for (i = 0; i < 256; i++)
- {
- for (j = 0; j < NumMatrixTypes; j++)
- {
- insProb[i][j] = (float)log((float)emitSingle[i]);
- }
- for (j = 0; j < 256; j++)
- {
- matchProb[i][j] = (float)log((float)emitPairs[i][j]);
- }
- }
- return 1;
-}
-
-
-int viterbi_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL)
-{
- char C1,c1, C2,c2;
- char *alphabet, *char_buf;
- char **al, **aln;
- int seq1Length, seq2Length, I, J;
- int i, j,ij, i1j1, i1j, ij1, k, a, b,l, LEN, r, c, m, state;
- int NumMatrixTypes=5;
- int NumInsertStates=2;
- int *traceback;
- float bestProb;
- static float **transMat, **insProb, **matchProb, *initialDistribution, **transProb, **emitPairs, *emitSingle, *TmatchProb, ***TinsProb;
- float *viterbi;
-
- ungap_sub_aln (A, ns[0],ls[0]);
- ungap_sub_aln (A, ns[1],ls[1]);
-
- seq1Length=I=strlen (A->seq_al[ls[0][0]]);
- seq2Length=J=strlen (A->seq_al[ls[1][0]]);
-
- if (!transMat)
- {
- alphabet=alphabetDefault;
- emitPairs=declare_float (256, 256);
- emitSingle=vcalloc (256, sizeof (float));
- for (i=0; i<256; i++)
- {
- emitSingle[i]=1e-5;
- for (j=0; j<256; j++)
- emitPairs[i][j]=1e-10;
- }
- l=strlen (alphabet);
-
- for (i=0; i<l; i++)
- {
-
- c1=tolower(alphabet[i]);
- C1=toupper(alphabet[i]);
- emitSingle[c1]=emitSingleDefault[i];
- emitSingle[C1]=emitSingleDefault[i];
- for (j=0; j<=i; j++)
- {
- c2=tolower(alphabet[j]);
- C2=toupper(alphabet[j]);
-
- emitPairs[c1][c2]=emitPairsDefault[i][j];
- emitPairs[C1][c2]=emitPairsDefault[i][j];
- emitPairs[C1][C2]=emitPairsDefault[i][j];
- emitPairs[c1][C2]=emitPairsDefault[i][j];
- emitPairs[c2][c1]=emitPairsDefault[i][j];
- emitPairs[C2][c1]=emitPairsDefault[i][j];
- emitPairs[C2][C1]=emitPairsDefault[i][j];
- emitPairs[c2][C1]=emitPairsDefault[i][j];
- }
- }
-
-
- transMat=declare_float (2*NumInsertStates+1, 2*NumInsertStates+1);
- transProb=declare_float (2*NumInsertStates+1,2* NumInsertStates+1);
- insProb=declare_float (256,NumMatrixTypes);
- matchProb=declare_float (256, 256);
- initialDistribution=vcalloc (2*NumMatrixTypes+1, sizeof (float));
-
- ProbabilisticModel (NumMatrixTypes,NumInsertStates,initDistrib2Default, emitSingle,emitPairs,gapOpen2Default,gapExtend2Default, transMat,initialDistribution,matchProb, insProb,transProb);
- }
-
-
- TmatchProb=vcalloc ((I+1)*(J+1), sizeof (float));
- TinsProb=declare_arrayN (3, sizeof (float),2,NumMatrixTypes,MAX(I,J)+1);
- get_tot_prob (A,A, ns,ls,NumMatrixTypes, matchProb, insProb,TmatchProb,TinsProb, CL);
-
- // create viterbi matrix
- l=NumMatrixTypes * (seq1Length+1) * (seq2Length+1);
- viterbi =vcalloc (l, sizeof (float));
- for (a=0; a<l; a++)viterbi[a]=LOG_ZERO;
- traceback=vcalloc (l, sizeof (int));
- for (a=0; a<l; a++)traceback[a]=-1;
-
- // initialization condition
- for (k = 0; k < NumMatrixTypes; k++)
- viterbi[k] = initialDistribution[k];
-
- // remember offset for each index combination
- ij = 0;
- i1j = -seq2Length - 1;
- ij1 = -1;
- i1j1 = -seq2Length - 2;
-
- ij *= NumMatrixTypes;
- i1j *= NumMatrixTypes;
- ij1 *= NumMatrixTypes;
- i1j1 *= NumMatrixTypes;
-
- // compute viterbi scores
- for (m=0,i = 0; i <= seq1Length; i++)
- {
- for ( j = 0; j <= seq2Length; j++, m++)
- {
- if (i > 0 && j > 0)
- {
- for (k = 0; k < NumMatrixTypes; k++)
- {
- float newVal = viterbi[k + i1j1] + transProb[k][0] + TmatchProb[m];
- if (viterbi[0 + ij] < newVal)
- {
- viterbi[0 + ij] = newVal;
- traceback[0 + ij] = k;
- }
- }
- }
- if (i > 0)
- {
- for (k = 0; k < NumInsertStates; k++)
- {
- float valFromMatch = TinsProb[0][k][i] + viterbi[0 + i1j] + transProb[0][2*k+1];
- float valFromIns = TinsProb[0][k][i] + viterbi[2*k+1 + i1j] + transProb[2*k+1][2*k+1];
- if (valFromMatch >= valFromIns){
- viterbi[2*k+1 + ij] = valFromMatch;
- traceback[2*k+1 + ij] = 0;
- }
- else {
- viterbi[2*k+1 + ij] = valFromIns;
- traceback[2*k+1 + ij] = 2*k+1;
- }
- }
- }
- if (j > 0)
- {
- for (k = 0; k < NumInsertStates; k++){
- float valFromMatch = TinsProb[1][k][j] + viterbi[0 + ij1] + transProb[0][2*k+2];
- float valFromIns = TinsProb[1][k][j] + viterbi[2*k+2 + ij1] + transProb[2*k+2][2*k+2];
- if (valFromMatch >= valFromIns){
- viterbi[2*k+2 + ij] = valFromMatch;
- traceback[2*k+2 + ij] = 0;
- }
- else
- {
- viterbi[2*k+2 + ij] = valFromIns;
- traceback[2*k+2 + ij] = 2*k+2;
- }
- }
- }
-
- ij += NumMatrixTypes;
- i1j += NumMatrixTypes;
- ij1 += NumMatrixTypes;
- i1j1 += NumMatrixTypes;
- }
- }
-
- // figure out best terminating cell
- bestProb = LOG_ZERO;
- state = -1;
- for (k = 0; k < NumMatrixTypes; k++)
- {
- float thisProb = viterbi[k + NumMatrixTypes * ((seq1Length+1)*(seq2Length+1) - 1)] + initialDistribution[k];
- if (bestProb < thisProb)
- {
- bestProb = thisProb;
- state = k;
- }
- }
-
-
-
- // compute traceback
- al=declare_char(2,seq1Length+seq2Length);
- LEN=0;
- r = seq1Length, c = seq2Length;
- while (r != 0 || c != 0)
- {
- int newState = traceback[state + NumMatrixTypes * (r * (seq2Length+1) + c)];
-
- if (state == 0){ c--; r--; al[0][LEN]=1;al[1][LEN]=1;}
- else if (state % 2 == 1) {r--; al[0][LEN]=1;al[1][LEN]=0;}
- else { c--; al[0][LEN]=0;al[1][LEN]=1;}
- LEN++;
- state = newState;
- }
-
-
- invert_list_char ( al[0], LEN);
- invert_list_char ( al[1], LEN);
- if ( A->declared_len<=LEN)A=realloc_aln2 ( A,A->max_n_seq, 2*LEN);
- aln=A->seq_al;
- char_buf= vcalloc (LEN+1, sizeof (char));
- for ( c=0; c< 2; c++)
- {
- for ( a=0; a< ns[c]; a++)
- {
- int ch=0;
- for ( b=0; b< LEN; b++)
- {
- if (al[c][b]==1)
- char_buf[b]=aln[ls[c][a]][ch++];
- else
- char_buf[b]='-';
- }
- char_buf[b]='\0';
- sprintf (aln[ls[c][a]],"%s", char_buf);
- }
- }
-
-
- A->len_aln=LEN;
- A->nseq=ns[0]+ns[1];
- vfree (char_buf);
- free_char (al, -1);
-
-
-
-
-
- return (int)(bestProb*(float)1000);
-}
-
-float ** get_emitPairs (char *mat, char *alp, float **p, float *s)
- {
- static char *rmat;
- float k=0, t=0;
- int a, b, c, l;
- int **M;
-
- if (!rmat)rmat=vcalloc (100, sizeof (char));
-
- if (!mat || !mat[0] || strm (mat, "default"))return p;
- else if (strm (rmat, mat))return p;
-
- sprintf (rmat,"%s", mat);
-
- M=read_matrice (mat);
- l=strlen (alp);
-
- k=log (2)/2;
- for (a=0; a<l; a++)
- for (b=0; b<l; b++)
- {
- int sc;
- float e;
- e=s[a]*s[b];
- sc=M[alp[a]-'A'][alp[b]-'A'];
- p[a][b]=e*exp ((double)sc*k);
- }
-
- for (a=0; a<l; a++)
- for (b=0; b<l; b++)
- t+=p[a][b];
-
- for (a=0; a<l; a++)
- for (b=0; b<l; b++)
- p[a][b]=p[a][b]/t;
-
- t=0;
-
- for (a=0; a<l; a++)
- for (b=0; b<l; b++)
- t+=p[a][b];
-
- return p;
- }
-
-/*********************************COPYRIGHT NOTICE**********************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Tue Oct 27 10:12:26 WEST 2009. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE 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.*/
-/**/
-/* T-COFFEE 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 Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/*********************************COPYRIGHT NOTICE**********************************/
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