--- /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;
+//DNA Alignment Models
+static float DNAinitDistrib2Default[] ={ 0.9588437676f, 0.0205782652f, 0.0205782652f };
+static float DNAgapOpen2Default[] = { 0.0190259293f, 0.0190259293f };
+static float DNAgapExtend2Default[] = { 0.3269913495f, 0.3269913495f };
+
+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 }
+};
+//RNA Alignment Models
+
+static float RNAinitDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
+static float RNAgapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
+static float RNAgapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
+
+static char RNAalphabetDefault[] = "ACGUTN";
+static float RNAemitSingleDefault[6] = {0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f};
+
+static float RNAemitPairsDefault[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 }
+};
+
+//Protein Alignment Models
+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+1, 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)
+{
+ static int NumMatrixTypes;
+ static int NumInsertStates;
+ 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;
+
+ int l;
+ 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")))
+ {
+ static float **p;
+ static float *s;
+ NumInsertStates=1;
+ NumMatrixTypes=3;
+ 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]=RNAemitPairsDefault[a][b];
+ }
+ }
+ p=get_emitPairs (CL->method_matrix, DNAalphabetDefault,p,s);
+ alphabet=RNAalphabetDefault;
+ 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++)
+ {
+ int 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(), "RNA")))
+ {
+ static float **p;
+ static float *s;
+ NumInsertStates=2;
+ NumMatrixTypes=5;
+
+ if (!p)
+ {
+ int l,a,b;
+ l=strlen (RNAalphabetDefault);
+ p=declare_float (l,l);
+ s=vcalloc (l, sizeof (float));
+ for (a=0; a<l; a++)
+ {
+ s[a]=RNAemitSingleDefault[a];
+ for (b=0; b<l; b++)
+ p[a][b]=RNAemitPairsDefault[a][b];
+ }
+ }
+ p=get_emitPairs (CL->method_matrix, RNAalphabetDefault,p,s);
+ alphabet=RNAalphabetDefault;
+ 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++)
+ {
+ int 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,RNAgapOpen2Default,RNAgapExtend2Default, transMat,initialDistribution,matchProb, insProb,transProb);
+ }
+ else if ( !transMat && strm (retrieve_seq_type(), "PROTEIN"))
+ {
+ static float **p;
+ static float *s;
+ NumInsertStates=2;
+ NumMatrixTypes=5;
+
+ 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++)
+ {
+ int 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;
+ int c1, c2;
+ int I, J;
+ int ***VA1,***VA2, *observed, index;
+ char *ss1=NULL;
+ char *ss2=NULL;
+ int uss=0;
+
+ //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;
+ char *sst1;
+ char *sst2;
+
+
+ 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);
+
+ sst1=seq2T_template_string((CL->S),s1);
+ sst2=seq2T_template_string((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;
+ NA1->seq_al[NA1->nseq]=sst1;
+ sprintf (NA1->name[NA1->nseq], "sst1");
+ }
+ 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;
+ NA2->seq_al[NA2->nseq]=sst2;
+ sprintf (NA2->name[NA2->nseq], "sst2");
+ }
+ 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;
+ }
+ }
+ if ( A1!=A2)
+ {
+ if (strm (A1->name[A1->nseq], "sst1"))ss1=A1->seq_al[A1->nseq];
+ if (strm (A2->name[A2->nseq], "sst2"))ss2=A2->seq_al[A2->nseq];
+ uss=(ss1&&ss2)?1:0;
+ }
+ else
+ uss=0;
+
+ 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=='-' || c1=='.' || 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
+ {
+ float sfac;
+ if (!uss)sfac=1;
+ else if (ss1[i-1]!=ss2[j-1])sfac=1;
+ else if (ss1[i-1]==ss2[j-1])sfac=1;
+ else sfac=1;
+
+
+ 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*sfac;
+ 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+1, 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;
+}
+
+
+
+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)
+{
+ int 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 */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*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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