void SCStat::PrintStatAll() {
PrintMain();
PrintPlace();
PrintTransition();
PrintDirected();
PrintEnd();
}
/* Function: DisplayPlan7PostAlign()
*
* Purpose: Print out posterior transition probabilities
* in modelpost format, for any set of alignments.
*
* Args: L - the length of the sequence
* hmm - the model
* forward - forward matrix
* backward - backward matrix
* alignment - array of traces
* A - size of alignment array
*
* Return: void
*
*/
void DisplayPlan7PostAlign(int L, struct plan7_s *hmm,
struct dpmatrix_s *forward,
struct dpmatrix_s *backward,
struct p7trace_s **alignment,
int A)
{
int sc;
int i;
int j;
int k;
int kmin;
int kmax;
int* min;
int* max;
int* on;
char state;
sc = forward->xmx[L][XMC] + hmm->xsc[XTC][MOVE]; /* total Forward score */
min = (int*) calloc (A, sizeof(int));
max = (int*) calloc (A, sizeof(int));
on = (int*) calloc (A, sizeof(int));
for (i = 0; i <= L; i++)
{
for (j = 0; j < A; j++) {
while (alignment[j]->pos[min[j]] < i - 1 && min[j] < alignment[j]->tlen - 1)
min[j]++;
while (alignment[j]->pos[max[j]] <= i + 1 && max[j] < alignment[j]->tlen - 1)
max[j]++;
}
for (state = STM; state <= STJ; state++)
{
if (state == STM || state == STB)
{
kmin = 1;
kmax = hmm->M;
}
else if (state == STD)
{
kmin = 2;
kmax = hmm->M - 1;
}
else if (state == STI)
{
kmin = 1;
kmax = hmm->M - 1;
}
else
kmin = kmax = 0;
for (k = kmin; k <= kmax; k++)
{
switch (state)
{
case STM:
if (i<L && k<hmm->M)
PrintTransition (STM,i,k, STM,i+1,k+1,
forward->mmx[i][k] + hmm->tsc[k][TMM] + backward->mmx[i+1][k+1] - sc,
alignment, min, max, on, A);
if (i<L && k<hmm->M)
PrintTransition (STM,i,k, STI,i+1,k,
forward->mmx[i][k] + hmm->tsc[k][TMI] + backward->imx[i+1][k] - sc,
alignment, min, max, on, A);
if (k<hmm->M-1)
PrintTransition (STM,i,k, STD,i,k+1,
forward->mmx[i][k] + hmm->tsc[k][TMD] + backward->dmx[i][k+1] - sc,
alignment, min, max, on, A);
PrintTransition (STM,i,k, STE,i,0,
forward->mmx[i][k] + hmm->esc[k] + backward->xmx[i][XME] - sc,
alignment, min, max, on, A);
break;
case STD:
if (i<L)
PrintTransition (STD,i,k, STM,i+1,k+1,
forward->dmx[i][k] + hmm->tsc[k][TDM] + backward->mmx[i+1][k+1] - sc,
alignment, min, max, on, A);
PrintTransition (STD,i,k, STD,i,k+1,
forward->dmx[i][k] + hmm->tsc[k][TDD] + backward->dmx[i][k+1] - sc,
alignment, min, max, on, A);
break;
case STI:
if (i<L)
PrintTransition (STI,i,k, STM,i+1,k+1,
forward->imx[i][k] + hmm->tsc[k][TIM] + backward->mmx[i+1][k+1] - sc,
alignment, min, max, on, A);
if (i<L)
PrintTransition (STI,i,k, STI,i+1,k,
forward->imx[i][k] + hmm->tsc[k][TII] + backward->imx[i+1][k] - sc,
alignment, min, max, on, A);
break;
case STB:
if (i<L)
PrintTransition (STB,i,0, STM,i+1,k,
forward->xmx[i][XMB] + hmm->bsc[k] + backward->mmx[i+1][k] - sc,
alignment, min, max, on, A);
break;
default:
break;
}
}
switch (state)
{
case STN:
PrintTransition (STN,i,0, STB,i,0,
forward->xmx[i][XMN] + hmm->xsc[XTN][MOVE] + backward->xmx[i][XMB] - sc,
alignment, min, max, on, A);
if (i<L)
PrintTransition (STN,i,0, STN,i+1,0,
forward->xmx[i][XMN] + hmm->xsc[XTN][LOOP] + backward->xmx[i+1][XMN] - sc,
alignment, min, max, on, A);
break;
case STJ:
PrintTransition (STJ,i,0, STB,i,0,
forward->xmx[i][XMJ] + hmm->xsc[XTJ][MOVE] + backward->xmx[i][XMB] - sc,
alignment, min, max, on, A);
if (i<L)
PrintTransition (STJ,i,0, STJ,i+1,0,
forward->xmx[i][XMJ] + hmm->xsc[XTJ][LOOP] + backward->xmx[i+1][XMJ] - sc,
alignment, min, max, on, A);
break;
case STC:
PrintTransition (STC,i,0, STT,i,0,
forward->xmx[i][XMC] + hmm->xsc[XTC][MOVE] - sc, /* should be 1 */
alignment, min, max, on, A);
if (i<L)
PrintTransition (STC,i,0, STC,i+1,0,
forward->xmx[i][XMC] + hmm->xsc[XTC][LOOP] + backward->xmx[i+1][XMC] - sc,
alignment, min, max, on, A);
break;
case STE:
PrintTransition (STE,i,0, STC,i,0,
forward->xmx[i][XME] + hmm->xsc[XTE][MOVE] + backward->xmx[i][XMC] - sc,
alignment, min, max, on, A);
PrintTransition (STE,i,0, STJ,i,0,
forward->xmx[i][XME] + hmm->xsc[XTE][LOOP] + backward->xmx[i][XMJ] - sc,
alignment, min, max, on, A);
break;
case STS:
if (i == 0)
PrintTransition (STS,i,0, STN,i,0,
backward->xmx[i][XMN] - sc, /* should be 1 */
alignment, min, max, on, A);
break;
case STM:
case STD:
case STI:
case STB:
case STT:
break;
default:
Die ("unknown state");
}
}
}
free (min);
free (max);
free (on);
}
