Revision 7c331b1ee58f504e2f77c8ec64224ad3b674463b authored by Ronny Lorenz on 04 May 2015, 13:34:30 UTC, committed by Ronny Lorenz on 04 May 2015, 13:34:30 UTC
1 parent fa00faf
plot_layouts.c
/**
* This file is a container for all plotting layout algorithms
*
* c Ronny Lorenz
* The ViennaRNA Package
*/
#include <config.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "utils.h"
#include "plot_layouts.h"
#ifdef _OPENMP
#include <omp.h>
#endif
#define PUBLIC
#define PRIVATE static
PUBLIC int rna_plot_type = 1; /* 0 = simple, 1 = naview, 2 = circular plot */
PRIVATE float *angle;
PRIVATE int *loop_size, *stack_size;
PRIVATE int lp, stk;
PRIVATE void loop(int i, int j, short *pair_table);
#ifdef _OPENMP
/* NOTE: all threadprivate variables are uninitialized when entering a thread! */
#pragma omp threadprivate(angle, loop_size, stack_size, lp, stk)
#endif
/*---------------------------------------------------------------------------*/
PUBLIC int simple_xy_coordinates(short *pair_table, float *x, float *y)
{
float INIT_ANGLE=0.; /* initial bending angle */
float INIT_X = 100.; /* coordinate of first digit */
float INIT_Y = 100.; /* see above */
float RADIUS = 15.;
int i, length;
float alpha;
length = pair_table[0];
angle = (float*) space( (length+5)*sizeof(float) );
loop_size = (int*) space( 16+(length/5)*sizeof(int) );
stack_size = (int*) space( 16+(length/5)*sizeof(int) );
lp = stk = 0;
loop(0, length+1, pair_table);
loop_size[lp] -= 2; /* correct for cheating with function loop */
alpha = INIT_ANGLE;
x[0] = INIT_X;
y[0] = INIT_Y;
for (i = 1; i <= length; i++) {
x[i] = x[i-1]+RADIUS*cos(alpha);
y[i] = y[i-1]+RADIUS*sin(alpha);
alpha += PI-angle[i+1];
}
free(angle);
free(loop_size);
free(stack_size);
return length;
}
/*---------------------------------------------------------------------------*/
PRIVATE void loop(int i, int j, short *pair_table)
/* i, j are the positions AFTER the last pair of a stack; i.e
i-1 and j+1 are paired. */
{
int count = 2; /* counts the VERTICES of a loop polygon; that's
NOT necessarily the number of unpaired bases!
Upon entry the loop has already 2 vertices, namely
the pair i-1/j+1. */
int r = 0, bubble = 0; /* bubble counts the unpaired digits in loops */
int i_old, partner, k, l, start_k, start_l, fill, ladder;
int begin, v, diff;
float polygon;
short *remember;
remember = (short *) space((1+(j-i)/5)*2*sizeof(short));
i_old = i-1, j++; /* j has now been set to the partner of the
previous pair for correct while-loop
termination. */
while (i != j) {
partner = pair_table[i];
if ((!partner) || (i==0))
i++, count++, bubble++;
else {
count += 2;
k = i, l = partner; /* beginning of stack */
remember[++r] = k;
remember[++r] = l;
i = partner+1; /* next i for the current loop */
start_k = k, start_l = l;
ladder = 0;
do {
k++, l--, ladder++; /* go along the stack region */
}
while (pair_table[k] == l);
fill = ladder-2;
if (ladder >= 2) {
angle[start_k+1+fill] += PIHALF; /* Loop entries and */
angle[start_l-1-fill] += PIHALF; /* exits get an */
angle[start_k] += PIHALF; /* additional PI/2. */
angle[start_l] += PIHALF; /* Why ? (exercise) */
if (ladder > 2) {
for (; fill >= 1; fill--) {
angle[start_k+fill] = PI; /* fill in the angles */
angle[start_l-fill] = PI; /* for the backbone */
}
}
}
stack_size[++stk] = ladder;
loop(k, l, pair_table);
}
}
polygon = PI*(count-2)/(float)count; /* bending angle in loop polygon */
remember[++r] = j;
begin = i_old < 0 ? 0 : i_old;
for (v = 1; v <= r; v++) {
diff = remember[v]-begin;
for (fill = 0; fill <= diff; fill++)
angle[begin+fill] += polygon;
if (v > r)
break;
begin = remember[++v];
}
loop_size[++lp] = bubble;
free(remember);
}
/*---------------------------------------------------------------------------*/
PUBLIC int simple_circplot_coordinates(short *pair_table, float *x, float *y){
unsigned int length = (unsigned int) pair_table[0];
unsigned int i;
float d = 2*PI/length;
for(i=0; i < length; i++){
x[i] = cos(i * d - PI/2);
y[i] = sin(i * d - PI/2);
}
return length;
}
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