WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / lib / plot_layouts.c

diff --git a/binaries/src/ViennaRNA/lib/plot_layouts.c b/binaries/src/ViennaRNA/lib/plot_layouts.c
new file mode 100644 (file)
index 0000000..1493467
--- /dev/null
+++ b/binaries/src/ViennaRNA/lib/plot_layouts.c
@@ -0,0 +1,157 @@
+/**
+ * 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;
+}