OpenMP changes.
Setting MAXTHREADS dynamically.
Removing drowlength
Delete correctly
Adding in two more options (ROW_LENGTH, MATRIX_FORMAT), made things way faster and changed default output.
probabilities[inputStructureDist % 2 ? 2 * i + 1 : 2 * i] = solutions[i].real() > 0 ? solutions[i].real() : 0;
Reverting the changes to make PRECISION 8 by default and to set neg. probabilities to 0.
Remove a free call
Ivan's performance changes
OPENMP_DEBUG
Fixes to the interiorloop function
Changes from Ivan.
Debug flag to turn off all the recursions.
Precalc energies.
Fixing memory requirements.
Updating the Readme
Cleaning up neighbors function.
Updating FFTbor2D to support ViennaRNA 2.1.x energy file formats and libRNA.a library.
Added an option for a simple output, which should be much easier to parse with R.
Formatting change, to clean up the consistency of +/- signs.