MFOLD

Flow chart for RNA folding - main
---------------------------------
         ----->  call device   ------------.
         ^           |                     |
         |           |              read energy files
         ^       (cont run)         |               |       
         |           |           (reg)           (save)
         ^      call cdump--.       |               |
         |                 call outputs             |         
         ^                  |       '--------- call menu
         |                  |-----------------------'             **
         ^                  |                                     |
         |               mrep = 1 --(multiple)-- read MREPth sequence
      err msg               |                         |
         ^            zero bit arrays <---------------'
         |            call process
   (n*2.gt.fldmax)----------' 
                           |
                    ----(n ok)-----
                    |              |
            (save or reg run)  (cont run)              
                    |              |
                call fill--(reg)-->|
                    |              |
  putcont<-----(save run)          |
    |                              |
  stop.                         rep = 1 
                               jump = 1
                               flag = .true.  
                                   |
                                   |<------ *
                                   | 
     (mult or n best)----------------(plot run)
       |                             |        |
    sortout(rep)               (jump.eq.1) (jump.eq.2)
     |        |                   |                |
  (err)     (no err)       dotplt(start)       dotplt(cross-hairs)
    |            |                '->  jump = 2  <-'
error message->rep++                      |
               mrep++                     |
              /      \                    |
         (reps done)  (more to go)        |
             |           |                |                  
     flag = .false.------------------------------->(not flag)->. 
                                       (flag)                  |
                                          |                    |
                         <----(err) <---trace1                 |
                        |                 |                    |
                    errmsg             (no err)                |
                        |                 |                    | 
                         -----------------|------->(not flag)->|
                                        (flag)                 |
                                        trace2                 |
                         <----(err) <---' |                    |
                    errmsg             (no err)                |
                        |                 |                    |
                        '-----------------|------->(not flag)->|
                                          |                    |
                                   calculate energy            |
                                   |              |            |
                            (plot or n-best)     (mult)        |
                                   |              |            |
                               mark basepairs     |            | 
                                   |              |            |
                                   '-- call selected outputs   |
                                                  |<-----------'
                                        ------------------
                                        |                |
                                  (plot or n-best)      (mult)------
                                   |          |         |           |
                                (flag)     (not flag) (done)    (not done)
                                goto *        '-> stop <-'       goto **