Integrate C DO 3D code from POY code base

[recursion-ninja]

• [x] Double check for segfaults
• [x] valgrind
• [x] Export an alias to the existing FFI binding
• [ ] Test FFI
• [x] Decide how/if this code will be used in one of our traversals
• [ ] Perform black box testing against POY 4/5
• [ ] Document
• [ ] Push memoized TCM into 3DO code.
• [ ] Switch 3DO from int that accepts up to 64 character states to unlimited by counting leading zeroes on input bit vectors.
• [ ] Add traversal code for 3DO
  • [x] Pseudocode
  • [ ] Actual code
• [x] What to do with gap character
• [ ] Decide where to disambiguate. If on C side use builtin: __builtin_clz, which only works on unsigned
• [x] Send characters_t as input as well as output to algn_3d_powell
• [x] Get actual sequences back from 3DO alignment
• [x] Update Python test harness
• [ ] Make sure my casting, from above, doesn't cause any problems.
• [ ] Consider moving all types to common library, as they're used all over.
• [x] Gapped and ungapped outputs are too short. Why?
• [x] Put asserts after all allocations.

[recursion-ninja]

Smoke test 3D DO using QuickCheck. If it doesn't SEGFAULT, we are good to go for now.

[ima-hima]

These are the steps I took to move code forward from Powell's original code here. This list also exists in ffi/external_direct_optimization/Changelog.md

#Changelog

Note: In all following, changes were made in both ukkCommon.c and ukkCommon_for_python.c, the latter of which is needed to do debugging using Python scripts. ukk_common.h and ukk.checkp.c are shared across both.

17/10/25

• Cloned
• Removed several unneeded compilation units.
• Removed inline directive
• Used modern limits library vs. values
• Edited makefile
  • Added new make command: test_powell
  • Removed extra cruft
  • Changed warnings
  • Updated to c11
• Got it to compile
• Tested with several dynamic characters that had failed my code. It ran.

17/10/27

• More code cleanup for legibility
• Added Python wrapper code for testing
  • Originally, Astr, Bstr & Cstr were globals, but I was unable to accept input strings due to allocation problems. So it forced me to make Astr, Bstr & Cstr local variables, with allocation happening in powell_3D_align. I put the three input characters into a struct, which I then passed around.
  • Removed original limit on input characters’ lengths.

17/10/27–31

• Valgrinded C code. Fixed all segfaults and bad memory reads. They were cause by my not sending the "global" struct through to traceback. Not sure why the compiler wasn’t bitching about that, but it wasn’t.
• Fixed segfaults when using Python ffi. step() exists in both GLIBC and Powell's code. The FFI needs GLIBC to work.
• Removed #FIXED_NUM_PLANES, which was always set to same value.

17/11/1

• Started to move to interface.
• Deleted dynamic_character_t type from 3DO code, as it's no longer needed.

17/11/3

• Updated all 3DO types in test_interface to use char instead of dynamic_char.
• Changed name of ukk.checkp.c to ukkCheckPoint.c.
• All code compiles including test_interface.

17/11/6

• Removed MAX_STR, but had to add it back in, as two array allocations (cost_vector and state_vector) rely on it, as well as the global MAX_COST.
• test_interface kept failing, either segfaulting or assertion errors. Step I took:
  • Built a separate file, test_c_only.c to run ukkCommon without the C interface.
  • Realized the problem had to do with align_io, which has elem_t, whereas Powell’s code has char.
  • Okay, so I can't convert from int to char. That conversion in C only allows for ASCII characters, so 33–126, inclusive. Can I just convert to int?
  • Gap character was hard coded as '-'. That's now been changed to (1 << alphabetSize) - 1.
  • Added gap_char_g global.

17/11/7–8

• Finished converting char strings to int arrays.

17/11/9

• First value in any alphabet is \(1 = 2^{0}\), i.e. first bit set.
• Set gap char, which is still global, to 1 << alphabetsize - 1.
• To get lengths of output characters need to return their values, which means passing a pointer to a data structure. Moving outputs to characters_t* since it has all the fields I need. I could use alignIO_t, but this gives me the option to move to a smaller type, like unsigned short later, to save space. At the same time, it would be cheaper computationally to use alignIO_t. That should be an easy change in future.
• Changed input type of algn_get_cost_medians_3d to accept characters_t*.

17/11/13

• Pushed through type change on input and output arrays from int to elem_t (unsigned int). This was to make translation from align_io to characters_t easier.
• In conjunction with that, was forced to use memcpy rather than just changing pointers on that translation.
• Cast several void * values in ukkCommon.h to char * to get rid of annoying warnings.
  • In allocFinal: flag, top and block.
  • In getPtr in return statement.
  • In getPtr: memset
• Renamed Astr, etc., Aidx, etc. and Alen, etc. to seq1, lenSeq1 and idxSeq1, respectively.
• Added new fn to reverse elem_t arrays.
• Cleared warnings in both gcc and clang

17/11/14

• Removed dead code
• Updated algn_3d_powell to accept characters_t as input
• Finally resolved annoying valgrind errors caused by bad indices in prints in ukkCheckPoint.c -> traceBack().
• Started getting actual sequences back from Powell. Actually, they were already coming back, but the lengths were set to 0, so they weren't getting copied correctly, and neither were gapped or ungapped getting computed.

17/11/16–17

• Issue with short gapped and ungapped chars was because of copying to/from align_io. 2D necessitates opening gap removal. 3D doesn't.