eternagame / cdsfold_su Goto Github PK

Translate Japanese comments

Should be possible to build on Mac, but clang is getting hung up on namespaces. If someone figures it out, please close this issue and provide tips in README.md.

May be related to changes in codon.cpp

• Change names of class attributes to have _ in front of the name
• Flip the if statement to check if opening the if stream failed and exit and have rest of the code not in an if statement

I've been accidentally merging in all of the commits from feature branches into the main branch. There's a github setting to automatically squash and merge to avoid having to manually squash.

Update so that the default is to use Vienna fold but that different build targets use the dummy energy model instead.

Problem.cpp

The code block:

 if (options_.nucleotide_constraints == 1 && i2r[R2_nuc] != NucConst_[j - 1]) {
                                       continue;
                                   }

                                   if (options_.DEPflg && Dep1_[ii2r[L_nuc * 10 + L2_nuc]][i] == 0) {
                                       continue;
                                   }
                                   if (options_.DEPflg && Dep1_[ii2r[R2_nuc * 10 + R_nuc]][j - 1] == 0) {
                                       continue;
                                   }

and variations of it are repeated a lot - make a helper function to remove this repeated code.

The exceptVector is converted to an exceptMap in codon.cpp. If a codon appears more than once in exceptVector, the integer the codon maps to in exceptMap is incremented but this count is never used. Remove the increment and update.

Need to figure out what's going on in this file.

Minor detail - iterator is using ints as bools

Comments were in Japanese and look like didn't convert correctly

Script can be based on the existing test script.

The script parses the run time, MFE, and other parameters, but the behavior is incorrect if there are multiple sequences in the same file.

Minor cosmetic detail