Documenting source code changes to handle trailing zeros and other input formatting corner cases

[maxieds]

@ceheitsch As requested, this is a follow up to my re-opening the pull request #12 to amend the sources mentioned to still have errors by @spoznan in issue #16. Basically, the new source to the function changed is as follows:

Rational get_rational_from_word(std::string word) {
        Rational result;
        std::size_t decimalpoint = word.find('.');
        bool negative = (word.find('-') != std::string::npos);
        if (decimalpoint != std::string::npos) {
            std::string intpart = word.substr(0, decimalpoint);
            std::string fracpart = word.substr(decimalpoint + 1);

            if (intpart == "") intpart = "0";
            Integer theint (intpart, 10);
            theint = abs(theint);

            // Carve out the fractional part. Surprisingly fiddly!
            // Handle a corner case where the fractional part is all zeros:
            int fracdenom = 1;
            int lastNonZeroPos = fracpart.find_last_of("0");
            while(lastNonZeroPos + 1 == fracpart.length() && lastNonZeroPos != std::string::npos) {
                 if(lastNonZeroPos == 0) {
                      fracpart = "";
                      break;
                 }
                 fracpart = fracpart.substr(0, lastNonZeroPos);
                 lastNonZeroPos = fracpart.find_last_of("0");
            } 
            fracdenom = pow(10, fracpart.length());
            if(fracpart == "") {
                 fracpart = "0";
            }
            Integer fracval (fracpart, 10);
            Rational thefrac (fracval, fracdenom);
            thefrac.canonicalize();

            result = theint + thefrac;
            if (negative) result *= -1;
        } else {
            Rational thevalue (word);
            result = thevalue;
        }
        result.canonicalize();
        return result;
    };

Compiling the new source on math-mulberry allows me to do the tests and ensure they pass as follows:

$ ./RunPMFECommand.sh pmfe-tests -a -s -o pmfe-tests-full-output-2020.11.02-v1.txt

  REQUIRE( seq.len() == 72 )
with expansion:
  72 == 72

-------------------------------------------------------------------------------
O. nivara tRNA (old) MFE
  onivara_old_33, d1
-------------------------------------------------------------------------------
src/test-pmfe.cc:589
...............................................................................

src/test-pmfe.cc:1167:
PASSED:
  REQUIRE( energy == pmfe::Rational(-861, 5) )
with expansion:
  -861/5 == -861/5

src/test-pmfe.cc:1171:
PASSED:
  REQUIRE( scored_structure.old_string() == "(.....(...)....(....).................................................)." )
with expansion:
  "(.....(...)....(....).................................................)."
  ==
  "(.....(...)....(....).................................................)."

-------------------------------------------------------------------------------
O. nivara tRNA (old) MFE
-------------------------------------------------------------------------------
src/test-pmfe.cc:589
...............................................................................

src/test-pmfe.cc:595:
PASSED:
  REQUIRE( seq.len() == 72 )
with expansion:
  72 == 72

-------------------------------------------------------------------------------
O. nivara tRNA (old) MFE
  onivara_old_34, d1
-------------------------------------------------------------------------------
src/test-pmfe.cc:589
...............................................................................

src/test-pmfe.cc:1184:
PASSED:
  REQUIRE( energy == pmfe::Rational(-567,10) )
with expansion:
  -567/10 == -567/10

src/test-pmfe.cc:1188:
PASSED:
  REQUIRE( scored_structure.old_string() == "((((((((......((....)).....................(....)..............))))))))." )
with expansion:
  "((((((((......((....)).....................(....)..............))))))))."
  ==
  "((((((((......((....)).....................(....)..............))))))))."

===============================================================================
All tests passed (174 assertions in 24 test cases)