gtfold/gtfold — pull request #108 by msoni3 (2012-09-09 05:47:29+00:00)
Title: Code enhancement, runtime improvement, optimization, restructuring and feature implementation

1. scaling added in partition function d2
2. scaling added in stochastic traceback d2
3. --scale option added to boltzmann and help message for --sampleenergy
4. Addition of DOUBLE_ONLY parameter
5. added calculation of mfe in gtboltzmann for scaleFactor
6. slightly optimized initialization of partition function
7. MyDouble for only native double
8. fixed bug in boltzmann (printing len of seqfile instead of seq in pri
9. Integer represented as double
10. Making partition function and stochastic traceback as generic templates
11. MyDouble removed before adding AdvancedDouble
12. AdvancedDouble file added
13. Makefile.am updated to take care of AdvancedDouble.cc
14. Three different implementation of AdvancedDouble implemented -- mainl
15. warnings removed
16. warnings removed, templatization completed
17. boltzmann rearranged, cleaned and warnings removed
18. improvements and warnings removed
19. implementation of --advancedouble INT option, deciding intelligently
20. templatization of partition function computation and traceback comput
21. to remove group of compile time warnings
22. updating help messages and example usages
23. partition function constructor added and removed warnings
24. additional warning removed