GitLab

correct some pb with gapOpening cost at sequence ends

git-svn-id: http://162.38.181.25/svn/macse@24 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@23 65091fd0-2642-4439-a783-786ed20c9932

-add trimSequence sub programm
-make enrich alignment a subfonction 

git-svn-id: http://162.38.181.25/svn/macse@22 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@21 65091fd0-2642-4439-a783-786ed20c9932

- begin/end gap cost all subprograms
- default gc for remove gappy seq sub programs

git-svn-id: http://162.38.181.25/svn/macse@20 65091fd0-2642-4439-a783-786ed20c9932

- add guessOneReadingFrame in the NT2AA subprogram
- handle profile with no sequence

git-svn-id: http://162.38.181.25/svn/macse@19 65091fd0-2642-4439-a783-786ed20c9932

- fix a minor bug in enrichAlignment (0 values was ignored as threshold)
- improve translateNT2AA to allow ignoring final stop (allow standard 3 step alignment strategy)
- print information concerning the genetic code used for the last sequence (last sequence information was previously missing)

git-svn-id: http://162.38.181.25/svn/macse@18 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@17 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@16 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@15 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@14 65091fd0-2642-4439-a783-786ed20c9932

add codingSequence basic statistic and (non parameterized) filtering during alignment enrichment based on those informations
add export functionality, to replace stop codon or FS codon in NT sequences, "!" in final codon are place at its end


git-svn-id: http://162.38.181.25/svn/macse@13 65091fd0-2642-4439-a783-786ed20c9932

ProfileAligner use double instead of float to limit rounding errors

git-svn-id: http://162.38.181.25/svn/macse@12 65091fd0-2642-4439-a783-786ed20c9932

-prog enrichAlignment
correct the determination of the sequence to be add

git-svn-id: http://162.38.181.25/svn/macse@11 65091fd0-2642-4439-a783-786ed20c9932

 - prog enrichAlignment => first version, does not question sequence order (pb of memory for building huge distance matrix)

git-svn-id: http://162.38.181.25/svn/macse@10 65091fd0-2642-4439-a783-786ed20c9932

- handle the case where the subset is empty or contains all sequences
- specify that a parameter follows the -out_subset and -out_other options

git-svn-id: http://162.38.181.25/svn/macse@9 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@8 65091fd0-2642-4439-a783-786ed20c9932

- SplitAlignment allows to specify a stretch of sites (useful for isolating section during debugging), todo anonimizing seq names (pb when names contains comma)
- translate NT2AA is implemented
- event costs are automatically turn into negative values
- minor bugs in option handling are fixed

git-svn-id: http://162.38.181.25/svn/macse@7 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@6 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@5 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@4 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@3 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@2 65091fd0-2642-4439-a783-786ed20c9932

git-svn-id: http://162.38.181.25/svn/macse@1 65091fd0-2642-4439-a783-786ed20c9932