Commits · ee5c527a84779997e3f871575402ea2d1cbd93e4 · phylo / fastcodeml

12 Dec, 2012 1 commit

Changed message output to cout from cerr. · ee5c527a

mvalle authored Dec 12, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5413 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ee5c527a

11 Dec, 2012 2 commits

Fixed problem with ambiguous codons. · ad0c251f

mvalle authored Dec 11, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5407 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ad0c251f

added paths for dev · 67cb81bc

hschabau authored Dec 11, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5394 95c5a404-1f88-0410-a6b0-c3f062b6f34a

67cb81bc

06 Dec, 2012 3 commits

Changed output of sites under positive selection so the site number starts from 1 and not zero. · a021808c
mvalle authored Dec 06, 2012
```
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5347 95c5a404-1f88-0410-a6b0-c3f062b6f34a
```
a021808c

Restructured few error messages. · 064a0a48

mvalle authored Dec 06, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5344 95c5a404-1f88-0410-a6b0-c3f062b6f34a

064a0a48

Added print num internal branches · 40acf8ea

mvalle authored Dec 06, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5343 95c5a404-1f88-0410-a6b0-c3f062b6f34a

40acf8ea

05 Dec, 2012 2 commits

· 98bf503e

hschabau authored Dec 05, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5333 95c5a404-1f88-0410-a6b0-c3f062b6f34a

98bf503e

· af416431

hschabau authored Dec 05, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5331 95c5a404-1f88-0410-a6b0-c3f062b6f34a

af416431

04 Dec, 2012 3 commits

Added print parameters. · a1a6de2f

mvalle authored Dec 04, 2012

Changed messages from Tree balancing.
Changed few BEB message formats.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5328 95c5a404-1f88-0410-a6b0-c3f062b6f34a

a1a6de2f

Changed variable name conflicting with reserved word · 6ca0ee3e

mvalle authored Dec 04, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5327 95c5a404-1f88-0410-a6b0-c3f062b6f34a

6ca0ee3e

Changed newick grammar to accept species names starting with number. · 7b82e33e

mvalle authored Dec 04, 2012

Better error message in parsing trees.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5324 95c5a404-1f88-0410-a6b0-c3f062b6f34a

7b82e33e

03 Dec, 2012 1 commit

Fixed bug that appears in beb only using -nr flag. · 2d27a5b2

mvalle authored Dec 03, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5303 95c5a404-1f88-0410-a6b0-c3f062b6f34a

2d27a5b2

01 Dec, 2012 1 commit

generated mpi version for castor · 31f394a2

hschabau authored Dec 01, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5289 95c5a404-1f88-0410-a6b0-c3f062b6f34a

31f394a2

30 Nov, 2012 1 commit

Fixed CMAKE_SKIP_RPATH for XMT · baf00e10

mvalle authored Nov 30, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5252 95c5a404-1f88-0410-a6b0-c3f062b6f34a

baf00e10

28 Nov, 2012 1 commit

Removed commented out test code (still BEB test code is still in place) · 357871ad

mvalle authored Nov 28, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5204 95c5a404-1f88-0410-a6b0-c3f062b6f34a

357871ad

24 Nov, 2012 1 commit

Removed testing code · 0b424b4e

mvalle authored Nov 24, 2012

Changed C style include to C++ style
Fixed few doxygen comments


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5191 95c5a404-1f88-0410-a6b0-c3f062b6f34a

0b424b4e

22 Nov, 2012 2 commits

update · fb6151d2

hschabau authored Nov 22, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5177 95c5a404-1f88-0410-a6b0-c3f062b6f34a

fb6151d2

update · c7c77395

hschabau authored Nov 22, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5176 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c7c77395

18 Nov, 2012 2 commits

Help message correction · 22fa4bd1

mvalle authored Nov 18, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5175 95c5a404-1f88-0410-a6b0-c3f062b6f34a

22fa4bd1

Added option -ps --no-pre-stop Don't stop H0 maximization if it cannot satisfy LRT (default: stop) · 5f1d3656
mvalle authored Nov 18, 2012
```
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5174 95c5a404-1f88-0410-a6b0-c3f062b6f34a
```
5f1d3656

15 Nov, 2012 1 commit

· 242dfbd1

hschabau authored Nov 15, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5149 95c5a404-1f88-0410-a6b0-c3f062b6f34a

242dfbd1

09 Nov, 2012 1 commit
- Removed variables used in testing, added printout arguments for a XMT compilation problem · 11012557
  mvalle authored Nov 09, 2012
```
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5102 95c5a404-1f88-0410-a6b0-c3f062b6f34a
```
  11012557
06 Nov, 2012 1 commit

Added support for ambiguous codons. · d1d7c9b6

mvalle authored Nov 06, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5085 95c5a404-1f88-0410-a6b0-c3f062b6f34a

d1d7c9b6

29 Oct, 2012 2 commits

Added mapping sites to original number · 85489f15

mvalle authored Oct 29, 2012

Removed divide and conquer command line option
Added default values on the command line options.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5025 95c5a404-1f88-0410-a6b0-c3f062b6f34a

85489f15

Cleaning · c34560cb

mvalle authored Oct 29, 2012

Added better support for XMT


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5019 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c34560cb

25 Oct, 2012 2 commits

Refactory changes (especially in Ming2) · ead0e2ec

mvalle authored Oct 25, 2012

Changed timer to return time_t
Added more catch cases
Different interface to BEB
Fixed warnings on windows
Changed BEB constructor
Partial porting to XMT
Fixed bug for testing


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4970 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ead0e2ec

· b7aa0327

hschabau authored Oct 25, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4964 95c5a404-1f88-0410-a6b0-c3f062b6f34a

b7aa0327

19 Oct, 2012 1 commit

Changed loading of std::map for efficiency. · 76ad1f34

mvalle authored Oct 19, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4929 95c5a404-1f88-0410-a6b0-c3f062b6f34a

76ad1f34

18 Oct, 2012 2 commits

Fixed bug in MPI results print · 331282bd

mvalle authored Oct 18, 2012

Added other symbols mapping for LAPACK/BLAS on Windows


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4925 95c5a404-1f88-0410-a6b0-c3f062b6f34a

331282bd

Added check for zero valid sites · 8ce34773

mvalle authored Oct 18, 2012

Upgraded doxygen and fixed doxygen comments
Fixed bug in write results
Changed computation order. First H1 then H0
Changed option init H1 from H0 to init H0 from H1
Added maximization forced stop if result does not already pass the LRT
Added MPI trace level and fixed messages
Added testing hooks to BEB.
Passed scale values from H1 to BEB
Fixed relative error default
Added initial map of internal to external site numbers
Changed iterator initialization


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4924 95c5a404-1f88-0410-a6b0-c3f062b6f34a

8ce34773

14 Oct, 2012 1 commit

Added exception for bad_alloc · 8fb3a6c0

mvalle authored Oct 14, 2012

Changed nul pointers from 0 to NULL (readability)
Fixed datatypes

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4896 95c5a404-1f88-0410-a6b0-c3f062b6f34a

8fb3a6c0

12 Oct, 2012 1 commit

Code restructuring · 6856879a

mvalle authored Oct 12, 2012

More on BEB computation
Changed null pointers from 0 to NULL


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4887 95c5a404-1f88-0410-a6b0-c3f062b6f34a

6856879a

11 Oct, 2012 2 commits

Removed vdExp usage that has problems with MPI · e5a7b966

mvalle authored Oct 11, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4839 95c5a404-1f88-0410-a6b0-c3f062b6f34a

e5a7b966

Changed comments, added cast · 6a482168

mvalle authored Oct 11, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4837 95c5a404-1f88-0410-a6b0-c3f062b6f34a

6a482168

10 Oct, 2012 3 commits

Finished fixing MPI for BEB. · 5e5adff6

mvalle authored Oct 10, 2012

Removed unneeded routines.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4835 95c5a404-1f88-0410-a6b0-c3f062b6f34a

5e5adff6

Added more code for BEB · f26764f5

mvalle authored Oct 10, 2012

Cleaned code
Started fixing design problem in MPI part


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4834 95c5a404-1f88-0410-a6b0-c3f062b6f34a

f26764f5

· 398b4e71

hschabau authored Oct 10, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4833 95c5a404-1f88-0410-a6b0-c3f062b6f34a

398b4e71

09 Oct, 2012 2 commits

testing fastcodeml · d11ae9d0

hschabau authored Oct 09, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4831 95c5a404-1f88-0410-a6b0-c3f062b6f34a

d11ae9d0

Cleared unused or moved code. · 038bec91

mvalle authored Oct 09, 2012

Cosmetic changes (variable names, variables access rights)
Added routines to support BEB
More validity controls on command line parameters

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4829 95c5a404-1f88-0410-a6b0-c3f062b6f34a

038bec91

05 Oct, 2012 1 commit

· 6a03fb31

hschabau authored Oct 05, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4814 95c5a404-1f88-0410-a6b0-c3f062b6f34a

6a03fb31