Implemented initialize h0 from h1 also for MPI.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5831 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added switches to compute a range of branches
Added branch selection (single branch or range of branches) to MPI.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5809 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed name to the internal variable mTimesFromFile to mBranchLengthFromFile.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5567 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added LRT output from MPI execution.
Readded --times-from-file to support old scripts.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5556 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed gene file to alignment file.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5470 95c5a404-1f88-0410-a6b0-c3f062b6f34a

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

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

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5174 95c5a404-1f88-0410-a6b0-c3f062b6f34a

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

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

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

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

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

Removed dependencies computation from Forest and created a standalone class
Added accessors to Forest
Removed unneeded methods
Write results do nothing if file not defined
Adjusted member visibility to various variables
Removed custom code for memalign
Added more tasking


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4784 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added initial routine to output results in a form suitable for automatic load into the database
Inital work on BEB


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4719 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4640 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4542 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Now links to ACML on windows
Removed unused entries in blas.h
Added option to enable fake omp_nesting in MKL
Added alternative routine that use DSYEVD instead of DSYEVR


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4541 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added new option to set the maximum number of MKL threads
Check for invalid times in file
Added definition for dsyevd
Added explanation for codon classes
Removed invalid test on parameters


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4537 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Fixed missing initialization in BranchSiteModelAltHyp.
Removed hardcoded value for relative error value.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4099 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed interface to BrancSiteModel.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@4003 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed various unsigned to size_t
For MPI passed the entire command line
Fixed local variable names
Added casts
Put save to Octave routines for testing


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3754 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Clarified Verbose levels.
Disabled balancing if run serial.
Move various initialization to be constructor initialization lists.
Fixed storage of results in MPI run.
All messages now go to cerr.
Different initialization of proportions. Now all classes have the same value.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3700 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Removed the NoMsg exception.
Added Fatal exception without argument.
Reduced tolerance in isDifferent.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3564 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3509 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3507 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added check on command line arguments that should not go together


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3505 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Put const in end value for iteration
Made loadTreeFromString private
Changed to C++ casts


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3504 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3410 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Removed no-aggressive option (so the reduction is always aggressive). Removed unneeded operation in compute LikelihoodWalker.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3404 95c5a404-1f88-0410-a6b0-c3f062b6f34a

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3265 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added command line switch to change the delta for the gradient computation.
Changed list of available optimization algorithms.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3247 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added option to have always the same starting point for optimization.
Added support for testing of variable h values.
Better check for parameters validity.
Small fixes.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3061 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Changed MPI structure
Aligned arrays
Added support for BLAS/LAPACK on windows.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3053 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Remove unused code and compilation options
Added USE_OLD_PROPORTIONS option
Streamlined Dependency between site classes computation
Correctly reinitialized BranchSiteModel variables



git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3043 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Simplified BranchSiteModel invocation.
Fixed OpenMP calls in main.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@3007 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Cleaned comments (for doxygen)
Changed few size_t into unsigned int
Moved preprocessing fields into anothed structure linked to ForestNode
Print active options improved
Moved to NLopt 2.2.4
Added RESTRICT keyword
Unrolled few loops for efficiency
Added new method to balance execution in the by-tree likelihood computation


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2892 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Use MKL VML functions
Better log messages formatting
Changed access method to children
New implementation of the 'same tree' flag
Fixed MKL directory and compilation line
Removed alignment for PGI compiler
Set slot (matrix and vector) length by experiment
Removed inline keywords
Added explicit to constructors
Aligned eigen decomposed matrices
Removed reversing of mD
Using STL map to convert codons to numbers
Reordered access to big vectors



git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2872 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Added attributes for alignment.
Reordered and cleaned variables.
Added placement new/delete and completed assignment operator for allocator (required by PGI)
Added print of compilation configuration at start of main.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2819 95c5a404-1f88-0410-a6b0-c3f062b6f34a

Used vector of bool for mGoodCodon. Added safeguard against negative likelihood. Added better shutdown of omp if so requested

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@2510 95c5a404-1f88-0410-a6b0-c3f062b6f34a