[med-svn] [raxml-ng] 01/03: New upstream version 0.2.0
Andreas Tille
tille at debian.org
Tue Apr 25 15:07:10 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository raxml-ng.
commit 56b3f904bc47b780e069019be013e8edabc69e67
Author: Andreas Tille <tille at debian.org>
Date: Tue Apr 25 17:06:23 2017 +0200
New upstream version 0.2.0
---
CMakeLists.txt | 19 +-
LICENSE.txt | 661 +++++++++++++++++++++++++++++++++++++
README.md | 98 +++++-
src/Model.cpp | 369 +++++++++++++++++----
src/Model.hpp | 50 ++-
src/PartitionInfo.hpp | 2 +-
src/TreeInfo.cpp | 19 +-
src/common.h | 2 +-
src/io/NewickStream.cpp | 34 +-
src/io/msa_streams.cpp | 3 +
src/main.cpp | 100 ++++--
src/version.h | 4 +-
test/src/CommandLineParserTest.cpp | 9 +-
test/src/ModelTest.cpp | 128 ++++++-
14 files changed, 1366 insertions(+), 132 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7bb0caa..909fa04 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,9 +3,9 @@ cmake_minimum_required (VERSION 2.8.10 FATAL_ERROR)
set(CMAKE_DISABLE_IN_SOURCE_BUILD ON)
set(CMAKE_DISABLE_SOURCE_CHANGES ON)
-set (ENABLE_PTHREADS ON CACHE BOOL "Enable multi-threading support (PTHREADS)")
-set (ENABLE_MPI ON CACHE BOOL "Enable MPI support")
-set (ENABLE_VCF OFF)
+set (USE_PTHREADS ON CACHE BOOL "Enable multi-threading support (PTHREADS)")
+set (USE_MPI ON CACHE BOOL "Enable MPI support")
+set (USE_VCF OFF)
# leave this disabled to build a portable binary
# (don't worry, libpll will still have full SIMD support!)
@@ -14,8 +14,19 @@ set (ENABLE_RAXML_SIMD OFF)
# build a portable static binary
set(STATIC_BUILD ON)
+set(ENABLE_PTHREADS ${USE_PTHREADS})
+
project (raxml-ng C CXX)
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ # no support for static linking on Mac
+ set(STATIC_BUILD OFF)
+ # MPI support on Macs seems to be tricky (and unnecessary)
+ set(ENABLE_MPI OFF)
+else()
+ set(ENABLE_MPI ${USE_MPI})
+endif()
+
#check for minimum compiler versions
message(STATUS "Compier: ${CMAKE_CXX_COMPILER_ID}")
@@ -67,7 +78,7 @@ if(ENABLE_MPI)
find_package(MPI)
if(MPI_CXX_FOUND)
# set( ENV{OMPI_CXX} "clang++" PARENT_SCOPE )
- set(CMAKE_CXX_COMPILER "mpicxx")
+ set(CMAKE_CXX_COMPILER "${MPI_CXX_COMPILER}")
include_directories(${MPI_CXX_INCLUDE_PATH})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_COMPILER_FLAGS} -D_RAXML_MPI")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_CXX_LINK_FLAGS}")
diff --git a/LICENSE.txt b/LICENSE.txt
new file mode 100644
index 0000000..dba13ed
--- /dev/null
+++ b/LICENSE.txt
@@ -0,0 +1,661 @@
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+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
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+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
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+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU AGPL, see
+<http://www.gnu.org/licenses/>.
diff --git a/README.md b/README.md
index 2d7524b..628ff75 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,96 @@
-# raxml-ng
-RAxML Next Generation: faster, easier-to-use and more flexible
+# RAxML New Generation
+
+[](http://www.gnu.org/licenses/agpl-3.0.en.html)
+
+## Introduction
+
+RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in [*libpll*](https://github.com/xflouris/libpll) (Flouri et al. 2014).
+
+RAxML-NG offers improvements in speed, flexibility and user-friendliness over the previous RAxML versions. It also implements some of the features previously available in ExaML (Kozlov et al. 2015), including checkpointing and efficient load balancing for partitioned alignments (Kobert et al. 2014).
+
+RAxML-NG is currently under active development, and the mid-term plan is to have most functionality of RAxML 8.x covered.
+You can see some of the planned features [here](https://github.com/amkozlov/raxml-ng/issues).
+
+## Installation instructions
+
+* For most desktop Unix/Linux and macOS systems, the easiest way to install RAxML-NG is by using the pre-compiled binary:
+[**Download 64-bit Linux binary**](https://github.com/amkozlov/raxml-ng/releases/download/0.1.0/raxml-ng_v0.1.0b_linux_x86_64.zip)
+[**Download 64-bit OSX/macOS binary**](https://github.com/amkozlov/raxml-ng/releases/download/0.1.0/raxml-ng_v0.1.0b_macos_x86_64.zip)
+
+* For clusters/supercomputers (i.e., if you want to use MPI), please use the following installation package which contains pre-built *libpll*. You will need `GCC 4.8+` and `CMake 2.8+` to compile RAxML-NG for your system.
+[**Download RAxML-NG-MPI for Linux**](https://github.com/amkozlov/raxml-ng/releases/download/0.1.0/raxml-ng_v0.1.0b_linux_x86_64_MPI.zip)
+
+* Binaries for Windows will become available later on
+
+* If neither of the above options worked for you, please clone this repository and build RAxML-NG from scratch:
+
+```
+git clone --recursive https://github.com/amkozlov/raxml-ng
+cd raxml-ng
+mkdir build && cd build
+cmake ..
+make
+```
+
+## Documentation and Support
+
+Documentation can be found in the [github wiki](https://github.com/amkozlov/raxml-ng/wiki) (work in progress).
+
+Also please check the online help with `raxml-ng -h`.
+
+If still in doubt, please feel free to post to the [RAxML google group](https://groups.google.com/forum/#!forum/raxml).
+
+## Usage examples
+
+ 1. Perform single tree inference on DNA alignment
+ (random starting tree, general time-reversible model, ML estimate of substitution rates and
+ nucleotide frequencies, discrete GAMMA model of rate heterogeneity with 4 categories):
+
+ `./raxml-ng --msa testDNA.fa --model GTR+G`
+
+ 2. Perform an all-in-one analysis (ML tree search + non-parametric bootstrap)
+ (10 randomized parsimony starting trees, fixed empirical substitution matrix (LG),
+ empirical aminoacid frequencies from alignment, 8 discrete GAMMA categories,
+ 200 bootstrap replicates):
+
+ `./raxml-ng --all --msa testAA.fa --model LG+G8+F --tree pars{10} --bs-trees 200`
+
+
+ 3. Optimize branch lengths and free model parameters on a fixed topology
+ (using multiple partitions with proportional branch lengths)
+
+ `./raxml-ng --evaluate --msa testAA.fa --model partitions.txt --tree test.tree --brlen scaled`
+
+## License and third party licenses
+
+The code is currently licensed under the GNU Affero General Public License version 3.
+
+## The team
+
+* Alexey Kozlov
+* Alexandros Stamatakis
+* Diego Darriba
+* Tomáš Flouri
+* Benoit Morel
+
+## References
+
+* Stamatakis A. (2014)
+**RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.**
+*Bioinformatics*, 30(9): 1312-1313.
+doi:[10.1093/bioinformatics/btu033](http://dx.doi.org/10.1093/bioinformatics/btu033)
+
+* Flouri T., Izquierdo-Carrasco F., Darriba D., Aberer AJ, Nguyen LT, Minh BQ, von Haeseler A., Stamatakis A. (2014)
+**The Phylogenetic Likelihood Library.**
+*Systematic Biology*, 64(2): 356-362.
+doi:[10.1093/sysbio/syu084](http://dx.doi.org/10.1093/sysbio/syu084)
+
+* Kozlov A.M., Aberer A.J., Stamatakis A. (2015)
+**ExaML version 3: a tool for phylogenomic analyses on supercomputers.**
+*Bioinformatics (2015) 31 (15): 2577-2579.*
+doi:[10.1093/bioinformatics/btv184](https://doi.org/10.1093/bioinformatics/btv184)
+
+* Kobert K., Flouri T., Aberer A., Stamatakis A. (2014)
+**The divisible load balance problem and its application to phylogenetic inference.**
+*Brown D., Morgenstern B., editors. (eds.) Algorithms in Bioinformatics, Vol. 8701 of Lecture Notes in Computer Science. Springer, Berlin, pp. 204–216*
+
diff --git a/src/Model.cpp b/src/Model.cpp
index 2ff89ff..a8be779 100644
--- a/src/Model.cpp
+++ b/src/Model.cpp
@@ -21,6 +21,58 @@ const unordered_map<DataType, const unsigned int *,EnumClassHash> DATATYPE_MAPS
{DataType::diploid10, pll_map_diploid10}
};
+
+// TODO move it out of here
+class parse_error {};
+static bool read_param(istringstream& s, double& val)
+{
+ if (s.peek() == '{' || s.peek() == '[')
+ {
+ s.get();
+ s >> val;
+ auto c = s.get();
+ if (c != '}' && c != ']')
+ throw parse_error();
+
+ return true;
+ }
+ else
+ return false;
+}
+
+static bool read_param(istringstream& s, doubleVector& vec)
+{
+ if (s.peek() == '{' || s.peek() == '[')
+ {
+ int c = s.get();
+ while (s && c != '}' && c != ']')
+ {
+ double val;
+ s >> val;
+ vec.push_back(val);
+ c = s.get();
+ }
+ if (c != '}' && c != ']')
+ throw parse_error();
+
+ return true;
+ }
+ else
+ return false;
+}
+
+static void print_param(ostringstream& s, const doubleVector& vec)
+{
+ s << "{";
+ size_t i = 0;
+ for (auto v: vec)
+ {
+ s << ((i > 0) ? "/" : "") << v;
+ ++i;
+ }
+ s << "}";
+}
+
Model::Model (DataType data_type, const std::string &model_string) :
_data_type(data_type)
{
@@ -37,7 +89,7 @@ const unsigned int * Model::charmap() const
void Model::init_from_string(const std::string &model_string)
{
- size_t pos = model_string.find_first_of("+");
+ size_t pos = model_string.find_first_of("+{[");
const string model_name = pos == string::npos ? model_string : model_string.substr(0, pos);
const string model_opts = pos == string::npos ? "" : model_string.substr(pos);
@@ -123,6 +175,9 @@ void Model::init_model_opts(const std::string &model_opts, const pllmod_mixture_
_brlen_scaler = 1.0;
_name = string(mix_model.name);
+ _ratecat_rates.clear();
+ _ratecat_weights.clear();
+
/* set rate heterogeneity defaults from model */
_num_ratecats = mix_model.ncomp;
_num_submodels = mix_model.ncomp;
@@ -143,83 +198,251 @@ void Model::init_model_opts(const std::string &model_opts, const pllmod_mixture_
mix_model.models[0]->rates ? ParamValue::model : ParamValue::ML;
const char *s = model_opts.c_str();
- const char *tmp;
+
+ istringstream ss(model_opts);
+
+ try
+ {
+ doubleVector user_srates;
+ if (read_param(ss, user_srates))
+ {
+ // TODO support multi-matrix models
+ if (_submodels.size() > 0)
+ runtime_error("User-defined rates for multi-matrix models are not supported yet!");
+
+ auto smodel = _submodels[0];
+ auto num_uniq_rates = smodel.num_uniq_rates();
+ if (user_srates.size() != num_uniq_rates)
+ {
+ throw runtime_error("Invalid number of substitution rates specified: " +
+ std::to_string(user_srates.size()) + " (expected: " +
+ std::to_string(num_uniq_rates) + ")\n");
+ }
+
+ // normalize the rates
+ auto last_rate = smodel.rate_sym().empty() ?
+ user_srates.back() : user_srates[smodel.rate_sym().back()];
+ for (auto& r: user_srates)
+ r /= last_rate;
+
+ for (auto& m: _submodels)
+ m.uniq_subst_rates(user_srates);
+
+ _param_mode[PLLMOD_OPT_PARAM_SUBST_RATES] = ParamValue::user;
+ }
+ }
+ catch(parse_error& e)
+ {
+ throw runtime_error(string("Invalid substitution rate specification: ") + s);
+ }
+
+ // skip "+"
+ ss.get();
/* parse the rest and set additional model params */
- int rate_cats;
ParamValue param_mode;
- while(*s != '\0')
+ while(ss.peek() != EOF)
{
- // skip "+"
- s++;
+ // set current string position, for error reporting
+ s = model_opts.c_str() + ss.tellg();
- switch(toupper(*s))
+ switch(toupper(ss.get()))
{
+ case EOF:
case '\0':
- case '+':
+ // end of model options
break;
+ case '+':
+ // proceed to the next token
+ continue;
case 'F':
- switch (toupper(*(s+1)))
+ try
{
- case '\0':
- case '+':
- case 'C':
- param_mode = ParamValue::empirical;
- break;
- case 'O':
- param_mode = ParamValue::ML;
- break;
- case 'E':
- param_mode = ParamValue::equal;
+ switch (toupper(ss.get()))
+ {
+ case EOF:
+ case '\0':
+ case '+':
+ case 'C':
+ param_mode = ParamValue::empirical;
+ break;
+ case 'O':
+ param_mode = ParamValue::ML;
+ break;
+ case 'E':
+ param_mode = ParamValue::equal;
+ break;
+ case 'U':
+ {
+ param_mode = ParamValue::user;
+
+ /* for now, read single set of frequencies */
+ doubleVector user_freqs;
+ if (read_param(ss, user_freqs))
+ {
+ if (user_freqs.size() != _num_states)
+ {
+ throw runtime_error("Invalid number of user frequencies specified: " +
+ std::to_string(user_freqs.size()) + "\n" +
+ "Number of frequencies must be equal to the number of states: " +
+ std::to_string(_num_states) + "\n");
+ }
+
+ double sum = 0.;
+ bool invalid = false;
+ for (auto v: user_freqs)
+ {
+ invalid |= (v <= 0. || v >= 1.);
+ sum += v;
+ }
+
+ if (invalid)
+ {
+ throw runtime_error("Invalid base frequencies specified! "
+ "Frequencies must be positive numbers between 0. and 1.");
+ }
+
+ // normalize freqs
+ for (auto& f: user_freqs)
+ f /= sum;
+
+ for (auto& m: _submodels)
+ m.base_freqs(user_freqs);
+ }
+ else
+ throw parse_error();
+ }
break;
- default:
- throw runtime_error(string("Invalid frequencies specification: ") + s);
+ default:
+ throw parse_error();
+ }
+ _param_mode[PLLMOD_OPT_PARAM_FREQUENCIES] = param_mode;
+ }
+ catch(parse_error& e)
+ {
+ throw runtime_error(string("Invalid frequencies specification: ") + s);
}
- _param_mode[PLLMOD_OPT_PARAM_FREQUENCIES] = param_mode;
break;
case 'I':
- switch (toupper(*(s+1)))
+ try
{
- case '\0':
- case '+':
- case 'O':
- param_mode = ParamValue::ML;
- break;
- case 'C':
- param_mode = ParamValue::empirical;
- break;
- case '{':
- if (sscanf(s+1, "{%lf}", &_pinv) == 1 && ((tmp = strchr(s, '}')) != NULL))
- {
- param_mode = ParamValue::user;
- s = tmp+1;
- }
- else
- throw runtime_error(string("Invalid p-inv specification: ") + s);
- break;
- default:
- throw runtime_error(string("Invalid p-inv specification: ") + s);
+ switch (toupper(ss.get()))
+ {
+ case EOF:
+ case '\0':
+ case '+':
+ case 'O':
+ param_mode = ParamValue::ML;
+ break;
+ case 'C':
+ param_mode = ParamValue::empirical;
+ break;
+ case 'U':
+ if (read_param(ss, _pinv))
+ param_mode = ParamValue::user;
+ else
+ throw parse_error();
+ break;
+ default:
+ throw parse_error();
+ }
+ _param_mode[PLLMOD_OPT_PARAM_PINV] = param_mode;
+ }
+ catch(parse_error& e)
+ {
+ throw runtime_error(string("Invalid p-inv specification: ") + s);
}
- _param_mode[PLLMOD_OPT_PARAM_PINV] = param_mode;
break;
- case 'R':
case 'G':
- /* allow to override mixture ratehet mode for now */
- _rate_het = toupper(*s) == 'R' ? PLLMOD_UTIL_MIXTYPE_FREE : PLLMOD_UTIL_MIXTYPE_GAMMA;
- if (sscanf(s+1, "%d", &rate_cats) == 1)
+ try
+ {
+ /* allow to override mixture ratehet mode for now */
+ _rate_het = PLLMOD_UTIL_MIXTYPE_GAMMA;
+ if (isdigit(ss.peek()))
+ {
+ ss >> _num_ratecats;
+ }
+ else if (_num_ratecats == 1)
+ _num_ratecats = 4;
+
+ if (read_param(ss, _alpha))
+ {
+ _param_mode[PLLMOD_OPT_PARAM_ALPHA] = ParamValue::user;
+ }
+ }
+ catch(parse_error& e)
+ {
+ throw runtime_error(string("Invalid GAMMA specification: ") + s);
+ }
+ break;
+ case 'R':
+ _rate_het = PLLMOD_UTIL_MIXTYPE_FREE;
+ if (isdigit(ss.peek()))
{
- _num_ratecats = rate_cats;
+ ss >> _num_ratecats;
}
else if (_num_ratecats == 1)
_num_ratecats = 4;
+
+ try
+ {
+ doubleVector v;
+ if (read_param(ss, v))
+ {
+ if (v.size() != _num_ratecats)
+ {
+ throw runtime_error("Invalid number of free rates specified: " +
+ std::to_string(v.size()) + " (expected: " +
+ std::to_string(_num_ratecats) + ")\n");
+ }
+
+ // TODO: maybe allow to optimize rates and weights separately
+ _param_mode[PLLMOD_OPT_PARAM_RATE_WEIGHTS] = ParamValue::user;
+ _param_mode[PLLMOD_OPT_PARAM_FREE_RATES] = ParamValue::user;
+
+ _ratecat_rates = v;
+
+ v.clear();
+ if (read_param(ss, v))
+ {
+ if (v.size() != _num_ratecats)
+ {
+ throw runtime_error("Invalid number of rate weights specified: " +
+ std::to_string(v.size()) + " (expected: " +
+ std::to_string(_num_ratecats) + ")\n");
+ }
+
+
+ // normalize weights
+ double sum = 0;
+ for (auto w: v)
+ sum += w;
+
+ for (auto& w: v)
+ w /= sum;
+
+ _ratecat_weights = v;
+ }
+ else
+ _ratecat_weights.assign(_num_ratecats, 1.0 / _num_ratecats);
+
+ // normalize weights + rates
+ double sum_weightrates = 0.0;
+ for (size_t i = 0; i < _num_ratecats; ++i)
+ sum_weightrates += _ratecat_rates[i] * _ratecat_weights[i];
+
+ for (auto& r: _ratecat_rates)
+ r /= sum_weightrates;
+ }
+ }
+ catch(parse_error& e)
+ {
+ throw runtime_error(string("Invalid FreeRate specification: ") + s);
+ }
break;
default:
throw runtime_error("Wrong model specification: " + model_opts);
}
-
- // rewind to next term
- while (*s != '+' && *s != '\0')
- s++;
}
switch (_param_mode.at(PLLMOD_OPT_PARAM_FREQUENCIES))
@@ -239,10 +462,10 @@ void Model::init_model_opts(const std::string &model_opts, const pllmod_mixture_
assert(0);
}
- const size_t num_srates = pllmod_util_subst_rate_count(_num_states);
switch (_param_mode.at(PLLMOD_OPT_PARAM_SUBST_RATES))
{
case ParamValue::user:
+ break;
case ParamValue::empirical:
case ParamValue::model:
/* nothing to do here */
@@ -251,15 +474,17 @@ void Model::init_model_opts(const std::string &model_opts, const pllmod_mixture_
case ParamValue::ML:
/* use equal rates as s a starting value for ML optimization */
for (auto& m: _submodels)
- m.subst_rates(doubleVector(num_srates, 1.0));
+ m.subst_rates(doubleVector(m.num_rates(), 1.0));
break;
default:
assert(0);
}
/* default: equal rates & weights */
- _ratecat_rates.assign(_num_ratecats, 1.0);
- _ratecat_weights.assign(_num_ratecats, 1.0 / _num_ratecats);
+ if (_ratecat_rates.empty())
+ _ratecat_rates.assign(_num_ratecats, 1.0);
+ if (_ratecat_weights.empty())
+ _ratecat_weights.assign(_num_ratecats, 1.0 / _num_ratecats);
_ratecat_submodels.assign(_num_ratecats, 0);
if (_num_ratecats > 1)
@@ -283,10 +508,14 @@ void Model::init_model_opts(const std::string &model_opts, const pllmod_mixture_
break;
case PLLMOD_UTIL_MIXTYPE_FREE:
- /* use GAMMA rates as inital values -> can be changed */
- pll_compute_gamma_cats(_alpha, _num_ratecats, _ratecat_rates.data());
- _param_mode[PLLMOD_OPT_PARAM_FREE_RATES] = ParamValue::ML;
- _param_mode[PLLMOD_OPT_PARAM_RATE_WEIGHTS] = ParamValue::ML;
+ if (_param_mode[PLLMOD_OPT_PARAM_FREE_RATES] == ParamValue::undefined)
+ {
+ /* use GAMMA rates as initial values -> can be changed */
+ pll_compute_gamma_cats(_alpha, _num_ratecats, _ratecat_rates.data());
+ _param_mode[PLLMOD_OPT_PARAM_FREE_RATES] = ParamValue::ML;
+ }
+ if (_param_mode[PLLMOD_OPT_PARAM_RATE_WEIGHTS] == ParamValue::undefined)
+ _param_mode[PLLMOD_OPT_PARAM_RATE_WEIGHTS] = ParamValue::ML;
break;
default:
@@ -304,13 +533,16 @@ void Model::init_model_opts(const std::string &model_opts, const pllmod_mixture_
std::string Model::to_string() const
{
- stringstream model_string;
+ ostringstream model_string;
model_string << name();
+ if (_param_mode.at(PLLMOD_OPT_PARAM_SUBST_RATES) == ParamValue::user)
+ print_param(model_string, submodel(0).uniq_subst_rates());
+
switch(_param_mode.at(PLLMOD_OPT_PARAM_FREQUENCIES))
{
case ParamValue::empirical:
- model_string << "+F";
+ model_string << "+FC";
break;
case ParamValue::ML:
model_string << "+FO";
@@ -318,6 +550,12 @@ std::string Model::to_string() const
case ParamValue::equal:
model_string << "+FE";
break;
+ case ParamValue::user:
+ {
+ model_string << "+FU";
+ print_param(model_string, base_freqs(0));
+ }
+ break;
default:
break;
}
@@ -331,7 +569,7 @@ std::string Model::to_string() const
model_string << "+I";
break;
case ParamValue::user:
- model_string << "+I{" << _pinv << "}";
+ model_string << "+IU{" << _pinv << "}";
break;
default:
break;
@@ -348,6 +586,11 @@ std::string Model::to_string() const
else if (_rate_het == PLLMOD_UTIL_MIXTYPE_FREE)
{
model_string << "+R" << _num_ratecats;
+ if (_param_mode.at(PLLMOD_OPT_PARAM_FREE_RATES) == ParamValue::user)
+ {
+ print_param(model_string, _ratecat_rates);
+ print_param(model_string, _ratecat_weights);
+ }
}
}
diff --git a/src/Model.hpp b/src/Model.hpp
index 283803c..d1d5832 100644
--- a/src/Model.hpp
+++ b/src/Model.hpp
@@ -1,6 +1,8 @@
#ifndef RAXML_MODEL_H_
#define RAXML_MODEL_H_
+#include <algorithm>
+
#include "common.h"
class SubstitutionModel
@@ -22,10 +24,33 @@ public:
// getters
unsigned int states() const;
std::string name() const;
- const doubleVector& base_freqs() const { return _base_freqs; };
- const doubleVector& subst_rates() const { return _subst_rates; };
- const intVector& rate_sym() const { return _rate_sym; };
- const intVector& freq_sym() const { return _freq_sym; };
+ const doubleVector& base_freqs() const { return _base_freqs; }
+ const doubleVector& subst_rates() const { return _subst_rates; }
+ const intVector& rate_sym() const { return _rate_sym; }
+ const intVector& freq_sym() const { return _freq_sym; }
+
+ unsigned int num_rates() const { return _states*(_states-1)/2; }
+ unsigned int num_uniq_rates() const
+ {
+ if (_rate_sym.empty())
+ return num_rates();
+ else
+ return *std::max_element(_rate_sym.cbegin(), _rate_sym.cend()) + 1;
+ }
+
+ doubleVector uniq_subst_rates() const
+ {
+ if (!_rate_sym.empty())
+ {
+ doubleVector uniq_rates(num_uniq_rates());
+ for (size_t i = 0; i < _subst_rates.size(); ++i)
+ uniq_rates[_rate_sym[i]] = _subst_rates[i];
+ return uniq_rates;
+ }
+ else
+ return _subst_rates;
+ };
+
// setters
void base_freqs(const doubleVector& v)
@@ -39,12 +64,27 @@ public:
void subst_rates(const doubleVector& v)
{
- if (v.size() != _states * (_states - 1) / 2)
+ if (v.size() != num_rates())
throw std::invalid_argument("Invalid size of subst_rates vector!");
_subst_rates = v;
};
+ void uniq_subst_rates(const doubleVector& v)
+ {
+ if (!_rate_sym.empty())
+ {
+ if (v.size() != num_uniq_rates())
+ throw std::invalid_argument("Invalid size of subst_rates vector!");
+
+ _subst_rates.resize(num_rates());
+ for (size_t i = 0; i < _subst_rates.size(); ++i)
+ _subst_rates[i] = v[_rate_sym[i]];
+ }
+ else
+ subst_rates(v);
+ };
+
private:
unsigned int _states;
std::string _name;
diff --git a/src/PartitionInfo.hpp b/src/PartitionInfo.hpp
index 7c8737b..4c56c35 100644
--- a/src/PartitionInfo.hpp
+++ b/src/PartitionInfo.hpp
@@ -25,7 +25,7 @@ public:
_name = std::move(other._name);
_range_string = std::move(other._range_string);
_model = std::move(other._model);
- _msa = std::move(_msa);
+ _msa = std::move(other._msa);
_stats = other._stats;
other._stats = nullptr;
}
diff --git a/src/TreeInfo.cpp b/src/TreeInfo.cpp
index 1d28b70..2a5e3ea 100644
--- a/src/TreeInfo.cpp
+++ b/src/TreeInfo.cpp
@@ -133,7 +133,8 @@ double TreeInfo::optimize_branches(double lh_epsilon, double brlen_smooth_factor
_pll_treeinfo->parallel_context,
_pll_treeinfo->parallel_reduce_cb
);
- DBG("\t - after brlen: logLH = %f\n", new_loglh);
+
+ LOG_DEBUG << "\t - after brlen: logLH = " << new_loglh << endl;
if (pll_errno)
throw runtime_error("ERROR in branch lenght optimization: " + string(pll_errmsg));
@@ -152,7 +153,7 @@ double TreeInfo::optimize_branches(double lh_epsilon, double brlen_smooth_factor
/* normalize scalers and scale the branches accordingly */
pllmod_treeinfo_normalize_brlen_scalers(_pll_treeinfo);
- DBG("\t - after brlen scalers: logLH = %f\n", new_loglh);
+ LOG_DEBUG << "\t - after brlen scalers: logLH = " << new_loglh << endl;
}
@@ -172,7 +173,8 @@ double TreeInfo::optimize_params(int params_to_optimize, double lh_epsilon)
PLLMOD_OPT_MAX_SUBST_RATE,
RAXML_BFGS_FACTOR,
RAXML_PARAM_EPSILON);
- DBG("\t - after rates: logLH = %f\n", new_loglh);
+
+ LOG_DEBUG << "\t - after rates: logLH = " << new_loglh << endl;
}
/* optimize BASE FREQS */
@@ -185,7 +187,7 @@ double TreeInfo::optimize_params(int params_to_optimize, double lh_epsilon)
RAXML_BFGS_FACTOR,
RAXML_PARAM_EPSILON);
- DBG("\t - after freqs: logLH = %f\n", new_loglh);
+ LOG_DEBUG << "\t - after freqs: logLH = " << new_loglh << endl;
}
/* optimize ALPHA */
@@ -196,7 +198,8 @@ double TreeInfo::optimize_params(int params_to_optimize, double lh_epsilon)
PLLMOD_OPT_MIN_ALPHA,
PLLMOD_OPT_MAX_ALPHA,
RAXML_PARAM_EPSILON);
- DBG("\t - after alpha: logLH = %f\n", new_loglh);
+
+ LOG_DEBUG << "\t - after alpha: logLH = " << new_loglh << endl;
}
if (params_to_optimize & PLLMOD_OPT_PARAM_PINV)
@@ -207,7 +210,7 @@ double TreeInfo::optimize_params(int params_to_optimize, double lh_epsilon)
PLLMOD_OPT_MAX_PINV,
RAXML_PARAM_EPSILON);
- DBG("\t - after p-inv: logLH = %f\n", new_loglh);
+ LOG_DEBUG << "\t - after p-inv: logLH = " << new_loglh << endl;
}
/* optimize FREE RATES and WEIGHTS */
@@ -224,8 +227,8 @@ double TreeInfo::optimize_params(int params_to_optimize, double lh_epsilon)
_pll_treeinfo->partition_count > 1)
pllmod_treeinfo_normalize_brlen_scalers(_pll_treeinfo);
- DBG("\t - after freeR: logLH = %f\n", new_loglh);
- DBG("\t - after freeR/crosscheck: logLH = %f\n", loglh());
+ LOG_DEBUG << "\t - after freeR: logLH = " << new_loglh << endl;
+// LOG_DEBUG << "\t - after freeR/crosscheck: logLH = " << loglh() << endl;
}
if (params_to_optimize & PLLMOD_OPT_PARAM_BRANCHES_ITERATIVE)
diff --git a/src/common.h b/src/common.h
index 488aebe..6fb90de 100644
--- a/src/common.h
+++ b/src/common.h
@@ -31,7 +31,7 @@ extern "C" {
// defaults
#define DEF_LH_EPSILON 0.1
#define OPT_LH_EPSILON 0.1
-#define RAXML_PARAM_EPSILON 0.01
+#define RAXML_PARAM_EPSILON 0.001 //0.01
#define RAXML_BFGS_FACTOR 1e7
#define RAXML_BRLEN_SMOOTHINGS 32
diff --git a/src/io/NewickStream.cpp b/src/io/NewickStream.cpp
index f31ef4d..8416114 100644
--- a/src/io/NewickStream.cpp
+++ b/src/io/NewickStream.cpp
@@ -1,5 +1,7 @@
#include "file_io.hpp"
+using namespace std;
+
NewickStream& operator<<(NewickStream& stream, const pll_utree_t& tree)
{
char * newick_str = pll_utree_export_newick(&tree);
@@ -16,13 +18,33 @@ NewickStream& operator<<(NewickStream& stream, const Tree& tree)
NewickStream& operator>>(NewickStream& stream, Tree& tree)
{
-// stream.getline()
-// char * newick_str = pll_utree_export_newick((pll_utree_t *) &tree);
-// stream << newick_str << std::endl;
-// free(newick_str);
- tree.fix_missing_brlens();
- assert(0);
+ string newick_str;
+
+ std::getline(stream, newick_str);
+
+ pll_utree_t * utree;
+ pll_rtree_t * rtree;
+
+ unsigned int tip_count;
+ if (!(utree = pll_utree_parse_newick_string(newick_str.c_str(), &tip_count)))
+ {
+ if (!(rtree = pll_rtree_parse_newick_string(newick_str.c_str(), &tip_count)))
+ {
+ throw runtime_error("ERROR reading tree file: " + string(pll_errmsg));
+ }
+ else
+ {
+ // LOG_INFO << "NOTE: You provided a rooted tree; it will be automatically unrooted." << endl;
+ utree = pll_rtree_unroot(rtree);
+
+ /* optional step if using default PLL clv/pmatrix index assignments */
+ pll_utree_reset_template_indices(utree, tip_count);
+ }
+ }
+
+ tree = Tree(tip_count, utree);
+
return stream;
}
diff --git a/src/io/msa_streams.cpp b/src/io/msa_streams.cpp
index 497ef55..e8d1077 100644
--- a/src/io/msa_streams.cpp
+++ b/src/io/msa_streams.cpp
@@ -223,6 +223,9 @@ MSA msa_load_from_file(const std::string &filename, const FileFormat format)
auto fmt_begin = msa_formats.cbegin();
auto fmt_end = msa_formats.cend();
+ if (!sysutil_file_exists(filename))
+ throw runtime_error("File not found: " + filename);
+
if (format != FileFormat::autodetect)
{
fmt_begin = std::find_if(msa_formats.begin(), msa_formats.end(),
diff --git a/src/main.cpp b/src/main.cpp
index d30a6e6..3778db4 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -49,6 +49,8 @@ struct RaxmlInstance
PartitionAssignmentList proc_part_assign;
unique_ptr<BootstrapTree> bs_tree;
+ unique_ptr<NewickStream> start_tree_stream;
+
/* this is just a dummy random tree used for convenience, e,g, if we need tip labels or
* just 'any' valid tree for the alignment at hand */
Tree random_tree;
@@ -176,10 +178,12 @@ void check_msa(RaxmlInstance& instance)
}
else
{
- for (auto e: gap_seqs)
+ for(auto it = gap_seqs.begin(); it != gap_seqs.end();)
{
- if (cur_gap_seq.find(e) == cur_gap_seq.end())
- gap_seqs.erase(e);
+ if(cur_gap_seq.find(*it) == cur_gap_seq.end())
+ it = gap_seqs.erase(it);
+ else
+ ++it;
}
}
@@ -197,9 +201,9 @@ void check_msa(RaxmlInstance& instance)
if (!gap_seqs.empty())
{
- LOG_WARN << "\nWARNING: Fully undetermined sequences found: " << stats->gap_seqs_count << endl;
+ LOG_WARN << "\nWARNING: Fully undetermined sequences found: " << gap_seqs.size() << endl;
for (auto c : gap_seqs)
- LOG_VERB << "WARNING: Sequence " << pll_msa->label[c] << " contains only gaps!" << endl;
+ LOG_VERB << "WARNING: Sequence " << c << " " << pll_msa->label[c] << " contains only gaps!" << endl;
}
@@ -211,7 +215,7 @@ void check_msa(RaxmlInstance& instance)
ps << instance.parted_msa;
- LOG_INFO << "\nNOTE: Reduced alignment (with gap-only sequences and columns removed) was printed to:\n";
+ LOG_INFO << "\nNOTE: Reduced alignment (with gap-only columns removed) was printed to:\n";
LOG_INFO << sysutil_realpath(reduced_msa_fname) << endl;
// save reduced partition file
@@ -289,11 +293,11 @@ Tree generate_tree(const RaxmlInstance& instance, StartingTree type)
{
case StartingTree::user:
{
- assert(!opts.tree_file.empty());
+ assert(instance.start_tree_stream);
/* parse the unrooted binary tree in newick format, and store the number
of tip nodes in tip_nodes_count */
- tree = Tree::loadFromFile(opts.tree_file);
+ *instance.start_tree_stream >> tree;
LOG_DEBUG << "Loaded user starting tree with " << tree.num_tips() << " taxa from: "
<< opts.tree_file << endl;
@@ -307,7 +311,6 @@ Tree generate_tree(const RaxmlInstance& instance, StartingTree type)
}
case StartingTree::random:
/* no starting tree provided, generate a random one */
- assert(opts.command != Command::evaluate);
LOG_DEBUG << "Generating a random starting tree with " << msa.size() << " taxa" << endl;
@@ -373,6 +376,9 @@ void build_start_trees(RaxmlInstance& instance, CheckpointManager& cm)
{
case StartingTree::user:
LOG_INFO_TS << "Loading user starting tree(s) from: " << opts.tree_file << endl;
+ if (!sysutil_file_exists(opts.tree_file))
+ throw runtime_error("File not found: " + opts.tree_file);
+ instance.start_tree_stream.reset(new NewickStream(opts.tree_file, std::ios::in));
break;
case StartingTree::random:
LOG_INFO_TS << "Generating random starting tree(s) with " << msa.size() << " taxa" << endl;
@@ -388,6 +394,13 @@ void build_start_trees(RaxmlInstance& instance, CheckpointManager& cm)
{
auto tree = generate_tree(instance, opts.start_tree);
+ // TODO use universal starting tree generator
+ if (opts.start_tree == StartingTree::user)
+ {
+ if (instance.start_tree_stream->peek() != EOF)
+ instance.opts.num_searches++;
+ }
+
// TODO: skip generation
if (i < cm.checkpoint().ml_trees.size())
continue;
@@ -463,6 +476,17 @@ void draw_bootstrap_support(RaxmlInstance& instance, const Checkpoint& checkp)
instance.bs_tree->calc_support();
}
+void save_ml_trees(const Options& opts, const Checkpoint& checkp)
+{
+ NewickStream nw(opts.ml_trees_file(), std::ios::out);
+ Tree ml_tree = checkp.tree;
+ for (auto topol: checkp.ml_trees)
+ {
+ ml_tree.topology(topol.second);
+ nw << ml_tree;
+ }
+}
+
void print_final_output(const RaxmlInstance& instance, const Checkpoint& checkp)
{
auto const& opts = instance.opts;
@@ -477,6 +501,13 @@ void print_final_output(const RaxmlInstance& instance, const Checkpoint& checkp)
LOG_INFO << checkp.models.at(p);
}
+ if (opts.command == Command::evaluate)
+ {
+ save_ml_trees(opts, checkp);
+
+ LOG_INFO << "\nAll optimized tree(s) saved to: " << sysutil_realpath(opts.ml_trees_file()) << endl;
+ }
+
if (opts.command == Command::search || opts.command == Command::all)
{
auto best = checkp.ml_trees.best();
@@ -492,13 +523,7 @@ void print_final_output(const RaxmlInstance& instance, const Checkpoint& checkp)
if (checkp.ml_trees.size() > 1)
{
- NewickStream nw(opts.ml_trees_file(), std::ios::out);
- Tree ml_tree = checkp.tree;
- for (auto topol: checkp.ml_trees)
- {
- ml_tree.topology(topol.second);
- nw << ml_tree;
- }
+ save_ml_trees(opts, checkp);
LOG_INFO << "All ML trees saved to: " << sysutil_realpath(opts.ml_trees_file()) << endl;
}
@@ -560,12 +585,20 @@ void thread_main(const RaxmlInstance& instance, CheckpointManager& cm)
/* get partitions assigned to the current thread */
auto const& part_assign = instance.proc_part_assign.at(ParallelContext::proc_id());
- if ((opts.command == Command::search || opts.command == Command::all) &&
- !instance.start_trees.empty())
+ if ((opts.command == Command::search || opts.command == Command::all ||
+ opts.command == Command::evaluate ) && !instance.start_trees.empty())
{
- LOG_INFO << "\nStarting ML tree search with " << opts.num_searches <<
- " distinct starting trees" << endl << endl;
+ if (opts.command == Command::evaluate)
+ {
+ LOG_INFO << "\nEvaluating " << opts.num_searches <<
+ " trees" << endl << endl;
+ }
+ else
+ {
+ LOG_INFO << "\nStarting ML tree search with " << opts.num_searches <<
+ " distinct starting trees" << endl << endl;
+ }
size_t start_tree_num = cm.checkpoint().ml_trees.size();
bool use_ckp_tree = cm.checkpoint().search_state.step != CheckpointStep::start;
@@ -589,19 +622,29 @@ void thread_main(const RaxmlInstance& instance, CheckpointManager& cm)
// treeinfo->tree(tree);
Optimizer optimizer(opts);
- if (opts.command == Command::search || opts.command == Command::all)
+ if (opts.command == Command::evaluate)
{
- optimizer.optimize_topology(*treeinfo, cm);
+ LOG_INFO_TS << "Tree #" << start_tree_num <<
+ ", initial LogLikelihood: " << FMT_LH(treeinfo->loglh()) << endl;
+ cm.search_state().loglh = optimizer.optimize(*treeinfo);
+ cm.update_and_write(*treeinfo);
}
else
{
- LOG_INFO << "\nInitial LogLikelihood: " << FMT_LH(treeinfo->loglh()) << endl << endl;
- optimizer.optimize(*treeinfo);
+ optimizer.optimize_topology(*treeinfo, cm);
}
LOG_PROGR << endl;
- LOG_INFO_TS << "ML tree search #" << start_tree_num <<
- ", logLikelihood: " << FMT_LH(cm.checkpoint().loglh()) << endl;
+ if (opts.command == Command::evaluate)
+ {
+ LOG_INFO_TS << "Tree #" << start_tree_num <<
+ ", final logLikelihood: " << FMT_LH(cm.checkpoint().loglh()) << endl;
+ }
+ else
+ {
+ LOG_INFO_TS << "ML tree search #" << start_tree_num <<
+ ", logLikelihood: " << FMT_LH(cm.checkpoint().loglh()) << endl;
+ }
LOG_PROGR << endl;
cm.save_ml_tree();
@@ -743,7 +786,10 @@ int main(int argc, char** argv)
/* now get to the real stuff */
srand(instance.opts.random_seed);
logger().set_log_level(instance.opts.log_level);
- logger().set_log_filename(instance.opts.log_file());
+
+ /* only master process writes the log file */
+ if (ParallelContext::master())
+ logger().set_log_filename(instance.opts.log_file());
print_banner();
LOG_INFO << instance.opts;
diff --git a/src/version.h b/src/version.h
index cb0e6c9..47ff98f 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1,2 +1,2 @@
-#define RAXML_VERSION "0.1.0 BETA"
-#define RAXML_DATE "18.03.2017"
+#define RAXML_VERSION "0.2.0 BETA"
+#define RAXML_DATE "04.04.2017"
diff --git a/test/src/CommandLineParserTest.cpp b/test/src/CommandLineParserTest.cpp
index 97773d9..536279e 100644
--- a/test/src/CommandLineParserTest.cpp
+++ b/test/src/CommandLineParserTest.cpp
@@ -71,10 +71,11 @@ TEST(CommandLineParserTest, search_minimal)
Options options;
// minimal valid command line
- string cmd = "raxml-ng --msa data.fa";
+ string cmd = "raxml-ng --msa data.fa --model GTR";
parse_options(cmd, parser, options, false);
EXPECT_EQ(Command::search, options.command);
EXPECT_EQ("data.fa", options.msa_file);
+ EXPECT_EQ("GTR", options.model_file);
}
TEST(CommandLineParserTest, search_complex1)
@@ -133,9 +134,10 @@ TEST(CommandLineParserTest, eval_minimal)
Options options;
// valid evaluate command line
- string cmd = "raxml-ng --evaluate --msa data.fa --tree start.tre";
+ string cmd = "raxml-ng --evaluate --msa data.fa --model GTR --tree start.tre";
parse_options(cmd, parser, options, false);
EXPECT_EQ(Command::evaluate, options.command);
+ EXPECT_EQ("GTR", options.model_file);
EXPECT_TRUE(options.optimize_model);
EXPECT_TRUE(options.optimize_brlen);
}
@@ -148,9 +150,10 @@ TEST(CommandLineParserTest, eval_complex)
// evaluate with more settings
string cmd = "raxml-ng --evaluate --msa data.fa --tree start.tre --opt-model OFF "
- "--opt-branches OFF --lh-epsilon 0.02";
+ "--opt-branches OFF --lh-epsilon 0.02 --model GTR";
parse_options(cmd, parser, options, false);
EXPECT_EQ(Command::evaluate, options.command);
+ EXPECT_EQ("GTR", options.model_file);
EXPECT_FALSE(options.optimize_model);
EXPECT_FALSE(options.optimize_brlen);
EXPECT_DOUBLE_EQ(0.02, options.lh_epsilon);
diff --git a/test/src/ModelTest.cpp b/test/src/ModelTest.cpp
index 70c9670..9084e58 100644
--- a/test/src/ModelTest.cpp
+++ b/test/src/ModelTest.cpp
@@ -10,7 +10,22 @@ TEST(ModelTest, defaults)
auto model = Model();
// tests
- EXPECT_EQ(model.to_string(), "GTR+F+G4");
+ EXPECT_EQ(model.to_string(), "GTR+FO");
+ EXPECT_EQ(model.data_type(), DataType::dna);
+ EXPECT_EQ(model.name(), "GTR");
+ EXPECT_EQ(model.num_states(), 4);
+ EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_FIXED);
+ EXPECT_EQ(model.num_ratecats(), 1);
+ EXPECT_EQ(model.params_to_optimize(), PLLMOD_OPT_PARAM_SUBST_RATES | PLLMOD_OPT_PARAM_FREQUENCIES);
+}
+
+TEST(ModelTest, GTR)
+{
+ // buildup
+ auto model = Model(DataType::autodetect, "GTR+F+G");
+
+ // tests
+ EXPECT_EQ(model.to_string(), "GTR+FC+G4");
EXPECT_EQ(model.data_type(), DataType::dna);
EXPECT_EQ(model.name(), "GTR");
EXPECT_EQ(model.num_states(), 4);
@@ -19,28 +34,30 @@ TEST(ModelTest, defaults)
EXPECT_EQ(model.params_to_optimize(), PLLMOD_OPT_PARAM_SUBST_RATES | PLLMOD_OPT_PARAM_ALPHA);
}
-TEST(ModelTest, GTR)
+TEST(ModelTest, GTR_R_user)
{
// buildup
- auto model = Model(DataType::autodetect, "GTR");
+ auto model = Model(DataType::autodetect, "GTR{0.1/0.5/1/2/3.5/0.5}+R3+Fc");
// tests
- EXPECT_EQ(model.to_string(), "GTR+FO");
+ EXPECT_EQ(model.to_string(), "GTR{0.2/1/2/4/7/1}+FC+R3");
EXPECT_EQ(model.data_type(), DataType::dna);
EXPECT_EQ(model.name(), "GTR");
EXPECT_EQ(model.num_states(), 4);
- EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_FIXED);
- EXPECT_EQ(model.num_ratecats(), 1);
- EXPECT_EQ(model.params_to_optimize(), PLLMOD_OPT_PARAM_SUBST_RATES | PLLMOD_OPT_PARAM_FREQUENCIES);
+ EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_FREE);
+ EXPECT_EQ(model.num_ratecats(), 3);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_SUBST_RATES), ParamValue::user);
+ EXPECT_EQ(model.params_to_optimize(), PLLMOD_OPT_PARAM_RATE_WEIGHTS | PLLMOD_OPT_PARAM_FREE_RATES);
}
+
TEST(ModelTest, JCI_user)
{
// buildup
- auto model = Model(DataType::autodetect, "JC+G+I{0.7}");
+ auto model = Model(DataType::autodetect, "JC+G+IU{0.7}");
// tests
- EXPECT_EQ(model.to_string(), "JC+I{0.7}+G4");
+ EXPECT_EQ(model.to_string(), "JC+IU{0.7}+G4");
EXPECT_EQ(model.data_type(), DataType::dna);
EXPECT_EQ(model.name(), "JC");
EXPECT_EQ(model.num_states(), 4);
@@ -50,13 +67,76 @@ TEST(ModelTest, JCI_user)
EXPECT_EQ(model.pinv(), 0.7);
}
+TEST(ModelTest, JCFG_user)
+{
+ // buildup
+ auto model = Model(DataType::autodetect, "JC+FC+G{2.5}");
+
+ // tests
+ EXPECT_EQ(model.to_string(), "JC+FC+G4{2.5}");
+ EXPECT_EQ(model.data_type(), DataType::dna);
+ EXPECT_EQ(model.name(), "JC");
+ EXPECT_EQ(model.num_states(), 4);
+ EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_GAMMA);
+ EXPECT_EQ(model.num_ratecats(), 4);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_FREQUENCIES), ParamValue::empirical);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_ALPHA), ParamValue::user);
+ EXPECT_EQ(model.params_to_optimize(), 0);
+ EXPECT_EQ(model.alpha(), 2.5);
+}
+
+TEST(ModelTest, HKY_user_freqs)
+{
+ // buildup
+ auto model = Model(DataType::autodetect, "HKY+FU{0.1/0.299/0.201/0.4}");
+
+ // tests
+ EXPECT_EQ(model.to_string(), "HKY+FU{0.1/0.299/0.201/0.4}");
+ EXPECT_EQ(model.data_type(), DataType::dna);
+ EXPECT_EQ(model.name(), "HKY");
+ EXPECT_EQ(model.num_states(), 4);
+ EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_FIXED);
+ EXPECT_EQ(model.num_ratecats(), 1);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_FREQUENCIES), ParamValue::user);
+ EXPECT_EQ(model.params_to_optimize(), PLLMOD_OPT_PARAM_SUBST_RATES);
+ EXPECT_EQ(model.base_freqs(0).size(), 4);
+ EXPECT_EQ(model.base_freqs(0)[0], 0.1);
+ EXPECT_EQ(model.base_freqs(0)[1], 0.299);
+ EXPECT_EQ(model.base_freqs(0)[2], 0.201);
+ EXPECT_EQ(model.base_freqs(0)[3], 0.4);
+}
+
+TEST(ModelTest, HKY_user_rates)
+{
+ // buildup
+ auto model = Model(DataType::autodetect, "HKY{1/2.424}+FC");
+
+ // tests
+ EXPECT_EQ(model.to_string(), "HKY{1/2.424}+FC");
+ EXPECT_EQ(model.data_type(), DataType::dna);
+ EXPECT_EQ(model.name(), "HKY");
+ EXPECT_EQ(model.num_states(), 4);
+ EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_FIXED);
+ EXPECT_EQ(model.num_ratecats(), 1);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_FREQUENCIES), ParamValue::empirical);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_SUBST_RATES), ParamValue::user);
+ EXPECT_EQ(model.params_to_optimize(), 0);
+ EXPECT_EQ(model.subst_rates(0).size(), 6);
+ EXPECT_EQ(model.subst_rates(0)[0], 1.0);
+ EXPECT_EQ(model.subst_rates(0)[1], 2.424);
+ EXPECT_EQ(model.subst_rates(0)[2], 1.0);
+ EXPECT_EQ(model.subst_rates(0)[3], 1.0);
+ EXPECT_EQ(model.subst_rates(0)[4], 2.424);
+ EXPECT_EQ(model.subst_rates(0)[5], 1.0);
+}
+
TEST(ModelTest, LGFI)
{
// buildup
auto model = Model(DataType::autodetect, "LG+F+I+G8");
// tests
- EXPECT_EQ(model.to_string(), "LG+F+I+G8");
+ EXPECT_EQ(model.to_string(), "LG+FC+I+G8");
EXPECT_EQ(model.data_type(), DataType::protein);
EXPECT_EQ(model.name(), "LG");
EXPECT_EQ(model.num_states(), 20);
@@ -79,3 +159,31 @@ TEST(ModelTest, LG4X)
EXPECT_EQ(model.num_ratecats(), 4);
EXPECT_EQ(model.params_to_optimize(), PLLMOD_OPT_PARAM_FREE_RATES | PLLMOD_OPT_PARAM_RATE_WEIGHTS);
}
+
+TEST(ModelTest, LG_R4_user)
+{
+ // buildup
+ auto model = Model(DataType::autodetect, "LG+R4{1/2/3/4}");
+
+ // tests
+ EXPECT_EQ(model.to_string(), "LG+R4{0.4/0.8/1.2/1.6}{0.25/0.25/0.25/0.25}");
+ EXPECT_EQ(model.data_type(), DataType::protein);
+ EXPECT_EQ(model.name(), "LG");
+ EXPECT_EQ(model.num_states(), 20);
+ EXPECT_EQ(model.ratehet_mode(), PLLMOD_UTIL_MIXTYPE_FREE);
+ EXPECT_EQ(model.num_ratecats(), 4);
+ EXPECT_EQ(model.params_to_optimize(), 0);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_FREE_RATES), ParamValue::user);
+ EXPECT_EQ(model.param_mode(PLLMOD_OPT_PARAM_RATE_WEIGHTS), ParamValue::user);
+ EXPECT_EQ(model.ratecat_weights().size(), 4);
+ EXPECT_EQ(model.ratecat_weights()[0], 1. / 4.);
+ EXPECT_EQ(model.ratecat_weights()[1], 1. / 4.);
+ EXPECT_EQ(model.ratecat_weights()[2], 1. / 4.);
+ EXPECT_EQ(model.ratecat_weights()[3], 1. / 4.);
+ EXPECT_EQ(model.ratecat_rates().size(), 4);
+ EXPECT_EQ(model.ratecat_rates()[0], 0.4);
+ EXPECT_EQ(model.ratecat_rates()[1], 0.8);
+ EXPECT_EQ(model.ratecat_rates()[2], 1.2);
+ EXPECT_EQ(model.ratecat_rates()[3], 1.6);
+}
+
--
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