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Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 19 Nov 2015 14:47:11 +0100
Description: Fix some spelling issues
--- a/libs/phylogeny/likeDist.cpp
+++ b/libs/phylogeny/likeDist.cpp
@@ -145,10 +145,10 @@ MDOUBLE likeDist::giveDistanceThroughCTC
const sequence& s2,
const vector<MDOUBLE> * weights,
MDOUBLE* score) const {
- // only in the case of homogenous model - work through pairwise EM like
+ // only in the case of homogeneous model - work through pairwise EM like
countTableComponentGam ctc;
if (_sp.categories() != 1) {
- errorMsg::reportError("this function only work for homogenous model.");
+ errorMsg::reportError("this function only work for homogeneous model.");
}
ctc.countTableComponentAllocatePlace(s1.getAlphabet()->size(),1);
for (int i=0; i<s1.seqLen(); ++i) {
--- a/programs/fastml/mainbb.cpp
+++ b/programs/fastml/mainbb.cpp
@@ -98,7 +98,7 @@ void mainbb::getStartingEvolTreeTopology
void mainbb::getStartingNJtreeNjMLdis() {
// note that here ALWAYS, the ML distances are computed using
- // an homogenous rate distribution.
+ // an homogeneous rate distribution.
uniDistribution lUni;
// const pijAccelerator* lpijAcc = _sp->getPijAccelerator();// note this is just a copy of the pointer.
const pijAccelerator* lpijAcc = _spVec[0].getPijAccelerator();// note this is just a copy of the pointer.
@@ -248,9 +248,9 @@ void mainbb::getStartingStochasticProces
int numberOfCategories = _options->gammaCategies;
MDOUBLE alpha = _options->gammaPar;
if (_options->distributionName == bb_options::hom) {
- numberOfCategories = 1; // forcing homogenous model.
+ numberOfCategories = 1; // forcing homogeneous model.
alpha = 1.0;
- cout<<"Using homogenous model (no among site rate variation)"<<endl;
+ cout<<"Using homogeneous model (no among site rate variation)"<<endl;
} else {
cout<<"Using a Gamma model with: "<<numberOfCategories<<" discrete categories "<<endl;
}
--- a/libs/phylogeny/numRec.cpp
+++ b/libs/phylogeny/numRec.cpp
@@ -134,7 +134,7 @@ int MyJacobi(VVdouble &Insym, VVdouble &
} // end of for (ip = ...
} // end of for (i = 0; i< MaxNumberOfSweeps ; ++i) {
vector<string> err;
- err.push_back("problems in function MyJacobi. more than MaxNumberOfSweeps were necesary.");
+ err.push_back("problems in function MyJacobi. more than MaxNumberOfSweeps were necessary.");
errorMsg::reportError(err);
return -1;
--- a/programs/fastml/bb_options_list.h
+++ b/programs/fastml/bb_options_list.h
@@ -9,7 +9,7 @@ static string usage() {
tmp +=" |-t tree input file |\n";
tmp +=" | (if tree is not given, a neighbor joining tree is computed). |\n";
tmp +=" |-g Assume among site rate variation model (Gamma) [By default the program |\n";
- tmp +=" | will assume an homogenous model. very fast, but less accurate!] |\n";
+ tmp +=" | will assume an homogeneous model. very fast, but less accurate!] |\n";
tmp += "|-m model name |\n";
tmp += "|-mj [JTT] |\n";
tmp += "|-ml LG |\n";
@@ -36,7 +36,7 @@ static string usage() {
tmp +=" | -qm = MOLPHY, -qs = MASE, -qp = PHLIYP, -qn = Nexus |\n";
tmp +=" +----------------------------------------------------------------------------+\n";
tmp +=" |Advances options: |\n";
- tmp +=" |-a Treshold for computing again marginal probabilities [0.9] |\n";
+ tmp +=" |-a Threshold for computing again marginal probabilities [0.9] |\n";
tmp +=" |-b Do not optimize branch lengths on starting tree |\n";
tmp +=" | [by default branches and alpha are ML optimized from the data] |\n";
tmp +=" |-c number of discrete Gamma categories for the gamma distribution [8] |\n";
--- a/programs/gainLoss/computeCorrelations.cpp
+++ b/programs/gainLoss/computeCorrelations.cpp
@@ -137,7 +137,7 @@ void computeCorrelations::runComputeCorr
numOfpositionsIn_B = _expChanges_PosNodeXY.size(); // if B is not given, it's copy
if(_isTwoSetsOfInputForCorrelation)
- LOGnOUT(3, <<"NOTE: Two seperate dataset input.\n Compute correl for selectedSites="<<numOfSitesSelected<<" subset of A="<<numOfpositionsIn_A<<" against B="<<numOfpositionsIn_B<<endl);
+ LOGnOUT(3, <<"NOTE: Two separate dataset input.\n Compute correl for selectedSites="<<numOfSitesSelected<<" subset of A="<<numOfpositionsIn_A<<" against B="<<numOfpositionsIn_B<<endl);
//// Mapping vectors
LOGnOUT(4, <<"Fill events vectors..."<<endl);
--- a/programs/gainLoss/gainLoss.cpp
+++ b/programs/gainLoss/gainLoss.cpp
@@ -4525,7 +4525,7 @@ void gainLoss::startSimultePosteriorExpe
LOGnOUT(4,<<(gainLossOptions::_userAlphaLoss/gainLossOptions::_userBetaLoss) / (gainLossOptions::_userAlphaGain/gainLossOptions::_userBetaGain)<<endl);
if(!gainLossOptions::_isRootFreqEQstationaryInSimulations){
if(gainLossOptions::_initRootFreqAtRandPointsInSimPostExpEachPos)
- LOGnOUT(4,<<"Root(1) freq is sampled seperatly for each pos"<<endl)
+ LOGnOUT(4,<<"Root(1) freq is sampled separately for each pos"<<endl)
else
LOGnOUT(4,<<"Root(1) freq is sampled once for the entire replication (sim all positions)"<<endl)
if(isComputeEmpiricalCorrection
--- a/libs/phylogeny/likeDistfixRoot.cpp
+++ b/libs/phylogeny/likeDistfixRoot.cpp
@@ -145,10 +145,10 @@ MDOUBLE likeDistfixRoot::evalLogLikeliho
// const sequence& s2,
// const vector<MDOUBLE> * weights,
// MDOUBLE* score) const {
-// // only in the case of homogenous model - work through pairwise EM like
+// // only in the case of homogeneous model - work through pairwise EM like
// countTableComponentGam ctc;
// if (_sp.categories() != 1) {
-// errorMsg::reportError("this function only work for homogenous model.");
+// errorMsg::reportError("this function only work for homogeneous model.");
// }
// ctc.countTableComponentAllocatePlace(s1.getAlphabet()->size(),1);
// for (int i=0; i<s1.seqLen(); ++i) {
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