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commit 8619180a4326fe3d11bdade6aa7084a7a53f4569 Author: Andreas Tille <[email protected]> Date: Thu Nov 19 08:33:19 2015 +0100 Fix some spelling issues --- debian/fastml.1 | 4 +- debian/patches/series | 1 + debian/patches/spelling.patch | 86 +++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 89 insertions(+), 2 deletions(-) diff --git a/debian/fastml.1 b/debian/fastml.1 index 7fb2f64..f29c8fa 100644 --- a/debian/fastml.1 +++ b/debian/fastml.1 @@ -30,7 +30,7 @@ sequences). \fB\-t\fR tree input file (if tree is not given, a neighbor joining tree is computed). .TP \fB\-g\fR Assume among site rate variation model (Gamma) [By default the program -will assume an homogenous model. very fast, but less accurate!] +will assume an homogeneous model. very fast, but less accurate!] .TP \fB\-m\fR model name .TP @@ -79,7 +79,7 @@ Controling the output options: .PP Advanced options: .TP -\fB\-a\fR Treshold for computing again marginal probabilities [0.9] +\fB\-a\fR Threshold for computing again marginal probabilities [0.9] .TP \fB\-b\fR Do not optimize branch lengths on starting tree [by default branches and alpha are ML optimized from the data] diff --git a/debian/patches/series b/debian/patches/series index e174b80..0d7e8d4 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ gcc_5.patch fix_makefile4test.patch fix_intall_target.patch +spelling.patch diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch new file mode 100644 index 0000000..17e6ed9 --- /dev/null +++ b/debian/patches/spelling.patch @@ -0,0 +1,86 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Mon, 22 Jun 2015 09:47:25 +0200 +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 +@@ -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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastml.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
