From: Michael R. Crusoe <crusoe@debian.org>
Subject: typo fixes
Forwarded: https://github.com/BioPP/bpp-phyl/pull/54
--- libbpp-phyl.orig/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
+++ libbpp-phyl/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
@@ -172,7 +172,7 @@
   {
     modelDescription = ApplicationTools::getStringParameter("model", params, "CodonRate(model=JC69)", suffix, suffixIsOptional, warn);
     if (!gCode)
-      throw Exception("PhylogeneticsApplicationTools::getSubstitutionModel(): a GeneticCode instance is required for instanciating a codon model.");
+      throw Exception("PhylogeneticsApplicationTools::getSubstitutionModel(): a GeneticCode instance is required for instantiating a codon model.");
     bIO.setGeneticCode(gCode);
   }
   else if (AlphabetTools::isWordAlphabet(alphabet))
@@ -201,7 +201,7 @@
   {
     modelDescription = ApplicationTools::getStringParameter("model", params, "CodonRate(model=JC69)", suffix, suffixIsOptional, warn);
     if (!gCode)
-      throw Exception("PhylogeneticsApplicationTools::getSubstitutionModel(): a GeneticCode instance is required for instanciating a codon model.");
+      throw Exception("PhylogeneticsApplicationTools::getSubstitutionModel(): a GeneticCode instance is required for instantiating a codon model.");
     bIO.setGeneticCode(gCode);
   }
   else if (AlphabetTools::isWordAlphabet(alphabet))
@@ -354,7 +354,7 @@
   if (AlphabetTools::isCodonAlphabet(alphabet))
   {
     if (!gCode)
-      throw Exception("PhylogeneticsApplicationTools::getFrequenciesSet(): a GeneticCode instance is required for instanciating a codon frequencies set.");
+      throw Exception("PhylogeneticsApplicationTools::getFrequenciesSet(): a GeneticCode instance is required for instantiating a codon frequencies set.");
     bIO.setGeneticCode(gCode);
   }
   unique_ptr<FrequenciesSet> pFS(bIO.read(alphabet, freqDescription, data, true));
@@ -453,7 +453,7 @@
   if (AlphabetTools::isCodonAlphabet(alphabet))
   {
     if (!gCode)
-      throw Exception("PhylogeneticsApplicationTools::setSubstitutionModelSet(): a GeneticCode instance is required for instanciating a codon model.");
+      throw Exception("PhylogeneticsApplicationTools::setSubstitutionModelSet(): a GeneticCode instance is required for instantiating a codon model.");
     bIO.setGeneticCode(gCode);
     tmpDesc = ApplicationTools::getStringParameter("model1", params, "CodonRate(model=JC69)", suffix, suffixIsOptional, warn);
   }
--- libbpp-phyl.orig/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
+++ libbpp-phyl/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
@@ -439,7 +439,7 @@
       }
       catch (SequenceNotFoundException& snfe)
       {
-        throw SequenceNotFoundException("TwoTreeLikelihood::initTreelikelihoods. Leaf name in tree not found in site conainer: ", snfe.getSequenceId());
+        throw SequenceNotFoundException("TwoTreeLikelihood::initTreelikelihoods. Leaf name in tree not found in site container: ", snfe.getSequenceId());
       }
     }
   }
--- libbpp-phyl.orig/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
+++ libbpp-phyl/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
@@ -385,7 +385,7 @@
     if (TextTools::isEmpty(nestedModelDescription))
       throw Exception("BppOSubstitutionModelFormat::read. Missing argument 'model' for model 'YpR_sym'.");
     if (verbose_)
-      ApplicationTools::displayResult("Symetric YpR model", modelName);
+      ApplicationTools::displayResult("Symmetric YpR model", modelName);
     BppOSubstitutionModelFormat nestedReader(NUCLEOTIDE, false, false, false, verbose_, warningLevel_);
     unique_ptr<NucleotideSubstitutionModel> nestedModel(dynamic_cast<NucleotideSubstitutionModel*>(nestedReader.read(&prny->getLetterAlphabet(), nestedModelDescription, data, false)));
     map<string, string> unparsedParameterValuesNested(nestedReader.getUnparsedArguments());
--- libbpp-phyl.orig/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
+++ libbpp-phyl/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
@@ -88,7 +88,7 @@
     if (delim_pos == string::npos)
     {
       ostringstream msg;
-      msg << "IOTreepuzzlePairedSiteLikelihoods::read: Couldn't find delimiter. The beggining of the line was : "
+      msg << "IOTreepuzzlePairedSiteLikelihoods::read: Couldn't find delimiter. The beginning of the line was : "
           << endl << line.substr(0, 100);
       throw Exception(msg.str());
     }
--- libbpp-phyl.orig/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
+++ libbpp-phyl/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
@@ -248,7 +248,7 @@
   virtual void setMinimumBranchLength(double minimum)
   {
     if (minimum > maximumBrLen_)
-      throw Exception("AbstractHomogeneousTreeLikelihood::setMinimumBranchLength. Minimum branch length sould be lower than the maximum one: " + TextTools::toString(maximumBrLen_));
+      throw Exception("AbstractHomogeneousTreeLikelihood::setMinimumBranchLength. Minimum branch length should be lower than the maximum one: " + TextTools::toString(maximumBrLen_));
     minimumBrLen_ = minimum;
     if (brLenConstraint_.get()) brLenConstraint_.release();
     brLenConstraint_.reset(new IntervalConstraint(minimumBrLen_, maximumBrLen_, true, true));
@@ -258,7 +258,7 @@
   virtual void setMaximumBranchLength(double maximum)
   {
     if (maximum < minimumBrLen_)
-      throw Exception("AbstractHomogeneousTreeLikelihood::setMaximumBranchLength. Maximum branch length sould be higher than the minimum one: " + TextTools::toString(minimumBrLen_));
+      throw Exception("AbstractHomogeneousTreeLikelihood::setMaximumBranchLength. Maximum branch length should be higher than the minimum one: " + TextTools::toString(minimumBrLen_));
     maximumBrLen_ = maximum;
     if (brLenConstraint_.get()) brLenConstraint_.release();
     brLenConstraint_.reset(new IntervalConstraint(minimumBrLen_, maximumBrLen_, true, true));
--- libbpp-phyl.orig/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
+++ libbpp-phyl/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
@@ -257,7 +257,7 @@
     virtual void setMinimumBranchLength(double minimum)
     {
       if (minimum > maximumBrLen_)
-        throw Exception("AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength. Minimum branch length sould be lower than the maximum one: " + TextTools::toString(maximumBrLen_));
+        throw Exception("AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength. Minimum branch length should be lower than the maximum one: " + TextTools::toString(maximumBrLen_));
       minimumBrLen_ = minimum;
       if (brLenConstraint_.get()) brLenConstraint_.release();
       brLenConstraint_.reset(new IntervalConstraint(minimumBrLen_, maximumBrLen_, true, true));
@@ -267,7 +267,7 @@
     virtual void setMaximumBranchLength(double maximum)
     {
       if (maximum < minimumBrLen_)
-        throw Exception("AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength. Maximum branch length sould be higher than the minimum one: " + TextTools::toString(minimumBrLen_));
+        throw Exception("AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength. Maximum branch length should be higher than the minimum one: " + TextTools::toString(minimumBrLen_));
       maximumBrLen_ = maximum;
       if (brLenConstraint_.get()) brLenConstraint_.release();
       brLenConstraint_.reset(new IntervalConstraint(minimumBrLen_, maximumBrLen_, true, true));
--- libbpp-phyl.orig/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
+++ libbpp-phyl/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
@@ -140,7 +140,7 @@
     }
     catch (SequenceNotFoundException& snfe)
     {
-      throw SequenceNotFoundException("DRASRTreeLikelihoodData::initTreelikelihoods. Leaf name in tree not found in site conainer: ", (node->getName()));
+      throw SequenceNotFoundException("DRASRTreeLikelihoodData::initTreelikelihoods. Leaf name in tree not found in site container: ", (node->getName()));
     }
     for (size_t i = 0; i < nbDistinctSites_; i++)
     {
@@ -243,7 +243,7 @@
     }
     catch (SequenceNotFoundException& snfe)
     {
-      throw SequenceNotFoundException("HomogeneousTreeLikelihood::initTreelikelihoodsWithPatterns. Leaf name in tree not found in site conainer: ", (node->getName()));
+      throw SequenceNotFoundException("HomogeneousTreeLikelihood::initTreelikelihoodsWithPatterns. Leaf name in tree not found in site container: ", (node->getName()));
     }
     for (size_t i = 0; i < nbSites; i++)
     {
--- libbpp-phyl.orig/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h
+++ libbpp-phyl/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h
@@ -62,7 +62,7 @@
   {
   private:
     /*
-     * The coordinates of the sustitutions or non-sustitutions that
+     * The coordinates of the substitutions or non-substitutions that
      * are NOT considered (ie for which the changes generator equals
      * the model one).
      *
--- libbpp-phyl.orig/src/Bpp/Phyl/Model/SubstitutionModelSet.h
+++ libbpp-phyl/src/Bpp/Phyl/Model/SubstitutionModelSet.h
@@ -273,7 +273,7 @@
     }
     catch (std::bad_cast& bc)
     {
-      throw Exception("SubstitutionModelSet::getSubstitutionModel : model is not a sustitution model " + getModel(i)->getName());
+      throw Exception("SubstitutionModelSet::getSubstitutionModel : model is not a substitution model " + getModel(i)->getName());
     }
   }
   
@@ -286,7 +286,7 @@
     }
     catch (std::bad_cast& bc)
     {
-      throw Exception("SubstitutionModelSet::getSubstitutionModel : model is not a sustitution model " + getModel(i)->getName());
+      throw Exception("SubstitutionModelSet::getSubstitutionModel : model is not a substitution model " + getModel(i)->getName());
     }
   }
 
