[med-svn] [Git][med-team/libbpp-popgen][master] d/patches/spelling: fix typos.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Aug 14 14:36:23 BST 2023
Michael R. Crusoe pushed to branch master at Debian Med / libbpp-popgen
Commits:
853b0f5f by Michael R. Crusoe at 2023-08-14T15:34:05+02:00
d/patches/spelling: fix typos.
- - - - -
3 changed files:
- debian/changelog
- debian/patches/series
- + debian/patches/spelling
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libbpp-popgen (2.4.1-10) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * d/patches/spelling: fix typos.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 14 Aug 2023 15:33:50 +0200
+
libbpp-popgen (2.4.1-9) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
unforce-cxxflags.patch
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,1066 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: fix spelling typos
+--- libbpp-popgen.orig/src/Bpp/PopGen/DataSet/DataSet.cpp
++++ libbpp-popgen/src/Bpp/PopGen/DataSet/DataSet.cpp
+@@ -388,7 +388,7 @@
+ for (size_t i = 0; i < individuals_selection.size(); i++)
+ {
+ if (individuals_selection[i] >= groups_[source_pos]->getNumberOfIndividuals())
+- throw IndexOutOfBoundsException("DataSet::splitGroup: individuals_selection excedes the number of individual in the group.", individuals_selection[i], 0, groups_[source_pos]->getNumberOfIndividuals());
++ throw IndexOutOfBoundsException("DataSet::splitGroup: individuals_selection exceeds the number of individual in the group.", individuals_selection[i], 0, groups_[source_pos]->getNumberOfIndividuals());
+ }
+ for (size_t i = 0; i < individuals_selection.size(); i++)
+ {
+@@ -471,7 +471,7 @@
+ }
+ catch (IndexOutOfBoundsException& ioobe)
+ {
+- throw IndexOutOfBoundsException("DataSet::getIndividualAtPositionFromGroup: individual_position out of bouds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
++ throw IndexOutOfBoundsException("DataSet::getIndividualAtPositionFromGroup: individual_position out of bounds.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
+ }
+ }
+
+@@ -1084,7 +1084,7 @@
+ void DataSet::initAnalyzedLoci(size_t number_of_loci)
+ {
+ if (analyzedLoci_ != 0)
+- throw Exception("DataSet::initAnalyzedLoci: analyzedLoci_ already initialyzed.");
++ throw Exception("DataSet::initAnalyzedLoci: analyzedLoci_ already initialized.");
+ analyzedLoci_ = new AnalyzedLoci(number_of_loci);
+ }
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp
++++ libbpp-popgen/src/Bpp/PopGen/MonoAlleleMonolocusGenotype.cpp
+@@ -49,7 +49,7 @@
+ MonoAlleleMonolocusGenotype::MonoAlleleMonolocusGenotype(std::vector<size_t> allele_index) : allele_index_(0)
+ {
+ if (allele_index.size() != 1)
+- throw BadSizeException("MonoAlleleMonolocusGenotype::MonoAlleleMonolocusGenotype: allele_index must conain one value.", allele_index.size(), 1);
++ throw BadSizeException("MonoAlleleMonolocusGenotype::MonoAlleleMonolocusGenotype: allele_index must contain one value.", allele_index.size(), 1);
+ allele_index_ = allele_index[0];
+ }
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/DataSet/DataSet.h
++++ libbpp-popgen/src/Bpp/PopGen/DataSet/DataSet.h
+@@ -121,7 +121,7 @@
+ *
+ * @return A const pointer to the locality matching the locality_position.
+ * @param locality_position The position of the Locality in the DataSet.
+- * @throw IndexOutOfBoundsException if locality_position excedes the number of locality of the DataSet.
++ * @throw IndexOutOfBoundsException if locality_position exceeds the number of locality of the DataSet.
+ */
+ const Locality<double>& getLocalityAtPosition(size_t locality_position) const;
+
+@@ -135,7 +135,7 @@
+ /**
+ * @brief Delete a Locality from the DataSet.
+ *
+- * @throw IndexOutOfBoundsException if locality_position excedes the number of Locality.
++ * @throw IndexOutOfBoundsException if locality_position exceeds the number of Locality.
+ */
+ void deleteLocalityAtPosition(size_t locality_position);
+
+@@ -199,14 +199,14 @@
+ /**
+ * @brief Get a group by position.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ */
+ const Group& getGroupAtPosition(size_t group_position) const;
+
+ /**
+ * @brief Delete a Group from the DataSet.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ */
+ void deleteGroupAtPosition(size_t group_position);
+
+@@ -231,7 +231,7 @@
+ * DataSet.
+ *
+ * @param group_ids A vector size_t listing the id of groups to merge.
+- * @throw IndexOutOfBoundsException if one of the int in groups excedes the number of groups.
++ * @throw IndexOutOfBoundsException if one of the int in groups exceeds the number of groups.
+ */
+ void mergeGroups(std::vector<size_t>& group_ids);
+
+@@ -241,7 +241,7 @@
+ * @param group_id The identifier of the source group.
+ * @param individuals_selection The positions of the Individuals to extract from the group to make the new group.
+ * @throw GroupNotFoundException if the group_id is not found.
+- * @throw IndexOutOfBoundsException if one position of the selection excedes the number of individuals of the group.
++ * @throw IndexOutOfBoundsException if one position of the selection exceeds the number of individuals of the group.
+ */
+ void splitGroup(size_t group_id, std::vector<size_t> individuals_selection);
+
+@@ -249,7 +249,7 @@
+ /**
+ * @brief Add an Individual to a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ * @throw BadIdentifierException if the individual's id is already in use.
+ */
+ void addIndividualToGroup(size_t group_position, const Individual& individual);
+@@ -257,7 +257,7 @@
+ /**
+ * @brief Add an empty Individual to a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ * @throw BadIdentifierException if the individual's id is already in use.
+ */
+ void addEmptyIndividualToGroup(size_t group_position, const std::string& individual_id);
+@@ -265,14 +265,14 @@
+ /**
+ * @brief Get the number of Individuals in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ */
+ size_t getNumberOfIndividualsInGroup(size_t group_position) const;
+
+ /**
+ * @brief Get the position of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ * @throw IndividualNotFoundException if individual_id is not found.
+ */
+ size_t getIndividualPositionInGroup(size_t group_position, const std::string& individual_id) const;
+@@ -280,15 +280,15 @@
+ /**
+ * @brief Get an Individual from a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ const Individual* getIndividualAtPositionFromGroup(size_t group_position, size_t individual_position) const;
+
+ /**
+ * @brief Get an Individual from a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ * @throw IndividualNotFoundException if individual_id is not found.
+ */
+ const Individual* getIndividualByIdFromGroup(size_t group_position, const std::string& individual_id) const;
+@@ -296,15 +296,15 @@
+ /**
+ * @brief Delete an Individual from a group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ void deleteIndividualAtPositionFromGroup(size_t group_position, size_t individual_position);
+
+ /**
+ * @brief Delete an Individual from a group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
+ * @throw IndividualNotFoundException if individual_id is not found.
+ */
+ void deleteIndividualByIdFromGroup(size_t group_position, const std::string& individual_id);
+@@ -312,32 +312,32 @@
+ /**
+ * @brief Set the sex of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ void setIndividualSexInGroup(size_t group_position, size_t individual_position, const unsigned short sex);
+
+ /**
+ * @brief Get the sex of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ unsigned short getIndividualSexInGroup(size_t group_position, size_t individual_position) const;
+
+ /**
+ * @brief Set the Date of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ void setIndividualDateInGroup(size_t group_position, size_t individual_position, const Date& date);
+
+ /**
+ * @brief Get the Date of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no date.
+ */
+ const Date* getIndividualDateInGroup(size_t group_position, size_t individual_position) const;
+@@ -345,16 +345,16 @@
+ /**
+ * @brief Set the coordinates of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ void setIndividualCoordInGroup(size_t group_position, size_t individual_position, const Point2D<double>& coord);
+
+ /**
+ * @brief Get the coordinate of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no coordinate.
+ */
+ const Point2D<double>* getIndividualCoordInGroup(size_t group_position, size_t individual_position) const;
+@@ -362,8 +362,8 @@
+ /**
+ * @brief Set the Locality of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw LocalityNotFoundException if locality_name is not found.
+ */
+ void setIndividualLocalityInGroupByName(size_t group_position, size_t individual_position, const std::string& locality_name);
+@@ -371,8 +371,8 @@
+ /**
+ * @brief Get the Locality of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no locality.
+ */
+ const Locality<double>* getIndividualLocalityInGroup(size_t group_position, size_t individual_position) const;
+@@ -380,8 +380,8 @@
+ /**
+ * @brief Add a Sequence to an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw AlphabetMismatchException if the sequence's alphabet doesn't match the container's alphabet.
+ * @throw BadIdentifierException if the sequence's name is already in use.
+ */
+@@ -391,8 +391,8 @@
+ /**
+ * @brief Get a Sequence from an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ * @throw SequenceNotFoundException if sequence_name is not found.
+ * @throw BadIntegerException if sequence_position is already in use.
+@@ -402,8 +402,8 @@
+ /**
+ * @brief Get a Sequence from an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ * @throw SequenceNotFoundException if sequence_position is not found.
+ */
+@@ -412,8 +412,8 @@
+ /**
+ * @brief Delete a Sequence of an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ * @throw SequenceNotFoundException if sequence_name is not found.
+ */
+@@ -422,8 +422,8 @@
+ /**
+ * @brief Delete a Sequence of an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ * @throw SequenceNotFoundException if sequence_position is not found.
+ */
+@@ -432,8 +432,8 @@
+ /**
+ * @brief Get the Sequences' names from an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ */
+ std::vector<std::string> getIndividualSequencesNamesInGroup(size_t group_position, size_t individual_position) const;
+@@ -441,8 +441,8 @@
+ /**
+ * @brief Get the position of a Sequence in an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ * @throw SequenceNotFoundException if sequence_name is not found.
+ */
+@@ -451,8 +451,8 @@
+ /**
+ * @brief Get the number of Sequences in an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no sequences.
+ */
+ size_t getIndividualNumberOfSequencesInGroup(size_t group_position, size_t individual_position) const;
+@@ -460,16 +460,16 @@
+ /**
+ * @brief Set the MultilocusGenotype of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ void setIndividualGenotypeInGroup(size_t group_position, size_t individual_position, const MultilocusGenotype& genotype);
+
+ /**
+ * @brief Initialyze the genotype of an Individual in a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw BadIntegerException if the number of loci is < 1;
+ * @throw NullPointerException if analyzed_loci is NULL.
+ * @throw Exception if the individual already has a genotype.
+@@ -479,28 +479,28 @@
+ /**
+ * @brief Delete the MultilocusGenotype of an Individual from a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ */
+ void deleteIndividualGenotypeInGroup(size_t group_position, size_t individual_position);
+
+ /**
+ * @brief Set a MonolocusGenotype of an Individual from a group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ */
+ void setIndividualMonolocusGenotypeInGroup(size_t group_position, size_t individual_position, size_t locus_position, const MonolocusGenotype& monogen);
+
+ /**
+ * @brief Set a MonolocusGenotype of an Individual from a group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ * @throw Exception if the ploidy doesn't match.
+ */
+ void setIndividualMonolocusGenotypeByAlleleKeyInGroup(size_t group_position, size_t individual_position, size_t locus_position, const std::vector<size_t> allele_keys);
+@@ -508,10 +508,10 @@
+ /**
+ * @brief Set a MonolocusGenotype of an Individual from a group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ * @throw Exception if there is no key in allele_keys.
+ */
+ void setIndividualMonolocusGenotypeByAlleleIdInGroup(size_t group_position, size_t individual_position, size_t locus_position, const std::vector<std::string> allele_id);
+@@ -519,10 +519,10 @@
+ /**
+ * @brief Get a MonolocusGenotype from an Individual of a Group.
+ *
+- * @throw IndexOutOfBoundsException if group_position excedes the number of groups.
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individual in the group.
++ * @throw IndexOutOfBoundsException if group_position exceeds the number of groups.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individual in the group.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ * @throw AlleleNotFoundException if at least one of the id is not found.
+ */
+ const MonolocusGenotype* getIndividualMonolocusGenotypeInGroup(size_t group_position, size_t individual_position, size_t locus_position) const;
+@@ -563,7 +563,7 @@
+ /**
+ * @brief Initialize the AnalyzedLoci for number of loci.
+ *
+- * @throw Exception if the AnalyzedLoci has already been initialyzed.
++ * @throw Exception if the AnalyzedLoci has already been initialized.
+ */
+ void initAnalyzedLoci(size_t number_of_loci);
+
+@@ -583,7 +583,7 @@
+ * @brief Set a LocusInfo.
+ *
+ * @throw NullPointerException if there is no AnalyzedLoci to setup.
+- * @throw IndexOutOfBoundsException if locus_position excedes the total of LocusInfo of the DataSet.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the total of LocusInfo of the DataSet.
+ */
+ void setLocusInfo(size_t locus_position, const LocusInfo& locus);
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/DataSet/Group.cpp
++++ libbpp-popgen/src/Bpp/PopGen/DataSet/Group.cpp
+@@ -507,7 +507,7 @@
+ }
+ catch (IndexOutOfBoundsException& ioobe)
+ {
+- throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotype: locus_position excedes the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
++ throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotype: locus_position exceeds the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
+ }
+ }
+
+@@ -525,7 +525,7 @@
+ }
+ catch (IndexOutOfBoundsException& ioobe)
+ {
+- throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotypeByAlleleKey: locus_position excedes the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
++ throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotypeByAlleleKey: locus_position exceeds the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
+ }
+ catch (Exception&)
+ {
+@@ -547,7 +547,7 @@
+ }
+ catch (IndexOutOfBoundsException& ioobe)
+ {
+- throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotypeByAlleleId: locus_position excedes the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
++ throw IndexOutOfBoundsException("Group::setIndividualMonolocusGenotypeByAlleleId: locus_position exceeds the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
+ }
+ catch (AlleleNotFoundException& anfe)
+ {
+@@ -569,7 +569,7 @@
+ }
+ catch (IndexOutOfBoundsException& ioobe)
+ {
+- throw IndexOutOfBoundsException("Group::getIndividualMonolocusGenotype: locus_position excedes the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
++ throw IndexOutOfBoundsException("Group::getIndividualMonolocusGenotype: locus_position exceeds the number of locus.", ioobe.getBadIndex(), ioobe.getBounds()[0], ioobe.getBounds()[1]);
+ }
+ }
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/DataSet/Group.h
++++ libbpp-popgen/src/Bpp/PopGen/DataSet/Group.h
+@@ -248,28 +248,28 @@
+ /**
+ * @brief Set the sex of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void setIndividualSexAtPosition(size_t individual_position, const unsigned short sex);
+
+ /**
+ * @brief Get the sex of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ unsigned short getIndividualSexAtPosition(size_t individual_position) const;
+
+ /**
+ * @brief Set the date of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void setIndividualDateAtPosition(size_t individual_position, const Date& date);
+
+ /**
+ * @brief Get the date of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the Individual has no date.
+ */
+ const Date& getIndividualDateAtPosition(size_t individual_position) const;
+@@ -277,14 +277,14 @@
+ /**
+ * @brief Set the coordinates of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void setIndividualCoordAtPosition(size_t individual_position, const Point2D<double>& coord);
+
+ /**
+ * @brief Get the coordinates of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the individual has no coordinate.
+ */
+ const Point2D<double>& getIndividualCoordAtPosition(size_t individual_position) const;
+@@ -292,14 +292,14 @@
+ /**
+ * @brief Set the locality of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void setIndividualLocalityAtPosition(size_t individual_position, const Locality<double>* locality);
+
+ /**
+ * @brief Get the locality of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the individual has no locality.
+ */
+ const Locality<double>& getIndividualLocalityAtPosition(size_t individual_position) const;
+@@ -307,7 +307,7 @@
+ /**
+ * @brief Add a sequence to an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw AlphabetMismatchException if the sequence's alphabet doesn't match the container's alphabet.
+ * @throw BadIdentifierException if the sequence's name is already in use.
+ * @throw BadIntegerException if sequence_position is already in use.
+@@ -319,7 +319,7 @@
+ /**
+ * @brief Get a sequence of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ * @throw SequenceNotFoundException if sequence_name is not found.
+ */
+@@ -330,7 +330,7 @@
+ /**
+ * @brief Get a sequence of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ * @throw SequenceNotFoundException if sequence_position is not found.
+ */
+@@ -341,7 +341,7 @@
+ /**
+ * @brief Delete a sequence of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ * @throw SequenceNotFoundException if sequence_name is not found.
+ */
+@@ -350,7 +350,7 @@
+ /**
+ * @brief Delete a sequence of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ * @throw SequenceNotFoundException if sequence_position is not found.
+ */
+@@ -359,14 +359,14 @@
+ /**
+ * @brief Tell if the Individual has some sequences.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ bool hasIndividualSequences(size_t individual_position) const;
+
+ /**
+ * @brief Get the sequences' names from an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ */
+ std::vector<std::string> getIndividualSequencesNames(size_t individual_position) const;
+@@ -374,7 +374,7 @@
+ /**
+ * @brief Get the position of a sequence in an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ * @throw SequenceNotFoundException if sequence_name is not found.
+ */
+@@ -385,7 +385,7 @@
+ /**
+ * @brief Get the number of sequences in an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if there is no sequence container defined in the individual.
+ */
+ size_t getIndividualNumberOfSequences(size_t individual_position) const;
+@@ -393,21 +393,21 @@
+ /**
+ * @brief Set all the sequences by copying an OrderedSequenceContainer.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void setIndividualSequences(size_t individual_position, const MapSequenceContainer& msc);
+
+ /**
+ * @brief Set the genotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void setIndividualGenotype(size_t individual_position, const MultilocusGenotype& genotype);
+
+ /**
+ * @brief Initialyze the genotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw BadIntegerException if loci_number < 1.
+ * @throw Exception if the individual already has a genotype.
+ */
+@@ -416,23 +416,23 @@
+ /**
+ * @brief Delete the genotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ void deleteIndividualGenotype(size_t individual_position);
+
+ /**
+ * @brief Tell if an Individual has a genotype.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ */
+ bool hasIndividualGenotype(size_t individual_position) const;
+
+ /**
+ * @brief Set a MonolocusGenotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ */
+ void setIndividualMonolocusGenotype(size_t individual_position, size_t locus_position,
+ const MonolocusGenotype& monogen);
+@@ -440,9 +440,9 @@
+ /**
+ * @brief Set a MonolocusGenotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ * @throw Exception if there is no key in allele_keys.
+ */
+ void setIndividualMonolocusGenotypeByAlleleKey(size_t individual_position, size_t locus_position,
+@@ -451,9 +451,9 @@
+ /**
+ * @brief Set a MonolocusGenotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ * @throw AlleleNotFoundException if at least one id is not found in locus_info.
+ */
+ void setIndividualMonolocusGenotypeByAlleleId(size_t individual_position, size_t locus_position,
+@@ -462,9 +462,9 @@
+ /**
+ * @brief Get a MonolocusGenotype of an Individual.
+ *
+- * @throw IndexOutOfBoundsException if individual_position excedes the number of individuals.
++ * @throw IndexOutOfBoundsException if individual_position exceeds the number of individuals.
+ * @throw NullPointerException if the individual has no genotype.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of locus.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of locus.
+ */
+ const MonolocusGenotype& getIndividualMonolocusGenotype(size_t individual_position,
+ size_t locus_position) const;
+--- libbpp-popgen.orig/src/Bpp/PopGen/DataSet/Individual.h
++++ libbpp-popgen/src/Bpp/PopGen/DataSet/Individual.h
+@@ -409,7 +409,7 @@
+ * @brief Set a MonolocusGenotype.
+ *
+ * @throw NullPointerException if there is no genotype defined.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ */
+ void setMonolocusGenotype(size_t locus_position, const MonolocusGenotype& monogen);
+
+@@ -417,7 +417,7 @@
+ * @brief Set a MonolocusGenotype.
+ *
+ * @throw NullPointerException if there is no genotype defined.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ * @throw Exception if there is no key in allele_keys.
+ */
+ void setMonolocusGenotypeByAlleleKey(
+@@ -428,7 +428,7 @@
+ * @brief Set a MonolocusGenotype.
+ *
+ * @throw NullPointerException if there is no genotype defined.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ * @throw AlleleNotFoundException if at least one the id is not found in the LocusInfo.
+ */
+ void setMonolocusGenotypeByAlleleId(
+@@ -440,7 +440,7 @@
+ * @brief Get a MonolocusGenotype.
+ *
+ * @throw NullPointerException if there is no genotype defined.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ */
+ const MonolocusGenotype& getMonolocusGenotype(size_t locus_position);
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/LocusInfo.h
++++ libbpp-popgen/src/Bpp/PopGen/LocusInfo.h
+@@ -124,7 +124,7 @@
+ /**
+ * @brief Retrieve an AlleleInfo object of the LocusInfo.
+ *
+- * @throw IndexOutOfBoundsException if key excedes the number of alleles.
++ * @throw IndexOutOfBoundsException if key exceeds the number of alleles.
+ */
+ const AlleleInfo& getAlleleInfoByKey(size_t key) const;
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/MultilocusGenotype.h
++++ libbpp-popgen/src/Bpp/PopGen/MultilocusGenotype.h
+@@ -96,7 +96,7 @@
+ /**
+ * @brief Set a MonolocusGenotype by allele keys.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ * @throw Exception if there is no key in allele_keys.
+ */
+ void setMonolocusGenotypeByAlleleKey(size_t locus_position,
+@@ -105,7 +105,7 @@
+ /**
+ * @brief Set a MonolocusGenotype by allele id.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ * @throw AlleleNotFoundException if at least one of the id is not found in the LocusInfo.
+ */
+ void setMonolocusGenotypeByAlleleId(size_t locus_position,
+@@ -115,14 +115,14 @@
+ /**
+ * @brief Set a MonolocusGenotype as missing data.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ */
+ void setMonolocusGenotypeAsMissing(size_t locus_position);
+
+ /**
+ * @brief Tell if a MonolocusGenotype is a missing data.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci.
+ */
+ bool isMonolocusGenotypeMissing(size_t locus_position) const;
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/MultilocusGenotypeStatistics.h
++++ libbpp-popgen/src/Bpp/PopGen/MultilocusGenotypeStatistics.h
+@@ -94,28 +94,28 @@
+ /**
+ * @brief Get the alleles' id at one locus for a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ */
+ static std::vector<size_t> getAllelesIdsForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+
+ /**
+ * @brief Count the number of allele (gametes) at a locus for a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ */
+ static size_t countGametesForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+
+ /**
+ * @brief Get a map of allele count for a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ */
+ static std::map<size_t, size_t> getAllelesMapForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+
+ /**
+ * @brief Get the alleles frequencies at one locus for a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static std::map<size_t, double> getAllelesFrqForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+@@ -123,28 +123,28 @@
+ /**
+ * @brief Count the number of non-missing data at a given locus for a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ */
+ static size_t countNonMissingForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+
+ /**
+ * @brief Counr the number of bi-allelic MonolocusGenotype at a given locus for a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ */
+ static size_t countBiAllelicForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+
+ /**
+ * @brief Count how many times each allele is found in an heterozygous MonolocusGenotype in a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ */
+ static std::map<size_t, size_t> countHeterozygousForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+
+ /**
+ * @brief Get the heterozygous frequencies for each allele at a locus in a set of groups.
+ *
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static std::map<size_t, double> getHeterozygousFrqForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+@@ -153,7 +153,7 @@
+ * @brief Compute the observed heterozygosity for one locus.
+ *
+ * This is the mean value of the getHeterozygousFrqForGroups map.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static double getHobsForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+@@ -166,7 +166,7 @@
+ * H_{exp}=1-\sum_{i=1}^{n}x_i^2
+ * @f]
+ * where @f$x_i at f$ is the frequency of the i<sup>th</sup> allele and @f$n at f$ the number of alleles.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static double getHexpForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+@@ -179,7 +179,7 @@
+ * H_{nb}=\frac{2n}{2n-1}\left(1-\sum_{i=1}^{n}x_i^2\right)=\frac{2n}{2n-1}H_{exp}
+ * @f]
+ * where @f$x_i at f$ is the frequency of the i<sup>th</sup> allele and @f$n at f$ the number of alleles.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static double getHnbForGroups(const PolymorphismMultiGContainer& pmgc, size_t locus_position, const std::set<size_t>& groups);
+@@ -194,7 +194,7 @@
+ * @f]
+ * where @f$x_i at f$ and @f$y_i at f$ are respectively the i<sup>th</sup> allele's frequency of the first and second group
+ * and @f$n at f$ the total number of alleles of both groups.
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static double getDnei72(const PolymorphismMultiGContainer& pmgc, std::vector<size_t> locus_positions, size_t grp1, size_t grp2);
+@@ -216,7 +216,7 @@
+ * \qquad\textrm{and}\qquad
+ * J_Y=\sum_{i=1}^{n}y_i^2
+ * @f]
+- * @throw IndexOutOfBoundsException if locus_position excedes the number of loci of one MultilocusGenotype.
++ * @throw IndexOutOfBoundsException if locus_position exceeds the number of loci of one MultilocusGenotype.
+ * @throw ZeroDivisionException if the number of considered alleles = 0.
+ */
+ static double getDnei78(const PolymorphismMultiGContainer& pmgc, std::vector<size_t> locus_positions, size_t grp1, size_t grp2);
+--- libbpp-popgen.orig/src/Bpp/PopGen/PolymorphismMultiGContainer.h
++++ libbpp-popgen/src/Bpp/PopGen/PolymorphismMultiGContainer.h
+@@ -102,21 +102,21 @@
+ /**
+ * @brief Get a MultilocusGenotype at a position.
+ *
+- * @throw IndexOutOfBoundsException if position excedes the size of the container.
++ * @throw IndexOutOfBoundsException if position exceeds the size of the container.
+ */
+ const MultilocusGenotype* getMultilocusGenotype(size_t position) const;
+
+ /**
+ * @brief Remove a MultilocusGenotype.
+ *
+- * @throw IndexOutOfBoundsException if position excedes the size of the container.
++ * @throw IndexOutOfBoundsException if position exceeds the size of the container.
+ */
+ MultilocusGenotype* removeMultilocusGenotype(size_t position);
+
+ /**
+ * @brief Delete a MultilocusGenotype.
+ *
+- * @throw IndexOutOfBoundsException if position excedes the size of the container.
++ * @throw IndexOutOfBoundsException if position exceeds the size of the container.
+ */
+ void deleteMultilocusGenotype(size_t position);
+
+@@ -135,14 +135,14 @@
+ /**
+ * @brief Get the Group id of a MultilocusGenotype.
+ *
+- * @throw IndexOutOfBoundsException if position excedes the size of the container.
++ * @throw IndexOutOfBoundsException if position exceeds the size of the container.
+ */
+ size_t getGroupId(size_t position) const;
+
+ /**
+ * @brief Set the Group id of a MultilocusGenotype.
+ *
+- * @throw IndexOutOfBoundsException if position excedes the size of the container.
++ * @throw IndexOutOfBoundsException if position exceeds the size of the container.
+ */
+ void setGroupId(size_t position, size_t group_id);
+
+--- libbpp-popgen.orig/src/Bpp/PopGen/PolymorphismSequenceContainer.h
++++ libbpp-popgen/src/Bpp/PopGen/PolymorphismSequenceContainer.h
+@@ -188,7 +188,7 @@
+ /**
+ * @brief Remove a sequence by index and return a pointer to this removed sequence.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences.
+ */
+ Sequence* removeSequence(size_t index);
+
+@@ -202,7 +202,7 @@
+ /**
+ * @brief Delete a sequence by index.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences.
+ */
+ void deleteSequence(size_t index);
+
+@@ -237,7 +237,7 @@
+ /**
+ * @brief Get the group identifier of the sequence.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ size_t getGroupId(size_t index) const;
+
+@@ -256,7 +256,7 @@
+ /**
+ * @brief Set the group identifier of a sequence.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ void setGroupId(size_t index, size_t group_id);
+
+@@ -280,7 +280,7 @@
+ /**
+ * @brief Tell if the sequence is ingroup by index.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ bool isIngroupMember(size_t index) const;
+
+@@ -294,7 +294,7 @@
+ /**
+ * @brief Set a sequence as ingroup member by index.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ void setAsIngroupMember(size_t index);
+
+@@ -308,7 +308,7 @@
+ /**
+ * @brief Set a sequence as outgroup member by index.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ void setAsOutgroupMember(size_t index);
+
+@@ -322,7 +322,7 @@
+ /**
+ * @brief Set the count of a sequence by index.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ * @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
+ */
+ void setSequenceCount(size_t index, unsigned int count);
+@@ -338,7 +338,7 @@
+ /**
+ * @brief Add 1 to the sequence count.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ void incrementSequenceCount(size_t index);
+
+@@ -352,7 +352,7 @@
+ /**
+ * @brief Removz 1 to the sequence count.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ * @throw BadIntegerException if count < 1 ... use deleteSequence instead of setting the count to 0.
+ */
+ void decrementSequenceCount(size_t index);
+@@ -368,7 +368,7 @@
+ /**
+ * @brief Get the count of a sequence by index.
+ *
+- * @throw IndexOutOfBoundsException if index excedes the number of sequences in the container.
++ * @throw IndexOutOfBoundsException if index exceeds the number of sequences in the container.
+ */
+ unsigned int getSequenceCount(size_t index) const;
+
View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/-/commit/853b0f5fdb7b1320bf11d17ca178675c7ce22104
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/-/commit/853b0f5fdb7b1320bf11d17ca178675c7ce22104
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