[med-svn] [seqan2] 02/05: more spelling; disable docs
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Feb 17 23:50:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository seqan2.
commit d97e992eb29e3881f62f0d75faf9569e7fdc9566
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Wed Feb 17 05:03:30 2016 -0800
more spelling; disable docs
---
debian/README.Debian | 2 +-
debian/changelog | 2 +-
debian/control | 39 +-
debian/patches/spelling.patch | 985 ++++++++++++++++++++++++++++++++++++++++++
debian/rules | 2 +-
5 files changed, 1008 insertions(+), 22 deletions(-)
diff --git a/debian/README.Debian b/debian/README.Debian
index 6c323e3..12c5300 100644
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -47,7 +47,7 @@ If you set your PATH like
PATH=${PATH}:/usr/lib/seqan/bin
-you can call all seqan tools straigth from command line with exception
+you can call all seqan tools straight from command line with exception
of /usr/lib/seqan/bin/join since there is a /usr/bin/join inside the
coreutils package which will be found first so you need to explicitly
specify the full path.
diff --git a/debian/changelog b/debian/changelog
index 6f4f481..8324fc9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,7 +3,7 @@ seqan2 (2.1.0+dfsg-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #811841
- * Seperate packaging from legacy seqan
+ * Separate packaging from legacy seqan
* cme fix dpkg-control
* moved debian/upstream to debian/upstream/metadata
* disable doc creation which works differently than in previous versions
diff --git a/debian/control b/debian/control
index 632850f..74af2a9 100644
--- a/debian/control
+++ b/debian/control
@@ -1,7 +1,8 @@
Source: seqan2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Soeren Sonnenburg <sonne at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Michael R. Crusoe <crusoe at ucdavis.edu>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
@@ -53,21 +54,21 @@ Description: C++ library for the analysis of biological sequences (development)
.
This package contains the developer files.
-Package: seqan2-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends},
- libjs-bootstrap,
- libjs-prettify,
- libjs-jquery
-Description: C++ library for the analysis of biological sequences (documentation)
- SeqAn is a C++ template library of efficient algorithms and data
- structures for the analysis of sequences with the focus on
- biological data. This library applies a unique generic design that
- guarantees high performance, generality, extensibility, and
- integration with other libraries. SeqAn is easy to use and
- simplifies the development of new software tools with a minimal loss
- of performance. This package contains the applications dfi, pair_align,
- micro_razers, seqan_tcoffee, seqcons, razers and tree_recon.
- .
- This package contains the documentation and examples.
+#Package: seqan2-doc
+#Architecture: all
+#Section: doc
+#Depends: ${misc:Depends},
+# libjs-bootstrap,
+# libjs-prettify,
+# libjs-jquery
+#Description: C++ library for the analysis of biological sequences (documentation)
+# SeqAn is a C++ template library of efficient algorithms and data
+# structures for the analysis of sequences with the focus on
+# biological data. This library applies a unique generic design that
+# guarantees high performance, generality, extensibility, and
+# integration with other libraries. SeqAn is easy to use and
+# simplifies the development of new software tools with a minimal loss
+# of performance. This package contains the applications dfi, pair_align,
+# micro_razers, seqan_tcoffee, seqcons, razers and tree_recon.
+# .
+# This package contains the documentation and examples.
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index de5fc97..506e421 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -93,3 +93,988 @@ Description: Fix some spelling issues
addDescription(parser, "(c) Copyright in 2014 by David Weese.");
+--- seqan2.orig/apps/fiona/compute_gain.cpp
++++ seqan2/apps/fiona/compute_gain.cpp
+@@ -1124,7 +1124,7 @@
+ std::cerr << "WARNING: Files not read completely!\n";
+ if (error)
+ {
+- std::cerr << "An error occured. Bailing out.\n";
++ std::cerr << "An error occurred. Bailing out.\n";
+ return 1;
+ }
+
+--- seqan2.orig/apps/fiona/fiona.cpp
++++ seqan2/apps/fiona/fiona.cpp
+@@ -2603,20 +2603,20 @@
+ double median = 0.0;
+ double mediumTotalOccs = 0.0;
+
+- std::map<unsigned, unsigned> vectorOccurences;
++ std::map<unsigned, unsigned> vectorOccurrences;
+
+ goBegin(iter);
+ for (; !atEnd(iter); ++iter)
+ {
+ unsigned numOccs = countOccurrences(iter);
+- ++vectorOccurences[numOccs];
++ ++vectorOccurrences[numOccs];
+ totalOccs += numOccs;
+ }
+
+ mediumTotalOccs = totalOccs / 2.0;
+
+ std::map<unsigned,unsigned>::iterator iterMap;
+- for (iterMap = vectorOccurences.begin (); iterMap != vectorOccurences.end (); ++iterMap)
++ for (iterMap = vectorOccurrences.begin (); iterMap != vectorOccurrences.end (); ++iterMap)
+ {
+ sumMedian += iterMap->second*iterMap->first;
+ if (sumMedian >= mediumTotalOccs)
+@@ -4193,7 +4193,7 @@
+ String<double> sd;
+ standardDeviation(sd, store.readSeqStore, options.genomeLength);
+
+- /*The strictness value allows to estimate the confidence intervall*/
++ /*The strictness value allows one to estimate the confidence intervall*/
+ for (unsigned i = 0; i < length(options.expectedTheoretical); ++i)
+ {
+ double expectedTemporary = options.expectedTheoretical[i] - options.strictness * sd[i];
+--- seqan2.orig/apps/mason2/README.mason_splicing
++++ seqan2/apps/mason2/README.mason_splicing
+@@ -19,7 +19,7 @@
+ 1. Overview
+ ------------------------------------------------------------------------------
+
+-Mason Splicing allows to construct transcripts from a GFF/GTF file, a
++Mason Splicing allows one to construct transcripts from a GFF/GTF file, a
+ reference sequence and an optional variant file.
+
+ ------------------------------------------------------------------------------
+--- seqan2.orig/apps/ngs_roi/project_spliced.h
++++ seqan2/apps/ngs_roi/project_spliced.h
+@@ -31,7 +31,7 @@
+ // ==========================================================================
+ // Author: Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
+ // ==========================================================================
+-// The ProjectSplicedRoi class allows to do the projection of ROIs to grouped
++// The ProjectSplicedRoi class allows one to do the projection of ROIs to grouped
+ // GTF/GFF intervals.
+ //
+ // This mode is enabled when the --gff-group-by KEY option is used. In this
+--- seqan2.orig/apps/pair_align/pair_align.cpp
++++ seqan2/apps/pair_align/pair_align.cpp
+@@ -33,7 +33,7 @@
+ addUsageLine(parser, "[\\fIOPTIONS\\fP] \\fB-s\\fP \\fIIN\\fP");
+ setCategory(parser, "Sequence Alignment");
+ addDescription(parser,
+- "The program allows to align two sequences using dyamic programming alignment algorithms while "
++ "The program allows one to align two sequences using dyamic programming alignment algorithms while "
+ "tweaking various parameters.");
+
+ addSection(parser, "Main Options");
+--- seqan2.orig/apps/rabema/README
++++ seqan2/apps/rabema/README
+@@ -112,7 +112,7 @@
+ alignments. The number of additional hits is 0. This is the number of hits in
+ the read mapper output with a valid error rate (below 3% in this case) that
+ are not found in the gold standard. If this number is greater than zero then
+-an error occured while building the gold standard or in the evaluation
++an error occurred while building the gold standard or in the evaluation
+ program. If you get such a number then please contact the Rabema authors.
+
+ The total number of reads is 8,840, the number of reads having an alignment
+@@ -136,4 +136,4 @@
+ Contact
+ ------
+
+- Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
+\ No newline at end of file
++ Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
+--- seqan2.orig/apps/rabema/rabema_build_gold_standard.cpp
++++ seqan2/apps/rabema/rabema_build_gold_standard.cpp
+@@ -986,7 +986,7 @@
+ "[\\fIOPTIONS\\fP] \\fB--out-gsi\\fP \\fIOUT.gsi\\fP \\fB--reference\\fP \\fIREF.fa\\fP "
+ "\\fB--in-bam\\fP \\fIPERFECT.{sam,bam}\\fP");
+ addDescription(parser,
+- "This program allows to build a RABEMA gold standard. The input is a reference FASTA file "
++ "This program allows one to build a RABEMA gold standard. The input is a reference FASTA file "
+ "and a perfect SAM/BAM map (e.g. created using RazerS 3 in full-sensitivity mode).");
+ addDescription(parser,
+ "The input SAM/BAM file must be \\fIsorted by coordinate\\fP. The program will create a "
+--- seqan2.orig/apps/rabema/ref_id_mapping.h
++++ seqan2/apps/rabema/ref_id_mapping.h
+@@ -24,7 +24,7 @@
+ // file. The order in the BAM file might not be the same as in the FASTA
+ // file.
+ //
+-// The function rebuildMapping() allows to rebuild the mapping from two
++// The function rebuildMapping() allows one to rebuild the mapping from two
+ // name store caches.
+ // ==========================================================================
+
+--- seqan2.orig/apps/sak/README
++++ seqan2/apps/sak/README
+@@ -1,6 +1,6 @@
+ Swiss Army Knife tool... It slices and dices and makes the laundry!
+
+-This tool allows to cut sequences and parts of sequences out of sequence
++This tool allows one to cut sequences and parts of sequences out of sequence
+ files. It supports all formats supported by the AutoSeqFormat class from
+ SeqAn, including FASTA, FASTQ and QSeq (Illumina format).
+
+--- seqan2.orig/apps/seqcons2/seqcons.cpp
++++ seqan2/apps/seqcons2/seqcons.cpp
+@@ -92,7 +92,7 @@
+ }
+ catch (std::runtime_error & e)
+ {
+- std::cerr << "\nERROR: An error occured during the program's execution:\n"
++ std::cerr << "\nERROR: An error occurred during the program's execution:\n"
+ << " " << e.what() << "\n";
+ return 1;
+ }
+--- seqan2.orig/dox/pages/index.dox
++++ seqan2/dox/pages/index.dox
+@@ -53,7 +53,7 @@
+ <tr><td><ul><li>@link localAlignment @endlink</li></ul></td><td></td></tr>
+ <tr><td><ul><li>@link LocalAlignmentEnumerator @endlink</li></ul></td><td>offers the Waterman-Eggert algorithm for enumerating suboptimal local alignments</td></tr>
+ <tr><td><ul><li>@link Align @endlink</li></ul></td><td>provides a data structure for tabular alignment of sequences with the same type</td></tr>
+- <tr><td><ul><li>@link Gaps @endlink</li></ul></td><td>allows to store gaps independent of the underlying sequence</td></tr>
++ <tr><td><ul><li>@link Gaps @endlink</li></ul></td><td>allows one to store gaps independent of the underlying sequence</td></tr>
+ </table>
+ </li>
+ <li>
+--- seqan2.orig/dox/pages/language_entities.dox
++++ seqan2/dox/pages/language_entities.dox
+@@ -16,7 +16,7 @@
+
+ @htmlonly <h2 data-lang-entity="typedef" id="typedef">Typedef</h2> @endhtmlonly
+
+-<strong>Typedefs are a common, standardized C++ language feature that allows to give custom names to arbitrary types.</strong>
++<strong>Typedefs are a common, standardized C++ language feature that allows one to give custom names to arbitrary types.</strong>
+
+ When programming SeqAn, they are often used for giving short names to complicated, nested template instantiations or to the result of a <a href="#metafunction">metafunction</a>.
+
+--- seqan2.orig/include/seqan/align/gaps_base.h
++++ seqan2/include/seqan/align/gaps_base.h
+@@ -112,7 +112,7 @@
+ * @tparam TSequence The type of the underlying sequence.
+ * @tparam TSpec Tag for specialization.
+ *
+- * Gaps wrap a @link ContainerConcept Sequence @endlink and allows to (1) insert gaps into the sequence and (2) select
++ * Gaps wrap a @link ContainerConcept Sequence @endlink and allows one to (1) insert gaps into the sequence and (2) select
+ * an infix of the gapped sequence (clipping). The gaps are not inserted into the underlying sequence (source) but
+ * stored separately. Using the clipping is optional and meant for selecting parts of the alignment as a part of the
+ * result of a local alignment algorithm.
+--- seqan2.orig/include/seqan/arg_parse/tool_doc.h
++++ seqan2/include/seqan/arg_parse/tool_doc.h
+@@ -568,7 +568,7 @@
+ *
+ * @section Remarks
+ *
+- * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows to store
++ * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows one to store
+ * and represent all information related to a command line tool that would normally go into a man page. It can be
+ * printed to STL streams in different formats, currently plain text, HTML and man pages are supported.
+ *
+--- seqan2.orig/include/seqan/basic/iterator_zip.h
++++ seqan2/include/seqan/basic/iterator_zip.h
+@@ -82,7 +82,7 @@
+ * @tparam TIteratorTypes A template parameter pack with one or more @link ContainerConcept#Iterator @endlink types.
+ *
+ * This iterator ties together different iterator types for different containers of the same size.
+- * It allows to operate on a single iterator, if multiple containers need to be traversed simultaneously.
++ * It allows one to operate on a single iterator, if multiple containers need to be traversed simultaneously.
+ * Note, that all operations are still executed in a serial fashion.
+ * If the zip iterator is dereferenced it returns a <a href="http://en.cppreference.com/w/cpp/utility/tuple">std::tuple</a>
+ * containing the dereferenced values of all embedded iterators.
+--- seqan2.orig/include/seqan/basic/metaprogramming_enable_if.h
++++ seqan2/include/seqan/basic/metaprogramming_enable_if.h
+@@ -252,7 +252,7 @@
+ * @param TCondition Boolean type, one of <tt>True</tt> and <tt>False</tt> or a metafunction returning such a tag
+ * type. If <tt>True</tt> then the constructor is visible, otherwise, it is not.
+ *
+- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a
++ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a
+ * href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must be used as the last dummy-argument of a constructor.
+ *
+ * To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
+@@ -280,7 +280,7 @@
+ * @param TCondition Boolean type, one of <tt>True</tt> and <tt>False</tt> or a metafunction returning such a tag
+ * type. If <tt>False</tt> then the constructor is visible, otherwise, it is not.
+ *
+- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a
++ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a
+ * href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must be used as the last dummy-argument of a constructor.
+ *
+ * To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
+@@ -309,7 +309,7 @@
+ * type. If <tt>True</tt> then the function is visible, otherwise, it is not.
+ * @param TResult The type that the function should have as the return type in case it is enabled.
+ *
+- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a
++ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a
+ * href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must occur as the return type definition of the function.
+ *
+ * To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
+@@ -338,7 +338,7 @@
+ * type. If <tt>False</tt> then the function is visible, otherwise, it is not.
+ * @param TResult The type that the function should have as the return type in case it is enabled.
+ *
+- * This macro allows to bind the visibility of a construtor to a boolean expression by using the <a
++ * This macro allows one to bind the visibility of a construtor to a boolean expression by using the <a
+ * href="http://en.wikipedia.org/wiki/Substitution_failure_is_not_an_error">SFINAE</a> principle for an optional argument with default value. The macro call must occur as the return type definition of the function.
+ *
+ * To avoid an unused argument warning, call <tt>ignoreUnusedVariableWarning(dummy)</tt> in the constructor's body.
+--- seqan2.orig/include/seqan/index/index_esa_base.h
++++ seqan2/include/seqan/index/index_esa_base.h
+@@ -169,7 +169,7 @@
+ typedef MaxRepeats_<void> MaxRepeats; // maximal repeat
+ struct MaxRepeatOccurrences;
+ typedef MaxRepeats_<MultiMems_> MultiMems; // Multiple Maximal Exact Match
+- struct MultiMemOccurences; // i.e. maximal match over different sequences
++ struct MultiMemOccurrences; // i.e. maximal match over different sequences
+
+
+ /*!
+@@ -197,7 +197,7 @@
+ template <typename TSize>
+ struct VertexEsa {
+ Pair<TSize> range; // current SA interval of hits (unique node identifier)
+- TSize parentRight; // right boundary of parent node's range (allows to go right)
++ TSize parentRight; // right boundary of parent node's range (allows one to go right)
+
+ SEQAN_HOST_DEVICE
+ VertexEsa() : range(0, 0), parentRight(0) {}
+--- seqan2.orig/include/seqan/index/index_esa_stree.h
++++ seqan2/include/seqan/index/index_esa_stree.h
+@@ -335,7 +335,7 @@
+ typedef typename HistoryStack_<Iter>::Type TStack;
+ typedef Iter iterator;
+
+- TStack history; // contains all previously visited intervals (allows to go up)
++ TStack history; // contains all previously visited intervals (allows one to go up)
+
+ //____________________________________________________________________________
+
+--- seqan2.orig/include/seqan/index/index_wotd.h
++++ seqan2/include/seqan/index/index_wotd.h
+@@ -311,7 +311,7 @@
+ TSize parentRepLen; // representative length of parent node
+ TSize edgeLen; // length of edge above current node
+ Pair<TSize> range; // current SA interval of hits
+- TSize parentRight; // right boundary of parent node's range (allows to go right)
++ TSize parentRight; // right boundary of parent node's range (allows one to go right)
+
+ VertexWotdModified_() :
+ node(0),
+--- seqan2.orig/include/seqan/parallel/parallel_splitting.h
++++ seqan2/include/seqan/parallel/parallel_splitting.h
+@@ -58,7 +58,7 @@
+ * to parallelize large for-loops that iterate over a contiguous range of elements. The interval and the number of
+ * subintervals can be set in the constructor @link Splitter::Splitter @endlink. @link Splitter#length @endlink and
+ * @link Splitter#resize @endlink can be used to retrieve or change the number of subintervals later. In contrast to
+- * other containers the Splitter allows to access one more element than its length would imply to allow to retrieve the
++ * other containers the Splitter allows one to access one more element than its length would imply to allow to retrieve the
+ * right boundary of each subinterval (see example code below).
+ *
+ * @section Examples
+--- seqan2.orig/include/seqan/sequence/sequence_interface.h
++++ seqan2/include/seqan/sequence/sequence_interface.h
+@@ -1101,7 +1101,7 @@
+ * @return TSize The amount of the requested capacity that was available. That is the function returns the minimum of
+ * <tt>newCapacity</tt> and <tt>capacity(me)</tt>.
+ *
+- * This function allows to increase the capacity but not the length of a container.
++ * This function allows one to increase the capacity but not the length of a container.
+ *
+ * Use @link StringConcept#resize @endlink if you want to change the size of a container.
+ *
+--- seqan2.orig/include/seqan/sequence/string_set_base.h
++++ seqan2/include/seqan/sequence/string_set_base.h
+@@ -69,7 +69,7 @@
+ * chromosomes of a genome. This facilitates writing generic data structures and algorithms to operate on single
+ * strings and genomes which is captured by the @link TextConcept @endlink.
+ *
+- * Second, the @link DependentStringSet @endlink specialization allows to create subsets of string sets without
++ * Second, the @link DependentStringSet @endlink specialization allows one to create subsets of string sets without
+ * storing copies of strings and identifying strings by a common id.
+ *
+ * @section Examples
+--- seqan2.orig/include/seqan/system/system_condition.h
++++ seqan2/include/seqan/system/system_condition.h
+@@ -32,7 +32,7 @@
+ // Author: David Weese <david.weese at fu-berlin.de>
+ // ==========================================================================
+ // Condition class. In conjunction with a critical section (given in the
+-// c'tor) this class allows to suspend a thread until another wakes it up via
++// c'tor) this class allows one to suspend a thread until another wakes it up via
+ // signal().
+ // ==========================================================================
+
+--- seqan2.orig/include/seqan/tabix_io/tabix_index_tbi.h
++++ seqan2/include/seqan/tabix_io/tabix_index_tbi.h
+@@ -33,7 +33,7 @@
+ // ==========================================================================
+ // (Read-only) Tabix index support.
+ //
+-// A Tabix index (Heng Li) allows to randomly seek in a tab-seperated genome
++// A Tabix index (Heng Li) allows one to randomly seek in a tab-seperated genome
+ // related file, e.g. VCF, GFF, SAM, BED, etc. The corresponding file only
+ // needs to be sorted by chromosomal position in advance and optionally
+ // compressed with 'bgzip'. The resulting file must be indexed with 'tabix'.
+--- seqan2.orig/manual/attic/Tutorial/IndicesOld.rst
++++ seqan2/manual/attic/Tutorial/IndicesOld.rst
+@@ -3,7 +3,7 @@
+ Indices
+ -------
+
+-A substring index is a datatype which allows to seek efficiently for all
++A substring index is a datatype which allows one to seek efficiently for all
+ occurrences of a pattern in a string or a set of strings. Substring
+ indices are very efficient for the exact string matching problem, i.e.
+ finding all exact occurrences of a pattern in a text or a text
+--- seqan2.orig/manual/source/HowTo/FixWhitespaceAutomatically.rst
++++ seqan2/manual/source/HowTo/FixWhitespaceAutomatically.rst
+@@ -11,7 +11,7 @@
+ This page describes how to use `Universal Indent GUI <http://universalindent.sourceforge.net/>`_ and `Uncrustify <http://uncrustify.sourceforge.net/>`_ to automatically fix whitespace such that code resembles the :ref:`style-guide-cpp` more closely.
+
+ * Uncrustify is a command line program that is given a style definition and a source file and reformats the source file according to the configuration.
+-* Universal Indent GUI is a graphical front-end to Uncrustify with life preview that allows to manipulate the configuration and immediately see the results.
++* Universal Indent GUI is a graphical front-end to Uncrustify with life preview that allows one to manipulate the configuration and immediately see the results.
+
+ Installing Universal Indent GUI
+ -------------------------------
+--- seqan2.orig/manual/source/StyleGuide/Cpp.rst
++++ seqan2/manual/source/StyleGuide/Cpp.rst
+@@ -154,7 +154,7 @@
+
+ Write const correct code.
+ Read the `C++ FAQ const correctness article <http://www.parashift.com/c ++-faq-lite/const-correctness.html>`_ for more information.
+-Besides other things, this allows to use temporary objects without copying in functions that do not need to change their arguments.
++Besides other things, this allows one to use temporary objects without copying in functions that do not need to change their arguments.
+
+ Compiler Warnings
+ ^^^^^^^^^^^^^^^^^
+--- seqan2.orig/manual/source/StyleGuide/DoxApiDocs.rst
++++ seqan2/manual/source/StyleGuide/DoxApiDocs.rst
+@@ -879,7 +879,7 @@
+ Our usability research indicates that some functionality is confusing
+ (e.g. see #1050) but cannot be removed. One example is the function
+ ``reserve()`` which can be used to *increase* the *capacity* of a
+-container whereas the function ``resize()`` allows to change the *size*
++container whereas the function ``resize()`` allows one to change the *size*
+ of a container, *increasing or decreasing* its size.
+
+ The documentation of such functions should contain a clarifying text and
+--- seqan2.orig/manual/source/Tutorial/BackgroundAndMotivation.rst
++++ seqan2/manual/source/Tutorial/BackgroundAndMotivation.rst
+@@ -68,14 +68,14 @@
+ Memory Management in SeqAn
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-C++ allows to allocate complex objects on the stack (in contrast to Java where objects are always constructed on the heap).
++C++ allows one to allocate complex objects on the stack (in contrast to Java where objects are always constructed on the heap).
+ The objects are constructed when the code execution enters the scope/block they are defined in and freed when the block is left.
+ Allocation of resources (e.g. memory) happens on construction and deallocation happens when the current block is left.
+ This is best explained in an example.
+
+ .. includefrags:: demos/tutorial/background_and_motivation/example.cpp
+
+-``seqan::String<char>`` is a class (actually an instantiation of the class template :dox:`String`) that allows to store strings of ``char`` values, similar to ``std::vector<char>`` or ``std::string``.
++``seqan::String<char>`` is a class (actually an instantiation of the class template :dox:`String`) that allows one to store strings of ``char`` values, similar to ``std::vector<char>`` or ``std::string``.
+
+ When the variable ``programName`` is allocated, the constructor of the ``String<char>`` class is called.
+ It allocates sufficient memory to store the value of ``argv[0]`` and then copies over the values from this string.
+--- seqan2.orig/manual/source/Tutorial/FileIOOverview.rst
++++ seqan2/manual/source/Tutorial/FileIOOverview.rst
+@@ -34,7 +34,7 @@
+ Formatted Files
+ """""""""""""""
+
+-SeqAn allows to read or write record-structured files through two types of classes: :dox:`FormattedFileIn` and :dox:`FormattedFileOut`.
++SeqAn allows one to read or write record-structured files through two types of classes: :dox:`FormattedFileIn` and :dox:`FormattedFileOut`.
+ Classes of type :dox:`FormattedFileIn` allow to read files, whereas classes of type :dox:`FormattedFileOut` allow to write files.
+ Note how these types of classes **do not allow to read and write the same file at the same time**.
+
+@@ -62,7 +62,7 @@
+
+ This tutorial shows the basic functionalities provided by any class of type :dox:`FormattedFileIn` or :dox:`FormattedFileOut`.
+ In particular, this tutorial adopts the classes :dox:`BamFileIn` and :dox:`BamFileOut` as concrete types.
+-The class :dox:`BamFileIn` allows to read files in SAM or BAM format, whereas the class :dox:`BamFileOut` allows to write them.
++The class :dox:`BamFileIn` allows one to read files in SAM or BAM format, whereas the class :dox:`BamFileOut` allows one to write them.
+ Nonetheless, **these functionalities are independent from the particular file format** and thus valid for all record-based file formats supported by SeqAn.
+
+ The demo application shown here is a simple BAM to SAM converter.
+--- seqan2.orig/manual/source/Tutorial/GffAndGtfIO.rst
++++ seqan2/manual/source/Tutorial/GffAndGtfIO.rst
+@@ -38,7 +38,7 @@
+
+ Format Version Support in SeqAn
+
+- :dox:`GffFileIn` allows to read GFF files in version 2 and 3 and GTF files.
++ :dox:`GffFileIn` allows one to read GFF files in version 2 and 3 and GTF files.
+ For writing, :dox:`GffFileOut` supports only GFF 3 and GTF.
+
+ GFF Format
+--- seqan2.orig/manual/source/Tutorial/IndexedFastaIO.rst
++++ seqan2/manual/source/Tutorial/IndexedFastaIO.rst
+@@ -27,7 +27,7 @@
+ If the FASTA file is named ``path/sequence.fasta``, the index file is usually named ``path/sequence.fasta.fai``.
+
+ Using such index files, it is possible to rapidly read parts of the given sequence file.
+-The module ``<seqan/seq_io.h>`` allows to create and read such ``.fai`` index files and exposes an API to read parts randomly of FASTA file.
++The module ``<seqan/seq_io.h>`` allows one to create and read such ``.fai`` index files and exposes an API to read parts randomly of FASTA file.
+
+ .. note::
+
+--- seqan2.orig/manual/source/Tutorial/SeedAndExtend.rst
++++ seqan2/manual/source/Tutorial/SeedAndExtend.rst
+@@ -34,7 +34,7 @@
+ :align: right
+ :width: 300px
+
+-The :dox:`Seed` class allows to store seeds. Seeds have a begin and end position in each sequence. Often, two or more close seeds are combined into a larger seed, possibly causing a shift in horizontal or vertical direction between the begin position of the upper left seed and the end position of the lower right seed. For this reason, the :dox:`Seed` class also stores an upper and a lower diagonal to reflect the expansion between those shifted seeds.
++The :dox:`Seed` class allows one to store seeds. Seeds have a begin and end position in each sequence. Often, two or more close seeds are combined into a larger seed, possibly causing a shift in horizontal or vertical direction between the begin position of the upper left seed and the end position of the lower right seed. For this reason, the :dox:`Seed` class also stores an upper and a lower diagonal to reflect the expansion between those shifted seeds.
+
+ The image to the right shows an example where three smaller seeds (black diagonals) were combined (or "chained locally") into one larger seed (green nine-sided area).
+ The first seed lies on the begin diagonal, the lowermost seed on the lower diagonal and the uppermost seed on the upper diagonal.
+--- seqan2.orig/manual/source/Tutorial/SimpleRnaSeq.rst
++++ seqan2/manual/source/Tutorial/SimpleRnaSeq.rst
+@@ -21,7 +21,7 @@
+ :ref:`tutorial-genome-annotations`, :ref:`tutorial-fragment-store`, experience with OpenMP (optional)
+
+ RNA-Seq refers to high-throughput sequencing of cDNA in order to get information about the RNA molecules available in a sample.
+-Knowing the sequence and abundance of mRNA allows to determine the (differential) expression of genes, to detect alternative splicing variants, or to annotate yet unknown genes.
++Knowing the sequence and abundance of mRNA allows one to determine the (differential) expression of genes, to detect alternative splicing variants, or to annotate yet unknown genes.
+
+ In the following tutorial you will develop a simple gene quantification tool.
+ It will load a file containing gene annotations and a file with RNA-Seq read alignments, computes abundances, and outputs RPKM values for each expressed gene.
+--- seqan2.orig/manual/source/Tutorial/VcfIO.rst
++++ seqan2/manual/source/Tutorial/VcfIO.rst
+@@ -38,7 +38,7 @@
+ For simple variants such as SNPs and small indels, each record corresponds to a variant.
+ More complex variants can be stored in multiple records (see the VCF standard on "breakends" for more information).
+
+-The ``vcf_io`` module of SeqAn allows to read and write VCF files record-wise.
++The ``vcf_io`` module of SeqAn allows one to read and write VCF files record-wise.
+ Since the structure of the fields in the VCF format often is very complex and the format undergoes changes in this respect, SeqAn only offers basic parsing functionality: The position is stored as a 0-based integer, reference names are stored in a reference name store (similar as in the :ref:`tutorial-sam-bam-io` Tutorial), and the quality is stored as a ``float`` value.
+
+ The remaining fields have to be parsed from and composed as strings in the user's application.
+--- seqan2.orig/tests/basic/test_basic_allocator.h
++++ seqan2/tests/basic/test_basic_allocator.h
+@@ -49,7 +49,7 @@
+ // ==========================================================================
+
+ // The following helper class is passed as the parent allocator to all tested
+-// allocators. It allows to count the number of allocations and deallocations
++// allocators. It allows one to count the number of allocations and deallocations
+ // and checks whether all allocated memory blocks are correctly deallocated
+ // when it is destructed.
+
+--- seqan2.orig/tests/realign/test_realign.cpp
++++ seqan2/tests/realign/test_realign.cpp
+@@ -42,7 +42,7 @@
+ static const bool PRINT_REALIGNMENTS = false;
+ static const bool DEBUG_REALIGNMENT = false;
+
+-// Helper function that allows to add gaps into the i-th read alignment in a fragmentStore.
++// Helper function that allows one to add gaps into the i-th read alignment in a fragmentStore.
+ template <typename TFragmentStore>
+ void addGaps(TFragmentStore & store, unsigned alignID, unsigned pos)
+ {
+--- seqan2.orig/util/cmake/FindSeqAn.cmake
++++ seqan2/util/cmake/FindSeqAn.cmake
+@@ -84,7 +84,7 @@
+ # SEQAN_DEFINITIONS
+ #
+ # Additionally, the following two variables are set. The first contains
+-# the include paths for SeqAn, the second for dependencies. This allows to
++# the include paths for SeqAn, the second for dependencies. This allows one to
+ # include the dependency headers using include_directories (SYSTEM ...),
+ # such that warnings from these headers do not appear in the nightly builds.
+ #
+--- seqan2.orig/util/py_lib/pyratemp.py
++++ seqan2/util/py_lib/pyratemp.py
+@@ -865,7 +865,7 @@
+ Since "import" is insecure, the PseudoSandbox does not allow to
+ import other modules. But since some functions need to import
+ other modules (e.g. "datetime.datetime.strftime" imports "time"),
+- this function replaces the builtin "import" and allows to use
++ this function replaces the builtin "import" and allows one to use
+ modules which are already accessible by the sandboxed code.
+
+ :Note:
+--- seqan2.orig/apps/fiona/error_rate_from_sam.cpp
++++ seqan2/apps/fiona/error_rate_from_sam.cpp
+@@ -71,7 +71,7 @@
+ unsigned totalReadCount = 0; // Number of reads read.
+ unsigned totalErrorneousReadCount = 0; // Number of reads with errors read, excluding unaligned reads.
+ unsigned totalUnalignedReadCount = 0; // Number of reads without alignments.
+- std::map<unsigned, unsigned> histo; // Histogram error count -> num occurences.
++ std::map<unsigned, unsigned> histo; // Histogram error count -> num occurrences.
+
+ // Read records
+
+--- seqan2.orig/apps/gustaf/msplazer_main.h
++++ seqan2/apps/gustaf/msplazer_main.h
+@@ -194,7 +194,7 @@
+ ++sizeCount[length(stellarMatches[i].matches)];
+ }
+ for(unsigned i = 0; i < length(sizeCount); ++ i){
+- std::cout << "Number of occurences for matches " << i << " : " << sizeCount[i] << std::endl;
++ std::cout << "Number of occurrences for matches " << i << " : " << sizeCount[i] << std::endl;
+ }
+ for(unsigned i = 0; i < length(distanceScores); ++i){
+ TScoreAlloc scores = distanceScores[i];
+--- seqan2.orig/apps/seqcons2/seqcons_options.cpp
++++ seqan2/apps/seqcons2/seqcons_options.cpp
+@@ -122,7 +122,7 @@
+ << "OVERLAP WINDOW SIZE \t" << overlapWindowSize << "\n"
+ << "\n"
+ << "K-MER SIZE \t" << kMerSize << "\n"
+- << "K-MER MAX OCCURENCES \t" << kMerMaxOcc << "\n"
++ << "K-MER MAX OCCURRENCES \t" << kMerMaxOcc << "\n"
+ << "\n"
+ << "REALIGNMENT BANDWIDTH \t" << reAlignmentBandwidth << "\n"
+ << "REALIGNMENT ENVIRONMENT\t" << reAlignmentEnvironment << "\n";
+@@ -208,7 +208,7 @@
+ setMinValue(parser, "k-mer-size", "5");
+ setDefaultValue(parser, "k-mer-size", "20");
+
+- addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore k-mer with higher occurence count, 0 to disable.",
++ addOption(parser, seqan::ArgParseOption("", "k-mer-max-occ", "Ignore k-mer with higher occurrence count, 0 to disable.",
+ seqan::ArgParseOption::INTEGER, "COUNT"));
+ setMinValue(parser, "k-mer-max-occ", "0");
+ setDefaultValue(parser, "k-mer-max-occ", "200");
+--- seqan2.orig/apps/seqcons2/seqcons_options.h
++++ seqan2/apps/seqcons2/seqcons_options.h
+@@ -100,7 +100,7 @@
+
+ // K-mer length to use for identifying overlap candidates.
+ int kMerSize;
+- // K-mers with a higher number of occurences are ignored.
++ // K-mers with a higher number of occurrences are ignored.
+ int kMerMaxOcc;
+
+ // -----------------------------------------------------------------------
+--- seqan2.orig/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.contig_consensus.sam.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.contig_consensus.txt.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.nop.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.nop.sam.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.nop.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.nop.txt.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.overlap_consensus.sam.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.overlap_consensus.txt.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.pos_consensus.sam.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.pos_consensus.txt.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.realign.sam.stderr
++++ seqan2/apps/seqcons2/tests/alns1.realign.sam.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/alns1.realign.txt.stderr
++++ seqan2/apps/seqcons2/tests/alns1.realign.txt.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/seqs1.align_consensus.stderr
++++ seqan2/apps/seqcons2/tests/seqs1.align_consensus.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/seqs1.nop.stderr
++++ seqan2/apps/seqcons2/tests/seqs1.nop.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
++++ seqan2/apps/seqcons2/tests/seqs1.overlap_consensus.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
++++ seqan2/apps/seqcons2/tests/seqs2.align_consensus.sam.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
++++ seqan2/apps/seqcons2/tests/seqs2.align_consensus.txt.stderr
+@@ -16,7 +16,7 @@
+ OVERLAP WINDOW SIZE 20
+
+ K-MER SIZE 20
+-K-MER MAX OCCURENCES 200
++K-MER MAX OCCURRENCES 200
+
+ REALIGNMENT BANDWIDTH 10
+ REALIGNMENT ENVIRONMENT 20
+--- seqan2.orig/apps/stellar/README
++++ seqan2/apps/stellar/README
+@@ -182,7 +182,7 @@
+ Remove overabundant query k-mers from the k-mer index. NUM must be a
+ value between 0 (remove all) and 1 (remove nothing, default). k-mers with
+ a relative abundance above NUM are removed. The relative abundance is
+- the absolute number of a k-mers occurences divided by the total number of
++ the absolute number of a k-mers occurrences divided by the total number of
+ k-mers in the query sequence(s). The total number of k-mers is about
+ the total length of the query sequence(s).
+
+--- seqan2.orig/demos/tutorial/basics/strings.cpp
++++ seqan2/demos/tutorial/basics/strings.cpp
+@@ -22,7 +22,7 @@
+ }
+ std::cout << std::endl;
+ //![iterate-and-replace]
+-//![count-occurences]
++//![count-occurrences]
+ typedef Size<TAminoAcidString>::Type TSize;
+ typedef String<TSize> TCounterString;
+ TCounterString counter;
+@@ -30,7 +30,7 @@
+ resize(counter, alphSize, 0);
+ for (TIter it = begin(sourceSeq); it != itEnd; goNext(it))
+ value(counter, ordValue(value(it))) += 1;
+-//![count-occurences]
++//![count-occurrences]
+ //![frequency-table]
+ typedef Iterator<TCounterString>::Type TCounterIter;
+ TCounterIter countIt = begin(counter);
+--- seqan2.orig/dox/pages/suffix_array.dox
++++ seqan2/dox/pages/suffix_array.dox
+@@ -13,7 +13,7 @@
+ * "Faster Suffix Sorting", 1999), and a quicksort based algorithm.
+ *
+ * The following example constructs a suffix array using the modified Skew algorithm and searches the interval of suffices
+- * beginning with $t="l"$. The start positions of these suffices are the occurences of $t$, which are outputted at last.
++ * beginning with $t="l"$. The start positions of these suffices are the occurrences of $t$, which are outputted at last.
+ * This is only an example for @link createSuffixArray @endlink and similar functions. For an index based substring search
+ * better use the more generic @link Finder @endlink class (see @Demo.Index Finder@ demo).
+ *
+--- seqan2.orig/include/seqan/find/find_base.h
++++ seqan2/include/seqan/find/find_base.h
+@@ -187,9 +187,9 @@
+ * @param[in] k Desired minimal score (for approximate matching). <tt>k</tt> is a number <tt><= 0</tt>.
+ * Differences are deletions, insertions, and substitutions.
+ *
+- * @return bool <tt>true</tt> if an occurence was found and <tt>false</tt> if not.
++ * @return bool <tt>true</tt> if an occurrence was found and <tt>false</tt> if not.
+ *
+- * Repeated calls of this function iterate through all occurences of <tt>pattern</tt>.
++ * Repeated calls of this function iterate through all occurrences of <tt>pattern</tt>.
+ *
+ * @section Examples
+ *
+--- seqan2.orig/include/seqan/find/find_begin.h
++++ seqan2/include/seqan/find/find_begin.h
+@@ -344,7 +344,7 @@
+ * @param[in,out] finder The Finder object to search through.
+ * @param[in,out] pattern The Pattern object to search for. This must be a pattern for approximate string matching.
+ * @param[in] limit The score limit. The default is the limit used during the last <tt>find</tt> call, see
+- * <tt>getScore</tt>. All occurences that score at least <tt>limit</tt> are reported.
++ * <tt>getScore</tt>. All occurrences that score at least <tt>limit</tt> are reported.
+ *
+ * @return bool <tt>true</tt> indicates a match, <tt>false</tt> indicates no match.
+ *
+--- seqan2.orig/include/seqan/index/index_esa_algs_multi.h
++++ seqan2/include/seqan/index/index_esa_algs_multi.h
+@@ -486,7 +486,7 @@
+
+
+ template <typename TSTree>
+- class Iter< MultiMem<TSTree>, MultiMemOccurences > {
++ class Iter< MultiMem<TSTree>, MultiMemOccurrences > {
+ public:
+
+ typedef typename Value<TSTree>::Type TValue;
+@@ -687,21 +687,21 @@
+
+
+ template < typename TRepeat >
+- inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
+- value(Iter<TRepeat, MultiMemOccurences> const &it) {
++ inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type &
++ value(Iter<TRepeat, MultiMemOccurrences> const &it) {
+ return it.tmp;
+ }
+
+ template < typename TRepeat >
+- inline typename Value< Iter<TRepeat, MultiMemOccurences> >::Type &
+- value(Iter<TRepeat, MultiMemOccurences> &it) {
++ inline typename Value< Iter<TRepeat, MultiMemOccurrences> >::Type &
++ value(Iter<TRepeat, MultiMemOccurrences> &it) {
+ return it.tmp;
+ }
+
+ //TODO:fix me
+ template < typename TRepeat >
+- inline Iter<TRepeat, MultiMemOccurences> &
+- goNext(Iter<TRepeat, MultiMemOccurences> &it) {
++ inline Iter<TRepeat, MultiMemOccurrences> &
++ goNext(Iter<TRepeat, MultiMemOccurrences> &it) {
+ if (it._innerStep()) {
+ // it.tmp.i1 = saAt(it.subState.parentPtr, container(*it.mmemIt));
+ // it.tmp.i2 = saAt(it.subState.childPtr, container(*it.mmemIt));
+@@ -715,23 +715,23 @@
+ }
+
+ template < typename TRepeat >
+- inline bool atEnd(Iter<TRepeat, MultiMemOccurences> const &it) {
++ inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> const &it) {
+ return it._atEnd;
+ }
+
+ template < typename TRepeat >
+- inline bool atEnd(Iter<TRepeat, MultiMemOccurences> &it) {
++ inline bool atEnd(Iter<TRepeat, MultiMemOccurrences> &it) {
+ return it._atEnd;
+ }
+
+
+ template <typename TSTree>
+ struct Iterator< MultiMem<TSTree> > {
+- typedef Iter<MultiMem<TSTree>, MultiMemOccurences> Type;
++ typedef Iter<MultiMem<TSTree>, MultiMemOccurrences> Type;
+ };
+
+ template <typename TSTree>
+- struct Size< Iter<MultiMem<TSTree>, MultiMemOccurences> > {
++ struct Size< Iter<MultiMem<TSTree>, MultiMemOccurrences> > {
+ typedef typename Size<TSTree>::Type Type;
+ };
+
+--- seqan2.orig/include/seqan/index/index_fm_dox.h
++++ seqan2/include/seqan/index/index_fm_dox.h
+@@ -475,7 +475,7 @@
+ * @param[in] character The character.
+ * @param[in] pos The position (which is included in the counting).
+ *
+- * @return TSize The number of occurences (Metafunction: @link Index#Size @endlink).
++ * @return TSize The number of occurrences (Metafunction: @link Index#Size @endlink).
+ */
+
+ /*!
+--- seqan2.orig/include/seqan/statistics/statistics_base.h
++++ seqan2/include/seqan/statistics/statistics_base.h
+@@ -83,13 +83,13 @@
+ }
+
+ /*
+- * @fn _numOccurences
++ * @fn _numOccurrences
+ * @headerfile <seqan/statistics.h>
+- * @brief Auxiliary function to compute the number of occurences of a set of patterns in a set of text strings.
++ * @brief Auxiliary function to compute the number of occurrences of a set of patterns in a set of text strings.
+ *
+- * @signature void _numOccurences(W, haystack, needle, algoTag);
++ * @signature void _numOccurrences(W, haystack, needle, algoTag);
+ *
+- * @param[in,out] W A counter, incremented by the number of occurences.
++ * @param[in,out] W A counter, incremented by the number of occurrences.
+ * @param[in] haystack The text strings.
+ * @param[in] needle The set of patterns.
+ * @param[in] algoTag The tag to select the online text search algorithm with.
+--- seqan2.orig/manual/source/Tutorial/ParsingCommandLineArguments.rst
++++ seqan2/manual/source/Tutorial/ParsingCommandLineArguments.rst
+@@ -143,7 +143,7 @@
+
+ # program -a 1 -a 2 -a 3
+
+-If the option ``a`` is not a list then the occurence ``-a 3`` overwrites all previous settings.
++If the option ``a`` is not a list then the occurrence ``-a 3`` overwrites all previous settings.
+
+ However, if ``a`` is marked to be a list, then all values (``1``, ``2``, and ``3``) are stored as its values.
+ We can get the number of elements using the function :dox:`ArgumentParser#getOptionValueCount` and then access the individual arguments using the function :dox:`ArgumentParser#getOptionValue`.
+--- seqan2.orig/util/py_lib/seqan/dox/proc_doc.py
++++ seqan2/util/py_lib/seqan/dox/proc_doc.py
+@@ -61,7 +61,7 @@
+ """Collection of the top-level documentation entries.
+
+ @ivar doc_processor The DocProcessor that created this ProcDoc.
+- @ivar local_name_counter Number of occurences for local names, used for
++ @ivar local_name_counter Number of occurrences for local names, used for
+ shortening @link display to second level entries.
+ """
+
+--- seqan2.orig/apps/sgip/sgip.cpp
++++ seqan2/apps/sgip/sgip.cpp
+@@ -72,7 +72,7 @@
+ struct SgipOption
+ {
+ // I/O options.
+- CharString orginalFile; // name of orginal file(first graph)
++ CharString originalFile; // name of original file(first graph)
+ CharString comparFile; // name of comparisive file(second graph)
+ CharString outputFile; // name of result file
+ CharString compareFolder;
+@@ -82,7 +82,7 @@
+ FileOption activeFile;
+ SearchingType searchingType;
+ CharString algorithm; // Search strategy for metric dimension,e.g. Greedy, genetic etc.
+- unsigned odimension; // metric dimension of orginal graph specified by user
++ unsigned odimension; // metric dimension of original graph specified by user
+ unsigned cdimension; // metric dimension of comparitive graph specified by user
+ bool showHelp;
+ bool showVersion;
+@@ -127,7 +127,7 @@
+ char const * file1, * file2;
+ if (!options.isoCheck)
+ {
+- file1 = toCString(options.orginalFile);
++ file1 = toCString(options.originalFile);
+ if (!_createGraph(g1, SivaLab(), file1))
+ return 1;
+
+@@ -137,7 +137,7 @@
+ }
+ else
+ {
+- file1 = toCString(options.orginalFile);
++ file1 = toCString(options.originalFile);
+ file2 = toCString(options.comparFile);
+ if (!_createGraph(g1, SivaLab(), file1))
+ return 1;
+@@ -169,9 +169,9 @@
+ {
+ setVersion(parser, SEQAN_APP_VERSION " [" SEQAN_REVISION "]");
+ addDescription(parser, " SGIP - Solution of Graph Isomorphism Problem");
+- addUsageLine(parser, "-o <orginal graph> [Option]");
++ addUsageLine(parser, "-o <original graph> [Option]");
+ addSection(parser, "Mandatory Options");
+- addOption(parser, ArgParseOption("o", "orginal", "File containing orginal graph", ArgParseArgument::INPUT_FILE,"IN"));
++ addOption(parser, ArgParseOption("o", "original", "File containing original graph", ArgParseArgument::INPUT_FILE,"IN"));
+ setRequired(parser, "o");
+ addSection(parser, "Main Options");
+ addOption(parser, ArgParseOption("a", "algorithm", "Algorithm used for searching metric dimension", ArgParseArgument::STRING));
+@@ -180,7 +180,7 @@
+ setDefaultValue(parser, "searching", "0");
+ addOption(parser, ArgParseOption("i", "isomorphism", "To check whether two given graphs are isomorphic"));
+ addOption(parser, ArgParseOption("c", "comparitive", "File containing comparitive graph", ArgParseArgument::INPUT_FILE,"IN"));
+- addOption(parser, ArgParseOption("od", "odimension", "Specified initial dimension of orginal graph by user", ArgParseArgument::INTEGER));
++ addOption(parser, ArgParseOption("od", "odimension", "Specified initial dimension of original graph by user", ArgParseArgument::INTEGER));
+ setDefaultValue(parser, "odimension", "3");
+ addOption(parser, ArgParseOption("cd", "cdimension", "Specified initial dimension of comparitive graph by user", ArgParseArgument::INTEGER));
+ setDefaultValue(parser, "cdimension", "3");
+@@ -212,7 +212,7 @@
+ return res;
+
+ // Extract option value.
+- getOptionValue(options.orginalFile, parser, "o");
++ getOptionValue(options.originalFile, parser, "o");
+ if (isSet(parser, "i"))
+ {
+ if (!isSet(parser, "c"))
diff --git a/debian/rules b/debian/rules
index cadd649..5fe4df6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -30,7 +30,7 @@ pkgdev=seqan-dev
override_dh_auto_build:
dh_auto_build
- cd obj-$(DEB_BUILD_GNU_TYPE); make dox # FIXME: This does nothing and no *.html files will be created at all
+ #cd obj-$(DEB_BUILD_GNU_TYPE); make dox # FIXME: This does nothing and no *.html files will be created at all
# This ends up in:
# Could not import extension sphinxcontrib.bibtex (exception: No module named sphinxcontrib.bibtex)
# Seems there is no sphinx module bibtex - thus deactivating creation of html manual
--
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