From 54c99cf41175326333c99b9a2dca4b9eac17d64c Mon Sep 17 00:00:00 2001 From: =?utf8?q?Carn=C3=AB=20Draug?= Date: Wed, 30 Aug 2017 19:17:37 +0100 Subject: [PATCH] maint: fix multiple typos identified by lintian --- Bio/AnalysisI.pm | 2 +- Bio/Annotation/OntologyTerm.pm | 2 +- Bio/AnnotationCollectionI.pm | 2 +- Bio/Assembly/Contig.pm | 6 +++--- Bio/Assembly/ScaffoldI.pm | 2 +- Bio/Assembly/Singlet.pm | 2 +- Bio/Assembly/Tools/ContigSpectrum.pm | 2 +- Bio/Cluster/UniGene.pm | 4 ++-- Bio/DB/EMBL.pm | 2 +- Bio/DB/Fasta.pm | 2 +- Bio/DB/GFF.pm | 6 +++--- Bio/DB/GFF/Adaptor/dbi.pm | 2 +- Bio/DB/GFF/Adaptor/dbi/mysql.pm | 2 +- Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm | 2 +- Bio/DB/GFF/Adaptor/dbi/oracle.pm | 2 +- Bio/DB/GFF/Adaptor/dbi/pg.pm | 2 +- Bio/DB/GFF/Segment.pm | 6 +++--- Bio/DB/GenBank.pm | 2 +- Bio/DB/GenPept.pm | 2 +- Bio/DB/HIV/HIVQueryHelper.pm | 2 +- Bio/DB/IndexedBase.pm | 2 +- Bio/DB/MeSH.pm | 4 ++-- Bio/DB/Qual.pm | 2 +- Bio/DB/Query/HIVQuery.pm | 2 +- Bio/DB/RefSeq.pm | 4 ++-- Bio/DB/SeqFeature/Store.pm | 2 +- Bio/DB/SeqFeature/Store/GFF2Loader.pm | 2 +- Bio/DB/SeqFeature/Store/GFF3Loader.pm | 2 +- Bio/DB/SeqFeature/Store/Loader.pm | 2 +- Bio/DB/TFBS/transfac_pro.pm | 8 ++++---- Bio/DB/Taxonomy/flatfile.pm | 2 +- Bio/DB/Taxonomy/sqlite.pm | 6 +++--- Bio/DB/WebDBSeqI.pm | 4 ++-- Bio/DescribableI.pm | 2 +- Bio/Factory/ObjectFactoryI.pm | 2 +- Bio/Index/Abstract.pm | 2 +- Bio/Index/AbstractSeq.pm | 2 +- Bio/Index/Blast.pm | 2 +- Bio/Index/BlastTable.pm | 2 +- Bio/Index/Hmmer.pm | 2 +- Bio/Index/Stockholm.pm | 2 +- Bio/LiveSeq/IO/Loader.pm | 2 +- Bio/LiveSeq/IO/README | 2 +- Bio/LiveSeq/Mutation.pm | 2 +- Bio/LiveSeq/SeqI.pm | 4 ++-- Bio/LocatableSeq.pm | 2 +- Bio/Location/Atomic.pm | 10 +++++----- Bio/Location/Fuzzy.pm | 2 +- Bio/Location/FuzzyLocationI.pm | 2 +- Bio/Location/Simple.pm | 6 +++--- Bio/Location/Split.pm | 2 +- Bio/Location/SplitLocationI.pm | 2 +- Bio/LocationI.pm | 2 +- Bio/Map/CytoMarker.pm | 2 +- Bio/Map/CytoPosition.pm | 6 +++--- Bio/Map/GeneRelative.pm | 4 ++-- Bio/Map/Microsatellite.pm | 2 +- Bio/Map/OrderedPosition.pm | 2 +- Bio/Map/Physical.pm | 2 +- Bio/Map/Position.pm | 2 +- Bio/Map/PositionI.pm | 2 +- Bio/Map/Relative.pm | 2 +- Bio/Map/TranscriptionFactor.pm | 2 +- Bio/Matrix/PSM/IO.pm | 2 +- Bio/Matrix/PSM/IO/masta.pm | 6 +++--- Bio/Matrix/PSM/InstanceSite.pm | 2 +- Bio/Matrix/PSM/ProtMatrix.pm | 6 +++--- Bio/Matrix/PSM/ProtPsm.pm | 2 +- Bio/Matrix/PSM/Psm.pm | 4 ++-- Bio/Matrix/PSM/PsmI.pm | 4 ++-- Bio/Matrix/PSM/SiteMatrix.pm | 12 ++++++------ Bio/Matrix/PSM/SiteMatrixI.pm | 4 ++-- Bio/Ontology/OntologyStore.pm | 2 +- Bio/Ontology/SimpleOntologyEngine.pm | 2 +- Bio/Ontology/Term.pm | 4 ++-- Bio/Ontology/TermI.pm | 2 +- Bio/OntologyIO/Handlers/BaseSAXHandler.pm | 2 +- Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm | 4 ++-- Bio/OntologyIO/obo.pm | 2 +- Bio/Perl.pm | 2 +- Bio/PhyloNetwork/muVector.pm | 2 +- Bio/PopGen/HtSNP.pm | 6 +++--- Bio/PopGen/Individual.pm | 2 +- Bio/PopGen/Population.pm | 4 ++-- Bio/PopGen/TagHaplotype.pm | 4 ++-- Bio/PrimarySeq.pm | 10 +++++----- Bio/PrimarySeqI.pm | 8 ++++---- Bio/PullParserI.pm | 2 +- Bio/Restriction/Analysis.pm | 2 +- Bio/Restriction/Enzyme.pm | 2 +- Bio/Restriction/EnzymeI.pm | 2 +- Bio/Restriction/IO/base.pm | 6 +++--- Bio/Restriction/IO/itype2.pm | 2 +- Bio/Root/Exception.pm | 2 +- Bio/Root/Root.pm | 2 +- Bio/Root/Storable.pm | 4 ++-- Bio/Root/Test.pm | 6 +++--- Bio/Root/Utilities.pm | 10 +++++----- Bio/Search/BlastUtils.pm | 2 +- Bio/Search/HSP/BlastPullHSP.pm | 2 +- Bio/Search/HSP/GenericHSP.pm | 2 +- Bio/Search/HSP/HMMERHSP.pm | 2 +- Bio/Search/HSP/HSPI.pm | 2 +- Bio/Search/HSP/ModelHSP.pm | 2 +- Bio/Search/HSP/PullHSPI.pm | 2 +- Bio/Search/Hit/GenericHit.pm | 2 +- Bio/Search/Hit/HMMERHit.pm | 2 +- Bio/Search/Hit/ModelHit.pm | 2 +- Bio/Search/Iteration/IterationI.pm | 2 +- Bio/Search/SearchUtils.pm | 2 +- Bio/Search/Tiling/TilingI.pm | 2 +- Bio/SearchDist.pm | 2 +- Bio/SearchIO/Writer/HTMLResultWriter.pm | 2 +- Bio/SearchIO/Writer/TextResultWriter.pm | 2 +- Bio/SearchIO/exonerate.pm | 2 +- Bio/SearchIO/hmmer3.pm | 2 +- Bio/Seq.pm | 6 +++--- Bio/Seq/EncodedSeq.pm | 2 +- Bio/Seq/Meta/Array.pm | 4 ++-- Bio/Seq/MetaI.pm | 8 ++++---- Bio/Seq/PrimaryQual.pm | 4 ++-- Bio/Seq/PrimedSeq.pm | 2 +- Bio/Seq/QualI.pm | 8 ++++---- Bio/Seq/RichSeqI.pm | 2 +- Bio/Seq/SeqBuilder.pm | 4 ++-- Bio/Seq/SeqWithQuality.pm | 14 +++++++------- Bio/Seq/SequenceTrace.pm | 6 +++--- Bio/Seq/SimulatedRead.pm | 2 +- Bio/SeqFeature/Computation.pm | 6 +++--- Bio/SeqFeature/Generic.pm | 4 ++-- Bio/SeqFeature/Lite.pm | 2 +- Bio/SeqFeature/PositionProxy.pm | 2 +- Bio/SeqFeature/SubSeq.pm | 2 +- Bio/SeqFeature/Tools/Unflattener.pm | 2 +- Bio/SeqFeature/TypedSeqFeatureI.pm | 2 +- Bio/SeqIO/ace.pm | 2 +- Bio/SeqIO/bsml.pm | 4 ++-- Bio/SeqIO/chadoxml.pm | 4 ++-- Bio/SeqIO/chaos.pm | 2 +- Bio/SeqIO/embl.pm | 4 ++-- Bio/SeqIO/fasta.pm | 2 +- Bio/SeqIO/fastq.pm | 2 +- Bio/SeqIO/game/gameHandler.pm | 2 +- Bio/SeqIO/gcg.pm | 4 ++-- Bio/SeqIO/genbank.pm | 6 +++--- Bio/SeqIO/interpro.pm | 2 +- Bio/SeqIO/lasergene.pm | 2 +- Bio/SeqIO/mbsout.pm | 2 +- Bio/SeqIO/msout.pm | 2 +- Bio/SeqIO/seqxml.pm | 2 +- Bio/SeqIO/swiss.pm | 4 ++-- Bio/SeqIO/tigr.pm | 4 ++-- Bio/SeqUtils.pm | 2 +- Bio/Structure/Entry.pm | 4 ++-- Bio/Structure/Residue.pm | 4 ++-- Bio/Structure/SecStr/STRIDE/Res.pm | 2 +- Bio/Taxonomy.pm | 4 ++-- Bio/Tools/Analysis/DNA/ESEfinder.pm | 2 +- Bio/Tools/Analysis/Protein/ELM.pm | 2 +- Bio/Tools/Analysis/Protein/NetPhos.pm | 4 ++-- Bio/Tools/ECnumber.pm | 2 +- Bio/Tools/GFF.pm | 4 ++-- Bio/Tools/Phylo/Gerp.pm | 2 +- Bio/Tools/Phylo/PAML/Result.pm | 2 +- Bio/Tools/SiRNA.pm | 2 +- Bio/Tools/Sigcleave.pm | 2 +- Bio/Tools/dpAlign.pm | 2 +- Bio/Tools/pSW.pm | 4 ++-- Bio/Tree/AlleleNode.pm | 2 +- Bio/Tree/NodeI.pm | 2 +- Bio/Tree/TreeFunctionsI.pm | 6 +++--- Bio/TreeIO/nexus.pm | 2 +- Bio/TreeIO/pag.pm | 2 +- Bio/Variation/AAReverseMutate.pm | 2 +- Bio/Variation/VariantI.pm | 6 +++--- scripts/DB/bp_flanks.pl | 2 +- scripts/index/bp_fetch.pl | 6 +++--- scripts/index/bp_index.pl | 4 ++-- scripts/seq/bp_unflatten_seq.pl | 2 +- 179 files changed, 281 insertions(+), 281 deletions(-) diff --git a/Bio/AnalysisI.pm b/Bio/AnalysisI.pm index c0fb99dbf..4b97957fb 100644 --- a/Bio/AnalysisI.pm +++ b/Bio/AnalysisI.pm @@ -676,7 +676,7 @@ keys: ended elapsed -See C for remarks on time formating. +See C for remarks on time formatting. An example - both for unformatted and formatted times: diff --git a/Bio/Annotation/OntologyTerm.pm b/Bio/Annotation/OntologyTerm.pm index a9c339ae1..752573253 100644 --- a/Bio/Annotation/OntologyTerm.pm +++ b/Bio/Annotation/OntologyTerm.pm @@ -341,7 +341,7 @@ sub definition { another Term (e.g. the top level of the ontology). Returns : The ontology of this Term [TermI]. Args : The ontology of this Term [TermI or scalar -- which - becomes the name of the catagory term] (optional). + becomes the name of the category term] (optional). =cut diff --git a/Bio/AnnotationCollectionI.pm b/Bio/AnnotationCollectionI.pm index 33acdfbdc..f1bc2e874 100644 --- a/Bio/AnnotationCollectionI.pm +++ b/Bio/AnnotationCollectionI.pm @@ -47,7 +47,7 @@ The Bioperl approach is that the "interesting facts" are represented by Bio::AnnotationI objects. The interface Bio::AnnotationI guarantees two methods - $obj->as_text(); # string formated to display to users + $obj->as_text(); # string formatted to display to users and diff --git a/Bio/Assembly/Contig.pm b/Bio/Assembly/Contig.pm index 052b87466..ad9fa58f8 100644 --- a/Bio/Assembly/Contig.pm +++ b/Bio/Assembly/Contig.pm @@ -103,7 +103,7 @@ of the aligned sequences that were used to do the assembly. "gapped consensus" refers to positions in the aligned consensus sequence, which is the consensus sequence including the gaps inserted -to align it agains the aligned sequences that were used to assemble +to align it against the aligned sequences that were used to assemble the contig. So, its limits are [ 1, (consensus length + number of gaps in consensus) ] @@ -424,7 +424,7 @@ sub downstream_neighbor { the feature attached to one of the contig aligned sequences, the feature is registered as an aligned sequence feature. If $flag is 0 and the feature is not - attched to any sequence in the contig, the feature is + attached to any sequence in the contig, the feature is simply added to the feature collection and no attachment or registration is made. @@ -1267,7 +1267,7 @@ sub purge { Usage : $contig->sort_alphabetically Function : - Changes the order of the alignemnt to alphabetical on name + Changes the order of the alignment to alphabetical on name followed by numerical by number. Returns : diff --git a/Bio/Assembly/ScaffoldI.pm b/Bio/Assembly/ScaffoldI.pm index dbfb48511..864c3988e 100644 --- a/Bio/Assembly/ScaffoldI.pm +++ b/Bio/Assembly/ScaffoldI.pm @@ -9,7 +9,7 @@ =head1 NAME -Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies +Bio::Assembly::ScaffoldI - Abstract Interface of Sequence Assemblies =head1 SYNOPSIS diff --git a/Bio/Assembly/Singlet.pm b/Bio/Assembly/Singlet.pm index 01225296b..f369f41f8 100644 --- a/Bio/Assembly/Singlet.pm +++ b/Bio/Assembly/Singlet.pm @@ -136,7 +136,7 @@ sub seqref { Title : _seq_to_singlet Usage : $singlet->seqref($seq) Function: Transform a sequence into a singlet - Returns : 1 for sucess + Returns : 1 for success Args : A Bio::Seq-compliant object =cut diff --git a/Bio/Assembly/Tools/ContigSpectrum.pm b/Bio/Assembly/Tools/ContigSpectrum.pm index 05cdb60ed..7467848c3 100644 --- a/Bio/Assembly/Tools/ContigSpectrum.pm +++ b/Bio/Assembly/Tools/ContigSpectrum.pm @@ -1819,7 +1819,7 @@ sub _update_overlap_stats { Args : Bio::Assembly::Contig object reference Bio::LocatableSeq contig sequence 1 Bio::LocatableSeq contig sequence 2 - minium overlap length [optional] + minimum overlap length [optional] minimum overlap identity percentage[optional] =cut diff --git a/Bio/Cluster/UniGene.pm b/Bio/Cluster/UniGene.pm index 1fedd353a..d4c64e88f 100644 --- a/Bio/Cluster/UniGene.pm +++ b/Bio/Cluster/UniGene.pm @@ -836,7 +836,7 @@ sub annotation{ Usage : Function: Adds a member object to the list of members. Example : - Returns : TRUE if the new member was successfuly added, and FALSE + Returns : TRUE if the new member was successfully added, and FALSE otherwise. Args : The member to add. @@ -1169,7 +1169,7 @@ sub namespace { Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious - user of this interface would not assumme this) and should be + user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) diff --git a/Bio/DB/EMBL.pm b/Bio/DB/EMBL.pm index 3b1fb3f1b..5d5eef56d 100644 --- a/Bio/DB/EMBL.pm +++ b/Bio/DB/EMBL.pm @@ -41,7 +41,7 @@ Bio::DB::EMBL - Database object interface for EMBL entry retrieval # or ... best when downloading very large files, prevents # keeping all of the file in memory - # also don't want features, just sequence so let's save bandwith + # also don't want features, just sequence so let's save bandwidth # and request Fasta sequence $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' , -format => 'fasta'); diff --git a/Bio/DB/Fasta.pm b/Bio/DB/Fasta.pm index 79d0413a3..e150d20dc 100644 --- a/Bio/DB/Fasta.pm +++ b/Bio/DB/Fasta.pm @@ -70,7 +70,7 @@ specific portion of the gi|gb|abc|xyz GenBank IDs. =head1 DATABASE CREATION AND INDEXING The object-oriented constructor is new(), the filehandle constructor is newFh() -and the tied hash constructor is tie(). They all allow to index a single Fasta +and the tied hash constructor is tie(). They all allow one to index a single Fasta file, several files, or a directory of files. See Bio::DB::IndexedBase. =head1 SEE ALSO diff --git a/Bio/DB/GFF.pm b/Bio/DB/GFF.pm index eb3751e99..6f35a1d59 100644 --- a/Bio/DB/GFF.pm +++ b/Bio/DB/GFF.pm @@ -696,7 +696,7 @@ adaptor-specific arguments: -refclass landmark Class; defaults to "Sequence" -The commonly used 'dbi::mysqlopt' adaptor also recogizes the following +The commonly used 'dbi::mysqlopt' adaptor also recognizes the following arguments. Argument Description @@ -2978,7 +2978,7 @@ sub get_features{ Status : abstract This method is used internally. The callback arguments are the same -as those used by make_feature(). This method must be overidden by +as those used by make_feature(). This method must be overridden by subclasses. =cut @@ -3008,7 +3008,7 @@ This method is used internally to fetch features either by their ID or their group ID. $ids is a arrayref containing a list of IDs, $type is one of "feature" or "group", and $callback is a callback. The callback arguments are the same as those used by make_feature(). This -method must be overidden by subclasses. +method must be overridden by subclasses. =cut diff --git a/Bio/DB/GFF/Adaptor/dbi.pm b/Bio/DB/GFF/Adaptor/dbi.pm index f31e9aaed..25ac3b12a 100644 --- a/Bio/DB/GFF/Adaptor/dbi.pm +++ b/Bio/DB/GFF/Adaptor/dbi.pm @@ -2165,7 +2165,7 @@ you want to calculate the coverage density. An object is returned corresponding to the requested region. It contains a tag called "coverage" that will return an array ref of "bins" length. Each element of the array describes the number of features that overlap the -bin at this postion. +bin at this position. Arguments: diff --git a/Bio/DB/GFF/Adaptor/dbi/mysql.pm b/Bio/DB/GFF/Adaptor/dbi/mysql.pm index 0c22ee137..cb43ceedd 100644 --- a/Bio/DB/GFF/Adaptor/dbi/mysql.pm +++ b/Bio/DB/GFF/Adaptor/dbi/mysql.pm @@ -111,7 +111,7 @@ This is the feature data table. Its columns are: fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) - fstop stop postion relative to reference (integer) + fstop stop position relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null diff --git a/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm b/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm index 96ed18711..a977b6d96 100644 --- a/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm +++ b/Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm @@ -112,7 +112,7 @@ This is the feature data table. Its columns are: fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) - fstop stop postion relative to reference (integer) + fstop stop position relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null diff --git a/Bio/DB/GFF/Adaptor/dbi/oracle.pm b/Bio/DB/GFF/Adaptor/dbi/oracle.pm index d9a8c47f8..0423e4da5 100644 --- a/Bio/DB/GFF/Adaptor/dbi/oracle.pm +++ b/Bio/DB/GFF/Adaptor/dbi/oracle.pm @@ -120,7 +120,7 @@ This is the feature data table. Its columns are: fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) - fstop stop postion relative to reference (integer) + fstop stop position relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null diff --git a/Bio/DB/GFF/Adaptor/dbi/pg.pm b/Bio/DB/GFF/Adaptor/dbi/pg.pm index 4dbc72703..d1784409f 100644 --- a/Bio/DB/GFF/Adaptor/dbi/pg.pm +++ b/Bio/DB/GFF/Adaptor/dbi/pg.pm @@ -176,7 +176,7 @@ This is the feature data table. Its columns are: fid feature ID (integer) fref reference sequence name (string) fstart start position relative to reference (integer) - fstop stop postion relative to reference (integer) + fstop stop position relative to reference (integer) ftypeid feature type ID (integer) fscore feature score (float); may be null fstrand strand; one of "+" or "-"; may be null diff --git a/Bio/DB/GFF/Segment.pm b/Bio/DB/GFF/Segment.pm index 364591b2f..9521097bf 100644 --- a/Bio/DB/GFF/Segment.pm +++ b/Bio/DB/GFF/Segment.pm @@ -593,7 +593,7 @@ sub seq_id { shift->refseq } Status : Public This indicates that the sequence was truncated during creation. The -returned flag is undef if no truncation occured. If truncation did +returned flag is undef if no truncation occurred. If truncation did occur, the flag is actually an array ref in which the first element is true if truncation occurred on the left, and the second element occurred if truncation occurred on the right. @@ -677,7 +677,7 @@ sub overlap_extent { Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their - own object ids in a way the implementaiton can control + own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should @@ -742,7 +742,7 @@ sub display_name { shift->seq_id } called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the - unique id for the implemetation, allowing multiple objects + unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return diff --git a/Bio/DB/GenBank.pm b/Bio/DB/GenBank.pm index a19a8fd52..653b529af 100644 --- a/Bio/DB/GenBank.pm +++ b/Bio/DB/GenBank.pm @@ -54,7 +54,7 @@ Bio::DB::GenBank - Database object interface to GenBank # or ... best when downloading very large files, prevents # keeping all of the file in memory - # also don't want features, just sequence so let's save bandwith + # also don't want features, just sequence so let's save bandwidth # and request Fasta sequence $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile' , -format => 'Fasta'); diff --git a/Bio/DB/GenPept.pm b/Bio/DB/GenPept.pm index 9f3e1bce6..dbb70e96d 100644 --- a/Bio/DB/GenPept.pm +++ b/Bio/DB/GenPept.pm @@ -184,7 +184,7 @@ sub default_format { Usage : $seq = $db->get_Seq_by_acc('AAC73346'); Function: Gets a Seq objects by accession number Returns : Bio::Seq object - Args : accession number to retrive by + Args : accession number to retrieve by =head1 Routines implemented by Bio::DB::NCBIHelper diff --git a/Bio/DB/HIV/HIVQueryHelper.pm b/Bio/DB/HIV/HIVQueryHelper.pm index 49c270ace..8e258fbd3 100755 --- a/Bio/DB/HIV/HIVQueryHelper.pm +++ b/Bio/DB/HIV/HIVQueryHelper.pm @@ -2046,7 +2046,7 @@ use Bio::Annotation::SimpleValue; Title : get_value Usage : $ac->get_value($tagname) -or- $ac->get_value( $tag_level1, $tag_level2,... ) - Function: access the annotation value assocated with the given tags + Function: access the annotation value associated with the given tags Example : Returns : a scalar Args : an array of tagnames that descend into the annotation tree diff --git a/Bio/DB/IndexedBase.pm b/Bio/DB/IndexedBase.pm index 2a33c0b04..88aea4a1e 100644 --- a/Bio/DB/IndexedBase.pm +++ b/Bio/DB/IndexedBase.pm @@ -126,7 +126,7 @@ use tied(%db) to recover the Bio::DB::IndexedBase object and call its methods. } In addition, you may invoke the FIRSTKEY and NEXTKEY tied hash methods directly -to retrieve the first and next ID in the database, respectively. This allows to +to retrieve the first and next ID in the database, respectively. This allows one to write the following iterative loop using just the object-oriented interface: my $db = Bio::DB::IndexedBase->new('/path/to/file'); diff --git a/Bio/DB/MeSH.pm b/Bio/DB/MeSH.pm index 1e9bd654d..767633e81 100644 --- a/Bio/DB/MeSH.pm +++ b/Bio/DB/MeSH.pm @@ -184,7 +184,7 @@ sub _set_cgi_base_url { Title : get_exact_term Usage : $s = $db->get_exact_term($value); - Function: Retrive a single MeSH term using a unique ID or exact name. + Function: Retrieve a single MeSH term using a unique ID or exact name. Example : Returns : a Bio::Phenotype::MeSH::Term object Args : scalar, UID or name of a MeSH term @@ -286,7 +286,7 @@ sub _run { sub result { my ($self,$value) = @_; - $self->throw("Could not retrive results") unless $self->status('COMPLETED'); + $self->throw("Could not retrieve results") unless $self->status('COMPLETED'); # no processing return $self->{'_content'} if $value && $value eq 'raw'; diff --git a/Bio/DB/Qual.pm b/Bio/DB/Qual.pm index 675b47074..729d7bc68 100644 --- a/Bio/DB/Qual.pm +++ b/Bio/DB/Qual.pm @@ -66,7 +66,7 @@ specific portion of the gi|gb|abc|xyz GenBank IDs. =head1 DATABASE CREATION AND INDEXING The object-oriented constructor is new(), the filehandle constructor is newFh() -and the tied hash constructor is tie(). They all allow to index a single Fasta +and the tied hash constructor is tie(). They all allow one to index a single Fasta file, several files, or a directory of files. See Bio::DB::IndexedBase. =head1 SEE ALSO diff --git a/Bio/DB/Query/HIVQuery.pm b/Bio/DB/Query/HIVQuery.pm index 64ec06834..8e142095a 100755 --- a/Bio/DB/Query/HIVQuery.pm +++ b/Bio/DB/Query/HIVQuery.pm @@ -590,7 +590,7 @@ sub remove_annotations { Title : get_value Usage : $ac->get_value($tagname) -or- $ac->get_value( $tag_level1, $tag_level2,... ) - Function: access the annotation value assocated with the given tags + Function: access the annotation value associated with the given tags Example : Returns : a scalar Args : an array of tagnames that descend into the annotation tree diff --git a/Bio/DB/RefSeq.pm b/Bio/DB/RefSeq.pm index 2b7ad4cbd..bc0acafc4 100644 --- a/Bio/DB/RefSeq.pm +++ b/Bio/DB/RefSeq.pm @@ -41,7 +41,7 @@ Bio::DB::RefSeq - Database object interface for RefSeq retrieval # or ... best when downloading very large files, prevents # keeping all of the file in memory - # also don't want features, just sequence so let's save bandwith + # also don't want features, just sequence so let's save bandwidth # and request Fasta sequence $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' , -format => 'fasta'); @@ -65,7 +65,7 @@ The functionality of this module is inherited from L which implements L. This module retrieves entries from EBI although it -retrives database entries produced at NCBI. When read into bioperl +retrieves database entries produced at NCBI. When read into bioperl objects, the parser for GenBank format it used. RefSeq is a NONSTANDARD GenBank file so be ready for surprises. diff --git a/Bio/DB/SeqFeature/Store.pm b/Bio/DB/SeqFeature/Store.pm index fcf11ff61..031c0ac66 100644 --- a/Bio/DB/SeqFeature/Store.pm +++ b/Bio/DB/SeqFeature/Store.pm @@ -2620,7 +2620,7 @@ you want to calculate the coverage density. An object is returned corresponding to the requested region. It contains a tag called "coverage" that will return an array ref of "bins" length. Each element of the array describes the number of features that overlap the -bin at this postion. +bin at this position. Arguments: diff --git a/Bio/DB/SeqFeature/Store/GFF2Loader.pm b/Bio/DB/SeqFeature/Store/GFF2Loader.pm index 174f8d0b8..6c9702556 100644 --- a/Bio/DB/SeqFeature/Store/GFF2Loader.pm +++ b/Bio/DB/SeqFeature/Store/GFF2Loader.pm @@ -196,7 +196,7 @@ The following read-only accessors return values passed or created during new(): =head2 Internal Methods -The following methods are used internally and may be overidden by +The following methods are used internally and may be overridden by subclasses. =over 4 diff --git a/Bio/DB/SeqFeature/Store/GFF3Loader.pm b/Bio/DB/SeqFeature/Store/GFF3Loader.pm index ba185064d..c14952859 100644 --- a/Bio/DB/SeqFeature/Store/GFF3Loader.pm +++ b/Bio/DB/SeqFeature/Store/GFF3Loader.pm @@ -263,7 +263,7 @@ The following read-only accessors return values passed or created during new(): =head2 Internal Methods -The following methods are used internally and may be overidden by +The following methods are used internally and may be overridden by subclasses. =over 4 diff --git a/Bio/DB/SeqFeature/Store/Loader.pm b/Bio/DB/SeqFeature/Store/Loader.pm index 33b6a0546..a47cd971b 100644 --- a/Bio/DB/SeqFeature/Store/Loader.pm +++ b/Bio/DB/SeqFeature/Store/Loader.pm @@ -284,7 +284,7 @@ sub verbose { shift->{verbose} } =head2 Internal Methods -The following methods are used internally and may be overidden by +The following methods are used internally and may be overridden by subclasses. =over 4 diff --git a/Bio/DB/TFBS/transfac_pro.pm b/Bio/DB/TFBS/transfac_pro.pm index 1883685e6..3e3658365 100644 --- a/Bio/DB/TFBS/transfac_pro.pm +++ b/Bio/DB/TFBS/transfac_pro.pm @@ -363,7 +363,7 @@ sub get_fragment { Function: Get a matrix that describes a binding site. Returns : Bio::Matrix::PSM::SiteMatrix Args : string - a matrix id ('M...'), optionally a sequence string from - which base frequencies will be calcualted for the matrix model + which base frequencies will be calculated for the matrix model (default 0.25 each) =cut @@ -781,7 +781,7 @@ sub _build_index { my ($self, $dat_dir, $force) = @_; # MLDBM would give us transparent complex data structures with DB_File, - # allowing just one index file, but its yet another requirment and we + # allowing just one index file, but its yet another requirement and we # don't strictly need it my $index_dir = $self->index_directory; @@ -1740,7 +1740,7 @@ sub _db_connect { =head2 index_directory Title : index_directory - Funtion : Get/set the location that index files are stored. (this module + Function : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) @@ -1789,7 +1789,7 @@ sub _species_to_taxid { } } else { - # some species lines are poorly formated so custom handling + # some species lines are poorly formatted so custom handling SWITCH: for ($raw_species) { # for speed, go by common first letters my $first_letter = substr($raw_species, 0, 1); diff --git a/Bio/DB/Taxonomy/flatfile.pm b/Bio/DB/Taxonomy/flatfile.pm index ab2e13a68..677b039f5 100644 --- a/Bio/DB/Taxonomy/flatfile.pm +++ b/Bio/DB/Taxonomy/flatfile.pm @@ -506,7 +506,7 @@ sub _db_connect { =head2 index_directory Title : index_directory - Funtion : Get/set the location that index files are stored. (this module + Function : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) diff --git a/Bio/DB/Taxonomy/sqlite.pm b/Bio/DB/Taxonomy/sqlite.pm index a0e24116e..4bf6ca1ca 100644 --- a/Bio/DB/Taxonomy/sqlite.pm +++ b/Bio/DB/Taxonomy/sqlite.pm @@ -460,7 +460,7 @@ SQL =head2 index_directory Title : index_directory - Funtion : Get/set the location that index files are stored. (this module + Function : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) @@ -478,7 +478,7 @@ sub index_directory { =head2 db_name Title : db_name - Funtion : Get/set the name of the SQLite3 database where data is stored + Function : Get/set the name of the SQLite3 database where data is stored Usage : $obj->db_name($newval) Returns : value of db_name (a scalar) Args : on set, new value (a scalar or undef, optional) @@ -498,7 +498,7 @@ sub db_name { =head2 cache_size Title : cache_size - Funtion : Get/set the cachesize used for loading the SQLite3 database + Function : Get/set the cachesize used for loading the SQLite3 database Usage : $obj->cache_size($newval) Returns : value of cache_size (a scalar) Args : on set, new value (a scalar or undef, optional) diff --git a/Bio/DB/WebDBSeqI.pm b/Bio/DB/WebDBSeqI.pm index e83110fe9..eff5189d0 100644 --- a/Bio/DB/WebDBSeqI.pm +++ b/Bio/DB/WebDBSeqI.pm @@ -26,7 +26,7 @@ for retrieving sequences =head1 DESCRIPTION Provides core set of functionality for connecting to a web based -database for retriving sequences. +database for retrieving sequences. Users wishing to add another Web Based Sequence Dabatase will need to extend this class (see L or L for @@ -344,7 +344,7 @@ sub get_Stream_by_gi { Returns : a Bio::SeqIO stream object Args : $ref : a reference to an array of accession.version strings for the desired sequence entries - Note : For GenBank, this is implemeted in NCBIHelper + Note : For GenBank, this is implemented in NCBIHelper =cut diff --git a/Bio/DescribableI.pm b/Bio/DescribableI.pm index 51911f369..09247cc62 100644 --- a/Bio/DescribableI.pm +++ b/Bio/DescribableI.pm @@ -80,7 +80,7 @@ define. Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious - user of this interface would not assumme this) and should be + user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) Returns : A scalar diff --git a/Bio/Factory/ObjectFactoryI.pm b/Bio/Factory/ObjectFactoryI.pm index 758cae123..e1b5ea329 100644 --- a/Bio/Factory/ObjectFactoryI.pm +++ b/Bio/Factory/ObjectFactoryI.pm @@ -101,7 +101,7 @@ sub create{ Usage : $obj = $factory->create_object(%args) Function: Create a new object. - This is supposed to supercede create(). Right now it only delegates + This is supposed to supersede create(). Right now it only delegates to create(). Returns : a new object Args : hash of initialization parameters diff --git a/Bio/Index/Abstract.pm b/Bio/Index/Abstract.pm index c9e7f0bc8..6ad2ba849 100644 --- a/Bio/Index/Abstract.pm +++ b/Bio/Index/Abstract.pm @@ -181,7 +181,7 @@ sub new { Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which - is wether the dbm file should be opened with + is whether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if diff --git a/Bio/Index/AbstractSeq.pm b/Bio/Index/AbstractSeq.pm index 7dcb93a9a..d1cfd0d7f 100644 --- a/Bio/Index/AbstractSeq.pm +++ b/Bio/Index/AbstractSeq.pm @@ -146,7 +146,7 @@ sub fetch { $seq = $seqio->next_seq(); } - # we essentially assumme that the primary_id for the database + # we essentially assume that the primary_id for the database # is the display_id if (ref($seq) && $seq->isa('Bio::PrimarySeqI') && $seq->primary_id =~ /^\D+$/) { diff --git a/Bio/Index/Blast.pm b/Bio/Index/Blast.pm index 531aefd81..77f1cf234 100644 --- a/Bio/Index/Blast.pm +++ b/Bio/Index/Blast.pm @@ -347,7 +347,7 @@ sub blast_parser_type { Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which - is wether the dbm file should be opened with + is whether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if diff --git a/Bio/Index/BlastTable.pm b/Bio/Index/BlastTable.pm index 8bd6bea8a..a531ccbc7 100644 --- a/Bio/Index/BlastTable.pm +++ b/Bio/Index/BlastTable.pm @@ -297,7 +297,7 @@ sub default_id_parser Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which - is wether the dbm file should be opened with + is whether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if diff --git a/Bio/Index/Hmmer.pm b/Bio/Index/Hmmer.pm index 8ec06cce5..8c48f940e 100644 --- a/Bio/Index/Hmmer.pm +++ b/Bio/Index/Hmmer.pm @@ -314,7 +314,7 @@ sub _index_file { Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which - is wether the dbm file should be opened with + is whether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if diff --git a/Bio/Index/Stockholm.pm b/Bio/Index/Stockholm.pm index 5d2ef2e44..a1fe668ae 100644 --- a/Bio/Index/Stockholm.pm +++ b/Bio/Index/Stockholm.pm @@ -307,7 +307,7 @@ sub default_id_parser { Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which - is wether the dbm file should be opened with + is whether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if diff --git a/Bio/LiveSeq/IO/Loader.pm b/Bio/LiveSeq/IO/Loader.pm index ab2f4f652..417b733ad 100644 --- a/Bio/LiveSeq/IO/Loader.pm +++ b/Bio/LiveSeq/IO/Loader.pm @@ -135,7 +135,7 @@ sub entry2liveseq { integer (optional) "flanking": amount of flanking bases to be kept boolean (optional) "getswissprotinfo": if set to "0" it will avoid trying to fetch information from a crossreference to a SwissProt - entry, avoding the process of creation of AARange objects + entry, avoiding the process of creation of AARange objects It is "1" (on) by default Alternative to a gene_name, a position can be given: an diff --git a/Bio/LiveSeq/IO/README b/Bio/LiveSeq/IO/README index 923811aff..4ca8ef11f 100644 --- a/Bio/LiveSeq/IO/README +++ b/Bio/LiveSeq/IO/README @@ -14,7 +14,7 @@ Bio::LiveSeq::IO::Loader Bio::LiveSeq::IO::BioPerl - is the preferred method which uses Bio::DB::EMBL to retrive + is the preferred method which uses Bio::DB::EMBL to retrieve sequences over the Web by accession number. Bio::LiveSeq::IO::SRS diff --git a/Bio/LiveSeq/Mutation.pm b/Bio/LiveSeq/Mutation.pm index b5b91c4c9..823ae8c5f 100644 --- a/Bio/LiveSeq/Mutation.pm +++ b/Bio/LiveSeq/Mutation.pm @@ -17,7 +17,7 @@ Bio::LiveSeq::Mutation - Mutation event descriptor class =head1 SYNOPSIS - # full descrition of a point mutation + # full description of a point mutation $mutation1a = Bio::LiveSeq::Mutation->new ( -seq => 'A', -seqori => 'T', -pos => 100, diff --git a/Bio/LiveSeq/SeqI.pm b/Bio/LiveSeq/SeqI.pm index 0197f7379..9536a96a4 100644 --- a/Bio/LiveSeq/SeqI.pm +++ b/Bio/LiveSeq/SeqI.pm @@ -248,7 +248,7 @@ sub labelsubseq { length, integer, '' or undef an optional strand (1 or -1) 4th argument if strand argument is not given, it will default to the object - argment. This argument is useful when a call is issued from a child + argument. This argument is useful when a call is issued from a child of a parent object containing the subseq method =cut @@ -386,7 +386,7 @@ sub display_id { Function: Returns the unique biological id for a sequence, commonly called the accession_number. Notice that primary_id() provides the unique id for the - implemetation, allowing multiple objects to have the same accession + implementation, allowing multiple objects to have the same accession number in a particular implementation. For objects with no accession_number this method returns "unknown". diff --git a/Bio/LocatableSeq.pm b/Bio/LocatableSeq.pm index 2d15f9b90..2fff64911 100644 --- a/Bio/LocatableSeq.pm +++ b/Bio/LocatableSeq.pm @@ -655,7 +655,7 @@ sub trunc { sub validate_seq { my ($self, $seqstr, $throw) = @_; $seqstr = '' if not defined $seqstr; - $throw = 0 if not defined $throw ; # 0 for backward compatiblity + $throw = 0 if not defined $throw ; # 0 for backward compatibility if ( (CORE::length $seqstr > 0 ) && ($seqstr !~ /^([$MATCHPATTERN]+)$/) ) { if ($throw) { diff --git a/Bio/Location/Atomic.pm b/Bio/Location/Atomic.pm index 205a317ff..54a107488 100644 --- a/Bio/Location/Atomic.pm +++ b/Bio/Location/Atomic.pm @@ -91,7 +91,7 @@ sub new { # Do # my $location = $f1->location->union($f2->location); # We get an error without the following code which - # explictly loads the Bio::Location::Simple class + # explicitly loads the Bio::Location::Simple class unless( $class->can('start') ) { eval { Bio::Root::Root->_load_module($class) }; if ( $@ ) { @@ -132,7 +132,7 @@ sub new { Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range - Args : optionaly allows the start to be set + Args : optionally allows the start to be set : using $loc->start($start) =cut @@ -149,7 +149,7 @@ sub start { Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range - Args : optionaly allows the end to be set + Args : optionally allows the end to be set : using $loc->end($start) =cut @@ -167,7 +167,7 @@ sub end { Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandidness (-1, 0, +1) - Args : optionaly allows the strand to be set + Args : optionally allows the strand to be set : using $loc->strand($strand) =cut @@ -480,7 +480,7 @@ sub valid_Location { The interface *does not* require implementing classes to accept setting of a different policy. The implementation - provided here does, however, allow to do so. + provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a diff --git a/Bio/Location/Fuzzy.pm b/Bio/Location/Fuzzy.pm index fa8166939..49129ddb1 100644 --- a/Bio/Location/Fuzzy.pm +++ b/Bio/Location/Fuzzy.pm @@ -438,7 +438,7 @@ sub end_pos_type { The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here - does, however, allow to do so. + does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation diff --git a/Bio/Location/FuzzyLocationI.pm b/Bio/Location/FuzzyLocationI.pm index 882279e40..2db6e9f83 100644 --- a/Bio/Location/FuzzyLocationI.pm +++ b/Bio/Location/FuzzyLocationI.pm @@ -182,7 +182,7 @@ Bio::LocationI methods follow The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here - does, however, allow to do so. + does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation diff --git a/Bio/Location/Simple.pm b/Bio/Location/Simple.pm index 18edf609b..c59c6098f 100644 --- a/Bio/Location/Simple.pm +++ b/Bio/Location/Simple.pm @@ -109,7 +109,7 @@ sub new { Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range - Args : optionaly allows the start to be set + Args : optionally allows the start to be set using $loc->start($start) =cut @@ -134,7 +134,7 @@ sub start { Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range - Args : optionaly allows the end to be set + Args : optionally allows the end to be set : using $loc->end($start) Note : If start is set but end is undefined, this now assumes that start is the same as end but throws a warning (i.e. it assumes this is @@ -173,7 +173,7 @@ sub end { Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandedness (-1, 0, +1) - Args : optionaly allows the strand to be set + Args : optionally allows the strand to be set : using $loc->strand($strand) =cut diff --git a/Bio/Location/Split.pm b/Bio/Location/Split.pm index 5ae46e958..dede2c405 100644 --- a/Bio/Location/Split.pm +++ b/Bio/Location/Split.pm @@ -798,7 +798,7 @@ sub seq_id { The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here - does, however, allow to do so. + does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation diff --git a/Bio/Location/SplitLocationI.pm b/Bio/Location/SplitLocationI.pm index 19303923e..41a45bc15 100644 --- a/Bio/Location/SplitLocationI.pm +++ b/Bio/Location/SplitLocationI.pm @@ -223,7 +223,7 @@ Bio::LocationI inherited methods follow The interface *does not* require implementing classes to accept setting of a different policy. The implementation provided here - does, however, allow to do so. + does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a CoordinatePolicyI object. The implementation diff --git a/Bio/LocationI.pm b/Bio/LocationI.pm index 48dedecb2..404e145d9 100644 --- a/Bio/LocationI.pm +++ b/Bio/LocationI.pm @@ -358,7 +358,7 @@ sub is_remote{ The interface *does not* require implementing classes to accept setting of a different policy. The implementation - provided here does, however, allow to do so. + provided here does, however, allow one to do so. Implementors of this interface are expected to initialize every new instance with a diff --git a/Bio/Map/CytoMarker.pm b/Bio/Map/CytoMarker.pm index 7466c3008..814e4e9ca 100644 --- a/Bio/Map/CytoMarker.pm +++ b/Bio/Map/CytoMarker.pm @@ -22,7 +22,7 @@ Bio::Map::CytoMarker - An object representing a marker. =head1 DESCRIPTION -This object handles markers with a positon in a cytogenetic map known. +This object handles markers with a position in a cytogenetic map known. This marker will have a name and a position. =head1 FEEDBACK diff --git a/Bio/Map/CytoPosition.pm b/Bio/Map/CytoPosition.pm index 82a8ab689..845ce5cfe 100644 --- a/Bio/Map/CytoPosition.pm +++ b/Bio/Map/CytoPosition.pm @@ -36,12 +36,12 @@ cytogenetic map. See L for more information. Cytogenetic locations are names of bands visible in stained mitotic eucaryotic chromosomes. The naming follows strict rules which are -consistant at least in higher vertebates, e.g. mammals. The chromosome +consistent at least in higher vertebates, e.g. mammals. The chromosome name preceds the band names. The shorter arm of the chromosome is called 'p' ('petit') and usually drawn pointing up. The lower arm is called 'q' ('queue'). The bands -are named from the region separting these, a centromere (cen), towards +are named from the region separating these, a centromere (cen), towards the tips or telomeric regions (ter) counting from 1 upwards. Depending of the resolution used the bands are identified with one or more digit. The first digit determines the major band and subsequent digits @@ -517,7 +517,7 @@ sub range2value { Title : value Usage : my $pos = $position->value; - Function: Get/Set the value for this postion + Function: Get/Set the value for this position Returns : scalar, value Args : none to get, OR scalar to set diff --git a/Bio/Map/GeneRelative.pm b/Bio/Map/GeneRelative.pm index 00d0859f8..2cab5a9ba 100755 --- a/Bio/Map/GeneRelative.pm +++ b/Bio/Map/GeneRelative.pm @@ -21,7 +21,7 @@ Bio::Map::GeneRelative - Represents being relative to named sub-regions of a use Bio::Map::GeneRelative; - # say that a somthing will have a position relative to the start of the + # say that a something will have a position relative to the start of the # gene on map my $rel = Bio::Map::GeneRelative->new(-gene => 0); @@ -202,7 +202,7 @@ sub absolute_conversion { return $self->SUPER::absolute_conversion($pos); } if (ref($value)) { - # psuedo-recurse + # pseudo-recurse my $rel = $value->relative; $value = $rel->absolute_conversion($value); } diff --git a/Bio/Map/Microsatellite.pm b/Bio/Map/Microsatellite.pm index db5949d78..ea7eaa402 100644 --- a/Bio/Map/Microsatellite.pm +++ b/Bio/Map/Microsatellite.pm @@ -103,7 +103,7 @@ use base qw(Bio::Map::Marker); default 'Unknown microsatellite') -positions => position(s) for this marker in maps[optional], An array reference of tuples (array refs themselves) - Each tuple conatins a Bio::Map::MapI-inherited object and a + Each tuple contains a Bio::Map::MapI-inherited object and a Bio::Map::PositionI-inherited obj, no default) -sequence => the sequence of this microsatellite (optional, scalar, no default) diff --git a/Bio/Map/OrderedPosition.pm b/Bio/Map/OrderedPosition.pm index c59a49b2b..1f54dd1e9 100644 --- a/Bio/Map/OrderedPosition.pm +++ b/Bio/Map/OrderedPosition.pm @@ -176,7 +176,7 @@ sub equals { # admittedly these aren't really the best comparisons in the world # but it is a first pass we'll need to refine the algorithm or not -# provide general comparisions and require these to be implemented +# provide general comparisons and require these to be implemented # by objects closer to the specific type of data =head2 less_than diff --git a/Bio/Map/Physical.pm b/Bio/Map/Physical.pm index d6429ac38..2f5e4bdce 100755 --- a/Bio/Map/Physical.pm +++ b/Bio/Map/Physical.pm @@ -19,7 +19,7 @@ Bio::Map::Physical - A class for handling a Physical Map (such as FPC) use Bio::MapIO; - # accquire a Bio::Map::Physical using Bio::MapIO::fpc + # acquire a Bio::Map::Physical using Bio::MapIO::fpc my $mapio = Bio::MapIO->new(-format => "fpc",-file => "rice.fpc", -readcor => 0); diff --git a/Bio/Map/Position.pm b/Bio/Map/Position.pm index 1a17e9173..575ec5e97 100644 --- a/Bio/Map/Position.pm +++ b/Bio/Map/Position.pm @@ -229,7 +229,7 @@ sub absolute { Title : value Usage : my $pos = $position->value; - Function: Get/Set the value for this postion + Function: Get/Set the value for this position Returns : scalar, value Args : [optional] new value to set diff --git a/Bio/Map/PositionI.pm b/Bio/Map/PositionI.pm index 3ac3018c3..466683bff 100644 --- a/Bio/Map/PositionI.pm +++ b/Bio/Map/PositionI.pm @@ -23,7 +23,7 @@ Bio::Map::PositionI - Abstracts the notion of a position having a value in the c =head1 DESCRIPTION -This object stores one of the postions that a mappable object +This object stores one of the positions that a mappable object (e.g. Marker) may have in a map. Positions can have non-numeric values or other methods to store the locations, diff --git a/Bio/Map/Relative.pm b/Bio/Map/Relative.pm index bbe3dcb2f..bc2463404 100755 --- a/Bio/Map/Relative.pm +++ b/Bio/Map/Relative.pm @@ -183,7 +183,7 @@ sub absolute_conversion { $self->throw("Relative to a Mappable, but this Mappable has no positions on the supplied Position's map") unless $value; } if (ref($value)) { - # psuedo-recurse + # pseudo-recurse my $rel = $value->relative; $value = $rel->absolute_conversion($value); } diff --git a/Bio/Map/TranscriptionFactor.pm b/Bio/Map/TranscriptionFactor.pm index 9769aa022..384108b11 100644 --- a/Bio/Map/TranscriptionFactor.pm +++ b/Bio/Map/TranscriptionFactor.pm @@ -48,7 +48,7 @@ element =head1 DESCRIPTION -A transcription factor modelled as a mappable element. It can have mulitple +A transcription factor modelled as a mappable element. It can have multiple binding sites (positions) near multiple genes (maps). =head1 FEEDBACK diff --git a/Bio/Matrix/PSM/IO.pm b/Bio/Matrix/PSM/IO.pm index 9639ab363..d1b8dc9b0 100644 --- a/Bio/Matrix/PSM/IO.pm +++ b/Bio/Matrix/PSM/IO.pm @@ -147,7 +147,7 @@ sub new { my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'scoring'; - $class->throw("$format format unrecognized or an argument error occured\n.") if (!grep(/$format/,@Bio::Matrix::PSM::IO::PSMFORMATS)); + $class->throw("$format format unrecognized or an argument error occurred\n.") if (!grep(/$format/,@Bio::Matrix::PSM::IO::PSMFORMATS)); $format = "\L$format"; # normalize capitalization to lower case # normalize capitalization diff --git a/Bio/Matrix/PSM/IO/masta.pm b/Bio/Matrix/PSM/IO/masta.pm index 0644c2856..9f418f711 100755 --- a/Bio/Matrix/PSM/IO/masta.pm +++ b/Bio/Matrix/PSM/IO/masta.pm @@ -195,7 +195,7 @@ sub next_psm { if ($line !~ /[^ACGTacgt]/g) { # This is a set of aligned sequences - $self->throw("Mixing between types is not allowed or a parsing error occured\n") + $self->throw("Mixing between types is not allowed or a parsing error occurred\n") if (($self->{_mtype} != 3) && ($mtype)) ; $self->throw("Bad sequence- different length: $line\n") if (($len) && ($len!=length($line))); @@ -209,12 +209,12 @@ sub next_psm { $line=~s/[\s\t]+/\t/g; my @data=split(/[\s\t]+/,$line); if ($#data==3) { - $self->throw("Mixing between types is not allowed or a parsing error occured\n") if (($mtype)&&($self->{_mtype} !=1)) ; + $self->throw("Mixing between types is not allowed or a parsing error occurred\n") if (($mtype)&&($self->{_mtype} !=1)) ; $self->{_mtype}=1; $mtype=1; } else { - $self->throw("Mixing between types is not allowedor a parsing error occured\n") if (($mtype)&&($self->{_mtype} !=2)) ; + $self->throw("Mixing between types is not allowedor a parsing error occurred\n") if (($mtype)&&($self->{_mtype} !=2)) ; $self->{_mtype}=2; $mtype=1; } diff --git a/Bio/Matrix/PSM/InstanceSite.pm b/Bio/Matrix/PSM/InstanceSite.pm index 123cb11ff..9b6318d0a 100644 --- a/Bio/Matrix/PSM/InstanceSite.pm +++ b/Bio/Matrix/PSM/InstanceSite.pm @@ -1,7 +1,7 @@ =head1 NAME -Bio::Matrix::PSM::InstanceSite - A PSM site occurance +Bio::Matrix::PSM::InstanceSite - A PSM site occurrence =head1 SYNOPSIS diff --git a/Bio/Matrix/PSM/ProtMatrix.pm b/Bio/Matrix/PSM/ProtMatrix.pm index 337d76c9b..2bd5eab7f 100644 --- a/Bio/Matrix/PSM/ProtMatrix.pm +++ b/Bio/Matrix/PSM/ProtMatrix.pm @@ -109,7 +109,7 @@ example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. -Summary of the methods I use most frequently (details bellow): +Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number @@ -316,7 +316,7 @@ sub _calculate_consensus { Title : next_pos Usage : - Function : Retrives the next position features: frequencies for all 20 amino + Function : Retrieves the next position features: frequencies for all 20 amino acids, log-odds scores for all 20 amino acids at this position, the main (consensus) letter at this position, the probability for the consensus letter to occur at this position and the relative @@ -720,7 +720,7 @@ sub _uncompress_string { Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one position. - Useful for relational database. Improvment of the previous 0..a coding. + Useful for relational database. Improvement of the previous 0..a coding. Throws : Example : my $strA=$self->get_compressed_freq('A'); Returns : String diff --git a/Bio/Matrix/PSM/ProtPsm.pm b/Bio/Matrix/PSM/ProtPsm.pm index cfadbe703..6c3268f34 100644 --- a/Bio/Matrix/PSM/ProtPsm.pm +++ b/Bio/Matrix/PSM/ProtPsm.pm @@ -53,7 +53,7 @@ mast, meme, transfac, theiresias, etc.? To me the best way is to return SiteMatrix object + arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but -it seems more straightforward. Hilmar does not like this beacause it is an +it seems more straightforward. Hilmar does not like this because it is an exception from the general BioPerl rules. Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other way, unless we want to create diff --git a/Bio/Matrix/PSM/Psm.pm b/Bio/Matrix/PSM/Psm.pm index fe5382369..1a427da4c 100644 --- a/Bio/Matrix/PSM/Psm.pm +++ b/Bio/Matrix/PSM/Psm.pm @@ -41,7 +41,7 @@ Bio::Matrix::PSM::Psm - handle combination of site matricies # where pA through pG are the respective frequencies of the matrix (see also # Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory, # except for -instances (reference to an array of - # Bio::Matrix::PSM::InstanceSite objects) which is documented bellow. + # Bio::Matrix::PSM::InstanceSite objects) which is documented below. =head1 DESCRIPTION @@ -67,7 +67,7 @@ arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but it seems more straightforward. Hilmar does not like -this beacause it is an exception from the general BioPerl rules Should +this because it is an exception from the general BioPerl rules Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other way, unless we want to create even one more diff --git a/Bio/Matrix/PSM/PsmI.pm b/Bio/Matrix/PSM/PsmI.pm index 9ced3f018..b3f64c142 100644 --- a/Bio/Matrix/PSM/PsmI.pm +++ b/Bio/Matrix/PSM/PsmI.pm @@ -41,7 +41,7 @@ Bio::Matrix::PSM::PsmI - abstract interface to handler of site matricies # Bio::Matrix::PSM::SiteMatrix), and everything else is self-explenatory, # except for #-instances (reference to an array of Bio::Matrix::PSM::InstanceSite objects) - # which is documented bellow. + # which is documented below. =head1 DESCRIPTION @@ -66,7 +66,7 @@ way is to return SiteMatrix object + arrray of InstanceSite objects and then mast will return undef for SiteMatrix and transfac will return undef for InstanceSite. Probably I cannot see some other design issues that might arise from such approach, but it seems more -straightforward. Hilmar does not like this beacause it is an +straightforward. Hilmar does not like this because it is an exception from the general BioPerl rules Should I leave this as an option? Also the header rightfully belongs the driver object, and could be retrieved as hashes. I do not think it can be done any other diff --git a/Bio/Matrix/PSM/SiteMatrix.pm b/Bio/Matrix/PSM/SiteMatrix.pm index 4e12b20ac..85b026cd3 100644 --- a/Bio/Matrix/PSM/SiteMatrix.pm +++ b/Bio/Matrix/PSM/SiteMatrix.pm @@ -17,7 +17,7 @@ position scoring matrix (or position weight matrix) and log-odds #or my ($a,$c,$g,$t,$score,$ic,$mid)=('05a011','110550','400001', '100104',0.001,19.2,'CRE1'); - #Where a stands for all (this frequency=1), see explanation bellow + #Where a stands for all (this frequency=1), see explanation below my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t, -lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l, -IC=>$ic,-e_val=>$score, -id=>$mid); @@ -75,7 +75,7 @@ Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. -Summary of the methods I use most frequently (details bellow): +Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number @@ -188,7 +188,7 @@ use base qw(Bio::Root::Root Bio::Matrix::PSM::SiteMatrixI); -sites => int, the number of sites that went into this matrix -model => hash ref, background frequencies for A, C, G and T -correction => number, the number to add to all positions to achieve - psuedo count correction (default 0: no correction) + pseudo count correction (default 0: no correction) NB: do not use correction when your input is frequences! -accession_number => string, an accession number @@ -273,7 +273,7 @@ sub new { $self->throw("Position meaningless-all frequencies are 0"); } - # apply psuedo-count correction to all values - this will result in + # apply pseudo-count correction to all values - this will result in # very bad frequencies if the input is already frequences and a # correction value as large as 1 is used! if ($self->{correction}) { @@ -360,7 +360,7 @@ sub calc_weight { Title : next_pos Usage : - Function: Retrives the next position features: frequencies for A,C,G,T, the + Function: Retrieves the next position features: frequencies for A,C,G,T, the main letter (as in consensus) and the probabilty for this letter to occur at this position and the current position Returns : hash (pA,pC,pG,pT,logA,logC,logG,logT,base,prob,rel) @@ -877,7 +877,7 @@ sub _uncompress_string { Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one - position. Useful for relational database. Improvment of the previous + position. Useful for relational database. Improvement of the previous 0..a coding. Example : my $strA=$self->get_compressed_freq('A'); Returns : String diff --git a/Bio/Matrix/PSM/SiteMatrixI.pm b/Bio/Matrix/PSM/SiteMatrixI.pm index 1bcff3b58..a41365e9e 100644 --- a/Bio/Matrix/PSM/SiteMatrixI.pm +++ b/Bio/Matrix/PSM/SiteMatrixI.pm @@ -30,7 +30,7 @@ Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. -Summary of the methods I use most frequently (details bellow): +Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number @@ -469,7 +469,7 @@ sub _uncompress_string { Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one position. - Useful for relational database. Improvment of the previous 0..a coding. + Useful for relational database. Improvement of the previous 0..a coding. Throws : Example : my $strA=$self->get_compressed_freq('A'); Returns : String diff --git a/Bio/Ontology/OntologyStore.pm b/Bio/Ontology/OntologyStore.pm index af9676578..4ebd5240e 100644 --- a/Bio/Ontology/OntologyStore.pm +++ b/Bio/Ontology/OntologyStore.pm @@ -28,7 +28,7 @@ Bio::Ontology::OntologyStore - A repository of ontologies my $cell_ontology = $io->next_ontology; #this is a singleton that caches the fact that you've created - #a 'Cell Ontology' intance... + #a 'Cell Ontology' instance... my $store = Bio::Ontology::OntologyStore->get_instance(); #...and it can hand you back a copy of it at any time. diff --git a/Bio/Ontology/SimpleOntologyEngine.pm b/Bio/Ontology/SimpleOntologyEngine.pm index 7abf54ee9..c4ba99ccf 100644 --- a/Bio/Ontology/SimpleOntologyEngine.pm +++ b/Bio/Ontology/SimpleOntologyEngine.pm @@ -535,7 +535,7 @@ sub get_all_relationships { Title : get_predicate_terms Usage : get_predicate_terms(): TermI - Function: Retrives all relationship types stored in the engine + Function: Retrieves all relationship types stored in the engine Example : Returns : reference to an array of Bio::Ontology::RelationshipType objects Args : diff --git a/Bio/Ontology/Term.pm b/Bio/Ontology/Term.pm index dfd106067..21f5136da 100644 --- a/Bio/Ontology/Term.pm +++ b/Bio/Ontology/Term.pm @@ -164,7 +164,7 @@ sub new { defined($is_obsolete) && $self->is_obsolete( $is_obsolete ); defined($comment) && $self->comment( $comment ); defined($dbxrefs) && $self->add_dbxref(-dbxrefs => $dbxrefs); - # deprecated methods, allow to pass on to get the dep. notification + # deprecated methods, allow one to pass on to get the dep. notification ref($dblinks) && $self->add_dblink(@$dblinks); ref($references) && $self->add_reference(@$references); @@ -938,7 +938,7 @@ sub description { =head1 Deprecated methods -Used for looking up the methods that supercedes them. +Used for looking up the methods that supersedes them. =cut diff --git a/Bio/Ontology/TermI.pm b/Bio/Ontology/TermI.pm index bf900129d..cc5338a07 100644 --- a/Bio/Ontology/TermI.pm +++ b/Bio/Ontology/TermI.pm @@ -340,7 +340,7 @@ sub get_secondary_ids { =head1 Deprecated methods -Used for looking up the methods that supercedes them. +Used for looking up the methods that supersedes them. =cut diff --git a/Bio/OntologyIO/Handlers/BaseSAXHandler.pm b/Bio/OntologyIO/Handlers/BaseSAXHandler.pm index 654a23e0c..dffd9d806 100644 --- a/Bio/OntologyIO/Handlers/BaseSAXHandler.pm +++ b/Bio/OntologyIO/Handlers/BaseSAXHandler.pm @@ -106,7 +106,7 @@ Juguang Xiao, juguang@tll.org.sg =head2 APPENDIX The rest of the documentation details each of the object methods. -Interal methods are usually preceded with a _ +Internal methods are usually preceded with a _ =cut diff --git a/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm b/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm index 0f74fdb41..8908ba878 100644 --- a/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm +++ b/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm @@ -58,7 +58,7 @@ Hilmar Lapp, hlapp at gmx.net =head2 APPENDIX The rest of the documentation details each of the object methods. -Interal methods are usually preceded with a _ +Internal methods are usually preceded with a _ =cut @@ -323,7 +323,7 @@ sub _persist_relationship { relationship types. Example : - Returns : the ontology as a peristent object with primary key + Returns : the ontology as a persistent object with primary key Args : the ontology to persist as a Bio::Ontology::OntologyI compliant object diff --git a/Bio/OntologyIO/obo.pm b/Bio/OntologyIO/obo.pm index 7c7e54910..6f4428555 100644 --- a/Bio/OntologyIO/obo.pm +++ b/Bio/OntologyIO/obo.pm @@ -465,7 +465,7 @@ sub _ont_engine { $self->{"_ont_engine"}; } -# Removes the escape chracters from the file +# Removes the escape characters from the file sub _filter_line { my ( $self, $line ) = @_; diff --git a/Bio/Perl.pm b/Bio/Perl.pm index e619dc483..c6826b0d5 100644 --- a/Bio/Perl.pm +++ b/Bio/Perl.pm @@ -58,7 +58,7 @@ Bio::Perl - Functional access to BioPerl for people who don't know objects $seq_object = get_sequence('genbank',"AI129902"); - # BLAST a sequence (assummes an internet connection) + # BLAST a sequence (assumes an internet connection) $blast_report = blast_sequence($seq_object); diff --git a/Bio/PhyloNetwork/muVector.pm b/Bio/PhyloNetwork/muVector.pm index d9eb4f8db..c5a39f897 100644 --- a/Bio/PhyloNetwork/muVector.pm +++ b/Bio/PhyloNetwork/muVector.pm @@ -168,7 +168,7 @@ This function is also overloaded to the - operator. =cut -sub substract { +sub subtract { my ($v1,$v2)=@_; $v1->throw("Vectors not the same size") unless ($v1->{dim} == $v2->{dim}); diff --git a/Bio/PopGen/HtSNP.pm b/Bio/PopGen/HtSNP.pm index 17241c15b..11da813c3 100644 --- a/Bio/PopGen/HtSNP.pm +++ b/Bio/PopGen/HtSNP.pm @@ -1133,7 +1133,7 @@ sub _remove_deg { Title : _rem_silent_snp Usage : _rem_silent_snp() - Function: there is the remote possibilty that one SNP won't be a + Function: there is the remote possibility that one SNP won't be a real SNP on this situation we have to remove this SNP, otherwise the program won't find any tag Returns : nonthing @@ -1174,7 +1174,7 @@ sub _rem_silent_snp { Usage : Function: list of snps that are not SNPs. All values for that SNPs on the set is the same one. Look stupid but can - happend and if this happend you will not find any tag + happened and if this happend you will not find any tag Returns : nothing Args : Status : @@ -1442,7 +1442,7 @@ sub compare_arrays { Title : _convert_to_numbers Usage : _convert_to_numbers() - Function: tranform the haplotype into numbers. before to do that + Function: transform the haplotype into numbers. before to do that we have to consider the variation on the set. Returns : nonthing Args : ref to an AoA and a ref to an array diff --git a/Bio/PopGen/Individual.pm b/Bio/PopGen/Individual.pm index 66c55321d..17632a431 100644 --- a/Bio/PopGen/Individual.pm +++ b/Bio/PopGen/Individual.pm @@ -113,7 +113,7 @@ sub new { if( ref($genotypes) =~ /array/i ) { $self->add_Genotype(@$genotypes); } else { - $self->warn("Must provide a valid array reference to set the genotypes value in the contructor"); + $self->warn("Must provide a valid array reference to set the genotypes value in the constructor"); } } return $self; diff --git a/Bio/PopGen/Population.pm b/Bio/PopGen/Population.pm index 9149802e6..b14989b75 100644 --- a/Bio/PopGen/Population.pm +++ b/Bio/PopGen/Population.pm @@ -244,7 +244,7 @@ sub set_Allele_Frequency { FREQUENCY FREQUENCIES )], @args); - if( defined $frequencies ) { # this supercedes the res + if( defined $frequencies ) { # this supersedes the res if( ref($frequencies) =~ /HASH/i ) { my ($markername,$alleles); while( ($markername,$alleles) = each %$frequencies ) { @@ -488,7 +488,7 @@ sub get_number_individuals{ Function: Fixes the number of individuals, call this with 0 to unset. Only use this if you know what you are doing, - this is only relavent when you are just adding + this is only relevant when you are just adding allele frequency data for a population and want to calculate something like theta Returns : none diff --git a/Bio/PopGen/TagHaplotype.pm b/Bio/PopGen/TagHaplotype.pm index 7d37c5d3f..e8f036e82 100644 --- a/Bio/PopGen/TagHaplotype.pm +++ b/Bio/PopGen/TagHaplotype.pm @@ -173,7 +173,7 @@ sub haplotype_block{ Title : input_block Usage : $obj->input_block() Function: returns haplotype block. By now will produce the same output than - $self->haplotype_block. but for compatiblity, this method is kept. + $self->haplotype_block. but for compatibility, this method is kept. This method is deprecated. Returns : reference to array of array with the haplotype input value Args : none @@ -367,7 +367,7 @@ sub _generateCombinations{ Usage : internal Function: take the haplotype and a list of possible combination for that length. Generate a subset and scan it to find if - the information is enought to define the haplotype set. + the information is enough to define the haplotype set. Returns : Args : none Status : private diff --git a/Bio/PrimarySeq.pm b/Bio/PrimarySeq.pm index adffedeef..3ac172cdf 100644 --- a/Bio/PrimarySeq.pm +++ b/Bio/PrimarySeq.pm @@ -546,7 +546,7 @@ sub display_id { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the - unique id for the implemetation, allowing multiple objects + unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should @@ -579,7 +579,7 @@ sub accession_number { Usage : $unique_key = $seqobj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their - own object ids in a way the implementaiton can control + own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no natural primary id, this method @@ -801,7 +801,7 @@ This comprises of display_name and description. Usage : $string = $seqobj->display_name(); Function: Get or set a string which is what should be displayed to the user. The string should have no spaces (ideally, though a cautious - user of this interface would not assumme this) and should be + user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea). @@ -852,8 +852,8 @@ actually implemented on Bio::PrimarySeqI sequences this throws an exception of "Sequence is a protein. Cannot revcom". - The id is the same id as the orginal sequence, and the - accession number is also indentical. If someone wants to + The id is the same id as the original sequence, and the + accession number is also identical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions. diff --git a/Bio/PrimarySeqI.pm b/Bio/PrimarySeqI.pm index d6991343a..8e58370a7 100644 --- a/Bio/PrimarySeqI.pm +++ b/Bio/PrimarySeqI.pm @@ -53,7 +53,7 @@ Bio::PrimarySeqI - Interface definition for a Bio::PrimarySeq This object defines an abstract interface to basic sequence information - for most users of the package the documentation (and methods) in this class are not useful - this is a developers-only -class which defines what methods have to be implmented by other Perl +class which defines what methods have to be implemented by other Perl objects to comply to the Bio::PrimarySeqI interface. Go "perldoc Bio::Seq" or "man Bio::Seq" for more information on the main class for sequences. @@ -213,7 +213,7 @@ sub display_id { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the - unique id for the implemetation, allowing multiple objects + unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return @@ -236,7 +236,7 @@ sub accession_number { Usage : $unique_implementation_key = $obj->primary_id; Function: Returns the unique id for this object in this implementation. This allows implementations to manage their - own object ids in a way the implementaiton can control + own object ids in a way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should @@ -347,7 +347,7 @@ are encouraged to override these methods protein. Cannot revcom". The id is the same id as the original sequence, and the - accession number is also indentical. If someone wants to + accession number is also identical. If someone wants to track that this sequence has be reversed, it needs to define its own extensions. diff --git a/Bio/PullParserI.pm b/Bio/PullParserI.pm index a22d251d9..08f3121a5 100644 --- a/Bio/PullParserI.pm +++ b/Bio/PullParserI.pm @@ -47,7 +47,7 @@ would need to cache some data or otherwise behave differently during a sequential read. The main method in the system is get_field(). This method relies on the -existance of a private hash reference accessible to it with the method +existence of a private hash reference accessible to it with the method _fields(). That hash ref should have as keys all the sorts of data you will want to parse (eg. 'score'), and prior to parsing the values would be undefined. A user of your module can then call either $module-Eget_field('score') or diff --git a/Bio/Restriction/Analysis.pm b/Bio/Restriction/Analysis.pm index 436b2b56a..1423f7271 100644 --- a/Bio/Restriction/Analysis.pm +++ b/Bio/Restriction/Analysis.pm @@ -383,7 +383,7 @@ sub cut { return $self; } -=head2 mulitple_digest +=head2 multiple_digest Title : multiple_digest Function : perform a multiple digest on a sequence diff --git a/Bio/Restriction/Enzyme.pm b/Bio/Restriction/Enzyme.pm index 7a18baf3b..c72bfa227 100644 --- a/Bio/Restriction/Enzyme.pm +++ b/Bio/Restriction/Enzyme.pm @@ -646,7 +646,7 @@ sub revcom_site { Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition -site. The forwad cut in the coordinates used here in Acc36I +site. The forward cut in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. Note that REBASE uses notation where cuts within symmetic sites are diff --git a/Bio/Restriction/EnzymeI.pm b/Bio/Restriction/EnzymeI.pm index b1eb36fa8..1136d6ec2 100644 --- a/Bio/Restriction/EnzymeI.pm +++ b/Bio/Restriction/EnzymeI.pm @@ -173,7 +173,7 @@ sub cuts_after { shift->throw_not_implemented; } Note that the common notation ACCTGC(4/8) means that the forward strand cut is four nucleotides after the END of the recognition -site. The forwad cut in the coordinates used here in Acc36I +site. The forward cut in the coordinates used here in Acc36I ACCTGC(4/8) is at 6+4 i.e. 10. Note that REBASE uses notation where cuts within symmetic sites are diff --git a/Bio/Restriction/IO/base.pm b/Bio/Restriction/IO/base.pm index 5942deb73..ea3fbc730 100644 --- a/Bio/Restriction/IO/base.pm +++ b/Bio/Restriction/IO/base.pm @@ -267,8 +267,8 @@ sub _cuts_from_site { Title : _meth Usage : ($pos, $meth) = $self->_meth('2(5)'); - Function: Separates methylation postion and coce from a string. - Adjusts the postion depending on enzyme site length + Function: Separates methylation position and coce from a string. + Adjusts the position depending on enzyme site length and symmetry Returns : array of position and methylation code Args : 1. reference to Enzyme object @@ -402,7 +402,7 @@ sub _make_multisites { The examples we have of multiply cutting enzymes cut only four times. This protected method deals only with a string of two -integers separated with a slash, e.g. '12/7'. The numbers represent the postions +integers separated with a slash, e.g. '12/7'. The numbers represent the positions BEFORE the start of the recognition site, i.e. negative positions. =cut diff --git a/Bio/Restriction/IO/itype2.pm b/Bio/Restriction/IO/itype2.pm index cb018eb08..748ecf1ef 100644 --- a/Bio/Restriction/IO/itype2.pm +++ b/Bio/Restriction/IO/itype2.pm @@ -116,7 +116,7 @@ sub read { chomp $line; my ($name, $prototype, $site, $meth, $vendor, $refs) = split /\t/, $line; - # we need mininum name and site + # we need minimum name and site unless ($site) { $self->warn("Can not parse line with name [$name]") if $self->verbose > 0; next; diff --git a/Bio/Root/Exception.pm b/Bio/Root/Exception.pm index f2458b1a8..75aa0ef07 100644 --- a/Bio/Root/Exception.pm +++ b/Bio/Root/Exception.pm @@ -119,7 +119,7 @@ Error.pm is not available. =head2 Throwing exceptions within Bioperl modules -Error.pm is not part of the Bioperl distibution, and may not be +Error.pm is not part of the Bioperl distribution, and may not be present within any given perl installation. So, when you want to throw an exception in a Bioperl module, the safe way to throw it is to use L which can use Error.pm diff --git a/Bio/Root/Root.pm b/Bio/Root/Root.pm index f8c9f2dc5..ce1a10063 100644 --- a/Bio/Root/Root.pm +++ b/Bio/Root/Root.pm @@ -64,7 +64,7 @@ if it has also been installed. If L has been installed, L() will use it. This causes an Error.pm-derived object to be thrown. This can be caught within a -C block, from wich you can extract useful bits of +C block, from which you can extract useful bits of information. If L is not installed, it will use the L-based exception throwing facilty. diff --git a/Bio/Root/Storable.pm b/Bio/Root/Storable.pm index bf11df8fe..6dbc3d635 100644 --- a/Bio/Root/Storable.pm +++ b/Bio/Root/Storable.pm @@ -26,7 +26,7 @@ should be called during object instantiation. Object storage is recursive; If the object being stored contains other storable objects, these will be stored separately, and replaced by a -skeleton object in the parent heirarchy. When the parent is later +skeleton object in the parent hierarchy. When the parent is later retrieved, its children remain in the skeleton state until explicitly retrieved by the parent. This lazy-retrieve approach has obvious memory efficiency benefits for certain applications. @@ -106,7 +106,7 @@ sub _initialise_storable { Arg [1] : string (optional) Function : Accessor for the file to write state into. - Should not normaly use as a setter - let Root::IO + Should not normally use as a setter - let Root::IO do this for you. Returntype: string Exceptions: diff --git a/Bio/Root/Test.pm b/Bio/Root/Test.pm index 9c00068d9..62ee3c884 100644 --- a/Bio/Root/Test.pm +++ b/Bio/Root/Test.pm @@ -189,7 +189,7 @@ our @TEMP_FILES; be skipped if either network tests haven't been enabled in Build.PL or an email hasn't been entered) - -excludes_os => str (default none, if OS suppied, all tests + -excludes_os => str (default none, if OS supplied, all tests will skip if running on that OS (eg. 'mswin')) -framework => str (default 'Test::Most', the Test module @@ -257,7 +257,7 @@ sub test_begin { presence of a binary, skips if absent) -requires_env => str (checks %ENV for a specific env. variable, skips if absent) - -excludes_os => str (default none, if OS suppied, desired num + -excludes_os => str (default none, if OS supplied, desired num of tests will skip if running on that OS (eg. 'mswin')) -requires_networking => 1 (if true the desired number of tests will @@ -484,7 +484,7 @@ sub _skip { "unknown argument '$key' supplied, did you mistake 'required...' for 'requires...'?\n"; } - # test user requirments and return + # test user requirements and return if ($os) { if ( $^O =~ /$os/i ) { return ( 'Not compatible with your Operating System', diff --git a/Bio/Root/Utilities.pm b/Bio/Root/Utilities.pm index cf7eb6cce..86bd72002 100644 --- a/Bio/Root/Utilities.pm +++ b/Bio/Root/Utilities.pm @@ -125,7 +125,7 @@ $Util = Bio::Root::Root->new(); Title : date_format Usage : $Util->date_format( [FMT], [DATE]) - Purpose : -- Get a string containing the formated date or time + Purpose : -- Get a string containing the formatted date or time : taken when this routine is invoked. : -- Provides a way to avoid using `date`. : -- Provides an interface to localtime(). @@ -331,7 +331,7 @@ sub num2month { : gzip, which is the default) : -OUTFILE => String (name of the output compressed file, full path). : -EXE => Name of executable for compression utility to use. - : Will supercede those in @COMPRESSION_UTILS defined by + : Will supersede those in @COMPRESSION_UTILS defined by : this module. If the absolute path to the executable is not provided, : it will be searched in the PATH env variable. Throws : Exception if file cannot be compressed. @@ -455,7 +455,7 @@ sub compress { : gzip, which is the default) : -OUTFILE => String (name of the output uncompressed file, full path). : -EXE => Name of executable for uncompression utility to use. - : Will supercede those in @UNCOMPRESSION_UTILS defined by + : Will supersede those in @UNCOMPRESSION_UTILS defined by : this module. If the absolute path to the executable is not provided, : it will be searched in the PATH env variable. Throws : Exception if file cannot be uncompressed. @@ -882,7 +882,7 @@ sub create_filehandle { : -FILE =>'usr/people/me/data.txt') Argument : Same arguemnts as for create_filehandle(). Returns : Reference to a FileHandle object. - Throws : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline(). + Throws : Propagates any exceptions thrown by Bio::Root::Utilities::get_newline(). See Also : L, L @@ -1039,7 +1039,7 @@ sub taste_file { : mac (\r or 015 or ^M) : unknown Throws : Exception if argument is not a file - : Propogates any exceptions thrown by Bio::Root::Utilities::get_newline(). + : Propagates any exceptions thrown by Bio::Root::Utilities::get_newline(). See Also : L, L diff --git a/Bio/Search/BlastUtils.pm b/Bio/Search/BlastUtils.pm index 6f756a0bc..6ae384cf8 100644 --- a/Bio/Search/BlastUtils.pm +++ b/Bio/Search/BlastUtils.pm @@ -486,7 +486,7 @@ sub collapse_nums { : be a standard, the structure of the HTML-formatted version : is even less so. Therefore, the use of this method to : reconstitute parsable Blast reports from HTML-format versions - : should be considered a temorary solution. + : should be considered a temporary solution. =cut diff --git a/Bio/Search/HSP/BlastPullHSP.pm b/Bio/Search/HSP/BlastPullHSP.pm index 4f2e5c748..9eac7019e 100644 --- a/Bio/Search/HSP/BlastPullHSP.pm +++ b/Bio/Search/HSP/BlastPullHSP.pm @@ -396,7 +396,7 @@ sub gaps { Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) - 'list' or 'array' to retreive both query and hit together + 'list' or 'array' to retrieve both query and hit together =cut diff --git a/Bio/Search/HSP/GenericHSP.pm b/Bio/Search/HSP/GenericHSP.pm index 23d102050..2989b0b9f 100644 --- a/Bio/Search/HSP/GenericHSP.pm +++ b/Bio/Search/HSP/GenericHSP.pm @@ -137,7 +137,7 @@ use base qw(Bio::Search::HSP::HSPI); -identical => # of residues that that matched identically -percent_identity => (optional) percent identity -conserved => # of residues that matched conservatively - (only protein comparisions; + (only protein comparisons; conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment diff --git a/Bio/Search/HSP/HMMERHSP.pm b/Bio/Search/HSP/HMMERHSP.pm index 70b2ef0e9..9eead3472 100644 --- a/Bio/Search/HSP/HMMERHSP.pm +++ b/Bio/Search/HSP/HMMERHSP.pm @@ -91,7 +91,7 @@ Plus Bio::Search::HSP::GenericHSP methods -hsp_length => Length of the HSP (including gaps) -identical => # of residues that that matched identically -conserved => # of residues that matched conservatively - (only protein comparisions - + (only protein comparisons - conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment diff --git a/Bio/Search/HSP/HSPI.pm b/Bio/Search/HSP/HSPI.pm index 171db0d58..a28b0c991 100644 --- a/Bio/Search/HSP/HSPI.pm +++ b/Bio/Search/HSP/HSPI.pm @@ -454,7 +454,7 @@ These methods come from L Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) - 'list' or 'array' to retreive both query and hit together + 'list' or 'array' to retrieve both query and hit together =cut diff --git a/Bio/Search/HSP/ModelHSP.pm b/Bio/Search/HSP/ModelHSP.pm index 0ea008447..c83905bb3 100644 --- a/Bio/Search/HSP/ModelHSP.pm +++ b/Bio/Search/HSP/ModelHSP.pm @@ -97,7 +97,7 @@ Plus Bio::Seach::HSP::ModelHSP methods -hsp_length=> Length of the HSP (including gaps) -identical => # of residues that that matched identically -conserved => # of residues that matched conservatively - (only protein comparisions; + (only protein comparisons; conserved == identical in nucleotide comparisons) -hsp_gaps => # of gaps in the HSP -query_gaps => # of gaps in the query in the alignment diff --git a/Bio/Search/HSP/PullHSPI.pm b/Bio/Search/HSP/PullHSPI.pm index 363a5d0ed..7a3ee0aea 100755 --- a/Bio/Search/HSP/PullHSPI.pm +++ b/Bio/Search/HSP/PullHSPI.pm @@ -651,7 +651,7 @@ sub bits { Returns : +1 or -1 (0 if unknown) Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject 'query' to retrieve the query strand (default) - 'list' or 'array' to retreive both query and hit together + 'list' or 'array' to retrieve both query and hit together =cut diff --git a/Bio/Search/Hit/GenericHit.pm b/Bio/Search/Hit/GenericHit.pm index bc2308873..cc6e42fee 100644 --- a/Bio/Search/Hit/GenericHit.pm +++ b/Bio/Search/Hit/GenericHit.pm @@ -281,7 +281,7 @@ sub accession { Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string - Args : [optional] scalar string to set the descrition + Args : [optional] scalar string to set the description =cut diff --git a/Bio/Search/Hit/HMMERHit.pm b/Bio/Search/Hit/HMMERHit.pm index b04776e03..d16e4a784 100644 --- a/Bio/Search/Hit/HMMERHit.pm +++ b/Bio/Search/Hit/HMMERHit.pm @@ -173,7 +173,7 @@ sub domains{ shift->hsps() } Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string - Args : [optional] scalar string to set the descrition + Args : [optional] scalar string to set the description =cut diff --git a/Bio/Search/Hit/ModelHit.pm b/Bio/Search/Hit/ModelHit.pm index a1f3233b0..e6b8c21cf 100644 --- a/Bio/Search/Hit/ModelHit.pm +++ b/Bio/Search/Hit/ModelHit.pm @@ -171,7 +171,7 @@ Implementation of Bio::Search::Hit::HitI methods Usage : $desc = $hit->description(); Function: Retrieve the description for the hit Returns : a scalar string - Args : [optional] scalar string to set the descrition + Args : [optional] scalar string to set the description =cut diff --git a/Bio/Search/Iteration/IterationI.pm b/Bio/Search/Iteration/IterationI.pm index c6fe71b57..59fbc54a4 100644 --- a/Bio/Search/Iteration/IterationI.pm +++ b/Bio/Search/Iteration/IterationI.pm @@ -154,7 +154,7 @@ are still not below threshold in the current iteration. =item * oldhits() [subset C] -All hits that occured in a previous iteration, whether below or above +All hits that occurred in a previous iteration, whether below or above threshold in the current iteration. Union of oldhits_below_threshold() + oldhits_newly_below_threshold() + oldhits_not_below_threshold() [subset H + subset I + subset G]. (Not applicable to the first diff --git a/Bio/Search/SearchUtils.pm b/Bio/Search/SearchUtils.pm index 57d44a98f..dee7351c3 100644 --- a/Bio/Search/SearchUtils.pm +++ b/Bio/Search/SearchUtils.pm @@ -703,7 +703,7 @@ sub collapse_nums { : be a standard, the structure of the HTML-formatted version : is even less so. Therefore, the use of this method to : reconstitute parsable Blast reports from HTML-format versions - : should be considered a temorary solution. + : should be considered a temporary solution. =cut diff --git a/Bio/Search/Tiling/TilingI.pm b/Bio/Search/Tiling/TilingI.pm index 092a4b1de..6ef9c3c64 100755 --- a/Bio/Search/Tiling/TilingI.pm +++ b/Bio/Search/Tiling/TilingI.pm @@ -19,7 +19,7 @@ Bio::Search::Tiling::TilingI - Abstract interface for an HSP tiling module Not used directly. Useful POD here for developers, however. -The interface is desgined to make the following code conversion as +The interface is designed to make the following code conversion as simple as possible: From: diff --git a/Bio/SearchDist.pm b/Bio/SearchDist.pm index fde16311b..1cc8ca9b0 100644 --- a/Bio/SearchDist.pm +++ b/Bio/SearchDist.pm @@ -48,7 +48,7 @@ The fitting procedure is better described in Sean Eddy's own code file in Compile/SW). Bascially it fits a EVD via a maximum likelhood method with pruning of the top end of the distribution so that real positives are discarded in the fitting procedure. This comes from -an orginally idea of Richard Mott's and the likelhood fitting +an originally idea of Richard Mott's and the likelhood fitting is from a book by Lawless [should ref here]. diff --git a/Bio/SearchIO/Writer/HTMLResultWriter.pm b/Bio/SearchIO/Writer/HTMLResultWriter.pm index 488f80466..c992a2b2e 100644 --- a/Bio/SearchIO/Writer/HTMLResultWriter.pm +++ b/Bio/SearchIO/Writer/HTMLResultWriter.pm @@ -438,7 +438,7 @@ sub to_string { if( defined $v->{'start'} ) { $start = $v->{'start'}; # since strand can be + or - use the direction - # to signify which whether to add or substract from end + # to signify which whether to add or subtract from end my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )* $baselens{$v->{'name'}}; if( length($piece) < $AlignmentLineWidth ) { diff --git a/Bio/SearchIO/Writer/TextResultWriter.pm b/Bio/SearchIO/Writer/TextResultWriter.pm index d6c1b9d42..411d638aa 100644 --- a/Bio/SearchIO/Writer/TextResultWriter.pm +++ b/Bio/SearchIO/Writer/TextResultWriter.pm @@ -416,7 +416,7 @@ Sequences producing significant alignments: (bits) value if( defined $v->{'start'} ) { $start = $v->{'start'}; # since strand can be + or - use the direction - # to signify which whether to add or substract from end + # to signify which whether to add or subtract from end my $d = $v->{'direction'} * ( $AlignmentLineWidth - $plen )* $baselens{$v->{'name'}}; if( length($piece) < $AlignmentLineWidth ) { diff --git a/Bio/SearchIO/exonerate.pm b/Bio/SearchIO/exonerate.pm index 9d96dffe1..c20796764 100644 --- a/Bio/SearchIO/exonerate.pm +++ b/Bio/SearchIO/exonerate.pm @@ -164,7 +164,7 @@ $MIN_INTRON=30; # This is the minimum intron size Usage : my $obj = Bio::SearchIO::exonerate->new(); Function: Builds a new Bio::SearchIO::exonerate object Returns : an instance of Bio::SearchIO::exonerate - Args : -min_intron => somewhat obselete option, how to determine if a + Args : -min_intron => somewhat obsolete option, how to determine if a an indel is an intron or a local gap. Use VULGAR rather than CIGAR to avoid this heuristic,default 30. -cigar => 1 set this to 1 if you want to parse diff --git a/Bio/SearchIO/hmmer3.pm b/Bio/SearchIO/hmmer3.pm index 35498177b..0ff6b2c12 100644 --- a/Bio/SearchIO/hmmer3.pm +++ b/Bio/SearchIO/hmmer3.pm @@ -1244,7 +1244,7 @@ sub end_document { Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results processed - Returns : interger + Returns : integer Args : none =cut diff --git a/Bio/Seq.pm b/Bio/Seq.pm index 0b020e0c9..348f6c651 100644 --- a/Bio/Seq.pm +++ b/Bio/Seq.pm @@ -69,7 +69,7 @@ Bio::Seq - Sequence object, with features # you can get truncations, translations and reverse complements, these # all give back Bio::Seq objects themselves, though currently with no - # features transfered + # features transferred my $trunc = $seqobj->trunc(100,200); my $rev = $seqobj->revcom(); @@ -669,7 +669,7 @@ sub display_id { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the - unique id for the implemetation, allowing multiple objects + unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return @@ -889,7 +889,7 @@ sub namespace{ Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious - user of this interface would not assumme this) and should be + user of this interface would not assume this) and should be less than thirty characters (though again, double checking this is a good idea) diff --git a/Bio/Seq/EncodedSeq.pm b/Bio/Seq/EncodedSeq.pm index cad3bd8fe..bf9f092d9 100644 --- a/Bio/Seq/EncodedSeq.pm +++ b/Bio/Seq/EncodedSeq.pm @@ -175,7 +175,7 @@ use base qw(Bio::LocatableSeq); gap ('G') or backward frameshift ('B') should have one or more gap characters; if the encoding specifies G or B, but no (or not enough) gap - characters exist, *they'll be added*; similary, + characters exist, *they'll be added*; similarly, if there are gap characters without a corresponding G or B encoding, G's will be inserted into the encoding. This allows some diff --git a/Bio/Seq/Meta/Array.pm b/Bio/Seq/Meta/Array.pm index 9f1c03588..9a65f7042 100644 --- a/Bio/Seq/Meta/Array.pm +++ b/Bio/Seq/Meta/Array.pm @@ -343,7 +343,7 @@ sub named_meta_text { should extend to the end of the sequence. The return value may be a string or an array reference, - depending on the implentation. If in doubt, use + depending on the implementation. If in doubt, use submeta_text() which is a variant guarantied to return a string. See L. @@ -469,7 +469,7 @@ sub named_submeta_text { Title : meta_names Usage : @meta_names = $obj->meta_names() - Function: Retrives an array of meta data set names. The default + Function: Retrieves an array of meta data set names. The default (unnamed) set name is guarantied to be the first name if it contains any data. Returns : an array of names diff --git a/Bio/Seq/MetaI.pm b/Bio/Seq/MetaI.pm index 221615f1d..daf8fa564 100644 --- a/Bio/Seq/MetaI.pm +++ b/Bio/Seq/MetaI.pm @@ -180,7 +180,7 @@ use base qw(Bio::Root::RootI); (reference). The return value may be a string or an array reference, - depending on the implentation. If in doubt, use meta_text() + depending on the implementation. If in doubt, use meta_text() which is a variant guarantied to return a string. See L. @@ -256,7 +256,7 @@ sub named_meta_text { shift->throw_not_implemented } sequence, they should be ignored. The return value may be a string or an array reference, - depending on the implentation. If in doubt, use + depending on the implementation. If in doubt, use submeta_text() which is a variant guarantied to return a string. See L. @@ -321,7 +321,7 @@ sub named_submeta_text { shift->throw_not_implemented } Title : meta_names Usage : @meta_names = $obj->meta_names() - Function: Retrives an array of meta data set names. The default (unnamed) + Function: Retrieves an array of meta data set names. The default (unnamed) set name is guarantied to be the first name. Returns : an array of names Args : none @@ -389,7 +389,7 @@ sub named_meta_length { shift->throw_not_implemented } =head1 Bio::PrimarySeqI methods -Implemeting classes will need to rewrite these Bio::PrimaryI methods. +Implementing classes will need to rewrite these Bio::PrimaryI methods. =cut diff --git a/Bio/Seq/PrimaryQual.pm b/Bio/Seq/PrimaryQual.pm index 4709a2a89..6a93d3489 100644 --- a/Bio/Seq/PrimaryQual.pm +++ b/Bio/Seq/PrimaryQual.pm @@ -327,7 +327,7 @@ sub header { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id - for the implemetation, allowing multiple objects to have the same + for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string @@ -354,7 +354,7 @@ sub accession_number { Usage : $unique_implementation_key = $obj->primary_id(); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a - way the implementaiton can control clients can expect one id to + way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. Returns : A string diff --git a/Bio/Seq/PrimedSeq.pm b/Bio/Seq/PrimedSeq.pm index 0990a2af5..7b18e7db8 100644 --- a/Bio/Seq/PrimedSeq.pm +++ b/Bio/Seq/PrimedSeq.pm @@ -300,7 +300,7 @@ sub get_primer { Title : annotated_sequence Usage : my $annotated_sequence_object = $primedseq->annotate_sequence(); - Function: Get an annotated sequence object containg the left and right + Function: Get an annotated sequence object containing the left and right primers Returns : An annotated sequence object or 0 if not defined. Args : diff --git a/Bio/Seq/QualI.pm b/Bio/Seq/QualI.pm index 27dedbd2e..ac6a909db 100644 --- a/Bio/Seq/QualI.pm +++ b/Bio/Seq/QualI.pm @@ -211,7 +211,7 @@ sub display_id { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id - for the implemetation, allowing multiple objects to have the same + for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". Returns : A string. @@ -240,7 +240,7 @@ sub accession_number { $unique_implementation_key = $obj->primary_id($new_prim_id); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a - way the implementaiton can control clients can expect one id to + way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. Returns : A string @@ -331,8 +331,8 @@ are encouraged to override these methods Usage : @rev = @{$qual->revcom()}; Function: Produces a new Bio::Seq::QualI implementing object which is reversed from the original quality array. - The id is the same id as the orginal sequence, and the accession number - is also indentical. If someone wants to track that this sequence has + The id is the same id as the original sequence, and the accession number + is also identical. If someone wants to track that this sequence has been reversed, it needs to define its own extensions To do an inplace edit of an object you can go: diff --git a/Bio/Seq/RichSeqI.pm b/Bio/Seq/RichSeqI.pm index 59873f468..849014f34 100644 --- a/Bio/Seq/RichSeqI.pm +++ b/Bio/Seq/RichSeqI.pm @@ -113,7 +113,7 @@ sub get_secondary_accessions{ Title : division Usage : - Function: Get (and set, depending on the implementation) the divison for + Function: Get (and set, depending on the implementation) the division for a sequence. Examples from GenBank are PLN (plants), PRI (primates), etc. diff --git a/Bio/Seq/SeqBuilder.pm b/Bio/Seq/SeqBuilder.pm index 551f3a8ce..9f201ad36 100644 --- a/Bio/Seq/SeqBuilder.pm +++ b/Bio/Seq/SeqBuilder.pm @@ -355,7 +355,7 @@ sub make_object{ =head1 Implementation specific methods -These methods allow to conveniently configure this sequence object +These methods allow one to conveniently configure this sequence object builder as to which slots are desired, and under which circumstances a sequence object should be abandoned altogether. The default mode is want_all(1), which means the builder will report all slots as wanted @@ -564,7 +564,7 @@ sub want_all{ Conditions in this implementation are closures (anonymous functions) which are passed one parameter, a hash reference the keys of which are equal to initialization - paramaters. The closure must return TRUE to make the object + parameters. The closure must return TRUE to make the object 'wanted.' Conditions will be implicitly ANDed. diff --git a/Bio/Seq/SeqWithQuality.pm b/Bio/Seq/SeqWithQuality.pm index abdb137b4..fd7c77e48 100644 --- a/Bio/Seq/SeqWithQuality.pm +++ b/Bio/Seq/SeqWithQuality.pm @@ -171,7 +171,7 @@ sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # default: turn OFF the warnings - $self->{supress_warnings} = 1; + $self->{suppress_warnings} = 1; my($qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet,$trace_indices) = $self->_rearrange([qw( QUAL SEQ DISPLAY_ID ACCESSION_NUMBER PRIMARY_ID DESC ID ALPHABET TRACE_INDICES )], @args); @@ -188,7 +188,7 @@ sub new { # Import sequence first if (!$seq) { my $id; - unless ($self->{supress_warnings} == 1) { + unless ($self->{suppress_warnings} == 1) { $self->warn("You did not provide sequence information during the ". "construction of a Bio::Seq::SeqWithQuality object. Sequence ". "components for this object will be empty."); @@ -427,7 +427,7 @@ sub display_id { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id - for the implemetation, allowing multiple objects to have the same + for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". This method sets the accession_number for the SeqWithQuality @@ -457,7 +457,7 @@ sub accession_number { Usage : $unique_implementation_key = $obj->primary_id(); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a - way the implementaiton can control clients can expect one id to + way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. This method sets the primary_id for the SeqWithQuality object. @@ -632,13 +632,13 @@ sub trace_indices { sub length { my $self = shift; if (!$self->{seq_ref}) { - unless ($self->{supress_warnings} == 1) { + unless ($self->{suppress_warnings} == 1) { $self->warn("Can't find {seq_ref} here in length()."); } return; } if (!$self->{qual_ref}) { - unless ($self->{supress_warnings} == 1) { + unless ($self->{suppress_warnings} == 1) { $self->warn("Can't find {qual_ref} here in length()."); } return; @@ -646,7 +646,7 @@ sub length { my $seql = $self->{seq_ref}->length(); if ($seql != $self->{qual_ref}->length()) { - unless ($self->{supress_warnings} == 1) { + unless ($self->{suppress_warnings} == 1) { $self->warn("Sequence length (".$seql.") is different from quality ". "length (".$self->{qual_ref}->length().") in the SeqWithQuality ". "object. This can only lead to problems later."); diff --git a/Bio/Seq/SequenceTrace.pm b/Bio/Seq/SequenceTrace.pm index 5f00549b4..ff78468f2 100755 --- a/Bio/Seq/SequenceTrace.pm +++ b/Bio/Seq/SequenceTrace.pm @@ -101,7 +101,7 @@ sub new { my ($class, @args) = @_; my $self = $class->SUPER::new(@args); # default: turn OFF the warnings - $self->{supress_warnings} = 1; + $self->{suppress_warnings} = 1; my($swq,$peak_indices,$trace_a,$trace_t, $trace_g,$trace_c,$acc_a,$acc_t,$acc_g,$acc_c) = $self->_rearrange([qw( @@ -343,7 +343,7 @@ sub display_id { called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id - for the implemetation, allowing multiple objects to have the same + for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return "unknown". This method sets the accession_number for the Quality @@ -373,7 +373,7 @@ sub accession_number { Usage : $unique_implementation_key = $obj->primary_id(); Function: Returns the unique id for this object in this implementation. This allows implementations to manage their own object ids in a - way the implementaiton can control clients can expect one id to + way the implementation can control clients can expect one id to map to one object. For sequences with no accession number, this method should return a stringified memory location. This method sets the primary_id for the Quality diff --git a/Bio/Seq/SimulatedRead.pm b/Bio/Seq/SimulatedRead.pm index fcc381e49..948749b36 100644 --- a/Bio/Seq/SimulatedRead.pm +++ b/Bio/Seq/SimulatedRead.pm @@ -376,7 +376,7 @@ sub _update_desc_mid { Substitutions and deletions are for a single residue, but additions can be additions of several residues. An alternative way to specify errors is by using array references - instead of scalar for the hash values. This allows to specify + instead of scalar for the hash values. This allows one to specify redundant mutations. For example, the case presented above would result in the same read sequence as the example below: $errors->{34}->{'%'} = ['C', 'T'] ; # substitution by a C and then a T diff --git a/Bio/SeqFeature/Computation.pm b/Bio/SeqFeature/Computation.pm index 6c0263071..189eba2ed 100644 --- a/Bio/SeqFeature/Computation.pm +++ b/Bio/SeqFeature/Computation.pm @@ -39,7 +39,7 @@ more types of score and subseqfeatures. It is compatible with the Generic SeqFeature object. The new way of storing score values is similar to the tag structure in the -Generic object. For storing sets of subseqfeatures the array containg the +Generic object. For storing sets of subseqfeatures the array containing the subseqfeatures is now a hash which contains arrays of seqfeatures Both the score and subSeqfeature methods can be called in exactly the same way, the value's will be stored as a 'default' score or subseqfeature. @@ -133,7 +133,7 @@ sub new { Title : has_score Usage : $value = $self->has_score('some_score') - Function: Tests wether a feature contains a score + Function: Tests whether a feature contains a score Returns : TRUE if the SeqFeature has the score, and FALSE otherwise. Args : The name of a score @@ -463,7 +463,7 @@ sub get_all_SeqFeature_types { Usage : @feats = $feat->get_SeqFeatures(); @feats = $feat->get_SeqFeatures('feature_type'); Function: Returns an array of sub Sequence Features of a specific - type or, if the type is ommited, all sub Sequence Features + type or, if the type is omitted, all sub Sequence Features Returns : An array Args : (optional) a SeqFeature type (ie exon, pattern) diff --git a/Bio/SeqFeature/Generic.pm b/Bio/SeqFeature/Generic.pm index 772d5fe66..c4564e55b 100644 --- a/Bio/SeqFeature/Generic.pm +++ b/Bio/SeqFeature/Generic.pm @@ -46,7 +46,7 @@ the information for a feature on a sequence. For many Features, this is all you will need to use (for example, this is fine for Repeats in DNA sequence or Domains in protein sequence). For other features, which have more structure, this is a -good base class to extend using inheritence to have new things: this +good base class to extend using inheritance to have new things: this is what is done in the L, L and L, which provide well coordinated classes to represent genes on DNA sequence (for @@ -553,7 +553,7 @@ sub source_tag { Title : has_tag Usage : my $value = $feat->has_tag('some_tag'); - Function: Tests wether a feature contaings a tag + Function: Tests whether a feature containings a tag Returns : TRUE if the SeqFeature has the tag, and FALSE otherwise. Args : The name of a tag diff --git a/Bio/SeqFeature/Lite.pm b/Bio/SeqFeature/Lite.pm index e74a5dac7..ed8885b6e 100644 --- a/Bio/SeqFeature/Lite.pm +++ b/Bio/SeqFeature/Lite.pm @@ -445,7 +445,7 @@ sub display_name { shift->name(@_) } called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the - unique id for the implemetation, allowing multiple objects + unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation. For sequences with no accession number, this method should return diff --git a/Bio/SeqFeature/PositionProxy.pm b/Bio/SeqFeature/PositionProxy.pm index 54c4275fd..aa1f23560 100644 --- a/Bio/SeqFeature/PositionProxy.pm +++ b/Bio/SeqFeature/PositionProxy.pm @@ -65,7 +65,7 @@ Ewan Birney Ebirney@sanger.ac.ukE =head1 DEVELOPERS -This class has been written with an eye out of inheritence. The fields +This class has been written with an eye out of inheritance. The fields the actual object hash are: _gsf_tag_hash = reference to a hash for the tags diff --git a/Bio/SeqFeature/SubSeq.pm b/Bio/SeqFeature/SubSeq.pm index 465135b6c..296a4061d 100644 --- a/Bio/SeqFeature/SubSeq.pm +++ b/Bio/SeqFeature/SubSeq.pm @@ -36,7 +36,7 @@ Bio::SeqFeature::SubSeq extends L features to represent a subsequence. When this feature is attached to a template sequence, the sequence of feature is the subsequence of the template at this location. The purpose of this class is to represent a sequence as a feature without having to -explictly store its sequence string. +explicitly store its sequence string. Of course, you might have reasons to explicitly set a sequence. In that case, note that the length of the sequence is allowed to not match the position of the diff --git a/Bio/SeqFeature/Tools/Unflattener.pm b/Bio/SeqFeature/Tools/Unflattener.pm index bf7e0cbb1..5cfc7fb85 100644 --- a/Bio/SeqFeature/Tools/Unflattener.pm +++ b/Bio/SeqFeature/Tools/Unflattener.pm @@ -410,7 +410,7 @@ Occasionally a GenBank entry will have both implicit exons (from the mRNA location) B explicit exon features. In this case, exons will still be transferred. Tag-value data from the -explicit exon will be transfered to the implicit exon. If exons are +explicit exon will be transferred to the implicit exon. If exons are shared between mRNAs these will be represented by different objects. Any inconsistencies between implicit and explicit will be reported. diff --git a/Bio/SeqFeature/TypedSeqFeatureI.pm b/Bio/SeqFeature/TypedSeqFeatureI.pm index 5acd14026..1bb216507 100644 --- a/Bio/SeqFeature/TypedSeqFeatureI.pm +++ b/Bio/SeqFeature/TypedSeqFeatureI.pm @@ -48,7 +48,7 @@ all the Bio::SeqFeatureI interface as well). It is suggested that the primary_tag() method of SeqFeatureI return the same as the ontology_term()-Ename() of the OntologyTypedI (ie, the "string" name of the ontology type is used as the primary -tag), but this should not be assummed by client code as they +tag), but this should not be assumed by client code as they are scenarios where one would like to maintain the difference. diff --git a/Bio/SeqIO/ace.pm b/Bio/SeqIO/ace.pm index 99ecd7040..c5734f209 100644 --- a/Bio/SeqIO/ace.pm +++ b/Bio/SeqIO/ace.pm @@ -24,7 +24,7 @@ from ace file format. It only parses a DNA or Peptide objects contained in the ace file, producing PrimarySeq objects from them. All other objects in the files will be ignored. It -doesn't attempt to parse any annotation attatched +doesn't attempt to parse any annotation attached to the containing Sequence or Protein objects, which would probably be impossible, since everyone's ACeDB schema can be different. diff --git a/Bio/SeqIO/bsml.pm b/Bio/SeqIO/bsml.pm index b35158b16..6e48cbcad 100644 --- a/Bio/SeqIO/bsml.pm +++ b/Bio/SeqIO/bsml.pm @@ -757,7 +757,7 @@ sub to_bsml { next if (defined $args->{SKIPTAGS} && $args->{SKIPTAGS} =~ /all/i); # Tags can consume a lot of CPU cycles, and can often be - # rather non-informative, so -skiptags can allow total or + # rather non-informative, so -skiptags can allow one total or # selective omission of tags. for my $tag ($bioFeat->all_tags()) { next if (exists $args->{SKIPTAGS}{$tag}); @@ -841,7 +841,7 @@ sub to_bsml { document, where $mimetype is the value designated by this key. For generic XML use text/xml, for BSML use text/x-bsml - -return This option will be supressed, since the nature of this + -return This option will be suppressed, since the nature of this method is to print out the XML document. If you wish to retrieve the objects generated, use the to_bsml method directly. diff --git a/Bio/SeqIO/chadoxml.pm b/Bio/SeqIO/chadoxml.pm index 707fd4eb5..ccdee718c 100644 --- a/Bio/SeqIO/chadoxml.pm +++ b/Bio/SeqIO/chadoxml.pm @@ -348,7 +348,7 @@ GenBank data file for a Drosophila melanogaster genome scaffold has the molecule type of "DNA", when converting to chadoxml, a $seqSOtype argument of "golden_path_region" can be supplied to save the scaffold as a feature of type "golden_path_region" in chadoxml, instead of "DNA". a feature with primary tag -of 'source' must be present in the sequence feature list of $seq, to decribe the +of 'source' must be present in the sequence feature list of $seq, to describe the whole sequence record. In the current implementation: @@ -495,7 +495,7 @@ EOUSAGE undef(my @top_featrels); undef (my %srcfhash); - local($^W) = 0; # supressing warnings about uninitialized fields. + local($^W) = 0; # suppressing warnings about uninitialized fields. if (!$name && $seq->can('attributes') ) { ($name) = $seq->attributes('Alias'); diff --git a/Bio/SeqIO/chaos.pm b/Bio/SeqIO/chaos.pm index 622bafa2f..ccf127515 100644 --- a/Bio/SeqIO/chaos.pm +++ b/Bio/SeqIO/chaos.pm @@ -367,7 +367,7 @@ sub write_seq { } qw(desc keywords division molecule is_circular); $prop{dates} = join("; ", $seq->get_dates) if $seq->can("get_dates"); - local($^W) = 0; # supressing warnings about uninitialized fields. + local($^W) = 0; # suppressing warnings about uninitialized fields. # Reference lines my $count = 1; diff --git a/Bio/SeqIO/embl.pm b/Bio/SeqIO/embl.pm index 36d373176..a856c1e64 100644 --- a/Bio/SeqIO/embl.pm +++ b/Bio/SeqIO/embl.pm @@ -926,7 +926,7 @@ sub write_seq { Title : _print_EMBL_FTHelper Usage : Function: Internal function - Returns : 1 if writing suceeded, otherwise undef + Returns : 1 if writing succeeded, otherwise undef Args : @@ -1433,7 +1433,7 @@ sub _read_FTHelper_EMBL { Usage : Function: internal function Example : - Returns : 1 if writing suceeded, else undef + Returns : 1 if writing succeeded, else undef Args : diff --git a/Bio/SeqIO/fasta.pm b/Bio/SeqIO/fasta.pm index 8b693d20c..fe58ae6e0 100644 --- a/Bio/SeqIO/fasta.pm +++ b/Bio/SeqIO/fasta.pm @@ -300,7 +300,7 @@ sub width { Usage : $obj->block($newval) Function: Get/Set the length of each block for FASTA output. Sequence blocks will be split with a space. Configuring block, to a value of 10 for - example, allows to easily indentify a position in a sequence by eye. + example, allows one to easily identify a position in a sequence by eye. Default : same value used for width. Returns : value of block Args : newvalue (optional) diff --git a/Bio/SeqIO/fastq.pm b/Bio/SeqIO/fastq.pm index c20f5d08c..f17d4e05c 100644 --- a/Bio/SeqIO/fastq.pm +++ b/Bio/SeqIO/fastq.pm @@ -475,7 +475,7 @@ methods. Internal methods are usually preceded with a _ quality data. Current values accepted are: - 'sanger' (orginal FASTQ) + 'sanger' (original FASTQ) ASCII encoding from 33-126, PHRED quality score from 0 to 93 'solexa' (aka illumina1.0) ASCII encoding from 59-104, SOLEXA quality score from -5 to 40 diff --git a/Bio/SeqIO/game/gameHandler.pm b/Bio/SeqIO/game/gameHandler.pm index 05c5db479..559c5ca61 100644 --- a/Bio/SeqIO/game/gameHandler.pm +++ b/Bio/SeqIO/game/gameHandler.pm @@ -114,7 +114,7 @@ sub end_document { Usage : $seqs = $handler->load Function: start parsing Returns : a ref to a list of sequence objects - Args : an optional flag to supress elements (not used yet) + Args : an optional flag to suppress elements (not used yet) =cut diff --git a/Bio/SeqIO/gcg.pm b/Bio/SeqIO/gcg.pm index f38454048..c95059aa1 100644 --- a/Bio/SeqIO/gcg.pm +++ b/Bio/SeqIO/gcg.pm @@ -273,10 +273,10 @@ sub GCG_checksum { Function: if parsed gcg sequence contains a checksum field : we compare it to a value computed here on the parsed : sequence. A checksum mismatch would indicate some - : type of parsing failure occured. + : type of parsing failure occurred. : Returns : 1 for success, 0 for failure - Args : string containing parsed seq, value of parsed cheksum + Args : string containing parsed seq, value of parsed checksum =cut diff --git a/Bio/SeqIO/genbank.pm b/Bio/SeqIO/genbank.pm index 84b84f71f..6bc8f37e1 100644 --- a/Bio/SeqIO/genbank.pm +++ b/Bio/SeqIO/genbank.pm @@ -89,7 +89,7 @@ associated Bio::AnnotationCollectionI object which is associated with Bio::Seq objects. If it is explicitly requested that no annotations should be stored when parsing a record of course they will not be available when you try and get them. If you are having this problem -look at the type of SeqBuilder that is being used to contruct your +look at the type of SeqBuilder that is being used to construct your sequence object. Comments Annotation 'comment' @@ -965,7 +965,7 @@ sub write_seq { my $circular = ($seq->is_circular) ? 'circular' : 'linear '; - local($^W) = 0; # supressing warnings about uninitialized fields. + local($^W) = 0; # suppressing warnings about uninitialized fields. my $temp_line; if ( $self->_id_generation_func ) { @@ -1330,7 +1330,7 @@ sub _read_GenBank_References { my (@refs); my $ref; - # assumme things are starting with RN + # assume things are starting with RN if ( $$buffer !~ /^REFERENCE/ ) { warn("Not parsing line '$$buffer' which maybe important"); } diff --git a/Bio/SeqIO/interpro.pm b/Bio/SeqIO/interpro.pm index 30138db24..cef76085a 100644 --- a/Bio/SeqIO/interpro.pm +++ b/Bio/SeqIO/interpro.pm @@ -120,7 +120,7 @@ sub next_seq { my $wingwhere = index($line, $wing); # the interpro XML is not fully formed, so we need to convert the - # extra double quotes and ampersands into appropriate XML chracter codes + # extra double quotes and ampersands into appropriate XML character codes if($where > 0){ my @linearray = split /$zinc/, $line; $finishedline = join ""zincins"", $linearray[0], $linearray[2]; diff --git a/Bio/SeqIO/lasergene.pm b/Bio/SeqIO/lasergene.pm index 1d3f0dcfa..bc2513b1b 100644 --- a/Bio/SeqIO/lasergene.pm +++ b/Bio/SeqIO/lasergene.pm @@ -25,7 +25,7 @@ Do not use this module directly. Use it via the L class. This object can product Bio::Seq::RichSeq objects from Lasergene sequence files. -IT DOES NOT PARSE ANY ATTIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE. +IT DOES NOT PARSE ANY ATTRIBUTE VALUE PAIRS IN THE HEADER OF THE LASERGENE FORMATTED FILE. IT DOES NOT WRITE THESE FILES EITHER. diff --git a/Bio/SeqIO/mbsout.pm b/Bio/SeqIO/mbsout.pm index 685905523..41b867cef 100644 --- a/Bio/SeqIO/mbsout.pm +++ b/Bio/SeqIO/mbsout.pm @@ -653,7 +653,7 @@ Function: returns a reference to a hash. The keys of the hash are the letters Bio::SeqIO::mbsout stream should be translated to. Returns : reference to a hash Args : NONE -Synopsys: +Synopsis: # retrieve the Bio::Seq object's sequence my $haplotype = $seq->seq; diff --git a/Bio/SeqIO/msout.pm b/Bio/SeqIO/msout.pm index 28568604c..8e8e58ecd 100644 --- a/Bio/SeqIO/msout.pm +++ b/Bio/SeqIO/msout.pm @@ -757,7 +757,7 @@ Function: returns a reference to a hash. The keys of the hash are the letters ' Bio::SeqIO::msout stream should be translated to. Returns : reference to a hash Args : NONE -Synopsys: +Synopsis: # retrieve the Bio::Seq object's sequence my $haplotype = $seq->seq; diff --git a/Bio/SeqIO/seqxml.pm b/Bio/SeqIO/seqxml.pm index c6cee856e..79a9e589e 100644 --- a/Bio/SeqIO/seqxml.pm +++ b/Bio/SeqIO/seqxml.pm @@ -906,7 +906,7 @@ sub element_property { push @{ $data->{'properties'} }, $annotation_obj; } else { - $self->throw("malformated property!"); + $self->throw("malformatted property!"); } } diff --git a/Bio/SeqIO/swiss.pm b/Bio/SeqIO/swiss.pm index 3e2648adf..8978f7c8d 100644 --- a/Bio/SeqIO/swiss.pm +++ b/Bio/SeqIO/swiss.pm @@ -478,7 +478,7 @@ sub next_seq { -annotation => $annotation, ); - # The annotation doesn't get added by the contructor + # The annotation doesn't get added by the constructor $seq->annotation($annotation); return $seq; @@ -549,7 +549,7 @@ sub write_seq { $self->_print( "ID $temp_line\n"); # if there, write the accession line - local($^W) = 0; # supressing warnings about uninitialized fields + local($^W) = 0; # suppressing warnings about uninitialized fields if ( $self->_ac_generation_func ) { $temp_line = &{$self->_ac_generation_func}($seq); diff --git a/Bio/SeqIO/tigr.pm b/Bio/SeqIO/tigr.pm index fea4d584c..88330012d 100644 --- a/Bio/SeqIO/tigr.pm +++ b/Bio/SeqIO/tigr.pm @@ -263,7 +263,7 @@ sub _process_pseudochromosome return; } - $self->throw("Reached end of _process_psuedochromosome"); + $self->throw("Reached end of _process_pseudochromosome"); } sub _process_assembly @@ -364,7 +364,7 @@ sub _process_assembly_seq() "with no in the stream"); } - # Protect agains lots of smaller lines + # Protect against lots of smaller lines my @chunks; do { diff --git a/Bio/SeqUtils.pm b/Bio/SeqUtils.pm index 287fcd899..b2ad21bca 100644 --- a/Bio/SeqUtils.pm +++ b/Bio/SeqUtils.pm @@ -51,7 +51,7 @@ Bio::SeqUtils - Additional methods for PrimarySeq objects my $revcomseq = Bio::SeqUtils->revcom_with_features($seq); # simulate cloning of a fragment into a vector. Cut the vector at - # positions 1000 and 1100 (deleting postions 1001 to 1099) and + # positions 1000 and 1100 (deleting positions 1001 to 1099) and # "ligate" a fragment into the sites. The fragment is # reverse-complemented in this example (option "flip"). # All features of the vector and fragment are preserved and diff --git a/Bio/Structure/Entry.pm b/Bio/Structure/Entry.pm index c913c81cd..aed8f9224 100644 --- a/Bio/Structure/Entry.pm +++ b/Bio/Structure/Entry.pm @@ -212,7 +212,7 @@ sub add_model { } push @{$self->{'model'}}, $m; # create a stringified version of our ref - # not used untill we get symbolic ref working + # not used until we get symbolic ref working #my $str_ref = "$self"; #$m->_grandparent($str_ref); } @@ -798,7 +798,7 @@ sub parent { $self->throw("parent: you need to supply an argument to get the parent from\n"); } - # for now we pass on to _parent, untill we get the symbolic ref thing working. + # for now we pass on to _parent, until we get the symbolic ref thing working. $self->_parent($obj); } diff --git a/Bio/Structure/Residue.pm b/Bio/Structure/Residue.pm index 0e239564f..a5e189b3f 100644 --- a/Bio/Structure/Residue.pm +++ b/Bio/Structure/Residue.pm @@ -116,7 +116,7 @@ sub new { Title : atom Usage : - Function: nothing useful untill I get symbolic references to do what I want + Function: nothing useful until I get symbolic references to do what I want Returns : Args : @@ -133,7 +133,7 @@ sub atom { Title : add_atom Usage : - Function: nothing useful untill I get symbolic references to do what I want + Function: nothing useful until I get symbolic references to do what I want Returns : Args : diff --git a/Bio/Structure/SecStr/STRIDE/Res.pm b/Bio/Structure/SecStr/STRIDE/Res.pm index 16e9b9310..78aa4850d 100644 --- a/Bio/Structure/SecStr/STRIDE/Res.pm +++ b/Bio/Structure/SecStr/STRIDE/Res.pm @@ -42,7 +42,7 @@ individual residues of a pdb structure file. STRIDE is available here: http://webclu.bio.wzw.tum.de/stride/ -Methods are then available for extracting all of the infomation +Methods are then available for extracting all of the information present within the output or convenient subsets of it. Although they are very similar in function, DSSP and STRIDE differ diff --git a/Bio/Taxonomy.pm b/Bio/Taxonomy.pm index 90419a16a..eba74b91c 100644 --- a/Bio/Taxonomy.pm +++ b/Bio/Taxonomy.pm @@ -389,7 +389,7 @@ sub add_node { Title : binomial Usage : my $val = $obj->binomial; - Function: returns the binomial name if this taxonomy reachs species level + Function: returns the binomial name if this taxonomy reaches species level Returns : the binomial name OR undef if taxonmy does not reach species level Args : [No arguments] @@ -410,7 +410,7 @@ sub binomial { Usage : $node = $taxonomy->get_node('species'); Function: get a Bio::Taxonomy::Node object according to rank name Returns : a Bio::Taxonomy::Node object or undef if null - Args : a vaild rank name + Args : a valid rank name =cut diff --git a/Bio/Tools/Analysis/DNA/ESEfinder.pm b/Bio/Tools/Analysis/DNA/ESEfinder.pm index 69cece20d..abfeb8da0 100644 --- a/Bio/Tools/Analysis/DNA/ESEfinder.pm +++ b/Bio/Tools/Analysis/DNA/ESEfinder.pm @@ -86,7 +86,7 @@ score] See L -This the second implentation of Bio::SimpleAnalysisI which hopefully +This the second implementation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from L. diff --git a/Bio/Tools/Analysis/Protein/ELM.pm b/Bio/Tools/Analysis/Protein/ELM.pm index 508af00b5..ef71958ee 100755 --- a/Bio/Tools/Analysis/Protein/ELM.pm +++ b/Bio/Tools/Analysis/Protein/ELM.pm @@ -205,7 +205,7 @@ sub compartment { name : species usage : $tool->species('9606'); - purpose : get/setter for species selction for ELM server + purpose : get/setter for species selection for ELM server arguments : none, taxon_id or Bio::Species object returns : a string of the ncbi taxon_id diff --git a/Bio/Tools/Analysis/Protein/NetPhos.pm b/Bio/Tools/Analysis/Protein/NetPhos.pm index 06faad06d..81543d70b 100644 --- a/Bio/Tools/Analysis/Protein/NetPhos.pm +++ b/Bio/Tools/Analysis/Protein/NetPhos.pm @@ -54,7 +54,7 @@ phosphorylation sites in eukaryotic proteins. See L. -This the first implentation of Bio::SimpleAnalysisI which hopefully +This the first implementation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from Bio::WebAgent. @@ -233,7 +233,7 @@ sub result { Usage : $job->threshold(...) Returns : The significance threshold of a prediction - Args : None (retrieves value) or a value beween 0 and 1. + Args : None (retrieves value) or a value between 0 and 1. Purpose : Get/setter of the threshold to be sumitted for analysis. =cut diff --git a/Bio/Tools/ECnumber.pm b/Bio/Tools/ECnumber.pm index ad198e7a2..ae918c375 100644 --- a/Bio/Tools/ECnumber.pm +++ b/Bio/Tools/ECnumber.pm @@ -69,7 +69,7 @@ Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification) =head1 DESCRIPTION L is a representation of EC numbers, -the numerical heirarchy for Enzyme Classification. +the numerical hierarchy for Enzyme Classification. See L for more details. diff --git a/Bio/Tools/GFF.pm b/Bio/Tools/GFF.pm index eeb27e563..f8cc0685c 100644 --- a/Bio/Tools/GFF.pm +++ b/Bio/Tools/GFF.pm @@ -1236,7 +1236,7 @@ sub get_seqs { Title : features_attached_to_seqs Usage : $obj->features_attached_to_seqs(1); - Function: For use with GFF3 containg sequence only + Function: For use with GFF3 containing sequence only Setting this B parsing ensures that all Bio::Seq object created will have the appropriate features added to them @@ -1265,7 +1265,7 @@ sub features_attached_to_seqs{ Title : ignore_sequence Usage : $obj->ignore_sequence(1); - Function: For use with GFF3 containg sequence only + Function: For use with GFF3 containing sequence only Setting this B parsing means that all sequence data will be ignored diff --git a/Bio/Tools/Phylo/Gerp.pm b/Bio/Tools/Phylo/Gerp.pm index b81261c4d..7dba25752 100755 --- a/Bio/Tools/Phylo/Gerp.pm +++ b/Bio/Tools/Phylo/Gerp.pm @@ -149,7 +149,7 @@ sub next_result { -end => $end, -strand => 1, -score => $rs_score, - #-type => 'conserved_region', ***causes 740x increase in SeqFeatureDB storage requirments! + #-type => 'conserved_region', ***causes 740x increase in SeqFeatureDB storage requirements! -source => 'GERP'); my $sv = Bio::Annotation::SimpleValue->new(-tagname => 'predicted', -value => 1); diff --git a/Bio/Tools/Phylo/PAML/Result.pm b/Bio/Tools/Phylo/PAML/Result.pm index fd0fbbd47..4aa52cb98 100644 --- a/Bio/Tools/Phylo/PAML/Result.pm +++ b/Bio/Tools/Phylo/PAML/Result.pm @@ -957,7 +957,7 @@ sub get_CodonFreqs{ } -=head2 BASEML Relavent values +=head2 BASEML Relevant values =cut diff --git a/Bio/Tools/SiRNA.pm b/Bio/Tools/SiRNA.pm index 8c768c4ce..55df1b98a 100644 --- a/Bio/Tools/SiRNA.pm +++ b/Bio/Tools/SiRNA.pm @@ -46,7 +46,7 @@ Bio::SeqFeature::SiRNA::Pair contains two subfeatures oligos. These objects provide accessors for the information on the individual reagent pairs. -This verion of Bio::Tools::SiRNA represents a major change in architecture. +This version of Bio::Tools::SiRNA represents a major change in architecture. Specific 'rulesets' for siRNA selection as developed by various groups are implemented as Bio::Tools::SiRNA::Ruleset objects, which inherit from Bio::Tools::SiRNA. This will make it easier to add new rule sets or modify diff --git a/Bio/Tools/Sigcleave.pm b/Bio/Tools/Sigcleave.pm index a3fb8bde5..301334cad 100644 --- a/Bio/Tools/Sigcleave.pm +++ b/Bio/Tools/Sigcleave.pm @@ -92,7 +92,7 @@ In both cases, the "threshold" setting controls the score reporting level. If no value for threshold is passed in by the user, the code defaults to a reporting value of 3.5. -In this implemntation the accessor will never return any +In this implementation the accessor will never return any score/position pair which does not meet the threshold limit. This is the slightly different from the behaviour of the 8.1 EGCG sigcleave program which will report the highest of the under-threshold results diff --git a/Bio/Tools/dpAlign.pm b/Bio/Tools/dpAlign.pm index bed31d6e4..9216bedd5 100644 --- a/Bio/Tools/dpAlign.pm +++ b/Bio/Tools/dpAlign.pm @@ -104,7 +104,7 @@ sequences overlap each other. Dynamic Programming was first introduced by Needleman-Wunsch (1970) to globally align two sequences. The idea of local alignment was later introduced by Smith-Waterman (1981). Gotoh (1982) improved both -algorithms by introducing auxillary arrays that reduced the time +algorithms by introducing auxiliary arrays that reduced the time complexity of the algorithms to O(m*n). Miller-Myers (1988) exploits the divide-and-conquer idea introduced by Hirschberg (1975) to solve the affine gap cost dynamic programming using only linear space. At diff --git a/Bio/Tools/pSW.pm b/Bio/Tools/pSW.pm index 48612572c..5a80b0a0a 100644 --- a/Bio/Tools/pSW.pm +++ b/Bio/Tools/pSW.pm @@ -254,14 +254,14 @@ sub pairwise_alignment{ if( $alc->alu(0)->text_label eq 'SEQUENCE' ) { push(@ostr1,$str1[$alc->alu(0)->start+1]); } else { - # assumme it is in insert! + # assume it is in insert! push(@ostr1,'-'); } if( $alc->alu(1)->text_label eq 'SEQUENCE' ) { push(@ostr2,$str2[$alc->alu(1)->start+1]); } else { - # assumme it is in insert! + # assume it is in insert! push(@ostr2,'-'); } $alctemp = $alc; diff --git a/Bio/Tree/AlleleNode.pm b/Bio/Tree/AlleleNode.pm index 706fea2cf..425da0663 100644 --- a/Bio/Tree/AlleleNode.pm +++ b/Bio/Tree/AlleleNode.pm @@ -381,7 +381,7 @@ Methods inherited from L. Function: The human readable identifier for the node Returns : value of human readable id Args : newvalue (optional) - Note : id cannot contain the chracters '();:' + Note : id cannot contain the characters '();:' "A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. Because you may diff --git a/Bio/Tree/NodeI.pm b/Bio/Tree/NodeI.pm index 82a94570f..0011d3eac 100644 --- a/Bio/Tree/NodeI.pm +++ b/Bio/Tree/NodeI.pm @@ -64,7 +64,7 @@ length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid branch length. Various implementations of NodeI may extend the basic functions and -allow storing of other information (like attatching a species object +allow storing of other information (like attaching a species object or full sequences used to build a tree or alternative sequences). If you don't know how to extend a Bioperl object please ask, happy to help, we would also greatly appreciate contributions with improvements diff --git a/Bio/Tree/TreeFunctionsI.pm b/Bio/Tree/TreeFunctionsI.pm index 8f4c87b2e..51508f108 100644 --- a/Bio/Tree/TreeFunctionsI.pm +++ b/Bio/Tree/TreeFunctionsI.pm @@ -31,7 +31,7 @@ Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree explorat =head1 DESCRIPTION -This interface provides a set of implementated Tree functions which +This interface provides a set of implemented Tree functions which only use the defined methods in the TreeI or NodeI interface. =head1 FEEDBACK @@ -129,7 +129,7 @@ sub find_node { } # could actually do this by testing $rootnode->can($type) but - # it is possible that a tree is implemeted with different node types + # it is possible that a tree is implemented with different node types # - although it is unlikely that the root node would be richer than the # leaf nodes. Can't handle NHX tags right now @@ -542,7 +542,7 @@ sub merge_lineage { Function: Splices out all nodes in the tree that have an ancestor and only one descendent. Returns : n/a - Args : none for normal behaviour, true to dis-regard the ancestor requirment + Args : none for normal behaviour, true to dis-regard the ancestor requirement and re-root the tree as necessary For example, if we are the tree $tree: diff --git a/Bio/TreeIO/nexus.pm b/Bio/TreeIO/nexus.pm index 6f497fc36..9f6f066e6 100644 --- a/Bio/TreeIO/nexus.pm +++ b/Bio/TreeIO/nexus.pm @@ -31,7 +31,7 @@ basically is just a remapping of trees. The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are -used to give a name for an internal node or record the bootstap value, +used to give a name for an internal node or record the bootstrap value, but other uses are possible. The FigTree program by Andrew Rambaut adds various rendering diff --git a/Bio/TreeIO/pag.pm b/Bio/TreeIO/pag.pm index 52ee3f598..ad944f2d3 100644 --- a/Bio/TreeIO/pag.pm +++ b/Bio/TreeIO/pag.pm @@ -255,7 +255,7 @@ sub next_tree{ Title : name_length Usage : $self->name_length(20); - Function: set mininum taxon name length + Function: set minimum taxon name length Returns : integer (length of name) Args : integer diff --git a/Bio/Variation/AAReverseMutate.pm b/Bio/Variation/AAReverseMutate.pm index 30e266cc2..13cf1b76d 100644 --- a/Bio/Variation/AAReverseMutate.pm +++ b/Bio/Variation/AAReverseMutate.pm @@ -192,7 +192,7 @@ sub aa_mut { Sets and returns codon_ori triplet. If value is not set, returns false. The string has to be three characters - long. The chracter content is not checked. + long. The character content is not checked. Example : Returns : string diff --git a/Bio/Variation/VariantI.pm b/Bio/Variation/VariantI.pm index 0586e0017..de8c65651 100644 --- a/Bio/Variation/VariantI.pm +++ b/Bio/Variation/VariantI.pm @@ -31,7 +31,7 @@ Bio::Variation::RNAChange and Bio::Variation::AAChange use them. See L, L, and L for more information. -These classes store information, heavy computation to detemine allele +These classes store information, heavy computation to determine allele sequences is done elsewhere. The database cross-references are implemented as @@ -199,10 +199,10 @@ sub each_Allele{ Function: Returns or sets the boolean value indicating that the - variant descibed is a canonical mutation with two alleles + variant described is a canonical mutation with two alleles assinged to be the original (wild type) allele and mutated allele, respectively. If this value is not set, it is - assumed that the Variant descibes polymorphisms. + assumed that the Variant describes polymorphisms. Returns : a boolean diff --git a/scripts/DB/bp_flanks.pl b/scripts/DB/bp_flanks.pl index da92d1de0..0f1415f74 100644 --- a/scripts/DB/bp_flanks.pl +++ b/scripts/DB/bp_flanks.pl @@ -246,7 +246,7 @@ sequence the subsequence was taken. The ID of the fasta entry is the name given at the command line joined by hyphen to the filename or accesion of the source sequence. If no id -is given a series of consequtive integers is used. +is given a series of consecutive integers is used. The tag=value pairs are: diff --git a/scripts/index/bp_fetch.pl b/scripts/index/bp_fetch.pl index b571616a9..86a5bbc9a 100644 --- a/scripts/index/bp_fetch.pl +++ b/scripts/index/bp_fetch.pl @@ -50,7 +50,7 @@ db information options only for expert use -dir - directory to find the index files - (overrides BIOPERL_INDEX environment varaible) + (overrides BIOPERL_INDEX environment variable) -type - type of DBM file to open (overrides BIOPERL_INDEX_TYPE environment variable) @@ -163,7 +163,7 @@ BEGIN { if ( $@ ) { if ( !exists $ENV{'BIOPERL_SAVVY'} ) { - print STDERR ("\nbp_fetch cannot find Bio::DB::GenBank and Bio::DB::EMBL modules\nThis is most likely because LWP has not been installed\nThis does not effect local indexing\nset environment variable BIOPERL_SAVVY to supress this message\n\n"); + print STDERR ("\nbp_fetch cannot find Bio::DB::GenBank and Bio::DB::EMBL modules\nThis is most likely because LWP has not been installed\nThis does not effect local indexing\nset environment variable BIOPERL_SAVVY to suppress this message\n\n"); } } } @@ -264,7 +264,7 @@ for my $arg ( @ARGV ) { }; /^local$/ && do { if ( !$dir ) { - die "\nNo directory specified for index\nDirectory must be specified by the environment varaible BIOPERL_INDEX or --dir option\ngo bp_index with no arguments for more help\n\n"; + die "\nNo directory specified for index\nDirectory must be specified by the environment variable BIOPERL_INDEX or --dir option\ngo bp_index with no arguments for more help\n\n"; } # diff --git a/scripts/index/bp_index.pl b/scripts/index/bp_index.pl index b636da0bf..3af1e227d 100644 --- a/scripts/index/bp_index.pl +++ b/scripts/index/bp_index.pl @@ -48,7 +48,7 @@ Options for expert use =head1 ENVIRONMENT bp_index and bp_fetch coordinate where the databases lie using the -enviroment variable BIOPERL_INDEX. This can be overridden using the +environment variable BIOPERL_INDEX. This can be overridden using the -dir option. There is no default value, so you must use the -dir option or set BIOPERL_INDEX. @@ -143,7 +143,7 @@ exec('perldoc',$0) unless @ARGV; my $name = shift; if( !$dir ) { - print STDERR "\nNo directory specified for index\nDirectory must be specified by the environment varaible BIOPERL_INDEX or -dir option\ngo bp_index with no arguments for more help\n\n"; + print STDERR "\nNo directory specified for index\nDirectory must be specified by the environment variable BIOPERL_INDEX or -dir option\ngo bp_index with no arguments for more help\n\n"; exit(1); } diff --git a/scripts/seq/bp_unflatten_seq.pl b/scripts/seq/bp_unflatten_seq.pl index 730a111a6..4bbebc729 100644 --- a/scripts/seq/bp_unflatten_seq.pl +++ b/scripts/seq/bp_unflatten_seq.pl @@ -88,7 +88,7 @@ input file (can also be specified as last argument) input format (defaults to genbank) -probably doesnt make so much sense to use this for non-flat formats; +probably doesn't make so much sense to use this for non-flat formats; ie other than embl/genbank =item -to FORMAT -- 2.11.4.GIT