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.\"
.IX Title "Ace::Sequence::FeatureList 3pm"
.TH Ace::Sequence::FeatureList 3pm "2021-02-20" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Ace::Sequence::FeatureList \- Lightweight Access to Features
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\&    # get a megabase from the middle of chromosome I
\&    $seq = Ace::Sequence\->new(\-name   => \*(AqCHROMOSOME_I,
\&                              \-db     => $db,
\&                              \-offset => 3_000_000,
\&                              \-length => 1_000_000);
\&
\&    # find out what\*(Aqs there
\&    $list = $seq\->feature_list;
\&
\&    # Scalar context: count all the features
\&    $feature_count = $list\->types;
\&
\&    # Array context: list all the feature types
\&    @feature_types = $list\->types;
\&
\&    # Scalar context, 1 argument.  Count this type
\&    $gene_cnt = $list\->types(\*(AqPredicted_gene\*(Aq);
\&    print "There are $gene_cnt genes here.\en";
\&
\&    # Array context, 1 argument.  Get list of subtypes
\&    @subtypes = $list\->types(\*(AqPredicted_gene\*(Aq);
\&
\&    # Two arguments. Count type & subtype
\&    $genefinder_cnt = $list\->types(\*(AqPredicted_gene\*(Aq,\*(Aqgenefinder\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fIAce::Sequence::FeatureList\fR is a small class that provides
statistical information about sequence features.  From it you can
obtain summary counts of the features and their types within a
selected region.
.SH "OBJECT CREATION"
.IX Header "OBJECT CREATION"
You will not ordinarily create an \fIAce::Sequence::FeatureList\fR object
directly.  Instead, objects will be created by calling a
\&\fIAce::Sequence\fR object's \fBfeature_list()\fR method.  If you wish to
create an \fIAce::Sequence::FeatureList\fR object directly, please consult
the source code for the \fI\f(BInew()\fI\fR method.
.SH "OBJECT METHODS"
.IX Header "OBJECT METHODS"
There are only two methods in \fIAce::Sequence::FeatureList\fR.
.IP "\fBtype()\fR" 4
.IX Item "type()"
This method has five distinct behaviors, depending on its context and
the number of parameters.  Usage should be intuitive
.Sp
.Vb 2
\& Context       Arguments       Behavior
\& \-\-\-\-\-\-\-       \-\-\-\-\-\-\-\-\-       \-\-\-\-\-\-\-\-
\&
\& scalar         \-none\-         total count of features in list
\& array          \-none\-         list feature types (e.g. "exon")
\& scalar          type          count features of this type
\& array           type          list subtypes of this type
\& \-any\-       type,subtype      count features of this type & subtype
.Ve
.Sp
For example, this code fragment will count the number of exons present
on the list:
.Sp
.Vb 1
\&  $exon_count = $list\->type(\*(Aqexon\*(Aq);
.Ve
.Sp
This code fragment will count the number of exons found by \*(L"genefinder\*(R":
.Sp
.Vb 1
\&  $predicted_exon_count = $list\->type(\*(Aqexon\*(Aq,\*(Aqgenefinder\*(Aq);
.Ve
.Sp
This code fragment will print out all subtypes of \*(L"exon\*(R" and their
counts:
.Sp
.Vb 3
\&  for my $subtype ($list\->type(\*(Aqexon\*(Aq)) {
\&      print $subtype,"\et",$list\->type(\*(Aqexon\*(Aq,$subtype),"\en";
\&  }
.Ve
.IP "\fBasString()\fR" 4
.IX Item "asString()"
.Vb 1
\&  print $list\->asString;
.Ve
.Sp
This dumps the list out in tab-delimited format.  The order of columns
is type, subtype, count.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Ace, Ace::Object, Ace::Sequence,
Ace::Sequence::Feature, \s-1GFF\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@w3.org> with extensive help from Jean
Thierry-Mieg <mieg@kaa.crbm.cnrs\-mop.fr>
.PP
Copyright (c) 1999, Lincoln D. Stein
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.