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.\" ========================================================================
.\"
.IX Title "Bio::Location::FuzzyLocationI 3pm"
.TH Bio::Location::FuzzyLocationI 3pm "2021-08-15" "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"
Bio::Location::FuzzyLocationI \- Abstract interface of a Location on a Sequence
which has unclear start/end location
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&    # Get a FuzzyLocationI object somehow
\&    print "Fuzzy FT location string is ", $location\->to_FTstring();
\&    print "location is of the type ", $location\->loc_type, "\en";
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This interface encapsulates the necessary methods for representing a
Fuzzy Location, one that does not have clear start and/or end points.
This will initially serve to handle features from Genbank/EMBL feature
tables that are written as 1^100 meaning between bases 1 and 100 or
<100..300 meaning it starts somewhere before 100.  Advanced
implementations of this interface may be able to handle the necessary
logic of overlaps/intersection/contains/union.  It was constructed to
handle fuzzy locations that can be represented in Genbank/EMBL.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists.  Your participation is much appreciated.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.
.SS "Reporting Bugs"
.IX Subsection "Reporting Bugs"
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SH "LocationI methods"
.IX Header "LocationI methods"
.SS "location_type"
.IX Subsection "location_type"
.Vb 5
\&  Title   : loc_type
\&  Usage   : my $location_type = $location\->location_type();
\&  Function: Get location type encoded as text
\&  Returns : string (\*(AqEXACT\*(Aq, \*(AqWITHIN\*(Aq, \*(AqIN\-BETWEEN\*(Aq)
\&  Args    : none
.Ve
.SH "Bio::LocationI methods"
.IX Header "Bio::LocationI methods"
Bio::LocationI methods follow
.SS "min_start"
.IX Subsection "min_start"
.Vb 5
\&  Title   : min_start
\&  Usage   : my $minstart = $location\->min_start();
\&  Function: Get minimum starting location of feature startpoint   
\&  Returns : integer or undef if no maximum starting point.
\&  Args    : none
.Ve
.SS "max_start"
.IX Subsection "max_start"
.Vb 5
\&  Title   : max_start
\&  Usage   : my $maxstart = $location\->max_start();
\&  Function: Get maximum starting location of feature startpoint  
\&  Returns : integer or undef if no maximum starting point.
\&  Args    : none
.Ve
.SS "start_pos_type"
.IX Subsection "start_pos_type"
.Vb 6
\&  Title   : start_pos_type
\&  Usage   : my $start_pos_type = $location\->start_pos_type();
\&  Function: Get start position type (ie <,>, ^) 
\&  Returns : type of position coded as text 
\&            (\*(AqBEFORE\*(Aq, \*(AqAFTER\*(Aq, \*(AqEXACT\*(Aq,\*(AqWITHIN\*(Aq, \*(AqBETWEEN\*(Aq)
\&  Args    : none
.Ve
.SS "min_end"
.IX Subsection "min_end"
.Vb 5
\&  Title   : min_end
\&  Usage   : my $minend = $location\->min_end();
\&  Function: Get minimum ending location of feature endpoint 
\&  Returns : integer or undef if no minimum ending point.
\&  Args    : none
.Ve
.SS "max_end"
.IX Subsection "max_end"
.Vb 5
\&  Title   : max_end
\&  Usage   : my $maxend = $location\->max_end();
\&  Function: Get maximum ending location of feature endpoint 
\&  Returns : integer or undef if no maximum ending point.
\&  Args    : none
.Ve
.SS "end_pos_type"
.IX Subsection "end_pos_type"
.Vb 6
\&  Title   : end_pos_type
\&  Usage   : my $end_pos_type = $location\->end_pos_type();
\&  Function: Get end position type (ie <,>, ^) 
\&  Returns : type of position coded as text 
\&            (\*(AqBEFORE\*(Aq, \*(AqAFTER\*(Aq, \*(AqEXACT\*(Aq,\*(AqWITHIN\*(Aq, \*(AqBETWEEN\*(Aq)
\&  Args    : none
.Ve
.SS "seq_id"
.IX Subsection "seq_id"
.Vb 5
\&  Title   : seq_id
\&  Usage   : my $seqid = $location\->seq_id();
\&  Function: Get/Set seq_id that location refers to
\&  Returns : seq_id
\&  Args    : [optional] seq_id value to set
.Ve
.SS "coordinate_policy"
.IX Subsection "coordinate_policy"
.Vb 4
\&  Title   : coordinate_policy
\&  Usage   : $policy = $location\->coordinate_policy();
\&            $location\->coordinate_policy($mypolicy); # set may not be possible
\&  Function: Get the coordinate computing policy employed by this object.
\&
\&            See Bio::Location::CoordinatePolicyI for documentation about
\&            the policy object and its use.
\&
\&            The interface *does not* require implementing classes to accept
\&            setting of a different policy. The implementation provided here
\&            does, however, allow one to do so.
\&
\&            Implementors of this interface are expected to initialize every
\&            new instance with a CoordinatePolicyI object. The implementation
\&            provided here will return a default policy object if none has
\&            been set yet. To change this default policy object call this
\&            method as a class method with an appropriate argument. Note that
\&            in this case only subsequently created Location objects will be
\&            affected.
\&
\&  Returns : A Bio::Location::CoordinatePolicyI implementing object.
\&  Args    : On set, a Bio::Location::CoordinatePolicyI implementing object.
.Ve
.SS "to_FTstring"
.IX Subsection "to_FTstring"
.Vb 5
\&  Title   : to_FTstring
\&  Usage   : my $locstr = $location\->to_FTstring()
\&  Function: returns the FeatureTable string of this location
\&  Returns : string
\&  Args    : none
.Ve