.\" Automatically generated by Pod::Man 4.14 (Pod::Simple 3.40) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "Bio::Coordinate::ExtrapolatingPair 3pm" .TH Bio::Coordinate::ExtrapolatingPair 3pm "2020-11-24" "perl v5.32.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::Coordinate::ExtrapolatingPair \- Continuous match between two coordinate sets. .SH "VERSION" .IX Header "VERSION" version 1.007001 .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& use Bio::Location::Simple; \& use Bio::Coordinate::ExtrapolatingPair; \& \& $match1 = Bio::Location::Simple\->new \& (\-seq_id => \*(Aqpropeptide\*(Aq, \-start => 21, \-end => 40, \-strand=>1 ); \& $match2 = Bio::Location::Simple\->new \& (\-seq_id => \*(Aqpeptide\*(Aq, \-start => 1, \-end => 20, \-strand=>1 ); \& \& $pair = Bio::Coordinate::ExtrapolatingPair\-> \& new(\-in => $match1, \& \-out => $match2, \& \-strict => 1 \& ); \& \& $pos = Bio::Location::Simple\->new \& (\-start => 40, \-end => 60, \-strand=> 1 ); \& $res = $pair\->map($pos); \& $res\->start eq 20; \& $res\->end eq 20; .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This class represents a one continuous match between two coordinate systems represented by Bio::Location::Simple objects. The relationship is directed and reversible. It implements methods to ensure internal consistency, and map continuous and split locations from one coordinate system to another. .PP This class is an elaboration of Bio::Coordinate::Pair. The map function returns only matches which is the mode needed most of tehtime. By default the matching regions between coordinate systems are boundless, so that you can say e.g. that gene starts from here in the chromosomal coordinate system and extends indefinetely in both directions. If you want to define the matching regions exactly, you can do that and set \fBstrict()\fR to true. .SH "METHODS" .IX Header "METHODS" .SS "new" .IX Subsection "new" .SS "strict" .IX Subsection "strict" .Vb 6 \& Title : strict \& Usage : $obj\->strict(1); \& Function: Set and read the strictness of the coordinate system. \& Example : \& Returns : value of input system \& Args : boolean .Ve .SS "map" .IX Subsection "map" .Vb 4 \& Title : map \& Usage : $newpos = $obj\->map($loc); \& Function: Map the location from the input coordinate system \& to a new value in the output coordinate system. \& \& In extrapolating coordinate system there is no location zero. \& Locations are... \& Example : \& Returns : new location in the output coordinate system or undef \& Args : Bio::Location::Simple .Ve .SH "INTERNAL METHODS" .IX Header "INTERNAL METHODS" .SS "_map" .IX Subsection "_map" .Vb 5 \& Title : _map \& Usage : $newpos = $obj\->_map($simpleloc); \& Function: Internal method that does the actual mapping. Called \& multiple times by map() if the location to be mapped is a \& split location \& \& Example : \& Returns : new location in the output coordinate system or undef \& Args : Bio::Location::Simple .Ve .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing lists" .IX Subsection "Mailing lists" User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. 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: \&\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 of the bugs and their resolution. Bug reports can be submitted via the web: .PP .Vb 1 \& https://github.com/bioperl/%%7Bdist%7D .Ve .SH "AUTHOR" .IX Header "AUTHOR" Heikki Lehvaslaiho .SH "COPYRIGHT" .IX Header "COPYRIGHT" This software is copyright (c) by Heikki Lehvaslaiho. .PP This software is available under the same terms as the perl 5 programming language system itself.