.\" Automatically generated by Pod::Man 2.27 (Pod::Simple 3.28)
.\"
.\" 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 turned on, 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
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "Bio::Coordinate::ExtrapolatingPair 3pm"
.TH Bio::Coordinate::ExtrapolatingPair 3pm "2014-07-13" "perl v5.18.2" "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 "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 \fIstrict()\fR to true.
.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 coodinate system there is no location zero.
\&           Locations are...
\& Example :
\& Returns : new location in the output coordinate system or undef
\& Args    : Bio::Location::Simple
.Ve
.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