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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/MailList.shtml - About the mailing lists
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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=head2 Reporting Bugs
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via
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of the bugs and their resolution. Bug reports can be submitted via the
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bioperl-bugs@bioperl.org
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http://bugzilla.bioperl.org/
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http://bugzilla.open-bio.org/
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=head1 AUTHOR - Chad Matsalla
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=head1 CONTRIBUTORS
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Heikki Lehvaslaiho heikki@ebi.ac.uk
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Heikki Lehvaslaiho heikki-at-bioperl-dot-org
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Lincoln Stein lstein@cshl.org
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Jason Stajich jason@bioperl.org
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Sendu Bala bix@sendu.me.uk
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=head2 Bio::Map::Marker methods
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Usage : my $position = $mappable->position($map); OR
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$mappable->position($map,$position); OR
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Function: Get/Set the Bio::Map::PositionI for a mappable element
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Returns : Bio::Map::PositionI
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Args : $map =Bio::Map::MapI # Map we are talking about
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$position = Bio::Map::PositionI # Position we want to set
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=head2 name($new_name)
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Title : name($new_name)
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Usage : $o_usat->name($new_name) _or_
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my $name = $o_usat->name()
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Function: Get/Set the name for this Microsatellite
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Returns : A scalar representing the current name of this Microsatellite
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Args : If provided, the current name of this Microsatellite
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will be set to $new_name.
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=head2 motif($new_motif)
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Title : motif($new_motif)
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Usage : my $motif = $o_usat->motif($new_motif) _or_
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my $motif = $o_usat->motif()
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Function: Get/Set the repeat motif for this Microsatellite
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Usage : $o_usat->motif($new_motif);
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my $motif = $o_usat->motif();
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Function: Get/Set the repeat motif for this Microsatellite.
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Returns : A scalar representing the current repeat motif of this
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Args : If provided, the current repeat motif of this Microsatellite
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will be set to $new_motif.
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Args : none to get, OR string to set
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return $self->{'_motif'};
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=head2 sequence($new_sequence)
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Title : sequence($new_sequence)
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Usage : my $sequence = $o_usat->sequence($new_sequence) _or_
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my $sequence = $o_usat->sequence()
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Function: Get/Set the sequence for this Microsatellite
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Usage : $o_usat->sequence($new_sequence);
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my $sequence = $o_usat->sequence();
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Function: Get/Set the sequence for this Microsatellite.
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Returns : A scalar representing the current sequence of this
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Args : If provided, the current sequence of this Microsatellite
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will be set to $new_sequence.
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Args : none to get, OR string to set
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return $self->{'_sequence'};
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=head2 repeats($new_repeats)
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Title : repeats($new_repeats)
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Usage : my $repeats = $o_usat->repeats($new_repeats) _or_
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my $repeats = $o_usat->repeats()
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Function: Get/Set the repeat repeats for this Microsatellite
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Usage : $o_usat->repeats($new_repeats);
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my $repeats = $o_usat->repeats()
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Function: Get/Set the repeat repeats for this Microsatellite.
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Returns : A scalar representing the current number of repeats of this
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Args : If provided, the current number of repeats of this
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Microsatellite will be set to $new_repeats.
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Args : none to get, OR int to set
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return $self->{'_repeats'};
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=head2 repeat_start_position($new_repeat_start_position)
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=head2 repeat_start_position
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Title : repeat_start_position($new_repeat_start_position)
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Usage : my $repeat_start_position =
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$o_usat->repeat_start_position($new_repeat_start_position) _or_
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my $repeat_start_position = $o_usat->repeat_start_position()
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Title : repeat_start_position
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Usage : $o_usat->repeat_start_position($new_repeat_start_position);
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my $repeat_start_position = $o_usat->repeat_start_position();
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Function: Get/Set the repeat repeat_start_position for this
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Returns : A scalar representing the repeat start position for this
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Args : If provided, the current repeat start position of this
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Microsatellite will be set to $new_repeat_start_position.
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This method will also try to set the repeat end position. This
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depends on having information for the motif and the number of
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repeats. If you want to use methods like get_trailing_flank or
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get_leading flank, be careful to include the right information.
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Args : none to get, OR string to set
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This method will also try to set the repeat end position. This
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depends on having information for the motif and the number of
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repeats. If you want to use methods like get_trailing_flank or
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get_leading flank, be careful to include the right information.
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return $self->{'_repeat_start_position'};
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=head2 repeat_end_position($value)
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=head2 repeat_end_position
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Title : repeat_end_position($set)
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Usage : $new_repeat_end_position =
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$o_usat->repeat_end_position("set"); _or_
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$new_repeat_end_position =
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$o_usat->repeat_end_position($value); _or_
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$current_repeat_end_position = $o_usat->repeat_end_position();
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Function: get/set the end position of the repeat in this sequence
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Title : repeat_end_position
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Usage : $o_usat->repeat_end_position("set");
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$o_usat->repeat_end_position($value);
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$current_repeat_end_position = $o_usat->repeat_end_position();
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Function: Get/set the end position of the repeat in this sequence.
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Returns : A scalar representing the base index of the end of the
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repeat in this Microsatellite. The first base in the sequence
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repeat in this Microsatellite. The first base in the sequence
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Args : A scalar representing a value, the string "set", or no
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argument (see Notes).
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argument (see Notes).
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Notes : If you do not provide an argument to this method, the current
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end position of the repeat in this Microsatellite will be
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If you provide the string "set" to this method it will set the
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end position based on the start position, the length of the
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motif, and the nuimber of repeats.
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If you specify a value the current end position of the repeat
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will be set to that value. This is a really bad idea. Don't do
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end position of the repeat in this Microsatellite will be
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If you provide the string "set" to this method it will set the
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end position based on the start position, the length of the
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motif, and the number of repeats.
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If you specify a value the current end position of the repeat
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will be set to that value. This is a really bad idea. Don't do
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sub repeat_end_position {
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my ($self,$caller) = @_;
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if( defined $caller ) {
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my ($self,@args) = @_;
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$self->warn("equals is not yet implemented in ".
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ref($self)." yet. Check back real soon!");
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$self->throw_not_implemented();
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Title : less_than
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Usage : if( $mappable->less_than($m2) ) ...
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Usage : if ($mappable->less_than($m2)) {...}
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Function: Tests if a position is less than another position
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Returns : boolean
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Args : Bio::Map::MappableI
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my ($self,@args) = @_;
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$self->warn("less_then is not yet implemented in ".
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ref($self)." yet. Check back real soon!");
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$self->throw_not_implemented();
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=head2 greater_than
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Title : greater_than
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Usage : if( $mappable->greater_than($m2) ) ...
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Usage : if ($mappable->greater_than($m2)) {...}
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Function: Tests if position is greater than another position
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Returns : boolean
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Args : Bio::Map::MappableI
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sub greater_than {
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my ($self,@args) = @_;
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$self->warn("greater_then is not yet implemented in ".
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ref($self)." yet. Check back real soon!");
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$self->throw_not_implemented();
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=head2 get_leading_flank()
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=head2 get_leading_flank
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Title : get_leading_flank()
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Title : get_leading_flank
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Usage : $leading_sequence = $o_usat->get_leading_flank();
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Returns : A scalar representing the sequence before the repeats in this
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sub get_leading_flank {
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my $self = shift;
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return substr $self->sequence(),0,$self->repeat_start_position-1;
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=head2 get_trailing_flank()
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=head2 get_trailing_flank
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Title : get_trailing_flank()
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Title : get_trailing_flank
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Usage : $trailing_flank = $o_usat->get_trailing_flank();
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Returns : A scalar representing the sequence after the repeats in this
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Bio/Map/Microsatellite.pm
