This is Info file pm.info, produced by Makeinfo version 1.68 from the input file bigpm.texi.  File: pm.info, Node: Bio/LiveSeq/Transcript, Next: Bio/LiveSeq/Translation, Prev: Bio/LiveSeq/SeqI, Up: Module List Transcript class for LiveSeq **************************** NAME ==== Bio::LiveSeq::Transcript - Transcript class for LiveSeq SYNOPSIS ======== # documentation needed DESCRIPTION =========== This stores informations about coding sequences (CDS). The implementation is that a Transcript object accesses a collection of Exon objects, inferring from them the nucleotide structure and sequence. AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new --- Title : new Usage : $transcript = Bio::LiveSeq::Transcript->new(-exons => \@obj_refs); Function: generates a new Bio::LiveSeq::Transcript Returns : reference to a new object of class Transcript Errorcode -1 Args : reference to an array of Exon object references all_Exons Title : all_Exons Usage : $transcript_obj->all_Exons() Function: returns references to all Exon objects the Transcript is composed of Example : foreach $exon ($transcript->all_Exons()) { do_something } Returns : array of object references Args : none =cut ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ sub all_Exons { my $self=shift; my $exonsref=$self->{'exons'}; my @exons=@{$exonsref}; my @newexons; my $exon; foreach $exon (@exons) { unless ($exon->obj_valid) { carp "$exon no more valid, start or end label lost, skipping...."; } else { push(@newexons,$exon); } } if ($#exons != $#newexons) { # update exons field $self->{'exons'}=\@newexons; } return (@newexons); } downstream_seq Title : downstream_seq Usage : $transcript_obj->downstream_seq() : $transcript_obj->downstream_seq(64) Function: returns a string of nucleotides downstream of the end of the CDS. If there is some information of the real mRNA, from features in an attached Gene object, it will return up to those boundaries. Otherwise it will return 1000 nucleotides. If an argument is given it will override the default 1000 number and return instead /that/ requested number of nucleotides. But if a Gene object is attached, this argument will be ignored. Returns : string Args : an optional integer number of nucleotides to be returned instead of the default if no gene attached --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- upstream_seq Title : upstream_seq Usage : $transcript_obj->upstream_seq() : $transcript_obj->upstream_seq(64) Function: just like downstream_seq but returns nucleotides before the ATG Note : the default, if no Gene information present and no nucleotides number given, is to return up to 400 nucleotides. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ get_Translation --------------- Title : valid Usage : $translation = $obj->get_Translation() Function: retrieves the reference to the object of class Translation (if any) attached to a LiveSeq object Returns : object reference Args : none translation_table ----------------- Title : translation_table Usage : $name = $obj->translation_table; : $name = $obj->translation_table(11); Function: Returns or sets the translation_table used for translating the transcript. If it has never been set, it will return undef. Returns : an integer frame ----- Title : frame Usage : $frame = $transcript->frame($label); Function: Returns the frame of a particular nucleotide. Frame can be 0 1 or 2 and means the position in the codon triplet of the particulat nucleotide. 0 is the first codon_position. Codon_position (1 2 3) is simply frame+1. If the label asked for is not inside the Transcript, -1 will be returned. Args : a label Returns : 0 1 or 2 Errorcode -1  File: pm.info, Node: Bio/LiveSeq/Translation, Next: Bio/LocatableSeq, Prev: Bio/LiveSeq/Transcript, Up: Module List Translation class for LiveSeq ***************************** NAME ==== Bio::LiveSeq::Translation - Translation class for LiveSeq SYNOPSIS ======== #documentation needed DESCRIPTION =========== This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate system and eventually its own ranges (protein domains). AUTHOR - Joseph A.L. Insana =========================== Email: Insana@ebi.ac.uk, jinsana@gmx.net Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new === Title : new Usage : $protein = Bio::LiveSeq::Translation->new(-transcript => $transcr); Function: generates a new Bio::LiveSeq::Translation Returns : reference to a new object of class Translation Errorcode -1 Args : reference to an object of class Transcript get_Transcript -------------- Title : valid Usage : $transcript = $obj->get_Transcript() Function: retrieves the reference to the object of class Transcript (if any) attached to a LiveSeq object Returns : object reference Args : none aa_ranges --------- Title : aa_ranges Usage : @proteinfeatures = $translation->aa_ranges() Function: to retrieve all the LiveSeq AARange objects attached to a Translation, usually created out of a SwissProt database entry crossreferenced from an EMBL CDS feature. Returns : an array Args : none  File: pm.info, Node: Bio/LocatableSeq, Next: Bio/Location/AvWithinCoordPolicy, Prev: Bio/LiveSeq/Translation, Up: Module List A Sequence object with start/end points on it ********************************************* NAME ==== Bio::LocatableSeq - A Sequence object with start/end points on it SYNOPSIS ======== Give standard usage here DESCRIPTION =========== # a normal sequence object $locseq->seq(); $locseq->id(); # has start,end points $locseq->start(); $locseq->end(); # inheriets off RangeI, so range operations possible $locseq->overlaps($seqfeature); FEEDBACK ======== Mailing Lists ------------- 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists The locatable sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this. It is, to be honest, not well integrated with the rest of bioperl, for example, the trunc() function does not return a LocatableSeq object, as some might have thought. There are all sorts of nasty gotcha's about interactions between coordinate systems when these sort of objects are used. 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start ----- Title : start Usage : $obj->start($newval) Function: Returns : value of start Args : newvalue (optional) end --- Title : end Usage : $obj->end($newval) Function: Returns : value of end Args : newvalue (optional) strand ------ Title : strand Usage : $obj->strand($newval) Function: Returns : value of strand Args : newvalue (optional) get_nse ------- Title : get_nse Usage : Function: Example : Returns : Args :  File: pm.info, Node: Bio/Location/AvWithinCoordPolicy, Next: Bio/Location/CoordinatePolicyI, Prev: Bio/LocatableSeq, Up: Module List class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise ************************************************************************************************************************************ NAME ==== Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise SYNOPSIS ======== See Bio::Location::CoordinatePolicyI DESCRIPTION =========== CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that for fuzzy locations of type WITHIN and BETWEEN the average of the two limits will be returned, and for all other locations it will return the widest possible range, but by using some common sense. This means that e.g. locations like "<5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp, Jason Stajich =================================== Email hlapp@gmx.net, jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start ----- Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. end --- Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object.  File: pm.info, Node: Bio/Location/CoordinatePolicyI, Next: Bio/Location/Fuzzy, Prev: Bio/Location/AvWithinCoordPolicy, Up: Module List Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location ****************************************************************************************************************** NAME ==== Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location SYNOPSIS ======== # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print "Location of feature ", $feature->primary_tag(), " employs a ", ref($location->coordinate_policy()), " instance for coordinate computation\n"; # change the policy, e.g. because the user chose to do so $location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new()); DESCRIPTION =========== Objects implementing this interface are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. While this may seem trivial for simple locations, there are different ways to do it for fuzzy or compound (split) locations. Classes implementing this interface implement a certain policy, like 'always widest range', 'always smallest range', 'mean for BETWEEN locations', etc. By installing a different policy object in a Location object, the behaviour of coordinate computation can be changed on-the-fly, and with a single line of code client-side. 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp, Jason Stajich =================================== Email hlapp@gmx.net, jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start ----- Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. end --- Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object.  File: pm.info, Node: Bio/Location/Fuzzy, Next: Bio/Location/FuzzyLocationI, Prev: Bio/Location/CoordinatePolicyI, Up: Module List Implementation of a Location on a Sequence which has unclear start and/or end locations *************************************************************************************** NAME ==== Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations SYNOPSIS ======== my $fuzzylocation = new Bio::Location::Fuzzy(-start => '<30', -end => 90, -loc_type => '.'); print "location string is ", $fuzzylocation->to_FTstring(); DESCRIPTION =========== This module contains 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. 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ loc_type -------- Title : loc_type Usage : my $location_type = $location->loc_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'BETWEEN') Args : none LocationI methods ================= length ------ Title : length Usage : $length = $fuzzy_loc->length(); Function: Get the length of this location. Note that the length of a fuzzy location will always depend on the currently active interpretation of start and end. The result will therefore vary for different CoordinatePolicy objects. Returns : an integer Args : none start ----- Title : start Usage : $start = $fuzzy->start(); Function: get/set start of this range, handling fuzzy_starts Returns : a positive integer representing the start of the location Args : start location on set (can be fuzzy point string) end --- Title : end Usage : $end = $fuzzy->end(); Function: get/set end of this range, handling fuzzy_ends Returns : a positive integer representing the end of the range Args : end location on set (can be fuzzy string) min_start --------- Title : min_start Usage : $min_start = $fuzzy->min_start(); Function: get/set the minimum starting point Returns : the minimum starting point from the contained sublocations Args : integer or undef on set max_start --------- Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get/set maximum starting location of feature startpoint Returns : integer or undef if no maximum starting point. Args : integer or undef on set start_pos_type -------------- Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get/set start position type. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : a string on set min_end ------- Title : min_end Usage : my $minend = $location->min_end(); Function: Get/set minimum ending location of feature endpoint Returns : integer or undef if no minimum ending point. Args : integer or undef on set max_end ------- Title : max_end Usage : my $maxend = $location->max_end(); Function: Get/set maximum ending location of feature endpoint Returns : integer or undef if no maximum ending point. Args : integer or undef on set end_pos_type ------------ Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get/set end position type. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : a string on set seq_id ------ 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 coordinate_policy ----------------- 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 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. to_FTstring ----------- Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: Get/Set seq_id that location refers to Returns : seq_id Args : [optional] seq_id value to set _fuzzypointdecode ----------------- Title : _fuzzypointdecode Usage : ($type,$min,$max) = $self->_fuzzypointdecode('<5'); Function: Decode a fuzzy string. Returns : A 3-element array consisting of the type of location, the minimum integer, and the maximum integer describing the range of coordinates this start or endpoint refers to. Minimum or maximum coordinate may be undefined. : Returns empty array on fail. Args : fuzzypoint string  File: pm.info, Node: Bio/Location/FuzzyLocationI, Next: Bio/Location/NarrowestCoordPolicy, Prev: Bio/Location/Fuzzy, Up: Module List Abstract interface of a Location on a Sequence which has unclear start/end location *********************************************************************************** NAME ==== Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location SYNOPSIS ======== # Get a FuzzyLocationI object somehow print "Fuzzy FT location string is ", $location->to_FTstring(); print "location is of the type ", $location->loc_type, "\n"; 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. 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ loc_type -------- Title : loc_type Usage : my $location_type = $location->loc_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'BETWEEN') Args : none LocationI methods ================= min_start --------- 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 max_start --------- 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 start_pos_type -------------- 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 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none min_end ------- 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 max_end ------- 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 end_pos_type ------------ 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 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none seq_id ------ 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 coordinate_policy ----------------- 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 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. to_FTstring ----------- Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none  File: pm.info, Node: Bio/Location/NarrowestCoordPolicy, Next: Bio/Location/Simple, Prev: Bio/Location/FuzzyLocationI, Up: Module List class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range ************************************************************************************************** NAME ==== Bio::Location::NarrowestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range SYNOPSIS ======== See Bio::Location::CoordinatePolicyI DESCRIPTION =========== CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that always the narrowest possible range is returned, but by using some common sense. This means that e.g. locations like ">5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp, Jason Stajich =================================== Email hlapp@gmx.net, jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start ----- Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. end --- Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object.  File: pm.info, Node: Bio/Location/Simple, Next: Bio/Location/Split, Prev: Bio/Location/NarrowestCoordPolicy, Up: Module List Implementation of a Simple Location on a Sequence ************************************************* NAME ==== Bio::Location::Simple - Implementation of a Simple Location on a Sequence SYNOPSIS ======== my $location = new Bio::Location::Simple(-start => 1, -end => 100, -strand => 1 ); if( $location->strand == -1 ) { printf "complement(%d..%d)\n", $location->start, $location->end; } else { printf "%d..%d\n", $location->start, $location->end; } DESCRIPTION =========== This is an implementation of Bio::LocationI to manage simple location information on a Sequence. 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start ----- Title : start Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range Args : optionaly allows the start to be set : using $loc->start($start) end --- Title : end Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range Args : optionaly allows the end to be set : using $loc->end($start) strand ------ Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandidness (-1, 0, +1) Args : optionaly allows the strand to be set : using $loc->strand($strand) length ------ Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none min_start --------- Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting location of feature startpoint Returns : integer or undef if no minimum starting point. Args : none max_start --------- Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint. In this implementation this is exactly the same as min_start(). Returns : integer or undef if no maximum starting point. Args : none start_pos_type -------------- Title : start_pos_type Usage : my $start_pos_type = $location->start_pos_type(); Function: Get start position type (ie <,>, ^). In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none min_end ------- 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 max_end ------- Title : max_end Usage : my $maxend = $location->max_end(); Function: Get maximum ending location of feature endpoint In this implementation this is exactly the same as min_end(). Returns : integer or undef if no maximum ending point. Args : none end_pos_type ------------ Title : end_pos_type Usage : my $end_pos_type = $location->end_pos_type(); Function: Get end position type (ie <,>, ^) In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none location_type ------------- Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'BETWEEN') Args : none to_FTstring ----------- Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none  File: pm.info, Node: Bio/Location/Split, Next: Bio/Location/SplitLocationI, Prev: Bio/Location/Simple, Up: Module List Implementation of a Location on a Sequence which has multiple locations (start/end points) ****************************************************************************************** NAME ==== Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points) SYNOPSIS ======== my $splitlocation = new Bio::Location::Split(); $splitlocation->add_sub_Location(new Bio::Location::Simple(-start=>1, -end=>30, -strand=>1)); $splitlocation->add_sub_Location(new Bio::Location::Simple(-start=>50, -end=>61, -strand=>1)); my @sublocs = $splitlocation->sub_Location(); my $count = 1; # print the start/end points of the sub locations foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { printf "sub feature %d [%d..%d]\n", $count, $location->start,$location->end, "\n"; $count++; } DESCRIPTION =========== This implementation handles locations which span more than one start/end location, or and/or lie on different sequences. 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ sub_Location ------------ Title : sub_Location Usage : @sublocs = $splitloc->sub_Location(); Function: Returns the array of sublocations making up this compound (split) location. Those sublocations referring to the same sequence as the root split location will be sorted by start position (forward sort) or end position (reverse sort) and come first (before those on other sequences). The sort order can be optionally specified or suppressed by the value of the first argument. The default is a forward sort. Returns : an array of Bio::LocationI implementing objects Args : Optionally 1, 0, or -1 for specifying a forward, no, or reverse sort order add_sub_Location ---------------- Title : add_sub_Location Usage : $splitloc->add_sub_Location(@locationIobjs); Function: add an additional sublocation Returns : number of current sub locations Args : list of Bio::LocationI implementing object(s) to add splittype --------- Title : splittype Usage : $splittype = $fuzzy->splittype(); Function: get/set the split splittype Returns : the splittype of split feature (join, order) Args : splittype to set is_single_sequence ------------------ Title : is_single_sequence Usage : if($splitloc->is_single_sequence()) { print "Location object $splitloc is split ". "but only across a single sequence\n"; } Function: Determine whether this location is split across a single or multiple sequences. This implementation ignores (sub-)locations that do not define seq_id(). The same holds true for the root location. Returns : TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise. Args : none LocationI methods ================= start ----- Title : start Usage : $start = $location->start(); Function: get the starting point of the first (sorted) sublocation Returns : integer Args : none end --- Title : end Usage : $end = $location->end(); Function: get the ending point of the last (sorted) sublocation Returns : integer Args : none min_start --------- Title : min_start Usage : $min_start = $location->min_start(); Function: get the minimum starting point Returns : the minimum starting point from the contained sublocations Args : none max_start --------- 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 start_pos_type -------------- 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 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none min_end ------- 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 max_end ------- 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 end_pos_type ------------ 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 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none seq_id ------ 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 coordinate_policy ----------------- 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 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. to_FTstring ----------- Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none  File: pm.info, Node: Bio/Location/SplitLocationI, Next: Bio/Location/WidestCoordPolicy, Prev: Bio/Location/Split, Up: Module List Abstract interface of a Location on a Sequence which has multiple locations (start/end points) ********************************************************************************************** NAME ==== Bio::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points) SYNOPSIS ======== # get a SplitLocationI somehow print $splitlocation->start, "..", $splitlocation->end, "\n"; my @sublocs = $splitlocation->sub_Location(); my $count = 1; # print the start/end points of the sub locations foreach my $location ( sort { $a->start <=> $b->start } @sublocs ) { printf "sub feature %d [%d..%d]\n", $location->start,$location->end; $count++; } DESCRIPTION =========== This interface encapsulates the necessary methods for representing the location of a sequence feature that has more that just a single start/end pair. Some examples of this are the annotated exons in a gene or the annotated CDS in a sequence file. 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Jason Stajich ====================== Email jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ sub_Location ------------ Title : sub_Location Usage : @locations = $feat->sub_Location(); Function: Returns an array of LocationI objects Returns : An array Args : none splittype --------- Title : splittype Usage : $splittype = $fuzzy->splittype(); Function: get/set the split splittype Returns : the splittype of split feature (join, order) Args : splittype to set is_single_sequence ------------------ Title : is_single_sequence Usage : if($splitloc->is_single_sequence()) { print "Location object $splitloc is split ". "but only across a single sequence\n"; } Function: Determine whether this location is split across a single or multiple sequences. Returns : TRUE if all sublocations lie on the same sequence as the root location (feature), and FALSE otherwise. Args : none LocationI methods ================= min_start --------- 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 max_start --------- 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 start_pos_type -------------- 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 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none min_end ------- 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 max_end ------- 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 end_pos_type ------------ 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 ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none seq_id ------ 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 coordinate_policy ----------------- 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 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. to_FTstring ----------- Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none  File: pm.info, Node: Bio/Location/WidestCoordPolicy, Next: Bio/LocationI, Prev: Bio/Location/SplitLocationI, Up: Module List class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range *********************************************************************************************** NAME ==== Bio::Location::WidestCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range SYNOPSIS ======== See Bio::Location::CoordinatePolicyI DESCRIPTION =========== CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that always the widest possible range is returned, but by using some common sense. This means that e.g. locations like "<5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). 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. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists 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 email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ AUTHOR - Hilmar Lapp, Jason Stajich =================================== Email hlapp@gmx.net, jason@chg.mc.duke.edu APPENDIX ======== The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start ----- Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. end --- Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object.