Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::SplicingTranscriptPair Class Reference
Inheritance diagram for Bio::EnsEMBL::SplicingTranscriptPair:

List of all members.


Class Summary

Synopsis

  my $ase = Bio::EnsEMBL::SplicingTranscriptPair-\>new(
    -START  =\> 123,
    -END    =\> 1045,
    -TRANSCRIPT_ID_1 =\> $tran1-\>dbID,
    -TRANSCRIPT_ID_2 =\> %tran2-\>dbID
  );

Description

A representation of an Alternative Splicing Transcrript Pair within the Ensembl system.
 

Definition at line 23 of file SplicingTranscriptPair.pm.

Available Methods

protected _deprecated_transform ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public add_sub_SeqFeature ()
public Bio::EnsEMBL::Analysis analysis ()
public contig ()
public String coord_system_name ()
public Int dbID ()
public String display_id ()
public end ()
public Boolean Or Undef equals ()
public Bio::EnsEMBL::Slice feature_Slice ()
public flush_sub_SeqFeature ()
public Reference get_all_alt_locations ()
public get_all_DAS_Features ()
public Bio::EnsEMBL::Gene get_nearest_Gene ()
public List get_overlapping_Genes ()
public id ()
public Boolean is_stored ()
public Int length ()
public void move ()
public Bio::EnsEMBL::Feature new ()
public Bio::EnsEMBL::Feature new_fast ()
public Boolean overlaps ()
public List project ()
public List project_to_slice ()
public Undef seq ()
public Int seq_region_end ()
public Unsigned seq_region_length ()
public String seq_region_name ()
public Int seq_region_start ()
public Boolean seq_region_strand ()
public String seqname ()
public Bio::EnsEMBL::Slice slice ()
public String species ()
public start ()
public Int strand ()
public sub_SeqFeature ()
public Hashref summary_as_hash ()
public transcript_id_1 ()
public transcript_id_2 ()
public Bio::EnsEMBL::Feature transfer ()
public Bio::EnsEMBL::Feature transform ()

Method Documentation

protected Bio::EnsEMBL::Feature::_deprecated_transform ( ) [inherited]

Undocumented method

Code:
click to view
public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Feature::add_sub_SeqFeature ( ) [inherited]

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Feature::analysis ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::Analysis $analysis
  Example    : $feature->analysis(new Bio::EnsEMBL::Analysis(...))
  Description: Getter/Setter for the analysis that is associated with 
               this feature.  The analysis describes how this feature 
               was derived.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DensityFeature.

public Bio::EnsEMBL::Feature::contig ( ) [inherited]

Undocumented method

Code:
click to view
public String Bio::EnsEMBL::Feature::coord_system_name ( ) [inherited]
  Arg [1]    : none
  Example    : print $feature->coord_system_name()
  Description: Gets the name of the coord_system which this feature is on.
               Returns undef if this Feature is not on a slice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Feature::display_id ( ) [inherited]
  Arg [1]    : none
  Example    : print $f->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  It is overridden by subclasses to
               return an appropriate value for objects of that particular 
               class.  If no appropriate display id is available an empty
               string is returned instead.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::FeaturePair, Bio::EnsEMBL::Gene, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::MarkerFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::RepeatFeature, Bio::EnsEMBL::SimpleFeature, and Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::SplicingTranscriptPair::end ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Feature.

public Boolean Or Undef Bio::EnsEMBL::Feature::equals ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::Feature object
  Example       : if ($featureA->equals($featureB)) { ... }
  Description   : Compares two features using various criteria.  The
                  test for eqality goes through the following list and
                  terminates at the first true match:
                  1. If the two features are the same object, they are
                     equal.
                  2. If they are of different types (e.g., transcript
                     and gene), they are *not* equal.
                  3. If they both have dbIDs: if these are the same,
                     then they are equal, otherwise not.
                  4. If they both have slices and analysis objects:
                     if the analysis dbIDs are the same and the
                     seq_region_id are the same, along with
                     seq_region_start and seq_region_end, then they are
                     equal, otherwise not.
                  If none of the above is able to determine equality,
                  undef is returned.
    Return type : tri-Boolean (0, 1, undef = "unknown")
    Exceptions  : Thrown if a non-feature is passed as the argument.
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::feature_Slice ( ) [inherited]
  Args       : none
  Example    : $slice = $feature->feature_Slice()
  Description: This is a convenience method to return a slice that covers the
               Area of this feature. The feature start will be at 1 on it, and
               it will have the length of this feature.
  Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached
               Slice.
  Exceptions : warning if Feature does not have attached slice.
  Caller     : web drawing code
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Feature::flush_sub_SeqFeature ( ) [inherited]

Undocumented method

Code:
click to view
public Reference Bio::EnsEMBL::Feature::get_all_alt_locations ( ) [inherited]
  Arg [1]    : none
  Example    : @features = @{$feature->get_all_alt_locations()};
               foreach $f (@features) {
                 print $f->slice->seq_region_name,' ',$f->start, $f->end,"\\n";
               }
  Description: Retrieves shallow copies of this feature in its alternate
               locations.  A feature can be considered to have multiple
               locations when it sits on a alternative structural haplotype
               or when it is on a pseudo autosomal region.  Most features will
               just return a reference to an empty list though.
               The features returned by this method will be on a slice which
               covers the entire alternate region.
               Currently this method does not take into account alternate
               locations on the alternate locations (e.g. a reference
               sequence may have multiple alternate haplotypes.  Asking
               for alternate locations of a feature on one of the alternate
               haplotypes will give you back the reference location, but not
               locations on the other alternate haplotypes).
  Returntype : reference to list of features of the same type of this feature.
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Feature::get_nearest_Gene ( ) [inherited]
  Description: Get all the nearest  gene to the feature
  Returntype : Bio::EnsEMBL::Gene
  Caller     : general
  Status     : UnStable
 
Code:
click to view
public List Bio::EnsEMBL::Feature::get_overlapping_Genes ( ) [inherited]
  Description: Get all the genes that overlap this feature.
  Returntype : list ref of Bio::EnsEMBL::Gene
  Caller     : general
  Status     : UnStable
 
Code:
click to view
public Bio::EnsEMBL::Feature::id ( ) [inherited]

Undocumented method

Code:
click to view
public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Feature::length ( ) [inherited]
  Arg [1]    : none
  Example    : $length = $feat->length();
  Description: Returns the length of this feature
  Returntype : Integer
  Exceptions : Throws if end < start and the feature is not on a
               circular slice
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Intron, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.

public void Bio::EnsEMBL::Feature::move ( ) [inherited]
  Arg [1]    : int start
  Arg [2]    : int end
  Arg [3]    : (optional) int strand
  Example    : None
  Description: Sets the start, end and strand in one call rather than in 
               3 seperate calls to the start(), end() and strand() methods.
               This is for convenience and for speed when this needs to be
               done within a tight loop.
  Returntype : none
  Exceptions : Thrown is invalid arguments are provided
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, and Bio::EnsEMBL::Map::QtlFeature.

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::new ( ) [inherited]
  Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
                feature is on. The coordinates of the created feature are
                relative to the start of the slice.
  Arg [-START]: The start coordinate of this feature relative to the start
                of the slice it is sitting on.  Coordinates start at 1 and
                are inclusive.
  Arg [-END]  : The end coordinate of this feature relative to the start of
                the slice it is sitting on.  Coordinates start at 1 and are
                inclusive.
  Arg [-STRAND]: The orientation of this feature.  Valid values are 1,-1,0.
  Arg [-SEQNAME] : A seqname to be used instead of the default name of the 
                of the slice.  Useful for features that do not have an 
                attached slice such as protein features.
  Arg [-dbID]   : (optional) internal database id
  Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
  Example    : $feature = Bio::EnsEMBL::Feature->new(-start    => 1, 
                                                     -end      => 100,
                                                     -strand   => 1,
                                                     -slice    => $slice,
                                                     -analysis => $analysis);
  Description: Constructs a new Bio::EnsEMBL::Feature.  Generally subclasses
               of this method are instantiated, rather than this class itself.
  Returntype : Bio::EnsEMBL::Feature
  Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
  Caller     : general, subclass constructors
  Status     : Stable
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::Storable.

Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::DnaDnaAlignFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::FeaturePair, Bio::EnsEMBL::Gene, Bio::EnsEMBL::Intron, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::MarkerFeature, Bio::EnsEMBL::Map::QtlFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::Operon, Bio::EnsEMBL::OperonTranscript, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::ProteinFeature, Bio::EnsEMBL::RepeatFeature, Bio::EnsEMBL::SimpleFeature, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::new_fast ( ) [inherited]
  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Feature
  Caller     : general, subclass constructors
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::DnaPepAlignFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::RepeatFeature, and Bio::EnsEMBL::SimpleFeature.

public Boolean Bio::EnsEMBL::Feature::overlaps ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Feature $f
               The other feature you want to check overlap with this feature
               for.
  Description: This method does a range comparison of this features start and
               end and compares it with another features start and end. It will
               return true if these ranges overlap and the features are on the
               same seq_region.
  Returntype : TRUE if features overlap, FALSE if they don't
  Exceptions : warning if features are on different seq_regions
  Caller     : general
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::Feature::project ( ) [inherited]
  Arg [1]    : string $name
               The name of the coordinate system to project this feature onto
  Arg [2]    : string $version (optional)
               The version of the coordinate system (such as 'NCBI34') to
               project this feature onto
  Example    :
    my $clone_projection = $feature->project('clone');
    foreach my $seg (@$clone_projection) {
      my $clone = $seg->to_Slice();
      print "Features current coords ", $seg->from_start, '-',
        $seg->from_end, " project onto clone coords " .
        $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
        $clone->strand, "\\n";
    }
  Description: Returns the results of 'projecting' this feature onto another
               coordinate system.  This is useful to see where a feature
               would lie in a coordinate system in which it
               crosses a boundary.
               This method returns a reference to a list of
               Bio::EnsEMBL::ProjectionSegment objects.
               ProjectionSegments are blessed arrays and can also be used as
               triplets [from_start,from_end,to_Slice]. The from_start and
               from_end are the coordinates relative to the feature start.
               For example, if a feature is current 100-200bp on a slice
               then the triplets returned might be:
               [1,50,$slice1],
               [51,101,$slice2]
               The to_Slice is a slice spanning the region on the requested
               coordinate system that this feature projected to.
               If the feature projects entirely into a gap then a reference to
               an empty list is returned.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
               which can also be used as [$start,$end,$slice] triplets
  Exceptions : slice does not have an adaptor
  Caller     : general
  Status     : Stable
 
Code:
click to view
public List Bio::EnsEMBL::Feature::project_to_slice ( ) [inherited]
  Arg [1]    : slice to project to
  Example    :
    my $clone_projection = $feature->project_to_slice($slice);
    foreach my $seg (@$clone_projection) {
      my $clone = $seg->to_Slice();
      print "Features current coords ", $seg->from_start, '-',
        $seg->from_end, " project onto clone coords " .
        $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
        $clone->strand, "\\n";
    }
  Description: Returns the results of 'projecting' this feature onto another
               slcie . This is useful to see where a feature
               would lie in a coordinate system in which it
               crosses a boundary.
               This method returns a reference to a list of
               Bio::EnsEMBL::ProjectionSegment objects.
               ProjectionSegments are blessed arrays and can also be used as
               triplets [from_start,from_end,to_Slice]. The from_start and
               from_end are the coordinates relative to the feature start.
               For example, if a feature is current 100-200bp on a slice
               then the triplets returned might be:
               [1,50,$slice1],
               [51,101,$slice2]
               The to_Slice is a slice spanning the region on the requested
               coordinate system that this feature projected to.
               If the feature projects entirely into a gap then a reference to
               an empty list is returned.
  Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
               which can also be used as [$start,$end,$slice] triplets
  Exceptions : slice does not have an adaptor
  Caller     : general
  Status     : At Risk
 
Code:
click to view
public Undef Bio::EnsEMBL::Feature::seq ( ) [inherited]
  Args       : none
  Example    : my $dna_sequence = $simple_feature->seq();
  Description: Returns the dna sequence from the attached slice and 
               attached database that overlaps with this feature.
               Returns undef if there is no slice or no database.
               Returns undef if this feature is unstranded (i.e. strand=0).
  Returntype : undef or string
  Exceptions : warning if this feature is not stranded
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Transcript.

public Int Bio::EnsEMBL::Feature::seq_region_end ( ) [inherited]
  Arg [1]    : none
  Example    : print $feature->seq_region_end();
  Description: Convenience method which returns the absolute end of this
               feature on the seq_region, as opposed to the relative (slice)
               position.
               Returns undef if this feature is not on a slice.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Unsigned Bio::EnsEMBL::Feature::seq_region_length ( ) [inherited]
  Arg [1]    : none
  Example    : print $feature->seq_region_length();
  Description: Returns the length of the seq_region which this feature is on 
               Returns undef if this Feature is not on a slice.
  Returntype : unsigned int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Feature::seq_region_name ( ) [inherited]
  Arg [1]    : none
  Example    : print $feature->seq_region_name();
  Description: Gets the name of the seq_region which this feature is on.
               Returns undef if this Feature is not on a slice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Feature::seq_region_start ( ) [inherited]
  Arg [1]    : none
  Example    : print $feature->seq_region_start();
  Description: Convenience method which returns the absolute start of this
               feature on the seq_region, as opposed to the relative (slice) 
               position.
               Returns undef if this feature is not on a slice.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Boolean Bio::EnsEMBL::Feature::seq_region_strand ( ) [inherited]
  Arg [1]    : none
  Example    : print $feature->seq_region_strand();
  Description: Returns the strand of the seq_region which this feature is on 
               (i.e. feature_strand * slice_strand)
               Returns undef if this Feature is not on a slice.
  Returntype : 1,0,-1 or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::Feature::seqname ( ) [inherited]
  Arg [1]    : (optional) $seqname
  Example    : $seqname = $feat->seqname();
  Description: Getter/Setter for the name of the sequence that this feature
               is on. Normally you can get away with not setting this value
               and it will default to the name of the slice on which this
               feature is on.  It is useful to set this value on features which
               do not ordinarily sit on features such as ProteinFeatures which
               sit on peptides.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::slice ( ) [inherited]
  Arg [1]    : (optional) Bio::EnsEMBL::Slice $slice
  Example    : $seqname = $feature->slice()->name();
  Description: Getter/Setter for the Slice that is associated with this 
               feature.  The slice represents the underlying sequence that this
               feature is on.  Note that this method call is analagous to the
               old SeqFeature methods contig(), entire_seq(), attach_seq(),
               etc.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Feature::species ( ) [inherited]
  Example			: $feature->species();
  Description	: Shortcut to the feature's DBAdaptor and returns its species name 
  Returntype 	: String the species name
  Exceptions 	: Thrown if there is no attached adaptor
  Caller      : Webcode
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::FeaturePair.

public Bio::EnsEMBL::SplicingTranscriptPair::start ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::Feature.

public Int Bio::EnsEMBL::Feature::strand ( ) [inherited]
  Arg [1]    : (optional) int $strand
  Example    : $feat->strand(-1);
  Description: Getter/Setter for the strand of this feature relative to the
               slice it is on.  0 is an unknown or non-applicable strand.  
               -1 is the reverse (negative) strand and 1 is the forward 
               (positive) strand.  No other values are permitted.
  Returntype : int
  Exceptions : thrown if an invalid strand argument is passed
  Caller     : general
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::QtlFeature, and Bio::EnsEMBL::ProteinFeature.

public Bio::EnsEMBL::Feature::sub_SeqFeature ( ) [inherited]

Undocumented method

Code:
click to view
public Hashref Bio::EnsEMBL::Feature::summary_as_hash ( ) [inherited]
  Example       : $feature_summary = $feature->summary_as_hash();
  Description   : Retrieves a textual summary of this Feature.
	              Should be overidden by subclasses for specific tweaking
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::SplicingTranscriptPair::transcript_id_1 ( )

Undocumented method

Code:
click to view
public Bio::EnsEMBL::SplicingTranscriptPair::transcript_id_2 ( )

Undocumented method

Code:
click to view
public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transfer ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice to transfer this feature to
  Example    : $feature = $feature->transfer($slice);
               next if(!defined($feature));
  Description: Returns a copy of this feature which has been shifted onto
               another slice.
               If the new slice is in a different coordinate system the
               feature is transformed first and then placed on the slice.
               If the feature would be split across a coordinate system
               boundary or mapped to a gap undef is returned instead.
               If the feature cannot be placed on the provided slice because
               it maps to an entirely different location, undef is returned
               instead.
  Returntype : Bio::EnsEMBL::Feature (or undef)
  Exceptions : throw on incorrect argument
               throw if feature does not have attached slice
  Caller     : general, transform()
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, and Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::transform ( ) [inherited]
  Arg [1]    : string $coord_system
               The coord system to transform this feature to.
  Arg [2]    : string $version (optional)
               The version of the coord system to transform this feature to.
  Example    : $feature = $feature->transform('contig');
               next if(!defined($feature));
  Description: Returns a copy of this feature, but converted to a different
               coordinate system. The converted feature will be placed on a
               slice which spans an entire sequence region of the new
               coordinate system. If the requested coordinate system is the
               same coordinate system it is simply placed on a slice which
               spans the entire seq_region (as opposed to the original slice
               which may have only partially covered the seq_region).
               If a feature spans a boundary in the new coordinate system,
               undef is returned instead.
               For example, transforming an exon in contig coordinates to one 
               in chromosomal coodinates will place the exon on a slice of an 
               entire chromosome.
  Returntype : Bio::EnsEMBL::Feature (or undef)
  Exceptions : thrown if an invalid coordinate system is provided
               warning if Feature is not attached to a slice
  Caller     : general, transfer()
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::Gene, Bio::EnsEMBL::PepDnaAlignFeature, Bio::EnsEMBL::PredictionExon, Bio::EnsEMBL::PredictionTranscript, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.


The documentation for this class was generated from the following file: