Inheritance diagram for Bio::EnsEMBL::IdMapping::ScoredMappingMatrix:

Public Member Functions
public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix	new ()

public void	flush ()

public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix	sub_matrix ()

public Float	add_Entry ()

public Float	update_Entry ()

public	remove_Entry ()

public Float	add_score ()

public Float	set_score ()

public Bio::EnsEMBL::IdMapping::Entry	get_Entry ()

public Float	get_score ()

public Arrayref	get_targets_for_source ()

public Arrayref	get_Entries_for_source ()

public Arrayref	get_sources_for_target ()

public Arrayref	get_Entries_for_target ()

public Arrayref	get_all_Entries ()

public Arrayref	get_all_sources ()

public Arrayref	get_all_targets ()

public Int	get_entry_count ()

public Int	size ()

public Int	get_source_count ()

public Int	get_target_count ()

public Arrayref	get_min_max_scores ()

public Float	get_average_score ()

public Int	merge ()

public void	log ()

public String	to_string ()

Public Member Functions inherited from Bio::EnsEMBL::IdMapping::Serialisable
public Bio::EnsEMBL::IdMapping::Serialisable	new ()

public String	write_to_file ()

public Bio::EnsEMBL::IdMapping::Serialisable	read_from_file ()

public String	dump_path ()

public String	cache_file_name ()

public String	cache_file ()

public Boolean	loaded ()

Detailed Description

Synopsis

# create a new ScoredMappingMatrix
my $gene_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
  -DUMP_PATH  => $dump_path,
  -CACHE_FILE => 'gene_scores.ser',
);
 
# add entries
my $gene_scores->add_Entry($entry1);
 
# serialise to file
$gene_scores->write_to_file;
 
# later, read these gene_scores from file
my $gene_scores1 = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
  -DUMP_PATH  => $dump_path,
  -CACHE_FILE => 'gene_gene_scores.ser',
);
$gene_scores1->read_from_file;

Description

This object represents a collection of scores between source and target
objects.  It holds a list of Bio::EnsEMBL::IdMapping::Entry objects and
has methods to retrieve indiviual or all Entries, as well as derived
data like number of unique sources or targets, or various counts and
averages.

It is the main collection for dealing with scored relationships in the
stable Id mapping application.

Definition at line 44 of file ScoredMappingMatrix.pm.

Member Function Documentation

◆ add_Entry()

public Float Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::add_Entry ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry $entry - Entry to add
  Example     :

$gene_scores->add_Entry($entry);

  Description : Adds an Entry to the scoring matrix.
  Return type : Float - the Entry's score
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ add_score()

public Float Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::add_score ( )

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Arg[2]      : Int $target - target object's internal Id ("dbID")
  Arg[3]      : Float $score - score for source/target pair
  Example     :

$gene_scores->add_score(1234, 5678, 0.997);

  Description : Adds a score for a source/target pair to the scoring matrix.
                This is a low-level version of add_Entry().
  Return type : Float - the score
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ flush()

public void Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::flush ( )

  Example     :

$gene_scores->flush;

  Description : Flushes (empties) the scoring matrix.
  Return type : none
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_all_Entries()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_all_Entries ( )

  Example     :

 foreach my $entry (@{ $gene_scores->get_all_Entries }) {
@section autotoc_md12 do something with the entry
                }

  Description : Returns a list of all Entries in the scoring matrix.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_all_sources()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_all_sources ( )

  Example     :

my @sources = @{ $gene_scores->get_all_sources };

  Description : Returns a list of all sources in the scoring matrix.
  Return type : Arrayref of Int (source objects' internal Ids)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_all_targets()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_all_targets ( )

  Example     :

my @targets = @{ $gene_scores->get_all_targets };

  Description : Returns a list of all targets in the scoring matrix.
  Return type : Arrayref of Int (target objects' internal Ids)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_average_score()

public Float Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_average_score ( )

  Example     :

my $avg_score = $gene_scores->get_average_score;

  Description : Returns the average (mean) score in the matrix.
  Return type : Float
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_Entries_for_source()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_Entries_for_source ( )

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Example     :

my @entries = @{ $gene_scores->get_Entries_for_source(1234) };

  Description : Returns a list of all Entries in the scoring matrix for a given
                source object.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_Entries_for_target()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_Entries_for_target ( )

  Arg[1]      : Int $target - target object's internal Id ("dbID")
  Example     :

my @entries = @{ $gene_scores->get_Entries_for_target(5678) };

  Description : Returns a list of all Entries in the scoring matrix for a given
                target object.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry objects
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_Entry()

public Bio::EnsEMBL::IdMapping::Entry Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_Entry ( )

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Arg[2]      : Int $target - target object's internal Id ("dbID")
  Example     :

my $entry = $gene_scores->get_Entry($source_gene->id,

$target_gene->id);

  Description : Gets an Entry from the scoring matrix for a given source and
                target object.
  Return type : Bio::EnsEMBL::IdMapping::Entry or undef
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_entry_count()

public Int Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_entry_count ( )

  Example     :

my $num_entries = $gene_scores->get_entry_count;

  Description : Returns the number of Entries in the scoring matrix.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_min_max_scores()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_min_max_scores ( )

  Example     :

my ($min_score, $max_score) =

@{ $gene_scores->get_min_max_scores };

  Description : Returns the mininum and maximum score in the scoring matrix.
  Return type : Arrayref of Float [min_score, max_score]
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_score()

public Float Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_score ( )

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Arg[2]      : Int $target - target object's internal Id ("dbID")
  Example     :

my $score = $gene_scores->get_score($source_gene->id,

$target_gene->id);

  Description : Gets the score from the scoring matrix for a given source and
                target object.
  Return type : Float or undef
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_source_count()

public Int Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_source_count ( )

  Example     :

my $num_sources = $gene_scores->get_source_count;

  Description : Returns the number of distinct sources in the scoring matrix.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_sources_for_target()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_sources_for_target ( )

  Arg[1]      : Int $target - target object's internal Id ("dbID")
  Example     :

my @sources = @{ $gene_scores->get_sources_for_target(5678) };

  Description : Returns a list of all sources which have a score against a given
                target object.
  Return type : Arrayref of Int (source objects' internal Ids)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_target_count()

public Int Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_target_count ( )

  Example     :

my $num_targets = $gene_scores->get_target_count;

  Description : Returns the number of distinct targets in the scoring matrix.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ get_targets_for_source()

public Arrayref Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::get_targets_for_source ( )

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Example     :

my @targets = @{ $gene_scores->get_targets_for_source(1234) };

  Description : Returns a list of all targets which have a score against a given
                source object.
  Return type : Arrayref of Int (target objects' internal Ids)
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ log()

public void Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::log ( )

  Arg[1]      : String $type - object type (e.g. 'gene')
  Arg[2]      : String $dump_path - path for writing output
  Example     :

$gene_scores->log('gene', $conf->param('basedir'));

  Description : Logs all Entries in the scoring matrix to a file. Used for
                debugging.
  Return type : none
  Exceptions  : thrown on I/0 error
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ merge()

public Int Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::merge ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::ScoredMappingMatrix $matrix - another
                matrix to merge with
  Example     :

my $update_count = $gene_scores->merge($more_gene_scores);

  Description : Merges two scoring matrices. If there's an Entry for a
                source/target pair in both matrices, the higher score will be
                retained.
  Return type : Int - number of Entries added or updated
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ new()

public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::new ( )

  Arg[1-N]    : see superclass
  Example     :

my $gene_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
                 -DUMP_PATH   => $dump_path,
                 -CACHE_FILE  => 'gene_scores.ser',
               );

  Description : Constructor.
  Return type : Bio::EnsEMBL::IdMapping::ScoredMappingMatrix
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ remove_Entry()

public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::remove_Entry ( )

Undocumented method

Code:

click to view

◆ set_score()

public Float Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::set_score ( )

  Arg[1]      : Int $source - source object's internal Id ("dbID")
  Arg[2]      : Int $target - target object's internal Id ("dbID")
  Arg[3]      : Float $score - score for source/target pair
  Example     :

$gene_scores->set_score(1234, 5678, 0.997);

  Description : Sets the score for a source/target pair in the scoring matrix.
                This method is similar to add_score, but assumes that the Entry
                has been added before, so won't update the sources and target
                lists.
  Return type : Float - the score
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ size()

public Int Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::size ( )

  Example     :

my $size = $gene_scores->size;

  Description : Returns the size of the scoring matrix. Same value as returned
                by get_entry_count().
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ sub_matrix()

public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::sub_matrix ( )

  Arg[1]      : Int $start - start index (inclusive)
  Arg[2]      : Int $end - end index (inclusive)
  Example     :

# get the first 1000 elements in the matrix

my $sub_matrix = $gene_scores->sub_matrix(1, 1000);

  Description : Returns a sub-matrix of the ScoredMappingMatrix. The arguments
                ($start and $end) specify the position of the first and last
                element to return (inclusive, counting starts with element 1,
                not 0)
  Return type : Bio::EnsEMBL::IdMapping::ScoredMappingMatrix
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ to_string()

public String Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::to_string ( )

  Example     :

print LOG $gene_scores->to_string, "\n";

  Description : Returns a string representation of the scoring matrix. This is
                simply a multi-line string, where each line is a stringified
                Entry.
                Useful for debugging and logging.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

◆ update_Entry()

public Float Bio::EnsEMBL::IdMapping::ScoredMappingMatrix::update_Entry ( )

  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry $entry - Entry to update
  Example     :

$gene_scores->update_Entry($entry);

  Description : Updates an Entry (or rather its score) in the scoring matrix.
                Actually delegates to add_Entry(), only there as an intuitively
                named wrapper.
  Return type : Float - the Entry's score
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

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

ensembl/modules/Bio/EnsEMBL/IdMapping/ScoredMappingMatrix.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ add_Entry()

◆ add_score()

◆ flush()

◆ get_all_Entries()

◆ get_all_sources()

◆ get_all_targets()

◆ get_average_score()

◆ get_Entries_for_source()

◆ get_Entries_for_target()

◆ get_Entry()

◆ get_entry_count()

◆ get_min_max_scores()

◆ get_score()

◆ get_source_count()

◆ get_sources_for_target()

◆ get_target_count()

◆ get_targets_for_source()

◆ log()

◆ merge()

◆ new()

◆ remove_Entry()

◆ set_score()

◆ size()

◆ sub_matrix()

◆ to_string()

◆ update_Entry()