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Summary

Bio::EnsEMBL::DBSQL::Funcgen::ResultSetAdaptor - A database adaptor for fetching and
storing ResultSet objects.

Package variables

Included modules

Inherit

Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor

Synopsis

my $rset_adaptor = $db->get_ResultSetAdaptor();
my @rsets = @{$rset_adaptor->fetch_all_ResultSets_by_Experiment()};
#my @displayable_rsets = @{$rset_adaptor->fetch_all_displayable_ResultSets()};
#Other methods?
#by FeatureType, CellType all with displayable flag?

Description

The ResultSetAdaptor is a database adaptor for storing and retrieving
ResultSet objects.

Methods

Methods description

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns a list of columns to use for queries.
  Returntype : List of strings
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns an additional table joining constraint to use for
			   queries.
  Returntype : List of strings
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns an ORDER BY clause. Sorting by oligo_feature_id would be
			   enough to eliminate duplicates, but sorting by location might
			   make fetching features on a slice faster.
  Returntype : String
  Exceptions : None
  Caller     : generic_fetch
  Status     : At Risk

  Arg [1]    : DBI statement handle object
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Creates Array objects from an executed DBI statement
			   handle.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Experiment objects
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns the names and aliases of the tables to use for queries.
  Returntype : List of listrefs of strings
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Arg[0]     : Bio::EnsEMBL::Slice - Slice to retrieve results from
  Arg[1]     : Bio::EnsEMBL::Funcgen::ResultSet - ResultSet to retrieve results from
  Arg[2]     : optional string - STATUS e.g. 'DIPLAYABLE'
  Example    : my @rfeatures = @{$rsa->fetch_ResultFeatures_by_Slice_ResultSet($slice, $rset, 'DISPLAYABLE')};
  Description: Gets a list of lightweight ResultFeatures from the ResultSet and Slice passed.
               Replicates are combined using a median of biological replicates based on 
               their mean techinical replicate scores
  Returntype : List of Bio::EnsEMBL::Funcgen::ResultFeature
  Exceptions : Warns if not experimental_chip ResultSet
               Throws if no Slice passed
               Warns if 
  Caller     : general
  Status     : At risk

  Arg [1]    : Bio::EnsEMBL::Funcgen::Experiment
  Example    : my @rsets = @{$rset_adaptor->fetch_all_by_Experiment($exp)};
  Description: Retrieves a list of Bio::EnsEMBL::Funcgen::ResultSets from the Experiment
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ResultSet objects
  Exceptions : None
  Caller     : general
  Status     : At Risk

  Arg [1]    : Bio::EnsEMBL::Funcgen::Experiment
  Arg [2]    : Bio::EnsEMBL::Analysis
  Example    : my @rsets = @{$rset_adaptor->fetch_all_by_Experiment_Analysis($exp, $anal)};
  Description: Retrieves a list of Bio::EnsEMBL::Funcgen::ResultSets with the given Analysis from the Experiment
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ResultSet objects
  Exceptions : Throws if Analysis is not valid and stored
  Caller     : general
  Status     : At Risk

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : string - type of array (e.g. AFFY or OLIGO)
  Arg [3]    : (optional) string - logic name
  Example    : my $slice = $sa->fetch_by_region('chromosome', '1');
               my $features = $ofa->fetch_by_Slice_type($slice, 'OLIGO');
  Description: Retrieves a list of features on a given slice that are created
               by probes from the specified type of array.
  Returntype : Listref of Bio::EnsEMBL::OligoFeature objects
  Exceptions : Throws if no array type is provided
  Caller     : General
  Status     : At Risk

  Arg [1]    : string - ResultSet name
  Example    : ($rset) = @{$rseta->fetch_all_by_name($exp->name().'_IMPORT')};
  Description: Retrieves ResultSets based on the name attribute
  Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::ResultSet objects
  Exceptions : Throws if no name provided
  Caller     : General
  Status     : At Risk - remove all, there should only be one?

  Arg [1]    : string - ResultSet name
  Arg [2]    : Bio::EnsEMBL::Funcgen::Analysis
  Example    : ($rset) = @{$rseta->fetch_by_name($exp->name().'_IMPORT')};
  Description: Retrieves a ResultSet based on the name attribute
  Returntype : Bio::EnsEMBL::Funcgen::ResultSet
  Exceptions : Throws if no name provided
  Caller     : General
  Status     : At Risk - remove all, there should only be one?

  Arg [1]    : Bio::EnsEMBL::Funcgen::ResultSet
  Arg [2]    : Bio::EnsEMBL::Analysis
  Example    : my @rsets = @{$rset_adaptor->fetch_all_by_Experiment_Analysis($exp, $anal)};
  Description: Retrieves a list of Bio::EnsEMBL::Funcgen::ResultSets with the given Analysis from the Experiment
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ResultSet objects
  Exceptions : Throws if ResultSet not valid or stored
  Caller     : general
  Status     : At Risk

  Example    : my @web_optimised_set = @{$rset_adaptor->fetch_all_result_feature_sets};
  Description: Retrieves a list of Bio::EnsEMBL::Funcgen::ResultSets which have been extracted 
               and compressed in the result_feature table.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::ResultSet objects
  Exceptions : None
  Caller     : general
  Status     : At Risk - remove and add status

  Arg [1]    : int - probe dbID
  Arg [2]    : Bio::EnsEMBL::Funcgen::ResultSet
  Example    : my @probe_results = @{$ofa->fetch_results_by_ProbeFeature_ResultSet($pid, $result_set)};
  Description: Gets result for a given probe in a ResultSet
  Returntype : ARRAYREF
  Exceptions : throws if args not valid
  Caller     : General
  Status     : At Risk - Change to take Probe?

  Args       : None
  Example    : my @rsets_ids = @{$rsa->list_dbIDs()};
  Description: Gets an array of internal IDs for all ProbeFeature objects in
               the current database.
  Returntype : List of ints
  Exceptions : None
  Caller     : general
  Status     : stable

  Arg[0]     : HASHREF - chip_channel_id => @scores pairs
  #Arg[1]     : Bio::EnsEMBL::Funcgen::ResultSet - ResultSet to retrieve results from
  Example    : my @rfeatures = @{$rsa->fetch_ResultFeatures_by_Slice_ResultSet($slice, $rset, 'DISPLAYABLE')};
  Description: Gets a list of lightweight ResultFeatures from the ResultSet and Slice passed.
               Replicates are combined using a median of biological replicates based on 
               their mean techinical replicate scores
  Returntype : List of Bio::EnsEMBL::Funcgen::ResultFeature
  Exceptions : None
  Caller     : general
  Status     : At risk

  Args       : List of Bio::EnsEMBL::Funcgen::ResultSet objects
  Example    : $rsa->store(@rsets);
  Description: Stores or updates previously stored ResultSet objects in the database. 
  Returntype : None
  Exceptions : Throws if a List of ResultSet objects is not provided or if
               an analysis is not attached to any of the objects
  Caller     : General
  Status     : At Risk

  Args       : Bio::EnsEMBL::Funcgen::ResultSet
  Example    : $rsa->store_chip_channel(@rset);
  Description: Convinience methods extracted from store to allow updating of chip_channel entries 
               during inline result processing which would otherwise be troublesome due to the need
               for a chip_channel_id in the result table before the ResultSet would normally be stored
               i.e. after it has been fully populated with data.
  Returntype : Bio::EnsEMBL::Funcgen::ResultSet
  Exceptions : Throws if a stored ResultSet object is not provided
  Caller     : General
  Status     : At Risk

Methods code

sub _columns {

	my $self = shift;

	return qw(
			  rs.result_set_id    rs.analysis_id
			  cc.table_name       cc.chip_channel_id
			  cc.table_id         rs.name
			  rs.cell_type_id     rs.feature_type_id
		 );

}

sub _default_where_clause {

  my $self = shift;
	
  #return 'rs.result_set_id = cc.result_set_id AND ((cc.table_name="experimental_chip" AND cc.table_id = ec.experimental_chip_id) OR (cc.table_name="channel" AND cc.table_id=c.channel_id AND ec.experimental_chip_id=c.experimental_chip_id))';

  
  #no need for complex join due to adding feature/cell_type columns to result_set
  #This was done to allow separation of top level rset with same name but different
  #cell or feature_types
  return 'rs.result_set_id = cc.result_set_id';

}

sub _final_clause {

  #do not mess with this!
  return ' GROUP by cc.chip_channel_id, cc.result_set_id ORDER BY rs.result_set_id, rs.cell_type_id, rs.feature_type_id';

}

sub _objs_from_sth {

  my ($self, $sth) = @_;
  
  my (@rsets, $last_id, $rset, $dbid, $anal_id, $anal, $ftype, $ctype, $table_id, $name);
  my ($sql, $table_name, $cc_id, $ftype_id, $ctype_id, $rf_set);
  my $a_adaptor = $self->db->get_AnalysisAdaptor();
  my $ft_adaptor = $self->db->get_FeatureTypeAdaptor();
  my $ct_adaptor = $self->db->get_CellTypeAdaptor(); 
  $sth->bind_columns(\$dbid,\$ anal_id,\$ table_name,\$ cc_id,\$ 
					 table_id,\$ name,\$ ctype_id,\$ ftype_id);
  
  #this fails if we delete entries from the joined tables
  #causes problems if we then try and store an rs which is already stored

  while ( $sth->fetch() ) {


    if(! $rset || ($rset->dbID() != $dbid)){
      
      push @rsets, $rset if $rset;

      $anal = (defined $anal_id) ? $a_adaptor->fetch_by_dbID($anal_id) : undef;
      $ftype = (defined $ftype_id) ? $ft_adaptor->fetch_by_dbID($ftype_id) : undef;
      $ctype = (defined $ctype_id) ? $ct_adaptor->fetch_by_dbID($ctype_id) : undef;
           

      $rset = Bio::EnsEMBL::Funcgen::ResultSet->new(
													-DBID         => $dbid,
													-NAME         => $name,
													-ANALYSIS     => $anal,
													-TABLE_NAME   => $table_name,
													-FEATURE_TYPE => $ftype,
													-CELL_TYPE    => $ctype,
													#-RESULT_FEATURE_SET => $rf_set,#Change to add_status
													-ADAPTOR      => $self,
												   );
    }
    
    #This assumes logical association between chip from the same exp, confer in store method?????????????????

    if(defined $rset->feature_type()){    
      throw("ResultSet does not accomodate multiple FeatureTypes") if ($ftype_id != $rset->feature_type->dbID());
    }
    
    if(defined $rset->cell_type()){
      throw("ResultSet does not accomodate multiple CellTypes") if ($ctype_id != $rset->cell_type->dbID());
    }

    #we're not controlling ctype and ftype during creating new ResultSets to store.
    #we should change add_table_id to add_ExperimentalChip and check in that method
    
    #add just the ids here, as we're aiming at quick web display.
    $rset->add_table_id($table_id, $cc_id);
  
  }

  push @rsets, $rset if $rset;
  
  return\@ rsets;

}

sub _tables {

  my $self = shift;
	
  return (
		  [ 'result_set',        'rs' ],
		  [ 'chip_channel',      'cc' ],
		  #[ 'experimental_chip', 'ec' ],
		  #[ 'channel',           'c'  ],
		  #This causes the N(no channelrecords) records to be returned when there is no linkable channel.
		  #solution is to create dummy channels for chip level import e.g. Sanger
		  #we can have channel here, but only if we make the link in the default where, otherwise we'll get spurious results
		  #must also make all the fetch methods use an OR constraint dependent on the table name
		  #this would also be in default where
		 );

}

sub fetch_ResultFeatures_by_Slice_ResultSet {

  my ($self, $slice, $rset, $ec_status, $with_probe) = @_;
  

  #warn "Using ResultSetAdaptor";

  return $self->db->get_ResultFeatureAdaptor->fetch_all_by_Slice_ResultSet($slice, $rset, $ec_status, $with_probe);


  if(! (ref($slice) && $slice->isa('Bio::EnsEMBL::Slice'))){
	throw('You must pass a valid Bio::EnsEMBL::Slice');
  }

  $self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::ResultSet', $rset);


  if($rset->table_name eq 'channel'){
	warn('Can only get ResultFeatures for an ExperimentalChip level ResultSet');
	return;
  }


  my (@rfeatures, %biol_reps, %rep_scores, @filtered_ids);
  my ($biol_rep, $score, $start, $end, $cc_id, $old_start, $old_end, $probe_field);


  my ($padaptor, $probe, $array,);
  my ($probe_id, $probe_set_id, $pname, $plength, $arraychip_id, $pclass, $probeset);
  my (%array_cache, %probe_set_cache, $ps_adaptor, $array_adaptor);

  my $ptable_syn = '';
  my $pjoin = '';
  my $pfields = '';

  if($with_probe){
	#This would be in BaseAdaptor? or core DBAdaptor?
	#This would work on assuming that the default foreign key would be the primary key unless specified
	
	#my($table_info, $fields, $adaptor) = @{$self->validate_and_get_join_fields('probe')};
	$padaptor = $self->db->get_ProbeAdaptor;
	$ps_adaptor = $self->db->get_ProbeSetAdaptor;
	$array_adaptor = $self->db->get_ArrayAdaptor;


	#This would return table and syn and syn.fields
	#Would also need access to obj_from_sth_values
	#could return code ref or adaptor
	$ptable_syn = ', probe p';
	
	#Some of these will be redundant: probe_id
	#Can we remove the foreign key from the returned fields?
	#But we need it here as it isn't being returned
	$pfields =  ', p.probe_id, p.probe_set_id, p.name, p.length, p.array_chip_id, p.class ';
  
	#will this make a difference if we join on pf instead of r?
	$pjoin = ' AND r.probe_id = p.probe_id ';
  }




  
  my @ids = @{$rset->table_ids()};
  #should we do some more optimisation of method here if we know about presence or lack or replicates?

  if($ec_status){
    @filtered_ids = @{$self->status_filter($ec_status, 'experimental_chip', @ids)};

    if(! @filtered_ids){

      warn("No ExperimentalChips have the $ec_status status, No ResultFeatures retrieved");
      return\@ rfeatures;
    }
  }


  #we need to build a hash of cc_id to biolrep value
  #Then we use the biolrep as a key, and push all techrep values.
  #this can then be resolved in the method below, using biolrep rather than cc_id


  my $sql = "SELECT ec.biological_replicate, cc.chip_channel_id from experimental_chip ec, chip_channel cc 
             WHERE cc.table_name='experimental_chip'
             AND ec.experimental_chip_id=cc.table_id
             AND cc.table_id IN(".join(', ', (map $_->dbID(), @{$rset->get_ExperimentalChips()})).")";

  
  my $sth = $self->prepare($sql);
  $sth->execute();
  $sth->bind_columns(\$biol_rep,\$ cc_id);
  #could maybe do a selecthashref here?

  while($sth->fetch()){
	$biol_rep ||= 'NO_REP_SET';

	$biol_reps{$cc_id} = $biol_rep;
  }

  if(grep(/^NO_REP_SET$/, values %biol_reps)){
	warn 'You have ExperimentalChips with no biological_replicate information, these will be all treated as one biological replicate';
  }

  #we don't need to account for strnadedness here as we're dealing with a double stranded feature
  #need to be mindful if we ever consider expression
  #we don't need X Y here, as X Y for probe will be unique for cc_id.
  #any result with the same cc_id will automatically be treated as a tech rep


  #This does not currently handle multiple CSs i.e. level mapping
  my $mcc =  $self->db->get_MetaCoordContainer();
  my $fg_cs = $self->db->get_FGCoordSystemAdaptor->fetch_by_name(
																$slice->coord_system->name(), 
																$slice->coord_system->version()
																);

  my $max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($fg_cs, 'probe_feature');


 #This join between sr and pf is causing the slow down.  Need to select right join for this.
  #just do two separate queries for now.

  $sql = "SELECT seq_region_id from seq_region where core_seq_region_id=".$slice->get_seq_region_id().
	" AND schema_build='".$self->db->_get_schema_build($slice->adaptor->db())."'";

   my ($seq_region_id) = $self->db->dbc->db_handle->selectrow_array($sql);




  #Can we push the median calculation onto the server?
  #group by pf.seq_region_start?
  #will it always be a median?


  $sql = 'SELECT STRAIGHT_JOIN r.score, pf.seq_region_start, pf.seq_region_end, cc.chip_channel_id '.$pfields.
	' FROM probe_feature pf, '.$rset->get_result_table().' r, chip_channel cc '.$ptable_syn.' WHERE cc.result_set_id = '.
	  $rset->dbID();

  $sql .= ' AND cc.table_id IN ('.join(' ,', @filtered_ids).')' if ((@filtered_ids != @ids) && $ec_status);


  $sql .= ' AND cc.chip_channel_id = r.chip_channel_id'.
	' AND r.probe_id=pf.probe_id'.$pjoin.
	  ' AND pf.seq_region_id='.$seq_region_id.
		' AND pf.seq_region_start<='.$slice->end();
  
  if($max_len){
	my $start = $slice->start - $max_len;
	$start = 0 if $start < 0;
	$sql .= ' AND pf.seq_region_start >= '.$start;
  }

  $sql .= ' AND pf.seq_region_end>='.$slice->start().
	' ORDER by pf.seq_region_start'; #do we need to add probe_id here as we may have probes which start at the same place

  #can we resolves replicates here by doing a median on the score and grouping by cc_id some how?
  #what if a probe_id is present more than once, i.e. on plate replicates?

  #To extend this to perform median calculation we'd have to group by probe_id, and ec.biological_replicate
  #THen perform means across biol reps.  This would require nested selects 
  #would this group correctly on NULL values if biol rep not set for a chip?
  #This would require an extra join too. 


  $sth = $self->prepare($sql);
  $sth->execute();
  
  if($with_probe){
	$sth->bind_columns(\$score,\$ start,\$ end,\$ cc_id,\$ probe_id,\$ probe_set_id,\$ 
					   pname,\$ plength,\$ arraychip_id,\$ pclass);
  }
  else{
	$sth->bind_columns(\$score,\$ start,\$ end,\$ cc_id);
  }
  my $position_mod = $slice->start() - 1;
  

  my $new_probe = 0;
  my $first_record = 1;

  while ( $sth->fetch() ) {

    #we need to get best result here if start and end the same
    #set start end for first result
    $old_start ||= $start;
    $old_end   ||= $end; 
    

	#This is assuming that a feature at the exact same locus is from the same probe
	#This may not be correct and will collapse probes with same sequence into one ResultFeature
	#This is okay for analysis purposes, but obscures the probe to result relationship
	#we arguably need to implement r.probe_id check here for normal ResultFeatures

    if(($start == $old_start) && ($end == $old_end)){#First result and duplicate result for same feature?

	  #only if with_probe(otherwise we have a genuine on plate replicate)
	  #if probe_id is same then we're just getting the extra probe for a different array?
	  #cc_id might be different for same probe_id?

	  #How can we differentiate between an on plate replicate and just the extra probe records?
	  #If array_chip_id is the same?  If it is then we have an on plate replicate (differing x/y vals in result)
	  #Otherwise we know we're getting another probe record from a different Array/ArrayChip.
	  #It is still possible for the extra probe record on a different ArrayChip to have a result, 
	  #the cc_id would be different and would be captured?
	  #This would still be the same probe tho, so still one RF

	  #When do we want to split?
	  #If probe_id is different...do we need to order by probe_id?	  
	  #probe will never be defined without with_probe
	  #so can omit from test

	  if(defined $probe && ($probe->dbID != $probe_id)){
		$new_probe = 1;
	  }
	  else{
		push @{$rep_scores{$biol_reps{$cc_id}}}, $score;
	  }
    }
	else{#Found new location
	  $new_probe = 1;
	}

	if($new_probe){
	  #store previous feature with best result from @scores
		#Do not change arg order, this is an array object!!

	  push @rfeatures, Bio::EnsEMBL::Funcgen::ResultFeature->new_fast
		(
		  ($old_start - $position_mod), 
		  ($old_end - $position_mod), undef,#strand needs adding
		  $self->resolve_replicates_by_ResultSet(\%rep_scores, $rset),
		  $probe,
		 );
	
	 
	  undef %rep_scores;
	  $old_start = $start;
      $old_end = $end;
	  
      #record new score

	  @{$rep_scores{$biol_reps{$cc_id}}} = ($score);
	}

	if($with_probe){

	  #This would be done via the ProbeAdaptor->obj_from_sth_values
	  #We need away ti maintain the Array/ProbeSet caches in obj_from_sth fetch
	  #Pulling into an array would increase memory usage over the fetch loop
	  #Can we maintain an object level cache which we would then have to reset?
	  #Wouldn't be the end of the world if it wasn't, but would use memory

	  
	  #This is recreating the Probe->_obj_frm_sth
	  #We need to be mindful that we can get multiple records for a probe
	  #So we need to check whether the probe_id is the same
	  #It may be possible to get two of the same probes contiguously
	  #So we would also have to check on seq_region_start

	  #Do we really need to set these?
	  #We are getting the advantage that we're cacheing
	  #Rather than a fetch for each object
	  #But maybe we don't need this information?
	  #Can we have two mode for obj_from_sth?

	  $array = $array_cache{$arraychip_id} || $self->db->get_ArrayAdaptor()->fetch_by_array_chip_dbID($arraychip_id);

	  if($probe_set_id){
		$probeset = $probe_set_cache{$probe_set_id} || $self->db->get_ProbeSetAdaptor()->fetch_by_dbID($probe_set_id);
	  }


	  if($first_record || $new_probe){

		$probe = Bio::EnsEMBL::Funcgen::Probe->new
			  (
			   -dbID          => $probe_id,
			   -name          => $pname,
			   -array_chip_id => $arraychip_id,
			   -array         => $array,
			   -probe_set     => $probeset,
			   -length        => $plength,
			   -class         => $pclass,
			   -adaptor       => $padaptor,
			);

	  } 
	  else {
		# Extend existing probe
		$probe->add_array_chip_probename($arraychip_id, $pname, $array);
	  }
	}

	$new_probe = 0;
	$first_record = 0;
  }
  
  #store last feature  
  #Do not change arg order, this is an array object!!
  #only if found previosu results
  if($old_start){
    push @rfeatures, Bio::EnsEMBL::Funcgen::ResultFeature->new_fast
      (
	   ($old_start - $position_mod), 
	   ($old_end - $position_mod),
	   $self->resolve_replicates_by_ResultSet(\%rep_scores, $rset),
	   $probe
	  );

	#(scalar(@scores) == 0) ? $scores[0] : $self->_get_best_result(\@scores)]);
  }
  
  return\@ rfeatures;

}

sub fetch_all_by_Experiment {

  my ($self, $exp) = @_;

  #my $constraint = "ec.experiment_id=".$exp->dbID();
  #This was much easier with the more complicated default where join
  #should we reinstate and just have a duplication of cell/feature_types?
	

  my $join = $self->get_Experiment_join_clause($exp);
  
  return ($join) ? $self->generic_fetch($join) : [];

}

sub fetch_all_by_Experiment_Analysis {

  my ($self, $exp, $analysis) = @_;

  if( !($analysis && $analysis->isa("Bio::EnsEMBL::Analysis") && $analysis->dbID())){
    throw("Need to pass a valid stored Bio::EnsEMBL::Analysis");
  }
  

  my $join = $self->get_Experiment_join_clause($exp)." AND rs.analysis_id=".$analysis->dbID();
	
  return ($join) ? $join." AND rs.analysis_id=".$analysis->dbID() : [];

}

sub fetch_all_by_FeatureType {

  my ($self, $ftype) = @_;

  if( !($ftype && $ftype->isa("Bio::EnsEMBL::Funcgen::FeatureType") && $ftype->dbID())){
    throw("Need to pass a valid stored Bio::EnsEMBL::Funcgen::FeatureType");
  }
	
  my $constraint = "rs.feature_type_id =".$ftype->dbID();
	
  return $self->generic_fetch($constraint);

}

sub fetch_all_by_name {

  my ($self, $name) = @_;

  if( ! defined $name){
    throw('Need to pass a ResultSet name');
  }

	
  my $constraint = "rs.name ='${name}'";
	
  return $self->generic_fetch($constraint);

}

sub fetch_all_by_name_Analysis {

  my ($self, $name, $anal) = @_;

  if( ! defined $name){
    throw('Need to pass a ResultSet name');
  }

  if(!($anal && $anal->isa('Bio::EnsEMBL::Analysis') && $anal->dbID())){
	throw('You must provide a valid, stored Bio::EnsEMBL::Analysis');
  }
	
  my $constraint = "rs.name ='${name}' AND rs.analysis_id=".$anal->dbID();
	
  return $self->generic_fetch($constraint);

}

sub fetch_all_linked_by_ResultSet {

  my ($self, $rset) = @_;

  $self->db->is_stored_an_valid('Bio::EnsEMBL::Funcgen::ResultSet', $rset);


  my $constraint = ' cc.result_set_id in (SELECT distinct(result_set_id) from chip_channel where chip_channel_id in('.join(', ', @{$rset->chip_channel_ids}).') ';
  
  my @tmp = @{$self->generic_fetch($constraint)};

  #Now remove query set
  my @linked_sets;

  map {push @linked_sets, $_ if $_->dbID != $rset->dbID} @tmp;

  return\@ linked_sets;

}

sub fetch_all_result_feature_sets {

  my $self = shift;
  
  throw('change to status call');
  return $self->generic_fetch('rs.result_feature_set=1');

}

sub fetch_results_by_probe_id_ResultSet {

  my ($self, $probe_id, $rset) = @_;
  
  throw("Need to pass a valid stored Bio::EnsEMBL::Funcgen::ResultSet") if (! ($rset  &&
									       $rset->isa("Bio::EnsEMBL::Funcgen::ResultSet")
									       && $rset->dbID()));
  
  throw('Must pass a probe dbID') if ! $probe_id;
  
  
  
  my $cc_ids = join(',', @{$rset->chip_channel_ids()});

  my $query = "SELECT r.score from result r where r.probe_id ='${probe_id}'".
    " AND r.chip_channel_id IN (${cc_ids}) order by r.score;";

  #without a left join this will return empty results for any probes which may have been remapped 
  #to the a chromosome, but no result exist for a given set due to only importing a subset of
  #a vendor specified mapping


  #This converts no result to a 0!

  my @results = map $_ = "@$_", @{$self->dbc->db_handle->selectall_arrayref($query)};
  

  return\@ results;
}





1;

}

sub get_Experiment_join_clause {

  my ($self, $exp) = @_;

  if( !($exp && $exp->isa("Bio::EnsEMBL::Funcgen::Experiment") && $exp->dbID())){
    throw("Need to pass a valid stored Bio::EnsEMBL::Funcgen::Experiment");
  }

  my @ecs = @{$exp->get_ExperimentalChips()};

  

  my $ec_ids = join(', ', (map $_->dbID, @ecs));#get ' separated list of ecids


  my @chans = map @$_, (map $_->get_Channels(), @ecs);
  my $chan_ids = join(', ', (map $_->dbID(), @chans));#get ' separated list of chanids
  #These give empty strings which are defined


  my $constraint;
  #This will not work for single IDs of 0, but this will never happen.

  if($ec_ids && $chan_ids){
	$constraint = '(((cc.table_name="experimental_chip" AND cc.table_id IN ('.$ec_ids.
	  ')) OR (cc.table_name="channel" AND cc.table_id IN ('.$chan_ids.'))))';
  }
  elsif($ec_ids){
	$constraint = 'cc.table_name="experimental_chip" AND cc.table_id IN ('.$ec_ids.')';
  }
  elsif($chan_ids){
	$constraint = 'cc.table_name="channel" AND cc.table_id IN ('.$chan_ids.')';
  }
  
  return $constraint;

}

sub list_dbIDs {

	my $self = shift;
	
	return $self->_list_dbIDs('result_set');

}

sub resolve_replicates_by_ResultSet {

  my ($self, $rep_ref) = @_;#, $rset) = @_;

  my ($score, @scores, $biol_rep);

  #deal with simplest case first and fastest?
  #can we front load this with the replicate set info, i.e. if we know we only have one then we don't' have to do all this testing and can do a mean

  if(scalar(keys %{$rep_ref}) == 1){
	
	($biol_rep) = keys %{$rep_ref};

	@scores = @{$rep_ref->{$biol_rep}};

	if (scalar(@scores) == 1){
	  $score = $scores[0];
	}else{
	  $score = mean(\@scores)
	}
  }else{#deal with biol replicates

	foreach $biol_rep(keys %{$rep_ref}){
	  push @scores, mean($rep_ref->{$biol_rep});
	}

	@scores = sort {$a<=>$b} @scores;

	$score = median(\@scores);

  }

  return $score;

}

sub store {

  my ($self, @rsets) = @_;

  throw("Must provide a list of ResultSet objects") if(scalar(@rsets == 0));
  
  my (%analysis_hash);
  
  my $sth = $self->prepare('INSERT INTO result_set (analysis_id, name, cell_type_id, feature_type_id) VALUES (?, ?, ?, ?)');
  
  my $db = $self->db();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();
  
 FEATURE: foreach my $rset (@rsets) {
    
    if( ! ref $rset || ! $rset->isa('Bio::EnsEMBL::Funcgen::ResultSet') ) {
      throw('Must be an ResultSet object to store');
    }
    
        
    if ( $rset->is_stored($db) ) {
      throw('ResultSet [' . $rset->dbID() . '] is already stored in the database\nResultSetAdaptor does not yet accomodate updating ResultSets');
      #would need to retrive stored result set and update table_ids
    }

    #above does not check if it has been generated from scratch but is identical i.e. recovery.
    #Need to check table_id and analysis and that it has the correct status


    
    if ( ! defined $rset->analysis() ) {
      throw('An analysis must be attached to the ResultSet objects to be stored.');
    }
    
    # Store the analysis if it has not been stored yet
    if ( ! $rset->analysis->is_stored($db) ) {
      warn("Will this not keep storing the same analysis if we keep passing the same unstored analysis?");
      $analysis_adaptor->store( $rset->analysis() );
    }
   

	my $ct_id = (defined $rset->cell_type()) ? $rset->cell_type->dbID() : undef;
	my $ft_id = (defined $rset->feature_type()) ? $rset->feature_type->dbID() : undef;

    $sth->bind_param(1, $rset->analysis->dbID(),   SQL_INTEGER);
    $sth->bind_param(2, $rset->name(),             SQL_VARCHAR);
	$sth->bind_param(3, $ct_id,                    SQL_INTEGER);
	$sth->bind_param(4, $ft_id,                    SQL_INTEGER);

	
    
    $sth->execute();
    
    $rset->dbID( $sth->{'mysql_insertid'} );
    $rset->adaptor($self);
    
	$self->store_states($rset);
    $self->store_chip_channels($rset);
	
    
  }
  
  return\@ rsets;

}

sub store_chip_channels {

  my ($self, $rset) = @_;
  
  if(! ($rset && $rset->isa("Bio::EnsEMBL::Funcgen::ResultSet"))){
    throw("You must pasas a valid Bio::EnsEMBL::Funcgen::ResultSet");
  }
  
  if ( ! $rset->is_stored($self->db()) ) {
    throw('ResultSet must be stored in the database before storing chip_channel entries');
  }
  
  my $sth = $self->prepare("
		INSERT INTO chip_channel (
			result_set_id, table_id, table_name
		) VALUES (?, ?, ?)
	");

  my $sth1 = $self->prepare("
		INSERT INTO chip_channel (
			chip_channel_id, result_set_id, table_id, table_name
		) VALUES (?, ?, ?, ?)
	");
  

  #Store and set all previously unstored table_ids
  foreach my $table_id(@{$rset->table_ids()}){
    my $cc_id = $rset->get_chip_channel_id($table_id);

    if(! defined $cc_id){
      $sth->bind_param(1, $rset->dbID(),       SQL_INTEGER);
      $sth->bind_param(2, $table_id,           SQL_INTEGER);
      $sth->bind_param(3, $rset->table_name(), SQL_VARCHAR);
      
      $sth->execute();

	  $cc_id = $sth->{'mysql_insertid'};
      $rset->add_table_id($table_id,  $sth->{'mysql_insertid'});
    }else{

	  #this should only store if not already stored for this rset
	  #this is because we may want to add chip_channels to a previously stored rset
	  my $sql = 'SELECT chip_channel_id from chip_channel where result_set_id='.$rset->dbID().
		" AND chip_channel_id=${cc_id}";
	  my ($loaded) = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)};

	  if(! $loaded){
		$sth1->bind_param(1, $cc_id,       SQL_INTEGER);
		$sth1->bind_param(2, $rset->dbID(),       SQL_INTEGER);
		$sth1->bind_param(3, $table_id,           SQL_INTEGER);
		$sth1->bind_param(4, $rset->table_name(), SQL_VARCHAR);
		$sth1->execute();#this could still fail is some one duplicates a result_set_id, table_id, table_name entry
	  }
	}
  }
  return $rset;

}

General documentation

This module was created by Nathan Johnson.
This module is part of the Ensembl project: /

Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk