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Commit c8a905ed authored by Arne Stabenau's avatar Arne Stabenau
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Special align features based on BaseAlignFeature.

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modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
+ 6
− 326
View file @ c8a905ed
......@@ -87,93 +87,15 @@ package Bio::EnsEMBL::DnaDnaAlignFeature;
=cut
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::SeqFeature;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::EnsEMBL::FeaturePair);
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($cigar_string,$features) = $self->_rearrange([qw(CIGAR_STRING FEATURES)],
@args);
if (defined($cigar_string) && defined($features)) {
$self->throw("Can't input cigar_string and an array of features to DnaDnaAlignFeature");
} elsif (defined($features)) {
$self->_parse_features($features);
} elsif (!defined($cigar_string)) {
$self->throw("A DnaDnaAlignFeature must have a cigar string defining the alignment");
} else {
$self->throw("DnaDnaAlignFeature has wrong arguments in constructor");
}
$self->cigar_string($cigar_string);
return $self;
}
=head2 cigar_string
Arg : Nothing (for just returning an existing cigar_string) or
A cigar string which looks something like
'100,200,3:110,210,11'
The cigar_string contains the ungapped pieces that make up the gapped alignment.
Its format is qstart,qend,length*strand.
So in the above example the gapped alignment contains 2 ungapped pieces from
100-102 in the query and 200-202 in the hit and
110-120 in the query and 210-220 in the hit.
The length parts of the cigar string are positive as the strand is +ve.
Usage : $dna_feat->cigar_string('100,200,3:110,210,11');
my $cigar_string = $dna_feat->cigar_string
Function : This module is for storing gapped dna-dna alignments. To save
space and memory all the structure of the gapped alignment
is stored in a string and the ->start and ->end values
are the minimum and maximum coords of all the gapped pieces.
This allows the gapped alignment to also function as
a feature pair. It is mostly used for storing Blast HSPs
(see Bio::EnsEMBL::Pipeline::Runnable::Blast)
If a cigar_string is defined it is returned otherwise an exception is thrown
Exception: If no cigar_string is defined an exception is thrown
Caller : Bio::EnsEMBL::Pipeline::Runnable::Blast
=cut
use Bio::EnsEMBL::BaseAlignFeature;
sub cigar_string {
my ($self,$arg) = @_;
if (defined($arg)) {
use vars qw(@ISA);
use strict;
# Do some checks to see whether this is valid
my $tmp = $arg;
$self->{_cigar_string} = $arg;
}
@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
if (!defined($self->{_cigar_string})) {
$self->throw("No cigar string defined - can't return one");
}
return $self->{_cigar_string};
}
=head2 _parse_cigar
......@@ -202,78 +124,7 @@ sub cigar_string {
sub _parse_cigar {
my ($self) = @_;
my $string = $self->cigar_string;
if (!defined($string)) {
$self->throw("No cigar string defined in object. This should be caught by the cigar_string method and never happen");
}
my @pieces = split(/:/,$string);
my @features;
foreach my $piece (@pieces) {
my $start1;
my $start2;
my $length;
if ($piece =~ /(\S+)\,(\S+)\,(\S+)/) {
$start1 = $1;
$start2 = $2;
$length = $3;
} else {
$self->throw("Can't parse cigar string element [$piece]. Invalid format. Should be start,end,length*strand");
}
my $strand = 1;
if ($length == 0) {
$self->throw("Length of piece is 0 - impossible");
}
if ($length < 0) {
$strand = -1;
}
$length = abs($length);
my $feature1 = new Bio::EnsEMBL::SeqFeature();
$feature1->start($start1);
$feature1->end ($start1 + $length - 1);
$feature1->strand($strand);
$feature1->score($self->score);
$feature1->seqname($self->seqname);
$feature1->phase($self->phase);
$feature1->p_value($self->p_value);
$feature1->percent_id($self->percent_id);
my $feature2 = new Bio::EnsEMBL::SeqFeature();
if ($strand == 1) {
$feature2->start($start2);
$feature2->end ($start2 + $strand*($length - 1));
} else {
$feature2->end ($start2);
$feature2->start($start2 + $strand*($length - 1));
}
$feature2->strand($strand);
$feature2->score($self->score);
$feature2->seqname($self->hseqname);
$feature2->phase($self->phase);
$feature2->p_value($self->p_value);
$feature2->percent_id($self->percent_id);
my $fp = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
-feature2 => $feature2);
$fp->analysis($self->analysis);
push(@features,$fp);
}
return @features;
return $self->_generic_parse_cigar( 1, 1 );
}
......@@ -312,178 +163,7 @@ sub _parse_cigar {
sub _parse_features {
my ($self,$features) = @_;
if (ref($features) ne "ARRAY") {
$self->throw("features must be an array reference not a [" . ref($features) . "]");
}
my @f = sort {$a->start <=> $b->start} @$features;
if (scalar(@f) == 0) {
$self->throw("No features in the array to parse");
}
my $hstrand = $f[0]->hstrand;
my $name = $f[0]->seqname;
my $hname = $f[0]->hseqname;
my $score = $f[0]->score;
my $percent = $f[0]->percent_id;
my $pvalue = $f[0]->p_value;
my $analysis = $f[0]->analysis;
my $phase = $f[0]->phase;
print STDERR "Analysis is $analysis\n";
print STDERR "Strand is $hstrand\n";
my $prev1;
my $prev2;
my $string;
my $f1start = $f[0]->start;
my $f1end = $f[$#f]->end;
my $f2start;
my $f2end;
if ($hstrand == 1) {
$f2start = $f[0]->hstart;
$f2end = $f[$#f]->hend;
} else {
$f2end = $f[0]->hend;
$f2start = $f[$#f]->hstart;
}
foreach my $f (@f) {
if (!$f->isa("Bio::EnsEMBL::FeaturePair")) {
$self->throw("Array element [$f] is not a Bio::EnsEMBL::FeaturePair");
}
print STDERR "Processing " . $f->gffstring . "\n";
if ($f->strand != $hstrand) {
$self->throw("Inconsistent strands in feature array");
}
if ($name ne $f->seqname) {
$self->throw("Inconsistent names in feature array [$name - " . $f->seqname . "]");
}
if ($hname ne $f->hseqname) {
$self->throw("Inconsistent names in feature array [$hname - " . $f->hseqname . "]");
}
if ($score ne $f->score) {
$self->throw("Inconsisent scores in feature array [$score - " . $f->score . "]");
}
if ($percent ne $f->percent_id) {
$self->throw("Inconsistent pids in feature array [$percent - " . $f->percent_id . "]");
}
my $start1 = $f->start;
my $start2;
if ($hstrand == 1) {
$start2 = $f->hstart;
} else {
$start2 = $f->hend;
}
if (defined($prev1)) {
if ($start1 < $prev1) {
$self->throw("Inconsistent coordinates in feature array $start1 < $prev1");
}
}
if (defined($prev2)) {
if ($hstrand == 1) {
if ($f->hstart < $prev2) {
$self->throw("Inconsistent coordinates in feature array " . $f->hstart . " < $prev2");
}
} else {
if ($f->hstart > $prev2) {
$self->throw("Inconsistent coordinates in feature array " . $f->hstart . " > $prev2");
}
}
}
my $length = ($f->end - $f->start + 1)*$hstrand;
my $hlength = ($f->hend - $f->hstart + 1)*$hstrand;
if ($length != $hlength) {
$self->throw("Hit length is different to the query length in DnaDnaAlignFeature");
}
$string = $string . $start1 . "," . $start2 . "," . $length . ":";
$prev1 = $f->end;
if ($hstrand == 1) {
$prev2 = $f->hend;
} else {
$prev2 = $f->hstart;
}
}
print STDERR "Making feature pair\n";
$string =~ s/:$//;
my $feature1 = new Bio::EnsEMBL::SeqFeature();
$feature1->start($f1start);
$feature1->end ($f1end);
$feature1->strand($hstrand);
$feature1->score($score);
$feature1->percent_id($percent);
$feature1->p_value($pvalue);
$feature1->seqname($name);
$feature1->percent_id($percent);
$feature1->p_value($pvalue);
$feature1->phase($phase);
$feature1->analysis($analysis);
my $feature2 = new Bio::EnsEMBL::SeqFeature();
$feature2->start($f2start);
$feature2->end ($f2end);
$feature2->strand($hstrand);
$feature2->score($score);
$feature2->seqname($hname);
$feature2->percent_id($percent);
$feature2->p_value($pvalue);
$feature2->phase($phase);
$feature2->analysis($analysis);
$self->feature1($feature1);
$self->feature2($feature2);
$self->cigar_string($string);
$self->_generic_parse_features( $features, 1, 1 );
}
=head2 ungapped_features
Arg : None.
Usage : my @feature_pairs = $dna_feat->ungapped_features;
Function : Converts the cigar_string contained by the module into
an array of ungapped Bio::EnsEMBL::FeaturePair.
All the work is done in the subroutine _parse_cigar_string
Exception: If no cigar string is defined
Caller : No specific caller.
=cut
sub ungapped_features {
my ($self) = @_;
if (defined($self->cigar_string)) {
my @features = $self->_parse_cigar;
return @features;
} else {
$self->throw("No cigar_string defined. Can't return ungapped features");
}
}
1;
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
+ 13
− 335
View file @ c8a905ed
package Bio::EnsEMBL::DnaPepAlignFeature;
# EnsEMBL module for storing dna-protein pairwise alignments
# EnsEMBL module for storing dna-dna pairwise alignments
#
# Cared for by Michele Clamp <michele@sanger.ac.uk>
#
......@@ -9,22 +9,22 @@ package Bio::EnsEMBL::DnaPepAlignFeature;
=head1 NAME
Bio::EnsEMBL::DnaPepAlignFeature - Ensembl specific dna-protein pairwise alignment feature
Bio::EnsEMBL::DnaDnaAlignFeature - Ensembl specific dna-dna pairwise alignment feature
=head1 SYNOPSIS
my $feat = new Bio::EnsEMBL::DnaPepAlignFeature(-seqname => 'myseq',
my $feat = new Bio::EnsEMBL::DnaDnaAlignFeature(-seqname => 'myseq',
-start => 100,
-end => 120,
-strand => 1,
-hstart => 200,
-hend => 220,
-analysis => $analysis,
-cigar_string => '100,200,3:109,203,12');
-cigar_string => '100,200,3:110,210,11');
# Alternatively if you have an array of ungapped features
my $feat = new Bio::EnsEMBL::DnaPepAlignFeature(-features => \@features);
my $feat = new Bio::EnsEMBL::DnaDnaAlignFeature(-features => \@features);
# Where @features is an array of Bio::EnsEMBL::FeaturePair
......@@ -45,8 +45,8 @@ package Bio::EnsEMBL::DnaPepAlignFeature;
#
# So in the above example the gapped alignment contains 2 ungapped pieces from
#
# 100-102 in the query and 200-200 in the hit and
# 109-120 in the query and 203-206 in the hit.
# 100-102 in the query and 200-202 in the hit and
# 110-120 in the query and 210-220 in the hit.
#
# The length parts of the cigar string are positive as the strand is +ve.
......@@ -87,93 +87,14 @@ package Bio::EnsEMBL::DnaPepAlignFeature;
=cut
use Bio::EnsEMBL::FeaturePair;
use Bio::EnsEMBL::SeqFeature;
use Bio::EnsEMBL::BaseAlignFeature;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::EnsEMBL::FeaturePair);
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($cigar_string,$features) = $self->_rearrange([qw(CIGAR_STRING FEATURES)],
@args);
if (defined($cigar_string) && defined($features)) {
$self->throw("Can't input cigar_string and an array of features to DnaPepAlignFeature");
} elsif (defined($features)) {
$self->_parse_features($features);
} elsif (!defined($cigar_string)) {
$self->throw("A DnaPepAlignFeature must have a cigar string defining the alignment");
} else {
$self->throw("DnaPepAlignFeature has wrong arguments in constructor");
}
$self->cigar_string($cigar_string);
return $self;
}
=head2 cigar_string
Arg : Nothing (for just returning an existing cigar_string) or
A cigar string which looks something like
'100,200,3:109,203,12'
The cigar_string contains the ungapped pieces that make up the gapped alignment.
Its format is qstart,qend,length*strand.
So in the above example the gapped alignment contains 2 ungapped pieces from
100-102 in the query and 200-200 in the hit and
109-120 in the query and 203-206 in the hit.
The length parts of the cigar string are positive as the strand is +ve.
Usage : $pep_feat->cigar_string('100,200,3:109,203,12');
my $cigar_string = $pep_feat->cigar_string
Function : This module is for storing gapped dna-protein alignments. To save
space and memory all the structure of the gapped alignment
is stored in a string and the ->start and ->end values
are the minimum and maximum coords of all the gapped pieces.
This allows the gapped alignment to also function as
a feature pair. It is mostly used for storing Blast HSPs
(see Bio::EnsEMBL::Pipeline::Runnable::Blast)
If a cigar_string is defined it is returned otherwise an exception is thrown
Exception: If no cigar_string is defined an exception is thrown
Caller : Bio::EnsEMBL::Pipeline::Runnable::Blast
=cut
sub cigar_string {
my ($self,$arg) = @_;
@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
if (defined($arg)) {
# Do some checks to see whether this is valid
my $tmp = $arg;
$self->{_cigar_string} = $arg;
}
if (!defined($self->{_cigar_string})) {
$self->throw("No cigar string defined - can't return one");
}
return $self->{_cigar_string};
}
=head2 _parse_cigar
......@@ -202,78 +123,7 @@ sub cigar_string {
sub _parse_cigar {
my ($self) = @_;
my $string = $self->cigar_string;
if (!defined($string)) {
$self->throw("No cigar string defined in object. This should be caught by the cigar_string method and never happen");
}
my @pieces = split(/:/,$string);
my @features;
foreach my $piece (@pieces) {
my $start1;
my $start2;
my $length;
if ($piece =~ /(\S+)\,(\S+)\,(\S+)/) {
$start1 = $1;
$start2 = $2;
$length = $3;
} else {
$self->throw("Can't parse cigar string element [$piece]. Invalid format. Should be start,end,length*strand");
}
my $strand = 1;
if ($length == 0) {
$self->throw("Length of piece is 0 - impossible");
}
if ($length < 0) {
$strand = -1;
}
$length = abs($length);
my $feature1 = new Bio::EnsEMBL::SeqFeature();
$feature1->start($start1);
$feature1->end ($start1 + $length - 1);
$feature1->strand($strand);
$feature1->score($self->score);
$feature1->seqname($self->seqname);
$feature1->phase($self->phase);
$feature1->p_value($self->p_value);
$feature1->percent_id($self->percent_id);
my $feature2 = new Bio::EnsEMBL::SeqFeature();
if ($strand == 1) {
$feature2->start($start2);
$feature2->end ($start2 + $strand*($length/3 - 1));
} else {
$feature2->end ($start2);
$feature2->start($start2 + $strand*($length/3 - 1));
}
$feature2->strand($strand);
$feature2->score($self->score);
$feature2->seqname($self->hseqname);
$feature2->phase($self->phase);
$feature2->p_value($self->p_value);
$feature2->percent_id($self->percent_id);
my $fp = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
-feature2 => $feature2);
$fp->analysis($self->analysis);
push(@features,$fp);
}
return @features;
return $self->_generic_parse_cigar( 3, 1 );
}
......@@ -303,7 +153,7 @@ sub _parse_cigar {
If there are no elements in the array
If the hit length is not exactly 3 times the query length
If the hit length is not equal to the query length
Caller : Called internally to the module by the constructor
......@@ -312,179 +162,7 @@ sub _parse_cigar {
sub _parse_features {
my ($self,$features) = @_;
if (ref($features) ne "ARRAY") {
$self->throw("features must be an array reference not a [" . ref($features) . "]");
}
my @f = sort {$a->start <=> $b->start} @$features;
if (scalar(@f) == 0) {
$self->throw("No features in the array to parse");
}
my $hstrand = $f[0]->hstrand;
my $name = $f[0]->seqname;
my $hname = $f[0]->hseqname;
my $score = $f[0]->score;
my $percent = $f[0]->percent_id;
my $pvalue = $f[0]->p_value;
my $analysis = $f[0]->analysis;
my $phase = $f[0]->phase;
print STDERR "Analysis is $analysis\n";
print STDERR "Strand is $hstrand\n";
my $prev1;
my $prev2;
my $string;
my $f1start = $f[0]->start;
my $f1end = $f[$#f]->end;
my $f2start;
my $f2end;
if ($hstrand == 1) {
$f2start = $f[0]->hstart;
$f2end = $f[$#f]->hend;
} else {
$f2end = $f[0]->hend;
$f2start = $f[$#f]->hstart;
}
foreach my $f (@f) {
if (!$f->isa("Bio::EnsEMBL::FeaturePair")) {
$self->throw("Array element [$f] is not a Bio::EnsEMBL::FeaturePair");
}
print STDERR "Processing " . $f->gffstring . "\n";
if ($f->strand != $hstrand) {
$self->throw("Inconsistent strands in feature array");
}
if ($name ne $f->seqname) {
$self->throw("Inconsistent names in feature array [$name - " . $f->seqname . "]");
}
if ($hname ne $f->hseqname) {
$self->throw("Inconsistent names in feature array [$hname - " . $f->hseqname . "]");
}
if ($score ne $f->score) {
$self->throw("Inconsisent scores in feature array [$score - " . $f->score . "]");
}
if ($percent ne $f->percent_id) {
$self->throw("Inconsistent pids in feature array [$percent - " . $f->percent_id . "]");
}
my $start1 = $f->start;
my $start2;
if ($hstrand == 1) {
$start2 = $f->hstart;
} else {
$start2 = $f->hend;
}
if (defined($prev1)) {
if ($start1 < $prev1) {
$self->throw("Inconsistent coordinates in feature array $start1 < $prev1");
}
}
if (defined($prev2)) {
if ($hstrand == 1) {
if ($f->hstart < $prev2) {
$self->throw("Inconsistent coordinates in feature array " . $f->hstart . " < $prev2");
}
} else {
if ($f->hstart > $prev2) {
$self->throw("Inconsistent coordinates in feature array " . $f->hstart . " > $prev2");
}
}
}
my $length = ($f->end - $f->start + 1)*$hstrand;
my $hlength = ($f->hend - $f->hstart + 1)*$hstrand;
if ($hlength/$length != 3) {
$self->throw("Hit length must be exactly 3 times the query length for a DnaPepAlignFeature");
}
$string = $string . $start1 . "," . $start2 . "," . $length . ":";
$prev1 = $f->end;
if ($hstrand == 1) {
$prev2 = $f->hend;
} else {
$prev2 = $f->hstart;
}
}
print STDERR "Making feature pair\n";
$string =~ s/:$//;
my $feature1 = new Bio::EnsEMBL::SeqFeature();
$feature1->start($f1start);
$feature1->end ($f1end);
$feature1->strand($hstrand);
$feature1->score($score);
$feature1->percent_id($percent);
$feature1->p_value($pvalue);
$feature1->seqname($name);
$feature1->percent_id($percent);
$feature1->p_value($pvalue);
$feature1->phase($phase);
$feature1->analysis($analysis);
my $feature2 = new Bio::EnsEMBL::SeqFeature();
$feature2->start($f2start);
$feature2->end ($f2end);
$feature2->strand($hstrand);
$feature2->score($score);
$feature2->seqname($hname);
$feature2->percent_id($percent);
$feature2->p_value($pvalue);
$feature2->phase($phase);
$feature2->analysis($analysis);
$self->feature1($feature1);
$self->feature2($feature2);
$self->cigar_string($string);
}
=head2 ungapped_features
Arg : None.
Usage : my @feature_pairs = $pep_feat->ungapped_features;
Function : Converts the cigar_string contained by the module into
an array of ungapped Bio::EnsEMBL::FeaturePair.
All the work is done in the subroutine _parse_cigar_string
Exception: If no cigar string is defined
Caller : No specific caller.
=cut
sub ungapped_features {
my ($self) = @_;
if (defined($self->cigar_string)) {
my @features = $self->_parse_cigar;
return @features;
} else {
$self->throw("No cigar_string defined. Can't return ungapped features");
}
$self->_generic_parse_features( $features, 3, 1 );
}
1;
modules/Bio/EnsEMBL/PepDnaAlignFeature.pm 0 → 100644
+ 168
− 0
View file @ c8a905ed
package Bio::EnsEMBL::PepDnaAlignFeature;
# EnsEMBL module for storing dna-dna pairwise alignments
#
# Cared for by Michele Clamp <michele@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
#
=head1 NAME
Bio::EnsEMBL::DnaDnaAlignFeature - Ensembl specific dna-dna pairwise alignment feature
=head1 SYNOPSIS
my $feat = new Bio::EnsEMBL::DnaDnaAlignFeature(-seqname => 'myseq',
-start => 100,
-end => 120,
-strand => 1,
-hstart => 200,
-hend => 220,
-analysis => $analysis,
-cigar_string => '100,200,3:110,210,11');
# Alternatively if you have an array of ungapped features
my $feat = new Bio::EnsEMBL::DnaDnaAlignFeature(-features => \@features);
# Where @features is an array of Bio::EnsEMBL::FeaturePair
# There is a method to manipulate the cigar_string into ungapped features
my @ungapped_features = $feat->ungapped_features;
# This converts the cigar string into an array of Bio::EnsEMBL::FeaturePair
# $analysis is a Bio::EnsEMBL::Analysis object
# Bio::EnsEMBL::SeqFeature methods can be used
# Bio::EnsEMBL::FeaturePair methods can be used
# The cigar_string contains the ungapped pieces that make up the gapped alignment
#
# It's format is qstart,qend,length*strand.
#
# So in the above example the gapped alignment contains 2 ungapped pieces from
#
# 100-102 in the query and 200-202 in the hit and
# 110-120 in the query and 210-220 in the hit.
#
# The length parts of the cigar string are positive as the strand is +ve.
# To make things clearer this is how a blast HSP would be parsed
#>AK014066
# Length = 146
# Minus Strand HSPs:
# Score = 76 (26.8 bits), Expect = 1.4, P = 0.74
# Identities = 20/71 (28%), Positives = 29/71 (40%), Frame = -1
#Query: 479 GLQAPPPTPQGCRLIPPPPLGLQAPLPTLRAVGSSHHHP*GRQGSSLSSFRSSLASKASA 300
# G APPP PQG R P P G + P L + + ++ R +A +
#Sbjct: 7 GALAPPPAPQG-RWAFPRPTG-KRPATPLHGTARQDRQVRRSEAAKVTGCRGRVAPHVAP 64
#Query: 299 SSPHNPSPLPS 267
# H P+P P+
#Sbjct: 65 PLTHTPTPTPT 75
#The alignment goes from 267 to 479 in sequence 1 and 7 to 75 in sequence 2 and the
#strand is -1.
#The alignment is made up of the following ungapped pieces :
#sequence 1 start 447 , sequence 2 start 7 , match length 33 , strand -1
#sequence 1 start 417 , sequence 2 start 18 , match length 27 , strand -1
#sequence 1 start 267 , sequence 2 start 27 , match length 137 , strand -1
#These ungapped pieces are made up into the following string (called a cigar string)
#447,7,-33:417,18,-27:267,27,-137
#i.e. seqstart1,seqstart2,length: etc
=cut
use Bio::EnsEMBL::BaseAlignFeature;
use vars qw(@ISA);
use strict;
@ISA = qw( Bio::EnsEMBL::BaseAlignFeature );
=head2 _parse_cigar
Arg : None.
Usage : Internal method - not used.
Function : Converts the cigar_string contained by the module into
an array of ungapped Bio::EnsEMBL::FeaturePair.
See sub cigar_string for an explanation of what that is.
Exception: If no cigar_string is returned from $self->cigar_string but
this should never happen as $self->cigar_string should throw
it first.
If the cigar string is the wrong format.
If the length of an ungapped piece is 0
Caller : Called internally to the module by ungapped_features
=cut
sub _parse_cigar {
my ($self) = @_;
return $self->_generic_parse_cigar( 1, 3 );
}
=head2 _parse_features
Arg : Array of Bio::EnsEMBL::FeaturePair
Usage : Internal method - not used.
Function : Converts an array of FeaturePairs into a gapped feature with
a cigar string describing the
See sub cigar_string for an explanation of what that is.
Exception: If the argument passed is not an array reference
All the features must have arisen from the same source
i.e. a blast HSP or some other alignment. Thus
exceptions are thrown when the scores,percent ids,p_values
seqnames , hseqnames and strands differ amongst the input
features.
All the features must not overlap in order to provide a
sane gapped alignment. An exception is thrown if they do.
If any element of the array is not a Bio::EnsEMBL::FeaturePair
If there are no elements in the array
If the hit length is not equal to the query length
Caller : Called internally to the module by the constructor
=cut
sub _parse_features {
my ($self,$features) = @_;
$self->_generic_parse_features( $features, 1, 3 );
}
1;
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