Skip to content

Commit

Permalink
Removed tabs
Browse files Browse the repository at this point in the history
  • Loading branch information
@fangly
fangly committed Mar 7, 2012
1 parent 5f115e2 commit 5ad8e23
Showing 1 changed file with 49 additions and 49 deletions.
98 changes: 49 additions & 49 deletions Bio/Seq.pm
View file
Expand Up @@ -32,7 +32,7 @@ Bio::Seq - Sequence object, with features
# make from strings in script
$seqobj = Bio::Seq->new( -display_id => 'my_id',
-seq => $sequence_as_string);
-seq => $sequence_as_string);
# gets sequence as a string from sequence object
$seqstr = $seqobj->seq(); # actual sequence as a string
Expand All @@ -43,8 +43,8 @@ Bio::Seq - Sequence object, with features
@features = $seqobj->get_SeqFeatures(); # just top level
foreach my $feat ( @features ) {
print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
$feat->end," strand ",$feat->strand,"\n";
print "Feature ",$feat->primary_tag," starts ",$feat->start," ends ",
$feat->end," strand ",$feat->strand,"\n";
# features retain link to underlying sequence object
print "Feature sequence is ",$feat->seq->seq(),"\n"
Expand All @@ -53,7 +53,7 @@ Bio::Seq - Sequence object, with features
# sequences may have a species
if( defined $seq->species ) {
print "Sequence is from ",$species->binomial," [",$species->common_name,"]\n";
print "Sequence is from ",$species->binomial," [",$species->common_name,"]\n";
}
# annotation objects are Bio::AnnotationCollectionI's
Expand All @@ -64,7 +64,7 @@ Bio::Seq - Sequence object, with features
# more information
foreach my $ref ( $ann->get_Annotations('reference') ) {
print "Reference ",$ref->title,"\n";
print "Reference ",$ref->title,"\n";
}
# you can get truncations, translations and reverse complements, these
Expand Down Expand Up @@ -136,8 +136,8 @@ exons it finds as sequence features in Genbank Flat File format.
print "Seen sequence ",$seqobj->display_id,", start of seq ",
substr($seqobj->seq,1,10),"\n";
if( $seqobj->alphabet eq 'dna') {
$rev = $seqobj->revcom;
$id = $seqobj->display_id();
$rev = $seqobj->revcom;
$id = $seqobj->display_id();
$id = "$id.rev";
$rev->display_id($id);
$seqout->write_seq($rev);
Expand All @@ -147,7 +147,7 @@ exons it finds as sequence features in Genbank Flat File format.
if( $feat->primary_tag eq 'exon' ) {
print STDOUT "Location ",$feat->start,":",
$feat->end," GFF[",$feat->gff_string,"]\n";
}
}
}
}
Expand Down Expand Up @@ -375,7 +375,7 @@ in order to retrieve the coordinates inside the Genbank or EMBL join()
statements (e.g. "CDS join(51..142,273..495,1346..1474)"):
if ( $feat->location->isa('Bio::Location::SplitLocationI') &&
$feat->primary_tag eq 'CDS' ) {
$feat->primary_tag eq 'CDS' ) {
foreach $loc ( $feat->location->sub_Location ) {
print $loc->start . ".." . $loc->end . "\n";
}
Expand Down Expand Up @@ -469,8 +469,8 @@ use base qw(Bio::Root::Root Bio::SeqI Bio::IdentifiableI Bio::DescribableI Bio::
Title : new
Usage : $seq = Bio::Seq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
-id => 'human_id',
-accession_number => 'AL000012',
);
-accession_number => 'AL000012',
);
Function: Returns a new Seq object from
basic constructors, being a string for the sequence
Expand All @@ -483,7 +483,7 @@ sub new {
my($caller,@args) = @_;

if( $caller ne 'Bio::Seq') {
$caller = ref($caller) if ref($caller);
$caller = ref($caller) if ref($caller);
}

# we know our inherietance hierarchy
Expand Down Expand Up @@ -512,23 +512,23 @@ sub new {
# gives a quick optimisation around testing things later on

if( defined $ann || defined $pid || defined $feat || defined $species ) {
$pid && $self->primary_id($pid);
$species && $self->species($species);
$ann && $self->annotation($ann);
if( defined $feat ) {
if( ref($feat) !~ /ARRAY/i ) {
if( ref($feat) && $feat->isa('Bio::SeqFeatureI') ) {
$self->add_SeqFeature($feat);
} else {
$self->warn("Must specify a valid Bio::SeqFeatureI or ArrayRef of Bio::SeqFeatureI's with the -features init parameter for ".ref($self));
}
} else {
foreach my $feature ( @$feat ) {
$self->add_SeqFeature($feature);
}
}
}
$pid && $self->primary_id($pid);
$species && $self->species($species);
$ann && $self->annotation($ann);
if( defined $feat ) {
if( ref($feat) !~ /ARRAY/i ) {
if( ref($feat) && $feat->isa('Bio::SeqFeatureI') ) {
$self->add_SeqFeature($feat);
} else {
$self->warn("Must specify a valid Bio::SeqFeatureI or ArrayRef of Bio::SeqFeatureI's with the -features init parameter for ".ref($self));
}
} else {
foreach my $feature ( @$feat ) {
$self->add_SeqFeature($feature);
}
}
}
}

return $self;
Expand Down Expand Up @@ -574,9 +574,9 @@ sub seq {
Title : validate_seq
Usage : if(! $seq->validate_seq($seq_str) ) {
print "sequence $seq_str is not valid for an object of type ",
ref($seq), "\n";
}
print "sequence $seq_str is not valid for an object of type ",
ref($seq), "\n";
}
Function: Validates a given sequence string. A validating sequence string
must be accepted by seq(). A string that does not validate will
lead to an exception if passed to seq().
Expand Down Expand Up @@ -752,19 +752,19 @@ sub primary_id {
Title : can_call_new
Usage : if ( $obj->can_call_new ) {
$newobj = $obj->new( %param );
}
$newobj = $obj->new( %param );
}
Function: can_call_new returns 1 or 0 depending
on whether an implementation allows new
constructor to be called. If a new constructor
is allowed, then it should take the followed hashed
constructor list.
$myobject->new( -seq => $sequence_as_string,
-display_id => $id
-accession_number => $accession
-alphabet => 'dna',
);
-display_id => $id
-accession_number => $accession
-alphabet => 'dna',
);
Example :
Returns : 1 or 0
Args : None
Expand Down Expand Up @@ -952,12 +952,12 @@ for more information
sub annotation {
my ($obj,$value) = @_;
if( defined $value ) {
$obj->throw("object of class ".ref($value)." does not implement ".
"Bio::AnnotationCollectionI. Too bad.")
unless $value->isa("Bio::AnnotationCollectionI");
$obj->{'_annotation'} = $value;
$obj->throw("object of class ".ref($value)." does not implement ".
"Bio::AnnotationCollectionI. Too bad.")
unless $value->isa("Bio::AnnotationCollectionI");
$obj->{'_annotation'} = $value;
} elsif( ! defined $obj->{'_annotation'}) {
$obj->{'_annotation'} = Bio::Annotation::Collection->new();
$obj->{'_annotation'} = Bio::Annotation::Collection->new();
}
return $obj->{'_annotation'};
}
Expand Down Expand Up @@ -1112,9 +1112,9 @@ sub feature_count {
my ($self) = @_;

if (defined($self->{'_as_feat'})) {
return ($#{$self->{'_as_feat'}} + 1);
return ($#{$self->{'_as_feat'}} + 1);
} else {
return 0;
return 0;
}
}

Expand All @@ -1140,7 +1140,7 @@ sub add_SeqFeature {

foreach my $feat ( @feat ) {
if( !$feat->isa("Bio::SeqFeatureI") ) {
$self->throw("$feat is not a SeqFeatureI and that's what we expect...");
$self->throw("$feat is not a SeqFeatureI and that's what we expect...");
}

# make sure we attach ourselves to the feature if the feature wants it
Expand Down Expand Up @@ -1268,15 +1268,15 @@ sub primary_seq {

if( defined $value) {
if( ! ref $value || ! $value->isa('Bio::PrimarySeqI') ) {
$obj->throw("$value is not a Bio::PrimarySeq compliant object");
$obj->throw("$value is not a Bio::PrimarySeq compliant object");
}

$obj->{'primary_seq'} = $value;
# descend down over all seqfeature objects, seeing whether they
# want an attached seq.

foreach my $sf ( $obj->get_SeqFeatures() ) {
$sf->attach_seq($value);
$sf->attach_seq($value);
}

}
Expand Down Expand Up @@ -1332,7 +1332,7 @@ sub all_SeqFeatures{
sub accession {
my $self = shift;
$self->warn(ref($self)."::accession is deprecated, ".
"use accession_number() instead");
"use accession_number() instead");
return $self->accession_number(@_);
}

Expand Down

0 comments on commit 5ad8e23

Please sign in to comment.