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Merge github.com:bioperl/bioperl-live into amplicons
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fangly committed Mar 14, 2012
2 parents 93fc11b + d3af015 commit 07dcf87
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Showing 14 changed files with 160 additions and 121 deletions.
2 changes: 1 addition & 1 deletion Bio/DB/SeqFeature/Store/DBI/SQLite.pm
Expand Up @@ -766,7 +766,7 @@ sub _name_sql {
my $from = "$name_table as n";
my ($match,$string) = $self->_match_sql($name);

my $where = "n.id=$join AND n.name $match";
my $where = "n.id=$join AND lower(n.name) $match";
$where .= " AND n.display_name>0" unless $allow_aliases;
return ($from,$where,'',$string);
}
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8 changes: 4 additions & 4 deletions Bio/FeatureHolderI.pm
Expand Up @@ -116,14 +116,14 @@ sub get_SeqFeatures {
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($subfeat,'EXPAND')
Function: adds a SeqFeature into the subSeqFeature array.
Function: Add a SeqFeature into the subSeqFeature array.
with no 'EXPAND' qualifer, subfeat will be tested
as to whether it lies inside the parent, and throw
an exception if not.
If EXPAND is used, the parent''s start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature
If EXPAND is used and the object implements Bio::RangeI
(which is not guaranteed), the parent''s start/end/strand
will be extended so that the new subFeature can be accomodated.
Example :
Returns : nothing
Args : a Bio::SeqFeatureI object
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