| line |
true |
false |
branch |
|
522
|
0 |
0 |
if ($db_name) |
|
523
|
0 |
0 |
unless $db_name =~ m[^[a-z0-9_/:.+-]+$]i |
|
526
|
0 |
0 |
if ($db_dir) { } |
|
527
|
0 |
0 |
unless -d $db_dir |
|
538
|
0 |
0 |
if ($db_name) |
|
540
|
0 |
0 |
unless $f |
|
545
|
0 |
0 |
if ('File::Spec'->file_name_is_absolute($db_name)) { } |
|
546
|
0 |
0 |
unless not $d or -d $d |
|
550
|
0 |
0 |
if $db_dir |
|
554
|
0 |
0 |
unless not $d or -d $d |
|
559
|
0 |
0 |
if ($masker) |
|
560
|
0 |
0 |
unless grep /^$masker$/, keys %AVAILABLE_MASKERS |
|
565
|
0 |
0 |
if ($program_dir) { } |
|
|
0 |
0 |
elsif ($ENV{'BLASTPLUSDIR'}) { } |
|
566
|
0 |
0 |
unless -d $program_dir |
|
577
|
0 |
0 |
if $db_make_args |
|
578
|
0 |
0 |
if $mask_make_args |
|
589
|
0 |
0 |
if (defined $self->check_db and $self->check_db == 0 and not $self->is_remote) |
|
590
|
0 |
0 |
unless $create or $overwrite |
|
592
|
0 |
0 |
unless ($self->db) |
|
594
|
0 |
0 |
unless ($self->db_data) |
|
602
|
0 |
0 |
if ($self->db_dir) { } |
|
691
|
0 |
0 |
if $fac |
|
697
|
0 |
0 |
if $fac |
|
719
|
0 |
0 |
if $self->check_db and not $self->overwrite |
|
721
|
0 |
0 |
unless $self->db_data |
|
729
|
0 |
0 |
$testio->next_seq->alphabet =~ /.na/ ? : |
|
745
|
0 |
0 |
if $usr_db_args |
|
755
|
0 |
0 |
if (%usr_args) |
|
763
|
0 |
0 |
if ($self->mask_file) { } |
|
|
0 |
0 |
elsif ($self->masker and $self->mask_data) { } |
|
769
|
0 |
0 |
unless $db_args{'-mask_data'} |
|
808
|
0 |
0 |
unless $data |
|
810
|
0 |
0 |
unless $masker |
|
813
|
0 |
0 |
if $usr_make_args |
|
814
|
0 |
0 |
unless (grep /^$masker$/, keys %AVAILABLE_MASKERS) |
|
817
|
0 |
0 |
if ($self->check_db($data)) { } |
|
818
|
0 |
0 |
unless ($masker eq 'segmasker') |
|
821
|
0 |
0 |
unless ($self->db_info($data)->{'_db_type'} eq $AVAILABLE_MASKERS{$masker}) |
|
832
|
0 |
0 |
if ($s->alphabet =~ /.na/) { } |
|
|
0 |
0 |
elsif ($s->alphabet =~ /protein/) { } |
|
841
|
0 |
0 |
unless ($type eq $AVAILABLE_MASKERS{$masker}) |
|
864
|
0 |
0 |
if (%usr_args) |
|
870
|
0 |
0 |
if (/dustmasker/) |
|
879
|
0 |
0 |
if (/windowmasker/) |
|
881
|
0 |
0 |
if ($mask_db) |
|
882
|
0 |
0 |
unless ($self->check_db($mask_db)) |
|
896
|
0 |
0 |
unless $status |
|
901
|
0 |
0 |
if ($mask_db) |
|
910
|
0 |
0 |
if (/segmasker/) |
|
924
|
0 |
0 |
$status ? : |
|
942
|
0 |
0 |
unless ($db) |
|
946
|
0 |
0 |
if ($self->is_remote) |
|
950
|
0 |
0 |
if ($db eq $self->db and $self->{'_db_info'}) |
|
960
|
0 |
0 |
if ($self->factory->stderr =~ /No alias or index file found/) |
|
969
|
0 |
0 |
if (/Database: (.*)/) |
|
973
|
0 |
0 |
if (/([0-9,]+) sequences; ([0-9,]+) total/) |
|
980
|
0 |
0 |
if (/Date: (.*?)\s+Longest sequence: ([0-9,]+)/) |
|
986
|
0 |
0 |
if (/Algorithm ID/) |
|
989
|
0 |
0 |
if (/\s*([0-9]+)\s+([a-z0-9_]+)\s+(.*)/i) { } |
|
1004
|
0 |
0 |
if (-e $db . '.psq') { } |
|
|
0 |
0 |
elsif (-e $db . '.nsq') { } |
|
1013
|
0 |
0 |
if ($db eq $self->db) |
|
1035
|
0 |
0 |
unless ref($args) =~ /^ARRAY|HASH$/ |
|
1037
|
0 |
0 |
if (ref $args eq 'HASH') |
|
1041
|
0 |
0 |
if @$args % 2 |
|
1062
|
0 |
0 |
unless ref($args) =~ /^ARRAY|HASH$/ |
|
1064
|
0 |
0 |
if (ref $args eq 'HASH') |
|
1068
|
0 |
0 |
if @$args % 2 |
|
1093
|
0 |
0 |
if ($db) { } |
|
1101
|
0 |
0 |
if ($db_path) |
|
1109
|
0 |
0 |
if $self->factory->stderr =~ /No alias or index file found/ |
|
1130
|
0 |
0 |
if @_ |
|
1152
|
0 |
0 |
unless (ref $_) |
|
1154
|
0 |
0 |
unless -e $data |
|
1156
|
0 |
0 |
unless $guesser->guess eq 'fasta' |
|
1162
|
0 |
0 |
if (ref $_ eq 'ARRAY' and ref $data->[0] and $data->[0]->isa('Bio::Seq') || $data->[0]->isa('Bio::PrimarySeq')) |
|
1170
|
0 |
0 |
unless my $fasio = 'Bio::SeqIO'->new(-'file', ">$fname", -'format', 'fasta') |
|
1184
|
0 |
0 |
if (ref $_) |
|
1186
|
0 |
0 |
if ($fmt eq 'fasta') { } |
|
1198
|
0 |
0 |
unless my $fasio = 'Bio::SeqIO'->new(-'file', ">$fname", -'format', 'fasta') |
|
1201
|
0 |
0 |
if ($data->isa('Bio::AlignIO')) { } |
|
|
0 |
0 |
elsif ($data->isa('Bio::SeqIO')) { } |
|
|
0 |
0 |
elsif ($data->isa('Bio::Align::AlignI')) { } |
|
|
0 |
0 |
elsif ($data->isa('Bio::Seq') or $data->isa('Bio::PrimarySeq')) { } |
|
1272
|
0 |
0 |
unless length $d |
|
1290
|
0 |
0 |
unless $self->{'_cleanup_list'} |
|
1293
|
0 |
0 |
if (exists $self->{'_results'}{'_file'}) |
|
1299
|
0 |
0 |
if ($self_file ne '' and $_ =~ /$self_file$/) |
|
1303
|
0 |
0 |
if (/(\.[a-z0-9_]+)+$/i) |
|
1308
|
0 |
0 |
if (-e $_ . '.psq') { } |
|
|
0 |
0 |
elsif (-e $_ . '.nsq') { } |
|
1354
|
0 |
0 |
if (grep /^$method$/, @Bio::Tools::Run::StandAloneBlastPlus::BlastMethods) |
|
1355
|
0 |
0 |
if $self->is_remote |
|
1358
|
0 |
0 |
if ($self->factory and $self->factory->can($method)) |
|
1361
|
0 |
0 |
if ($self->db_info and grep /^$method$/, keys %{$self->db_info;}) |