| line |
true |
false |
branch |
|
120
|
0 |
0 |
if (scalar @method_args > 0 and ref($method_args[0]) =~ /foundation/i) { } |
|
132
|
0 |
0 |
if (scalar @method_args > 0 and ref($method_args[0]) =~ /array/i) { } |
|
144
|
0 |
0 |
if (scalar @method_args > 0 and not ref $method_args[0]) { } |
|
147
|
0 |
0 |
if (defined $filename) { } |
|
164
|
0 |
0 |
if (scalar @method_args > 0) { } |
|
|
0 |
0 |
elsif (defined $self->{'db_file_name'} and not defined $self->open($self->{'db_file_name'}, 'r')) { } |
|
174
|
0 |
0 |
$error_condition == 0 ? : |
|
194
|
0 |
0 |
unless (defined $open_flags and $open_flags =~ /^r$/i) |
|
202
|
0 |
0 |
if (defined $self->{'db_handle'}) |
|
208
|
0 |
0 |
if (not defined $db_file_name && ($self->{'db_file_name'} = $db_file_name) && defined $self->{'db_file_name'} && defined($self->{'db_handle'} = 'IO::File'->new($self->{'db_file_name'}, $open_flags))) { } |
|
|
0 |
0 |
elsif (defined $self->{'db_file_name'} and defined $self->{'db_handle'} and $self->_parseDBfile == 0) { } |
|
228
|
0 |
0 |
if ($error_condition == 1) |
|
232
|
0 |
0 |
$error_condition == 1 ? : |
|
249
|
0 |
0 |
if (defined $self->{'db_handle'}) |
|
251
|
0 |
0 |
unless ($return_val) |
|
276
|
0 |
0 |
if (defined $self->{'active_record'}) { } |
|
301
|
0 |
0 |
if (defined $active_num and $active_num =~ /^\d+$/ || $active_num == -1 and $active_num < $self->count) { } |
|
312
|
0 |
0 |
unless (defined $active_num) |
|
336
|
0 |
0 |
if (defined $self->hasNext) { } |
|
360
|
0 |
0 |
if (defined $self->{'active_record'} and $self->{'active_record'} >= -1 and $self->{'active_record'} < $self->count - 1) { } |
|
390
|
0 |
0 |
if (defined $identifier) { } |
|
393
|
0 |
0 |
if (defined $seek_result and $seek_result == 1) |
|
419
|
0 |
0 |
if (defined $identifier and exists $self->{'identifier_to_number_hash'}{$identifier}) |
|
441
|
0 |
0 |
defined $self->{'db_handle'} ? : |
|
450
|
0 |
0 |
unless (defined $db_handle) |
|
457
|
0 |
0 |
if (defined $self->{'active_record'} and $self->{'active_record'} > -1 and $self->{'active_record'} < $self->count and defined $db_handle and defined($pos_str = $self->{'number_to_fp_array'}{$self->{'active_record'}})) |
|
468
|
0 |
0 |
if (defined $pos_arr[0] and defined $db_handle->seek($pos_arr[0], 0) and defined $pos_arr[1] and defined read($db_handle, $record, $pos_arr[1] - $pos_arr[0] + 1)) |
|
548
|
0 |
0 |
defined $self->{'db_handle'} ? : |
|
569
|
0 |
0 |
if (defined $record_identifier and not $record_identifier =~ // and &isValidFASTAdata($line) != 0) { } |
|
|
0 |
0 |
elsif (&isValidFASTAheader($line) != 0) { } |
|
|
0 |
0 |
elsif ($line eq '') { } |
|
574
|
0 |
0 |
if ($empty_line_found == 1) |
|
583
|
0 |
0 |
if ($preceding_header_flag == 1) |
|
588
|
0 |
0 |
if (defined $first_data_line_length) |
|
589
|
0 |
0 |
if ($last_line_length_lt_std_flag == 1) |
|
602
|
0 |
0 |
if ($line_len > $first_data_line_length) { } |
|
|
0 |
0 |
elsif ($line_len < $first_data_line_length) { } |
|
623
|
0 |
0 |
unless (defined $self->{'active_record'}) |
|
629
|
0 |
0 |
if (defined $line_number and $line_number > 1) |
|
634
|
0 |
0 |
if (defined $pos1 and defined $string) |
|
642
|
0 |
0 |
if (defined $pos1) |
|
647
|
0 |
0 |
if ($preceding_header_flag == 1) |
|
653
|
0 |
0 |
if ($empty_line_found == 1) |
|
664
|
0 |
0 |
if (defined $self->{'identifier_to_number_hash'}{$record_identifier}) { } |
|
693
|
0 |
0 |
if ($empty_line_found == 1) |
|
703
|
0 |
0 |
if ($line =~ /$UNBOUND_FASTA_SEPARATOR/) { } |
|
|
0 |
0 |
elsif ($last_line_length_lt_std_flag == 1) { } |
|
|
0 |
0 |
elsif (defined $record_identifier and not $record_identifier =~ //) { } |
|
733
|
0 |
0 |
if (defined $pos1 and defined $string) |
|
740
|
0 |
0 |
if ($preceding_header_flag == 1) |
|
746
|
0 |
0 |
$self->{'error_cnt'} == 0 ? : |
|
764
|
0 |
0 |
if (defined $self->{'number_to_identifier_array'}{$active_num}) { } |
|
773
|
0 |
0 |
if (defined $line_number) { } |
|
774
|
0 |
0 |
if (defined $active_num and $active_num < $self->{'active_record'}) { } |
|
|
0 |
0 |
elsif (defined $active_num and $active_num == $self->{'active_record'}) { } |
|
788
|
0 |
0 |
if ($self->{'db_handle'}->eof == 1) { } |
|
822
|
0 |
0 |
if (defined $message and defined $tf_level and defined $log_facility) |
|
826
|
0 |
0 |
if (defined $self->{'foundation'}) |
|
827
|
0 |
0 |
if ($log_facility != $USR_ERR) { } |
|
835
|
0 |
0 |
if (defined $self->{'error_ref'} and $log_facility == $USR_ERR) |