| line |
true |
false |
branch |
|
207
|
0 |
1 |
if (defined $ENV{'TRIBEDIR'}) |
|
209
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
210
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
235
|
0 |
2 |
if $attr =~ /^-/ |
|
236
|
0 |
2 |
if ($attr =~ /MCL/i) |
|
240
|
0 |
2 |
if ($attr =~ /MATRIX/i) |
|
246
|
1 |
0 |
unless defined $self->weight |
|
255
|
0 |
5 |
unless $Bio::Tools::Run::TribeMCL::OK_FIELD{$attr} |
|
256
|
4 |
1 |
if @_ |
|
274
|
0 |
0 |
if (defined $exe) |
|
277
|
0 |
0 |
unless (defined $self->{'_mcl_exe'}) |
|
279
|
0 |
0 |
if ($Bio::Tools::Run::TribeMCL::MCLPROGRAM and -e $Bio::Tools::Run::TribeMCL::MCLPROGRAM and -x $Bio::Tools::Run::TribeMCL::MCLPROGRAM) { } |
|
283
|
0 |
0 |
if ($exe = $self->io->exists_exe($Bio::Tools::Run::TribeMCL::MCLPROGRAM_NAME) and -x $exe) { } |
|
287
|
0 |
0 |
if $warn |
|
309
|
0 |
1 |
if (defined $exe) |
|
312
|
1 |
0 |
unless (defined $self->{'_matrix_exe'}) |
|
314
|
0 |
1 |
if ($Bio::Tools::Run::TribeMCL::MATRIXPROGRAM and -e $Bio::Tools::Run::TribeMCL::MATRIXPROGRAM and -x $Bio::Tools::Run::TribeMCL::MATRIXPROGRAM) { } |
|
318
|
0 |
1 |
if ($exe = $self->io->exists_exe($Bio::Tools::Run::TribeMCL::MATRIXPROGRAM_NAME) and -x $exe) { } |
|
322
|
0 |
1 |
if $warn |
|
343
|
0 |
0 |
if ($self->description_file) |
|
347
|
0 |
0 |
unless defined $file |
|
350
|
0 |
0 |
unless -e $index_file |
|
352
|
0 |
0 |
unless -e $mcl_infile |
|
357
|
0 |
0 |
if ($self->description) { } |
|
372
|
0 |
0 |
if ($consensus) { } |
|
390
|
0 |
0 |
if $taxon_str |
|
391
|
0 |
0 |
if $taxon_str |
|
393
|
0 |
0 |
$taxon{'taxon_classification'} ? : |
|
398
|
0 |
0 |
if $name |
|
399
|
0 |
0 |
if $sub_species |
|
400
|
0 |
0 |
if $tax_id |
|
401
|
0 |
0 |
if @classification |
|
439
|
0 |
0 |
if ($@) |
|
447
|
0 |
0 |
if ($self->use_db) |
|
460
|
0 |
0 |
if ($self->use_db) { } |
|
461
|
0 |
0 |
if ($use_db{$description{$member}[0]}) |
|
462
|
0 |
0 |
if $description{$member}[1] |
|
463
|
0 |
0 |
if $description{$member}[1] |
|
467
|
0 |
0 |
if $description{$member}[1] |
|
468
|
0 |
0 |
if $description{$member}[1] |
|
472
|
0 |
0 |
if ($#desc < 0) |
|
477
|
0 |
0 |
if ($#desc == 0) |
|
480
|
0 |
0 |
if ($consensus{$i}{'desc'} eq 'UNKNOWN') { } |
|
491
|
0 |
0 |
if (keys %desc == 1) |
|
539
|
0 |
0 |
if ($lcs eq $candidate_consensus or index($orig_desc, $candidate_consensus) != -1) |
|
557
|
0 |
0 |
if $length == 0 |
|
558
|
0 |
0 |
if ($perc_with_desc >= 40 and $length >= 1) |
|
559
|
0 |
0 |
if ($score > $best_score) |
|
566
|
0 |
0 |
if ($best_perc == 0 or $best_perc >= 100) |
|
569
|
0 |
0 |
if ($best_annotation eq '') |
|
583
|
0 |
0 |
unless open FILE, "$filter | " |
|
588
|
0 |
0 |
unless $description |
|
591
|
0 |
0 |
if ($description{$acc}) |
|
643
|
0 |
0 |
unless (defined $self->o) |
|
650
|
0 |
0 |
unless (defined $self->I) |
|
655
|
0 |
0 |
if (defined $self->$param) |
|
659
|
0 |
0 |
if ($self->quiet or $self->verbose < 0) |
|
662
|
0 |
0 |
unless ($^O =~ /Mac/) |
|
663
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
670
|
0 |
0 |
unless $status == 0 |
|
689
|
0 |
0 |
unless (defined $self->ind) |
|
696
|
0 |
0 |
unless (defined $self->out) |
|
704
|
0 |
0 |
if (defined $self->$param) |
|
708
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
712
|
0 |
0 |
unless $status == 0 |
|
735
|
0 |
0 |
if ($type =~ /scorefile/i) |
|
736
|
0 |
0 |
unless -e $self->scorefile |
|
740
|
0 |
0 |
if ($type =~ /blastfile/i) { } |
|
|
0 |
0 |
elsif ($type =~ /searchio/i) { } |
|
|
0 |
0 |
elsif ($type =~ /pairs/i) { } |
|
|
0 |
0 |
elsif ($type =~ /hsp/i) { } |
|
|
0 |
0 |
elsif ($type =~ /hit/i) { } |
|
767
|
0 |
0 |
unless ($rc) |
|
793
|
0 |
0 |
if ($expect == 0) |
|
815
|
0 |
0 |
if ($expect == 0) |
|
848
|
0 |
0 |
if ($expect == 0) |
|
880
|
0 |
0 |
unless open FILE, $file |
|
886
|
0 |
0 |
if (/Query=\s+(\S+)/) |
|
889
|
0 |
0 |
if (/^>(\S+)/) |
|
892
|
0 |
0 |
if (/Expect = (\S+)/) |
|
896
|
0 |
0 |
if ($expect == 0) |
|
924
|
0 |
0 |
unless open MCL, $mcl |
|
929
|
0 |
0 |
if ($start) |
|
933
|
0 |
0 |
if (/^\d+/) |
|
938
|
0 |
0 |
if (/\$$/) |
|
941
|
0 |
0 |
if /^\(mclruninfo/ |
|
943
|
0 |
0 |
unless open IND, $ind |