Removed Camel-case from Bigfile parsers

Former-commit-id: d21187738e8884dbde97cef325c26e3edce89f07

getters.txt

@@ -200,18 +200,18 @@ get_next_column
 
 BigBed Parser (Daniel)
 
-getChrom
-getStart
-getEnd
-getScore
-getParts
-getName
-getRGB
-getBedFeature
+get_chrom
+get_start
+get_end
+get_score
+get_parts
+get_name
+get_rgb
+get_bedFeature
 
 BigWig Parser (Daniel)
 
-getRawChrom
-getStart
-getEnd
-getScore
+get_chrom
+get_start
+get_end
+get_score

modules/Bio/EnsEMBL/IO/Parser/BigBed.pm

@@ -85,87 +85,87 @@ sub next {
   }
 }
 
-sub getRawChrom {
+sub get_raw_chrom {
   my $self = shift;
   return $self->{current}->seq_id;
 }
 
-sub getChrom {
+sub get_chrom {
   my $self = shift;
-  return $self->getRawChrom;
+  return $self->get_raw_chrom;
 }
 
-sub getRawStart {
+sub get_raw_start {
   my $self = shift;
   return $self->{current}->start;
 }
 
-sub getStart {
+sub get_start {
   my $self = shift;
-  return $self->getRawStart;
+  return $self->get_raw_start;
 }
 
-sub getRawEnd {
+sub get_raw_end {
   my $self = shift;
   return $self->{current}->end;
 }
 
-sub getEnd {
+sub get_end {
   my $self = shift;
-  return $self->getRawEnd;
+  return $self->get_raw_end;
 }
 
-sub getRawScore {
+sub get_raw_score {
   my $self = shift;
   return $self->{current}->score;
 }
 
-sub getScore {
+sub get_score {
   my $self = shift;
-  return $self->getRawScore;
+  return $self->get_raw_score;
 }
 
-sub getRawStrand {
+sub get_raw_strand {
   my $self = shift;
   return $self->{current}->strand;
 }
 
-sub getStrand {
+sub get_strand {
   my $self = shift;
-  return $self->getRawStrand;
+  return $self->get_raw_strand;
 }
 
-sub getRawParts {
+sub get_raw_parts {
   my $self = shift;
   return $self->{current}->get_SeqFeatures;
 }
 
-sub getParts {
+sub get_parts {
   my $self = shift;
-  return $self->getRawParts;
+  return $self->get_raw_parts;
 }
 
-sub getRawName {
+sub get_raw_name {
   my $self = shift;
   return $self->{current}->name;
 }
 
-sub getName {
+sub get_name {
   my $self = shift;
-  return $self->getRawName;
+  return $self->get_raw_name;
 }
 
-sub getRawRGB {
+sub get_raw_rgb {
   my $self = shift;
   return $self->{current}->attributes('RGB');
 }
 
-sub getRGB {
+sub get_rgb {
   my $self = shift;
-  return $self->getRawRGB;
+  return $self->get_raw_rgb;
 }
 
-sub getBEDFeature {
+sub get_bed_feature {
   my $self = shift;
   return $self->{current};
 }
@@ -176,7 +176,7 @@ sub getBEDFeature {
 sub munge_chr_id {
   my ($self, $chr_id) = @_;
 
-  # Check we get values back for seq region. Maybe need to add 'chr' 
+  # Check we get_ values back for seq region. Maybe need to add 'chr' 
   if ($self->{_cache}->{_bigbed_handle}->chromSize($chr_id)) {
       return $chr_id;
   } elsif ($self->{_cache}->{_bigbed_handle}->chromSize("chr$chr_id")) {
@@ -207,7 +207,7 @@ sub fetch_features  {
 
   my @features;
   while ($self->next) {
-    push @features,$self->getBEDFeature;
+    push @features,$self->get_bed_feature;
   }
   return \@features;
 }

modules/Bio/EnsEMBL/IO/Parser/BigWig.pm

@@ -85,44 +85,44 @@ sub next {
   }
 }
 
-sub getRawChrom {
+sub get_raw_chrom {
   my $self = shift;
   return $self->{current} ? $self->{current}->seq_id : undef;
 }
 
-sub getChrom {
+sub get_chrom {
   my $self = shift;
-  return $self->getRawChrom;
+  return $self->get_raw_chrom;
 }
 
-sub getRawStart {
+sub get_raw_start {
   my $self = shift;
   return $self->{current}->start;
 }
 
-sub getStart {
+sub get_start {
   my $self = shift;
-  return $self->getRawStart;
+  return $self->get_raw_start;
 }
 
-sub getRawEnd {
+sub get_raw_end {
   my $self = shift;
   return $self->{current}->end;
 }
 
-sub getEnd {
+sub get_end {
   my $self = shift;
-  return $self->getRawEnd;
+  return $self->get_raw_end;
 }
 
-sub getRawScore {
+sub get_raw_score {
   my $self = shift;
   return $self->{current}->score;
 }
 
-sub getScore {
+sub get_score {
   my $self = shift;
-  return $self->getRawScore;
+  return $self->get_raw_score;
 }
 
 # UCSC prepend 'chr' on human chr ids. These are in some of the BigBed
@@ -131,7 +131,7 @@ sub getScore {
 sub munge_chr_id {
   my ($self, $chr_id) = @_;
 
-  # Check we get values back for seq region. Maybe need to add 'chr' 
+  # Check we get_ values back for seq region. Maybe need to add 'chr' 
   if ($self->{_cache}->{_bigbed_handle}->chromSize($chr_id)) {
       return $chr_id;
   } elsif ($self->{_cache}->{_bigbed_handle}->chromSize("chr$chr_id")) {

modules/t/bigbed.t

@@ -10,28 +10,28 @@ use Bio::EnsEMBL::IO::Parser::BigBed;
 my $parser = Bio::EnsEMBL::IO::Parser::BigBed->open('modules/t/data.bb');
 
 ok($parser->next());
-ok($parser->getChrom eq 'chr1');
-ok($parser->getStart == 3);
-ok($parser->getEnd == 6);
-ok($parser->getStrand == 0);
-ok($parser->getName eq 'Mo');
-ok($parser->getScore == 1000);
+ok($parser->get_chrom eq 'chr1');
+ok($parser->get_start == 3);
+ok($parser->get_end == 6);
+ok($parser->get_strand == 0);
+ok($parser->get_name eq 'Mo');
+ok($parser->get_score == 1000);
 
 ok($parser->next);
-ok($parser->getChrom eq 'chr1');
-ok($parser->getStart == 4);
-ok($parser->getEnd == 8);
-ok($parser->getStrand);
-ok($parser->getName eq 'Larry');
-ok($parser->getScore == 1000);
+ok($parser->get_chrom eq 'chr1');
+ok($parser->get_start == 4);
+ok($parser->get_end == 8);
+ok($parser->get_strand);
+ok($parser->get_name eq 'Larry');
+ok($parser->get_score == 1000);
 
 ok($parser->next);
-ok($parser->getChrom eq 'chr2');
-ok($parser->getStart == 2);
-ok($parser->getEnd == 7);
-ok($parser->getStrand == -1);
-ok($parser->getName eq 'Curly');
-ok($parser->getScore == 1000);
+ok($parser->get_chrom eq 'chr2');
+ok($parser->get_start == 2);
+ok($parser->get_end == 7);
+ok($parser->get_strand == -1);
+ok($parser->get_name eq 'Curly');
+ok($parser->get_score == 1000);
 
 ok(!$parser->next);
 

modules/t/bigwig.t

@@ -10,17 +10,17 @@ use Bio::EnsEMBL::IO::Parser::BigWig;
 my $parser = Bio::EnsEMBL::IO::Parser::BigWig->open("modules/t/data-variableStep.bw");
 
 ok($parser->next);
-ok($parser->getChrom eq 'chr1');
-ok($parser->getStart == 1);
-ok($parser->getEnd == 1);
-ok($parser->getScore == 1);
+ok($parser->get_chrom eq 'chr1');
+ok($parser->get_start == 1);
+ok($parser->get_end == 1);
+ok($parser->get_score == 1);
 
 for (my $i = 0; $i < 4; $i++) {
   ok($parser->next);
-  ok($parser->getChrom eq 'chr1');
-  ok($parser->getStart == 2 + 2 * $i);
-  ok($parser->getEnd == 2 + 2 * $i);
-  ok($parser->getScore == 2 + $i);
+  ok($parser->get_chrom eq 'chr1');
+  ok($parser->get_start == 2 + 2 * $i);
+  ok($parser->get_end == 2 + 2 * $i);
+  ok($parser->get_score == 2 + $i);
 }
 
 ok(!$parser->next);
@@ -34,10 +34,10 @@ $parser = Bio::EnsEMBL::IO::Parser::BigWig->open('modules/t/data-fixedStep.bw');
 
 for (my $i = 0; $i < 10; $i ++) {
   ok($parser->next);
-  ok($parser->getChrom eq 'chr1');
-  ok($parser->getStart == 1 + $i);
-  ok($parser->getEnd == 1 + $i);
-  ok($parser->getScore == $i);
+  ok($parser->get_chrom eq 'chr1');
+  ok($parser->get_start == 1 + $i);
+  ok($parser->get_end == 1 + $i);
+  ok($parser->get_score == $i);
 }
 
 ok(!$parser->next);