view release on metacpan or search on metacpan
t/SearchIO/blastxml.t view on Meta::CPAN
is($iter->number, $iter_count);
is($iter->num_hits, shift @$di);
is($iter->num_hits_new, shift @$di);
is($iter->num_hits_old, shift @$di);
is(scalar($iter->newhits_below_threshold), shift @$di);
is(scalar($iter->newhits_not_below_threshold), shift @$di);
is(scalar($iter->newhits_unclassified), shift @$di);
is(scalar($iter->oldhits_below_threshold), shift @$di);
is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
is(scalar($iter->oldhits_not_below_threshold), shift @$di);
my $hit_count = 0;
if ($iter_count == 1) {
while( my $hit = $result->next_hit ) {
my $d = shift @valid_hit_data;
is($hit->name, shift @$d);
t/SearchIO/blastxml.t view on Meta::CPAN
is($iter->number, $iter_count);
is($iter->num_hits, shift @$di);
is($iter->num_hits_new, shift @$di);
is($iter->num_hits_old, shift @$di);
is(scalar($iter->newhits_below_threshold), shift @$di);
is(scalar($iter->newhits_not_below_threshold), shift @$di);
is(scalar($iter->newhits_unclassified), shift @$di);
is(scalar($iter->oldhits_below_threshold), shift @$di);
is(scalar($iter->oldhits_newly_below_threshold), shift @$di);
is(scalar($iter->oldhits_not_below_threshold), shift @$di);
my $hit_count = 0;
if ($iter_count == 1) {
while( my $hit = $result->next_hit ) {
my $d = shift @valid_hit_data;
is($hit->name, shift @$d);
view release on metacpan or search on metacpan
lib/Bio/SearchIO/hmmer3.pm view on Meta::CPAN
elsif ( $buffer =~ /Domain( and alignment)? annotation for each/
or $buffer =~ /Annotation for each hit\s+\(and alignments\)/
) {
@hsp_list = (); # Here for multi-query reports
my $name;
my $annot_counter = 0;
while ( defined( $buffer = $self->_readline ) ) {
if ( $buffer =~ /\[No targets detected/
|| $buffer =~ /Internal pipeline statistics/ )
{
lib/Bio/SearchIO/hmmer3.pm view on Meta::CPAN
}
if ( $buffer =~ m/^\>\>\s(\S*)\s+(.*)/ ) {
$name = $1;
my $desc = $2;
$annot_counter++;
$domaincounter{"$name.$annot_counter"} = 0;
# The Hit Description from the Scores table can be truncated if
# its too long, so use the '>>' line description when its longer
if (length $hit_list[
$hitinfo{"$name.$annot_counter"}
]
[1] < length $desc
) {
$hit_list[ $hitinfo{"$name.$annot_counter"} ][1] = $desc;
}
while ( defined( $buffer = $self->_readline ) ) {
if ( $buffer =~ m/Internal pipeline statistics/
|| $buffer =~ m/Alignments for each domain/
lib/Bio/SearchIO/hmmer3.pm view on Meta::CPAN
else {
print STDERR "Missed this line: $buffer\n";
next;
}
my $info = $hit_list[ $hitinfo{"$name.$annot_counter"} ];
if ( !defined $info ) {
$self->warn(
"Incomplete information: can't find HSP $name in list of hits\n"
);
next;
}
$domaincounter{"$name.$annot_counter"}++;
my $hsp_key
= $name . "_" . $domaincounter{"$name.$annot_counter"};
# Keep it simple for now. let's customize later
@vals = (
$hmm_start, $hmm_stop,
$seq_start, $seq_stop,
lib/Bio/SearchIO/hmmer3.pm view on Meta::CPAN
$hitlength, '',
'', '',
'', ''
);
push @hsp_list, [ $name, @vals ];
$hspinfo{"$hsp_key.$annot_counter"} = $#hsp_list;
}
}
}
elsif ( $buffer =~ /Alignment(?:s for each domain)?:/ ) {
#line counter
lib/Bio/SearchIO/hmmer3.pm view on Meta::CPAN
or $buffer =~ /\s\sscore:\s\S+\s+/
) {
my $domainnum = $1 || 1;
$count = 0;
my $key = $name . "_" . $domainnum;
$hsp = $hsp_list[ $hspinfo{"$key.$annot_counter"} ];
$csline = $$hsp[-5];
$hline = $$hsp[-4];
$midline = $$hsp[-3];
$qline = $$hsp[-2];
$pline = $$hsp[-1];
view release on metacpan or search on metacpan
scripts/correlate_position_data.pl view on Meta::CPAN
# variables for reporting the summary of results
my @correlations;
my @optimal_shifts;
my @optimal_correlations;
my $count = 0;
my $not_enough_data = 0;
my $no_variance = 0;
$pm->run_on_finish(
sub {
my ( $pid, $exit_code, $ident, $exit_signal, $core_dump, $result ) = @_;
push @correlations, @{ $result->[0] };
push @optimal_shifts, @{ $result->[1] };
push @optimal_correlations, @{ $result->[2] };
$count += $result->[3];
$not_enough_data += $result->[4];
$no_variance += $result->[5];
}
);
# Split the input data into parts and execute in parallel in separate forks
scripts/correlate_position_data.pl view on Meta::CPAN
my $new_count = $Data->reload_children(@files);
printf " reloaded %s features from children\n", format_with_commas($new_count);
# summarize the results
summarize_results( \@correlations, \@optimal_shifts, \@optimal_correlations,
$count, $not_enough_data, $no_variance );
}
sub single_execution {
# run in a single thread
scripts/correlate_position_data.pl view on Meta::CPAN
# Set variables for summary analysis
my @correlations;
my @optimal_shifts;
my @optimal_correlations;
my $count = 0;
my $not_enough_data = 0;
my $no_variance = 0;
# check that we can collect information
unless ( $Data->feature_type eq 'named' or $Data->feature_type eq 'coordinate' ) {
die " Unable to identify the type of features in the input file."
scripts/correlate_position_data.pl view on Meta::CPAN
$row->value( $p_i, '.' ) if ($find_pvalue);
if ($find_shift) {
$row->value( $shift_i, '.' );
$row->value( $shiftr_i, '.' );
}
$not_enough_data++;
next;
}
# Calculate Paired T-Test P value
# going to try this before normalizing
scripts/correlate_position_data.pl view on Meta::CPAN
$count++;
}
# Return correlation results for summary
return ( \@correlations, \@optimal_shifts, \@optimal_correlations,
$count, $not_enough_data, $no_variance );
}
sub add_new_columns {
# Required columns
scripts/correlate_position_data.pl view on Meta::CPAN
sub summarize_results {
# the results from the correlation analysis
my ( $correlations, $optimal_shifts, $optimal_correlations,
$count, $not_enough_data, $no_variance )
= @_;
# Summary analyses
printf " Correlated %s features\n", format_with_commas($count);
printf " Mean Pearson correlation was %.3f +/- %.3f\n",
scripts/correlate_position_data.pl view on Meta::CPAN
mean( map {abs} @{$optimal_shifts} ),
stddevp( map {abs} @{$optimal_shifts} );
printf " Mean optimal Pearson correlation was %.3f +/- %.3f\n",
mean( @{$optimal_correlations} ), stddevp( @{$optimal_correlations} );
}
if ($not_enough_data) {
printf " %s features did not have enough data points\n",
format_with_commas($not_enough_data);
}
if ($no_variance) {
printf " %s features had no variance in the reference data points\n",
format_with_commas($no_variance);
}
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use 5.006;
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open( my $fh, '<', $filename )
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
}
}
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
TODO: {
local $TODO = "Need to replace the boilerplate text";
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
module_boilerplate_ok('lib/Bio/Tools/Alignment/Overview.pm');
view release on metacpan or search on metacpan
lib/Bio/Tools/Run/Alignment/Clustalw.pm view on Meta::CPAN
# previous alignments.
sub anchored_align {
my @local_array = ();
my @seqs_not_matched = ();
print "\n Beginning anchored-alignment example... \n";
for ($seq_num = 0; $seq_num < scalar(@seq_array); $seq_num++) {
my $seqobj = $seq_array[$seq_num];
lib/Bio/Tools/Run/Alignment/Clustalw.pm view on Meta::CPAN
my $id = $seqobj->id();
# if $regex is not found in the sequence, save sequence id name and set
# array value =0 for later
unless ($seq =~/$regex/) {
$local_array[$seq_num] = 0;
push (@seqs_not_matched, $id) ;
next;
}
# find positions of start and of subsequence to be aligned
my $match_start_pos = length($`);
my $match_stop_pos = length($`) + length($&);
lib/Bio/Tools/Run/Alignment/Clustalw.pm view on Meta::CPAN
# Perform alignment on the local segments of the sequences which match "anchor"
$aln = $factory->align(\@local_array);
my $consensus = $aln->consensus_string(); # Get consensus of local alignment
if (scalar(@seqs_not_matched) ) {
print " Sequences not matching $regex : @seqs_not_matched \n"
} else {
print " All sequences match $regex : @seqs_not_matched \n"
}
print "Consensus sequence of local alignment: $consensus \n";
return 1;
}
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open my $fh, "<", $filename
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
} else {
pass("$filename contains no boilerplate text");
}
}
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
view release on metacpan or search on metacpan
t/Bio/Tradis/RunTradisBWA.t view on Meta::CPAN
DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
$obj = Bio::Tradis::RunTradis->new(
fastqfile => $fastqfile,
reference => "not_really_a_ref.fa",
tag => $tag,
outfile => $outfile,
output_directory => $output_directory,
_temp_directory => $temp_directory,
_stats_handle => $stats_handle,
view release on metacpan or search on metacpan
lib/Bio/Translator.pm view on Meta::CPAN
);
$codon = uc $codon;
# Set up the translation table given the strand and whether this is
# searching for stop codons. Set up the not_found string by whether this
# is a start or not.
my $rc = $p{strand} == 1 ? 0 : 1;
my ( $table, $not_found );
unless ( $p{start} ) {
$table = $self->table->codon2aa->[$rc];
$not_found = 'X';
}
else {
$table = $self->table->codon2start->[$rc];
$not_found = '-';
}
return $self->table->_unroll( $codon, $table, { start => $p{start} } )
|| $not_found;
}
1;
=head1 AUTHOR
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open my $fh, "<", $filename
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
} else {
pass("$filename contains no boilerplate text");
}
}
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
view release on metacpan or search on metacpan
t/boilerplate.t view on Meta::CPAN
use strict;
use warnings;
use Test::More tests => 3;
sub not_in_file_ok {
my ($filename, %regex) = @_;
open my $fh, "<", $filename
or die "couldn't open $filename for reading: $!";
my %violated;
t/boilerplate.t view on Meta::CPAN
} else {
pass("$filename contains no boilerplate text");
}
}
not_in_file_ok(README =>
"The README is used..." => qr/The README is used/,
"'version information here'" => qr/to provide version information/,
);
not_in_file_ok(Changes =>
"placeholder date/time" => qr(Date/time)
);
sub module_boilerplate_ok {
my ($module) = @_;
not_in_file_ok($module =>
'the great new $MODULENAME' => qr/ - The great new /,
'boilerplate description' => qr/Quick summary of what the module/,
'stub function definition' => qr/function[12]/,
);
}
view release on metacpan or search on metacpan
lib/Bio/Variation/VariantI.pm view on Meta::CPAN
=cut
sub label {
my ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 status
view release on metacpan or search on metacpan
lib/Bio/VertRes/Config/CommandLine/StudyNameSearch.pm view on Meta::CPAN
has 'default_database_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'study_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'config_base' => ( is => 'ro', isa => 'Str', required => 1 );
sub get_study_database_name_or_default_if_not_found {
my ($self) = @_;
#Â In the normal case the study will be in the default database, so check it first to save on IO
if (
Bio::VertRes::Config::RegisterStudy->new(
lib/Bio/VertRes/Config/CommandLine/StudyNameSearch.pm view on Meta::CPAN
my $obj = Bio::VertRes::Config::CommandLine::StudyNameSearch->new(
default_database_name => 'pathogen_rnd_track',
config_base => $destination_directory,
study_name => 'Unseen study'
);
$obj->get_study_database_name_or_default_if_not_found;
=head1 METHODS
=head2 get_study_database_name_or_default_if_not_found
Lookup the study name in all the standard databases. If its found then return that database. If its a new study return the default.
=head1 AUTHOR
view release on metacpan or search on metacpan
$ make test
$ sudo make install
The second command (`make test`) performs a number of basic tests of the software on your
system. These should all pass without problems. If you do encounter issues, it is best
_not_ to proceed to the following step for the actual installation, but rather to try to
resolve the outstanding problems, for example by submitting an
[issue report](https://github.com/naturalis/wgs2ncbi/issues), so that the authors can help
you out.
In addition to the preceding steps, you also need to install the `tbl2asn` program. The
view release on metacpan or search on metacpan
lib/Bio/DB/BioSQL/BaseDriver.pm view on Meta::CPAN
# copy the static mapping tables into our private hashs
# you may then change individual mappings in your derived adaptor driver
$self->objrel_map(\%object_entity_map);
$self->slot_attribute_map(\%slot_attribute_map);
$self->not_select_attrs(\%dont_select_attrs);
$self->association_entity_map(\%association_entity_map);
return $self;
}
lib/Bio/DB/BioSQL/BaseDriver.pm view on Meta::CPAN
my @slots = $adp->get_persistent_slots();
# get the slot/attribute map
my $table = $self->table_name($adp);
my $slotmap = $self->slot_attribute_map();
# get the map of columns excluded from SELECTs
my $dont_select_attrs = $self->not_select_attrs();
# default the entity-alias map if not provided
if(! $entitymap) {
$entitymap = {};
$entitymap->{$table} = [$table];
}
lib/Bio/DB/BioSQL/BaseDriver.pm view on Meta::CPAN
$map = $self->{'_slot_attr_map'};
}
return $map;
}
=head2 not_select_attrs
Title : not_select_attrs
Usage : $obj->not_select_attrs($newval)
Function: Get/set a map of all columns that should not be included in
SELECT lists.
Example :
Returns : value of not_select_attrs (a reference to a hash map)
Args : new value (a reference to a hash map, optional)
=cut
sub not_select_attrs{
my ($self,$value) = @_;
if( defined $value) {
$self->{'not_select_attrs'} = $value;
}
return $self->{'not_select_attrs'};
}
=head2 association_entity_map
Title : association_entity_map
view release on metacpan or search on metacpan
t/lib/Test/Harness/Straps.pm view on Meta::CPAN
# sometimes the 'not ' and the 'ok' are on different lines,
# happens often on VMS if you do:
# print "not " unless $test;
# print "ok $num\n";
if ( $self->{lone_not_line} && ($self->{lone_not_line} == $self->{line} - 1) ) {
$point->set_ok( 0 );
}
if ( $self->{todo}{$point->number} ) {
$point->set_directive_type( 'todo' );
t/lib/Test/Harness/Straps.pm view on Meta::CPAN
} # test point
elsif ( $line =~ /^not\s+$/ ) {
$linetype = 'other';
# Sometimes the "not " and "ok" will be on separate lines on VMS.
# We catch this and remember we saw it.
$self->{lone_not_line} = $self->{line};
}
elsif ( $self->_is_header($line) ) {
$linetype = 'header';
$self->{saw_header}++;
t/lib/Test/Harness/Straps.pm view on Meta::CPAN
delete @{$self}{qw(max skip_all todo too_many_tests)};
$self->{line} = 0;
$self->{saw_header} = 0;
$self->{saw_bailout}= 0;
$self->{lone_not_line} = 0;
$self->{bailout_reason} = '';
$self->{'next'} = 1;
}
=head1 EXAMPLES
view release on metacpan or search on metacpan
lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm view on Meta::CPAN
Returns : scalar string (class name)
Args : none
=cut
sub obj_class { shift->throw_not_implemented }
=head2 next_obj()
Title : next_obj
Usage : $obj = $adaptor->next_obj
lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm view on Meta::CPAN
Returns : object of class obj_class()
Args : none
=cut
sub next_obj { shift->throw_not_implemented }
=head2 rewind()
Title : rewind
Usage :
lib/Bio/DB/SoapEUtilities/FetchAdaptor.pm view on Meta::CPAN
Returns :
Args : none
=cut
sub rewind { shift->throw_not_implemented }
=head2 result()
Title : result
Usage :
view release on metacpan or search on metacpan
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub add_seq {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 remove_seq
Title : remove_seq
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub remove_seq {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 purge
Title : purge
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub purge {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 sort_alphabetically
Title : sort_alphabetically
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub sort_alphabetically {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Sequence selection methods
Methods returning one or more sequences objects.
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub each_seq {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 each_alphabetically
Title : each_alphabetically
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub each_alphabetically {
my($self) = @_;
$self->throw_not_implemented();
}
=head2 each_seq_with_id
Title : each_seq_with_id
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub each_seq_with_id {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 get_seq_by_pos
Title : get_seq_by_pos
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub get_seq_by_pos {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Create new alignments
The result of these methods are horizontal or vertical subsets of the
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub select {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 select_noncont
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub select_noncont {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 slice
Title : slice
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub slice {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Change sequences within the MSE
These methods affect characters in all sequences without changing the
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub map_chars {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 uppercase
Title : uppercase()
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub uppercase {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 match_line
Title : match_line()
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub match_line {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 match
Title : match()
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub match {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 unmatch
Title : unmatch()
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub unmatch {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 MSE attibutes
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub id {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 missing_char
Title : missing_char
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub missing_char {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 match_char
Title : match_char
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub match_char {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 gap_char
Title : gap_char
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub gap_char {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 symbol_chars
Title : symbol_chars
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub symbol_chars{
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Alignment descriptors
These read only methods describe the MSE in various ways.
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub consensus_string {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 consensus_iupac
Title : consensus_iupac
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub consensus_iupac {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 is_flush
Title : is_flush
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub is_flush {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 length
Title : length()
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub length {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 maxname_length
Title : maxname_length
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub maxname_length {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 num_residues
Title : num_residues
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub num_residues {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 num_sequences
Title : num_sequences
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub num_sequences {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 percentage_identity
Title : percentage_identity
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub percentage_identity{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 overall_percentage_identity
Title : overall_percentage_identity
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub overall_percentage_identity{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 average_percentage_identity
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub average_percentage_identity{
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Alignment positions
Methods to map a sequence position into an alignment column and back.
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub column_from_residue_number {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Sequence names
Methods to manipulate the display name. The default name based on the
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub displayname {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 set_displayname_count
Title : set_displayname_count
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub set_displayname_count {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 set_displayname_flat
Title : set_displayname_flat
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub set_displayname_flat {
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 set_displayname_normal
Title : set_displayname_normal
Bio/Align/AlignI.pm view on Meta::CPAN
=cut
sub set_displayname_normal {
my ($self) = @_;
$self->throw_not_implemented();
}
=head1 Deprecated methods
=head2 no_residues