[Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.11, 1.12 IO.pm, 1.6, 1.7

Mauricio Herrera Cuadra mauricio at dev.open-bio.org
Tue Aug 29 23:40:35 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Assembly
In directory dev.open-bio.org:/tmp/cvs-serv514/Bio/Assembly

Modified Files:
	Contig.pm IO.pm 
Log Message:
Updating emails


Index: IO.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/IO.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** IO.pm	4 Jul 2006 22:23:13 -0000	1.6
--- IO.pm	30 Aug 2006 03:40:33 -0000	1.7
***************
*** 4,8 ****
  #
  #   based on the Bio::SeqIO module
! #       by Ewan Birney <birney at sanger.ac.uk>
  #       and Lincoln Stein  <lstein at cshl.org>
  #
--- 4,8 ----
  #
  #   based on the Bio::SeqIO module
! #       by Ewan Birney <birney at ebi.ac.uk>
  #       and Lincoln Stein  <lstein at cshl.org>
  #
***************
*** 24,30 ****
  
      $in  = Bio::Assembly::IO->new(-file=>"<inputfilename",
!                                 -format=>'phrap');
      $out = Bio::Assembly::IO->new(-file=>">outputfilename",
!                                 -format=>'phrap');
  
      while ( my $seq = $in->next_seq() ) {
--- 24,30 ----
  
      $in  = Bio::Assembly::IO->new(-file=>"<inputfilename",
!                                   -format=>'phrap');
      $out = Bio::Assembly::IO->new(-file=>">outputfilename",
!                                   -format=>'phrap');
  
      while ( my $seq = $in->next_seq() ) {
***************
*** 88,92 ****
   Usage   : Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
   Function: Returns a new assembly stream
!  Returns : A Bio::Assembly::IO::Handler initialised 
             with the appropriate format
   Args    : -file => $filename
--- 88,92 ----
   Usage   : Bio::Assembly::IO->new(-file =>$filename,-format=>'format')
   Function: Returns a new assembly stream
!  Returns : A Bio::Assembly::IO::Handler initialised
             with the appropriate format
   Args    : -file => $filename
***************
*** 98,109 ****
      my ($caller, at args) = @_;
      my $class = ref($caller) || $caller;
!     
      # or do we want to call SUPER on an object if $caller is an
      # object?
      if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
! 	my ($self) = $class->SUPER::new(@args);	
  	$self->_initialize(@args);
  	return $self;
!     } else { 
  
  	my %param = @args;
--- 98,109 ----
      my ($caller, at args) = @_;
      my $class = ref($caller) || $caller;
! 
      # or do we want to call SUPER on an object if $caller is an
      # object?
      if( $class =~ /Bio::Assembly::IO::(\S+)/ ) {
! 	my ($self) = $class->SUPER::new(@args);
  	$self->_initialize(@args);
  	return $self;
!     } else {
  
  	my %param = @args;
***************
*** 113,117 ****
  	    unless (defined $param{'-file'} || defined $ARGV[0]);
  
! 	my $format = $param{'-format'} || 
  	    $class->_guess_format( $param{-file} || $ARGV[0] );
  	$format = "\L$format";	# normalize capitalization to lower case
--- 113,117 ----
  	    unless (defined $param{'-file'} || defined $ARGV[0]);
  
! 	my $format = $param{'-format'} ||
  	    $class->_guess_format( $param{-file} || $ARGV[0] );
  	$format = "\L$format";	# normalize capitalization to lower case

Index: Contig.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/Contig.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Contig.pm	7 Aug 2006 21:30:11 -0000	1.11
--- Contig.pm	30 Aug 2006 03:40:33 -0000	1.12
***************
*** 34,52 ****
  
      use Bio::Assembly::Contig;
!     $c = Bio::Assembly::Contig->new(-id=>"1"); 
  
      $ls  = Bio::LocatableSeq->new(-seq=>"ACCG-T",
! 				  -id=>"r1",
! 				  -alphabet=>'dna');
      $ls2 = Bio::LocatableSeq->new(-seq=>"ACA-CG-T",
! 				  -id=>"r2",
! 				  -alphabet=>'dna');
  
      $ls_coord = Bio::SeqFeature::Generic->new(-start=>3,
! 	   				      -end=>8,
                                                -strand=>1);
      $ls2_coord = Bio::SeqFeature::Generic->new(-start=>1,
! 					       -end=>8,
! 					       -strand=>1);
      $c->add_seq($ls);
      $c->add_seq($ls2);
--- 34,52 ----
  
      use Bio::Assembly::Contig;
!     $c = Bio::Assembly::Contig->new(-id=>"1");
  
      $ls  = Bio::LocatableSeq->new(-seq=>"ACCG-T",
!                                   -id=>"r1",
!                                   -alphabet=>'dna');
      $ls2 = Bio::LocatableSeq->new(-seq=>"ACA-CG-T",
!                                   -id=>"r2",
!                                   -alphabet=>'dna');
  
      $ls_coord = Bio::SeqFeature::Generic->new(-start=>3,
!                                               -end=>8,
                                                -strand=>1);
      $ls2_coord = Bio::SeqFeature::Generic->new(-start=>1,
!                                                -end=>8,
!                                                -strand=>1);
      $c->add_seq($ls);
      $c->add_seq($ls2);
***************
*** 55,59 ****
  
      $con = Bio::LocatableSeq->new(-seq=>"ACACCG-T",
! 				  -alphabet=>'dna');
      $c->set_consensus_sequence($con);
  
--- 55,59 ----
  
      $con = Bio::LocatableSeq->new(-seq=>"ACACCG-T",
!                                   -alphabet=>'dna');
      $c->set_consensus_sequence($con);
  
***************
*** 350,354 ****
   Function  : Get/Set a contig neighbor for the current contig when
               building a scaffold. The upstream neighbor is
!              located before $contig first base 
   Returns   : nothing
   Argument  : Bio::Assembly::Contig
--- 350,354 ----
   Function  : Get/Set a contig neighbor for the current contig when
               building a scaffold. The upstream neighbor is
!              located before $contig first base
   Returns   : nothing
   Argument  : Bio::Assembly::Contig
***************
*** 395,399 ****
   Title     : add_features
   Usage     : $contig->add_features($feat,$flag)
!  Function  : 
  
               Add an array of features to the contig feature
--- 395,399 ----
   Title     : add_features
   Usage     : $contig->add_features($feat,$flag)
!  Function  :
  
               Add an array of features to the contig feature
***************
*** 413,417 ****
  
   Returns   : number of features added.
!  Argument  : 
               $feat : A reference to an array of Bio::SeqFeatureI
               $flag : boolean - true if consensus sequence object
--- 413,417 ----
  
   Returns   : number of features added.
!  Argument  :
               $feat : A reference to an array of Bio::SeqFeatureI
               $flag : boolean - true if consensus sequence object
***************
*** 502,506 ****
   Title     : change_coord
   Usage     : $contig->change_coord($in,$out,$query)
!  Function  : 
  
               Change coordinate system for $query.  This method
--- 502,506 ----
   Title     : change_coord
   Usage     : $contig->change_coord($in,$out,$query)
!  Function  :
  
               Change coordinate system for $query.  This method
***************
*** 516,520 ****
  
   Returns   : integer
!  Argument  : 
               $in    : [string]  input coordinate system
               $out   : [string]  output coordinate system
--- 516,520 ----
  
   Returns   : integer
!  Argument  :
               $in    : [string]  input coordinate system
               $out   : [string]  output coordinate system
***************
*** 530,534 ****
  
      # Parsing arguments
!     # Loading read objects (these calls will throw exceptions whether $read_in or 
      # $read_out is not found
      my ($read_in,$read_out) = (undef,undef);
--- 530,534 ----
  
      # Parsing arguments
!     # Loading read objects (these calls will throw exceptions whether $read_in or
      # $read_out is not found
      my ($read_in,$read_out) = (undef,undef);
***************
*** 538,542 ****
      if ($in_ID  ne 'consensus') {
  	$read_in  = $self->get_seq_coord( $self->get_seq_by_name($in_ID)  );
! 	$self->throw("Can't change coordinates without sequence location for $in_ID") 
  	    unless (defined $read_in);
      }
--- 538,542 ----
      if ($in_ID  ne 'consensus') {
  	$read_in  = $self->get_seq_coord( $self->get_seq_by_name($in_ID)  );
! 	$self->throw("Can't change coordinates without sequence location for $in_ID")
  	    unless (defined $read_in);
      }
***************
*** 583,587 ****
  	   last SWITCH1;
         };
!       (($type_in =~ /^aligned /) && defined($read_in) && 
         ($type_out eq 'ungapped consensus')) && do {
  	   $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
--- 583,587 ----
  	   last SWITCH1;
         };
!       (($type_in =~ /^aligned /) && defined($read_in) &&
         ($type_out eq 'ungapped consensus')) && do {
  	   $query = $self->change_coord("aligned $in_ID",'gapped consensus',$query);
***************
*** 615,619 ****
  	   last SWITCH1;
         };
!       (defined($read_in)  && ($type_in  =~ /^unaligned /) && 
         defined($read_out) && ($type_out =~ /^aligned /))  && do {
  	   my $list_in = $self->{'_elem'}{$in_ID}{'_gaps'};
--- 615,619 ----
  	   last SWITCH1;
         };
!       (defined($read_in)  && ($type_in  =~ /^unaligned /) &&
         defined($read_out) && ($type_out =~ /^aligned /))  && do {
  	   my $list_in = $self->{'_elem'}{$in_ID}{'_gaps'};
***************
*** 710,714 ****
   Title     : set_seq_coord
   Usage     : $contig->set_seq_coord($feat,$seq);
!  Function  : 
  
               Set "gapped consensus" location for an aligned
--- 710,714 ----
   Title     : set_seq_coord
   Usage     : $contig->set_seq_coord($feat,$seq);
!  Function  :
  
               Set "gapped consensus" location for an aligned
***************
*** 719,726 ****
  
   Returns   : Bio::SeqFeature::Generic for old coordinates or undef.
!  Argument  : 
               $feat  : a Bio::SeqFeature::Generic object
                        representing a location for the
!                       aligned sequence, in "gapped 
                        consensus" coordinates.
  
--- 719,726 ----
  
   Returns   : Bio::SeqFeature::Generic for old coordinates or undef.
!  Argument  :
               $feat  : a Bio::SeqFeature::Generic object
                        representing a location for the
!                       aligned sequence, in "gapped
                        consensus" coordinates.
  
***************
*** 956,960 ****
      my ($self, @args) = @_;
  
!     my ($type,$start,$end) = 
  	$self->_rearrange([qw(TYPE START END)], @args);
  
--- 956,960 ----
      my ($self, @args) = @_;
  
!     my ($type,$start,$end) =
  	$self->_rearrange([qw(TYPE START END)], @args);
  
***************
*** 983,990 ****
   Title     : get_seq_feat_by_tag
   Usage     : $seq = $contig->get_seq_feat_by_tag($seq,"_aligned_coord:$seqID")
!  Function  : 
  
               Get a sequence feature based on its primary_tag.
!              When you add 
  
   Returns   : a Bio::SeqFeature object
--- 983,990 ----
   Title     : get_seq_feat_by_tag
   Usage     : $seq = $contig->get_seq_feat_by_tag($seq,"_aligned_coord:$seqID")
!  Function  :
  
               Get a sequence feature based on its primary_tag.
!              When you add
  
   Returns   : a Bio::SeqFeature object
***************
*** 1067,1072 ****
   Function  :
  
!              Adds a sequence to the contig. *Does* 
!              *not* align it - just adds it to the 
               hashes.
  
--- 1067,1072 ----
   Function  :
  
!              Adds a sequence to the contig. *Does*
!              *not* align it - just adds it to the
               hashes.
  
***************
*** 1158,1162 ****
  
      # Updating residue count
!     $self->{'_nof_residues'} -= $seq->length() + 
  	&_nof_gaps( $self->{'_elem'}{$seqID}{'_gaps'}, $seq->length );
  
--- 1158,1162 ----
  
      # Updating residue count
!     $self->{'_nof_residues'} -= $seq->length() +
  	&_nof_gaps( $self->{'_elem'}{$seqID}{'_gaps'}, $seq->length );
  
***************
*** 1199,1209 ****
   Title     : sort_alphabetically
   Usage     : $contig->sort_alphabetically
!  Function  : 
  
!              Changes the order of the alignemnt to alphabetical on name 
               followed by numerical by number.
  
!  Returns   : 
!  Argument  : 
  
  =cut
--- 1199,1209 ----
   Title     : sort_alphabetically
   Usage     : $contig->sort_alphabetically
!  Function  :
  
!              Changes the order of the alignemnt to alphabetical on name
               followed by numerical by number.
  
!  Returns   :
!  Argument  :
  
  =cut
***************
*** 1221,1228 ****
  
   Title     : each_seq
!  Usage     : foreach $seq ( $contig->each_seq() ) 
   Function  : Gets an array of Seq objects from the alignment
   Returns   : an array
!  Argument  : 
  
  =cut
--- 1221,1228 ----
  
   Title     : each_seq
!  Usage     : foreach $seq ( $contig->each_seq() )
   Function  : Gets an array of Seq objects from the alignment
   Returns   : an array
!  Argument  :
  
  =cut
***************
*** 1246,1255 ****
   Function  :
  
!              Returns an array of sequence object sorted alphabetically 
               by name and then by start point.
               Does not change the order of the alignment
  
!  Returns   : 
!  Argument  : 
  
  =cut
--- 1246,1255 ----
   Function  :
  
!              Returns an array of sequence object sorted alphabetically
               by name and then by start point.
               Does not change the order of the alignment
  
!  Returns   :
!  Argument  :
  
  =cut
***************
*** 1263,1268 ****
  
   Title     : each_seq_with_id
!  Usage     : foreach $seq ( $contig->each_seq_with_id() ) 
!  Function  : 
  
               Gets an array of Seq objects from the
--- 1263,1268 ----
  
   Title     : each_seq_with_id
!  Usage     : foreach $seq ( $contig->each_seq_with_id() )
!  Function  :
  
               Gets an array of Seq objects from the
***************
*** 1284,1288 ****
   Title     : get_seq_by_pos
   Usage     : $seq = $contig->get_seq_by_pos(3)
!  Function  : 
  
               Gets a sequence based on its position in the alignment.
--- 1284,1288 ----
   Title     : get_seq_by_pos
   Usage     : $seq = $contig->get_seq_by_pos(3)
!  Function  :
  
               Gets a sequence based on its position in the alignment.
***************
*** 1317,1321 ****
   Title     : select
   Usage     : $contig2 = $contig->select(1, 3) # three first sequences
!  Function  : 
  
               Creates a new alignment from a continuous subset of
--- 1317,1321 ----
   Title     : select
   Usage     : $contig2 = $contig->select(1, 3) # three first sequences
!  Function  :
  
               Creates a new alignment from a continuous subset of
***************
*** 1339,1343 ****
   Title     : select_noncont
   Usage     : $contig2 = $contig->select_noncont(1, 3) # first and 3rd sequences
!  Function  : 
  
               Creates a new alignment from a subset of
--- 1339,1343 ----
   Title     : select_noncont
   Usage     : $contig2 = $contig->select_noncont(1, 3) # first and 3rd sequences
!  Function  :
  
               Creates a new alignment from a subset of
***************
*** 1359,1363 ****
   Title     : slice
   Usage     : $contig2 = $contig->slice(20, 30)
!  Function  : 
  
               Creates a slice from the alignment inclusive of start and
--- 1359,1363 ----
   Title     : slice
   Usage     : $contig2 = $contig->slice(20, 30)
!  Function  :
  
               Creates a slice from the alignment inclusive of start and
***************
*** 1368,1373 ****
  
   Returns   : a Bio::Assembly::Contig object
!  Argument  : positive integer for start column 
!              positive integer for end column 
  
  =cut
--- 1368,1373 ----
  
   Returns   : a Bio::Assembly::Contig object
!  Argument  : positive integer for start column
!              positive integer for end column
  
  =cut
***************
*** 1388,1392 ****
   Title     : map_chars
   Usage     : $contig->map_chars('\.','-')
!  Function  : 
  
               Does a s/$arg1/$arg2/ on the sequences. Useful for gap
--- 1388,1392 ----
   Title     : map_chars
   Usage     : $contig->map_chars('\.','-')
!  Function  :
  
               Does a s/$arg1/$arg2/ on the sequences. Useful for gap
***************
*** 1397,1401 ****
               $contig->map_chars('.','-') wont do what you want)
  
!  Returns   : 
   Argument  : 'from' rexexp
               'to' string
--- 1397,1401 ----
               $contig->map_chars('.','-') wont do what you want)
  
!  Returns   :
   Argument  : 'from' rexexp
               'to' string
***************
*** 1413,1418 ****
   Usage     : $contig->uppercase()
   Function  : Sets all the sequences to uppercase
!  Returns   : 
!  Argument  : 
  
  =cut
--- 1413,1418 ----
   Usage     : $contig->uppercase()
   Function  : Sets all the sequences to uppercase
!  Returns   :
!  Argument  :
  
  =cut
***************
*** 1444,1448 ****
   Title     : match()
   Usage     : $contig->match()
!  Function  : 
  
               Goes through all columns and changes residues that are
--- 1444,1448 ----
   Title     : match()
   Usage     : $contig->match()
!  Function  :
  
               Goes through all columns and changes residues that are
***************
*** 1469,1473 ****
   Title     : unmatch()
   Usage     : $contig->unmatch()
!  Function  : 
  
               Undoes the effect of method match. Unsets match_char.
--- 1469,1473 ----
   Title     : unmatch()
   Usage     : $contig->unmatch()
!  Function  :
  
               Undoes the effect of method match. Unsets match_char.
***************
*** 1517,1522 ****
   Usage     : $contig->missing_char("?")
   Function  : Gets/sets the missing_char attribute of the alignment
!              It is generally recommended to set it to 'n' or 'N' 
!              for nucleotides and to 'X' for protein. 
   Returns   : An missing_char string,
   Argument  : An missing_char string (optional)
--- 1517,1522 ----
   Usage     : $contig->missing_char("?")
   Function  : Gets/sets the missing_char attribute of the alignment
!              It is generally recommended to set it to 'n' or 'N'
!              for nucleotides and to 'X' for protein.
   Returns   : An missing_char string,
   Argument  : An missing_char string (optional)
***************
*** 1576,1580 ****
  =head2 Alignment descriptors
  
! These read only methods describe the MSE in various ways. 
  
  
--- 1576,1580 ----
  =head2 Alignment descriptors
  
! These read only methods describe the MSE in various ways.
  
  
***************
*** 1583,1588 ****
   Title     : consensus_string
   Usage     : $str = $contig->consensus_string($threshold_percent)
!  Function  : Makes a strict consensus 
!  Returns   : 
   Argument  : Optional treshold ranging from 0 to 100.
               The consensus residue has to appear at least threshold %
--- 1583,1588 ----
   Title     : consensus_string
   Usage     : $str = $contig->consensus_string($threshold_percent)
!  Function  : Makes a strict consensus
!  Returns   :
   Argument  : Optional treshold ranging from 0 to 100.
               The consensus residue has to appear at least threshold %
***************
*** 1602,1606 ****
   Title     : consensus_iupac
   Usage     : $str = $contig->consensus_iupac()
!  Function  : 
  
               Makes a consensus using IUPAC ambiguity codes from DNA
--- 1602,1606 ----
   Title     : consensus_iupac
   Usage     : $str = $contig->consensus_iupac()
!  Function  :
  
               Makes a consensus using IUPAC ambiguity codes from DNA
***************
*** 1629,1640 ****
   Title     : is_flush
   Usage     : if( $contig->is_flush() )
-            : 
             :
!  Function  : Tells you whether the alignment 
             : is flush, ie all of the same length
!            : 
             :
   Returns   : 1 or 0
!  Argument  : 
  
  =cut
--- 1629,1640 ----
   Title     : is_flush
   Usage     : if( $contig->is_flush() )
             :
!            :
!  Function  : Tells you whether the alignment
             : is flush, ie all of the same length
!            :
             :
   Returns   : 1 or 0
!  Argument  :
  
  =cut
***************
*** 1648,1656 ****
  
   Title     : length()
!  Usage     : $len = $contig->length() 
   Function  : Returns the maximum length of the alignment.
               To be sure the alignment is a block, use is_flush
!  Returns   : 
!  Argument  : 
  
  =cut
--- 1648,1656 ----
  
   Title     : length()
!  Usage     : $len = $contig->length()
   Function  : Returns the maximum length of the alignment.
               To be sure the alignment is a block, use is_flush
!  Returns   :
!  Argument  :
  
  =cut
***************
*** 1666,1670 ****
   Title     : maxdisplayname_length
   Usage     : $contig->maxdisplayname_length()
!  Function  : 
  
               Gets the maximum length of the displayname in the
--- 1666,1670 ----
   Title     : maxdisplayname_length
   Usage     : $contig->maxdisplayname_length()
!  Function  :
  
               Gets the maximum length of the displayname in the
***************
*** 1672,1676 ****
  
   Returns   : integer
!  Argument  : 
  
  =cut
--- 1672,1676 ----
  
   Returns   : integer
!  Argument  :
  
  =cut
***************
*** 1687,1691 ****
   Function  : number of residues in total in the alignment
   Returns   : integer
!  Argument  : 
  
  =cut
--- 1687,1691 ----
   Function  : number of residues in total in the alignment
   Returns   : integer
!  Argument  :
  
  =cut
***************
*** 1718,1722 ****
   Usage   : $id = $contig->percentage_identity
   Function: The function calculates the percentage identity of the alignment
!  Returns : The percentage identity of the alignment (as defined by the 
  						     implementation)
   Argument: None
--- 1718,1722 ----
   Usage   : $id = $contig->percentage_identity
   Function: The function calculates the percentage identity of the alignment
!  Returns : The percentage identity of the alignment (as defined by the
  						     implementation)
   Argument: None
***************
*** 1734,1738 ****
   Title   : percentage_identity
   Usage   : $id = $contig->percentage_identity
!  Function: The function calculates the percentage identity of 
             the conserved columns
   Returns : The percentage identity of the conserved columns
--- 1734,1738 ----
   Title   : percentage_identity
   Usage   : $id = $contig->percentage_identity
!  Function: The function calculates the percentage identity of
             the conserved columns
   Returns : The percentage identity of the conserved columns
***************
*** 1751,1755 ****
   Title   : average_percentage_identity
   Usage   : $id = $contig->average_percentage_identity
!  Function: The function uses a fast method to calculate the average 
             percentage identity of the alignment
   Returns : The average percentage identity of the alignment
--- 1751,1755 ----
   Title   : average_percentage_identity
   Usage   : $id = $contig->average_percentage_identity
!  Function: The function uses a fast method to calculate the average
             percentage identity of the alignment
   Returns : The average percentage identity of the alignment
***************
*** 1841,1850 ****
   Title     : set_displayname_count
   Usage     : $contig->set_displayname_count
!  Function  : 
  
               Sets the names to be name_# where # is the number of
               times this name has been used.
  
!  Returns   : None 
   Argument  : None
  
--- 1841,1850 ----
   Title     : set_displayname_count
   Usage     : $contig->set_displayname_count
!  Function  :
  
               Sets the names to be name_# where # is the number of
               times this name has been used.
  
!  Returns   : None
   Argument  : None
  
***************
*** 1873,1877 ****
  
   Title     : set_displayname_normal
!  Usage     : $contig->set_displayname_normal() 
   Function  : Makes all the sequences be displayed as name/start-end
   Returns   : None
--- 1873,1877 ----
  
   Title     : set_displayname_normal
!  Usage     : $contig->set_displayname_normal()
   Function  : Makes all the sequences be displayed as name/start-end
   Returns   : None
***************
*** 1889,1893 ****
   Title     : _binary_search
   Usage     : _binary_search($list,$query)
!  Function  : 
  
               Find a number in a sorted list of numbers.  Return values
--- 1889,1893 ----
   Title     : _binary_search
   Usage     : _binary_search($list,$query)
!  Function  :
  
               Find a number in a sorted list of numbers.  Return values
***************
*** 1903,1907 ****
  
   Returns   : array of integers
!  Argument  : 
               $list  : array reference
               $query : integer
--- 1903,1907 ----
  
   Returns   : array of integers
!  Argument  :
               $list  : array reference
               $query : integer
***************
*** 1956,1962 ****
      Function: number of gaps found before position $query
      Returns : integer
!     Args    : 
                $array_ref : gap registry reference
!               $query     : [integer] a position in a sequence 
  
  =cut
--- 1956,1962 ----
      Function: number of gaps found before position $query
      Returns : integer
!     Args    :
                $array_ref : gap registry reference
!               $query     : [integer] a position in a sequence
  
  =cut
***************
*** 1988,1999 ****
      Title   : _padded_unpadded
      Usage   : _padded_unpadded($array_ref, $query)
!     Function: 
  
                Returns a coordinate corresponding to
!               position $query after gaps were 
                removed from a sequence.
  
      Returns : integer
!     Args    : 
                $array_ref : reference to this gap registry
                $query     : [integer] coordionate to change
--- 1988,1999 ----
      Title   : _padded_unpadded
      Usage   : _padded_unpadded($array_ref, $query)
!     Function:
  
                Returns a coordinate corresponding to
!               position $query after gaps were
                removed from a sequence.
  
      Returns : integer
!     Args    :
                $array_ref : reference to this gap registry
                $query     : [integer] coordionate to change
***************
*** 2016,2026 ****
      Title   : _unpadded_padded
      Usage   : _unpadded_padded($array_ref, $query)
!     Function: 
  
!               Returns the value corresponding to 
                ungapped position $query when gaps are
                counted as valid sites in a sequence
  
!     Returns : 
      Args    : $array_ref = a reference to this sequence's gap registry
                $query = [integer] location to change
--- 2016,2026 ----
      Title   : _unpadded_padded
      Usage   : _unpadded_padded($array_ref, $query)
!     Function:
  
!               Returns the value corresponding to
                ungapped position $query when gaps are
                counted as valid sites in a sequence
  
!     Returns :
      Args    : $array_ref = a reference to this sequence's gap registry
                $query = [integer] location to change
***************
*** 2055,2059 ****
      Function: stores gap locations for a sequence
      Returns : number of gaps found
!     Args    : 
                $seq       : sequence string
                $array_ref : a reference to an array,
--- 2055,2059 ----
      Function: stores gap locations for a sequence
      Returns : number of gaps found
!     Args    :
                $seq       : sequence string
                $array_ref : a reference to an array,



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