[Bioperl-guts-l] bioperl-live/Bio/Tools/Blast HSP.pm, 1.23, 1.24 HTML.pm, 1.19, 1.20

Mauricio Herrera Cuadra mauricio at dev.open-bio.org
Sun Sep 24 11:36:34 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Blast
In directory dev.open-bio.org:/tmp/cvs-serv15026/Bio/Tools/Blast

Modified Files:
	HSP.pm HTML.pm 
Log Message:
Updating URLs


Index: HTML.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Blast/HTML.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** HTML.pm	4 Jul 2006 22:23:25 -0000	1.19
--- HTML.pm	24 Sep 2006 15:36:32 -0000	1.20
***************
*** 6,10 ****
  # STATUS  : Alpha
  # REVISION: $Id$
! # 
  # For the latest version and documentation, visit the distribution site:
  #    http://bio.perl.org/Projects/Blast/
--- 6,10 ----
  # STATUS  : Alpha
  # REVISION: $Id$
! #
  # For the latest version and documentation, visit the distribution site:
  #    http://bio.perl.org/Projects/Blast/
***************
*** 20,24 ****
  #
  # Copyright (c) 1996-98 Steve Chervitz. All Rights Reserved.
! #           This module is free software; you can redistribute it and/or 
  #           modify it under the same terms as Perl itself.
  #-------------------------------------------------------------------------------
--- 20,24 ----
  #
  # Copyright (c) 1996-98 Steve Chervitz. All Rights Reserved.
! #           This module is free software; you can redistribute it and/or
  #           modify it under the same terms as Perl itself.
  #-------------------------------------------------------------------------------
***************
*** 28,32 ****
  use Exporter;
  
! use Bio::Tools::WWW  qw(:obj); 
  
  use vars qw( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS
--- 28,32 ----
  use Exporter;
  
! use Bio::Tools::WWW  qw(:obj);
  
  use vars qw( @ISA @EXPORT @EXPORT_OK %EXPORT_TAGS
***************
*** 91,95 ****
  Swiss-Prot, PIR, PDB, SGD).
  
! This module is intended for use by Bio::Tools::Blast.pm and related modules, 
  which provides a front-end to the methods in Bio::Tools::Blast::HTML.pm.
  
--- 91,95 ----
  Swiss-Prot, PIR, PDB, SGD).
  
! This module is intended for use by Bio::Tools::Blast.pm and related modules,
  which provides a front-end to the methods in Bio::Tools::Blast::HTML.pm.
  
***************
*** 111,121 ****
   Bio::Tools::WWW.pm      - URL repository.
  
!  http://bio.perl.org/Projects/modules.html  - Online module documentation
!  http://bio.perl.org/Projects/Blast/        - Bioperl Blast Project     
   http://bio.perl.org/                       - Bioperl Project Homepage
  
  =head1 FEEDBACK
  
! =head2 Mailing Lists 
  
  User feedback is an integral part of the evolution of this and other
--- 111,120 ----
   Bio::Tools::WWW.pm      - URL repository.
  
!  http://bio.perl.org/Projects/Blast/        - Bioperl Blast Project
   http://bio.perl.org/                       - Bioperl Project Homepage
  
  =head1 FEEDBACK
  
! =head2 Mailing Lists
  
  User feedback is an integral part of the evolution of this and other
***************
*** 132,136 ****
  web:
  
!   http://bugzilla.open-bio.org/           
  
  =head1 AUTHOR
--- 131,135 ----
  web:
  
!   http://bugzilla.open-bio.org/
  
  =head1 AUTHOR
***************
*** 141,145 ****
  
  Copyright (c) 1998-2000 Steve Chervitz. All Rights Reserved.
! This module is free software; you can redistribute it and/or 
  modify it under the same terms as Perl itself.
  
--- 140,144 ----
  
  Copyright (c) 1998-2000 Steve Chervitz. All Rights Reserved.
! This module is free software; you can redistribute it and/or
  modify it under the same terms as Perl itself.
  
***************
*** 175,180 ****
             : raw Blast report line-by-line.
             : Utility method used by to_html() in Bio::Tools::Blast.pm.
!  Returns   : Reference to an anonymous function to be used while reading in  
!            : the raw report. 
             : The function itself operates on the Blast report line-by-line
             : HTML-ifying it and printing it to STDOUT (or saving in the supplied
--- 174,179 ----
             : raw Blast report line-by-line.
             : Utility method used by to_html() in Bio::Tools::Blast.pm.
!  Returns   : Reference to an anonymous function to be used while reading in
!            : the raw report.
             : The function itself operates on the Blast report line-by-line
             : HTML-ifying it and printing it to STDOUT (or saving in the supplied
***************
*** 184,190 ****
             : If no argument is supplied, HTML output is sent to STDOUT.
   Throws    : Croaks if an argument is supplied and is not an array ref.
!            : The anonymous function returned by this method croaks if 
             : the Blast output appears to be HTML-formatted already.
!  Comments  : Adapted from a script by Keith Robison  November 1993 
             : krobison at nucleus.harvard.edu; http://golgi.harvard.edu/gilbert.html
             : Modified extensively by Steve Chervitz and Mike Cherry.
--- 183,189 ----
             : If no argument is supplied, HTML output is sent to STDOUT.
   Throws    : Croaks if an argument is supplied and is not an array ref.
!            : The anonymous function returned by this method croaks if
             : the Blast output appears to be HTML-formatted already.
!  Comments  : Adapted from a script by Keith Robison  November 1993
             : krobison at nucleus.harvard.edu; http://golgi.harvard.edu/gilbert.html
             : Modified extensively by Steve Chervitz and Mike Cherry.
***************
*** 207,214 ****
      my $found_data  = 0;  # Nothing is done until this is true
      my $skip        = 0;  # Skipping various items in the report header
!     my $ref_skip    = 0;  # so we can include nice HTML versions 
!                           # (e.g., references for the BLAST program). 
!     my $getNote     = 0; 
!     my $getGenBankAlert = 0; 
      my $str = '';
      my $gi_link = \$_gi_link;
--- 206,213 ----
      my $found_data  = 0;  # Nothing is done until this is true
      my $skip        = 0;  # Skipping various items in the report header
!     my $ref_skip    = 0;  # so we can include nice HTML versions
!                           # (e.g., references for the BLAST program).
!     my $getNote     = 0;
!     my $getGenBankAlert = 0;
      my $str = '';
      my $gi_link = \$_gi_link;
***************
*** 234,238 ****
  		$ref_skip = 0 if /^\s+$/;
  	    }
! 	    if($getNote) { 
  		## SAC: created this test since we are no longer reading from STDIN.
  		$out_aref ? push(@$out_aref, $_) : print $_;
--- 233,237 ----
  		$ref_skip = 0 if /^\s+$/;
  	    }
! 	    if($getNote) {
  		## SAC: created this test since we are no longer reading from STDIN.
  		$out_aref ? push(@$out_aref, $_) : print $_;
***************
*** 251,255 ****
  		$prog = $2;
  		if($prog =~ /BLASTN/) {
! 		    ## Prevent the error at Entrez when you ask for a nucl 
  		    ## entry with a protein GI number.
  		    $$gi_link = $DbUrl{'gb_n'};  # nucleotide
--- 250,254 ----
  		$prog = $2;
  		if($prog =~ /BLASTN/) {
! 		    ## Prevent the error at Entrez when you ask for a nucl
  		    ## entry with a protein GI number.
  		    $$gi_link = $DbUrl{'gb_n'};  # nucleotide
***************
*** 268,273 ****
  		&_markup_database(\$_);
  		$out_aref ? push(@$out_aref, $_) : print $_;
! 		if ( /non-redundant genbank/i and $prog =~ /TBLAST[NX]/i) { 
! 		    $getGenBankAlert = 1; 
  		}
  		$skip = 1;
--- 267,272 ----
  		&_markup_database(\$_);
  		$out_aref ? push(@$out_aref, $_) : print $_;
! 		if ( /non-redundant genbank/i and $prog =~ /TBLAST[NX]/i) {
! 		    $getGenBankAlert = 1;
  		}
  		$skip = 1;
***************
*** 286,293 ****
  		$found_table = 1;
  		$skip = 0;
! 		$out_aref ? push(@$out_aref, $refs) : print $refs; 
! 		if($getGenBankAlert) { 
  		    $str = &_genbank_alert;
! 		    $out_aref ? push(@$out_aref, $str) : print $str; 
  		}
  		$str = "\n<p><pre>";
--- 285,292 ----
  		$found_table = 1;
  		$skip = 0;
! 		$out_aref ? push(@$out_aref, $refs) : print $refs;
! 		if($getGenBankAlert) {
  		    $str = &_genbank_alert;
! 		    $out_aref ? push(@$out_aref, $str) : print $str;
  		}
  		$str = "\n<p><pre>";
***************
*** 315,319 ****
             : to raw Blast output.
   Returns   : n/a
!  Comments  : These items need be set only once. 
  
  See Also   : L<get_html_func()|get_html_func>
--- 314,318 ----
             : to raw Blast output.
   Returns   : n/a
!  Comments  : These items need be set only once.
  
  See Also   : L<get_html_func()|get_html_func>
***************
*** 327,331 ****
      %SGDUrl     = $BioWWW->sgd_url('all');
  
!     $Signif  = '[\de.-]{3,}';        # Regexp for a P-value or Expect value. 
      $Int     = ' *\d\d*';            # Regexp for an integer.
      $Descrip = ' +.* {2,}?';         # Regexp for a description line.
--- 326,330 ----
      %SGDUrl     = $BioWWW->sgd_url('all');
  
!     $Signif  = '[\de.-]{3,}';        # Regexp for a P-value or Expect value.
      $Int     = ' *\d\d*';            # Regexp for an integer.
      $Descrip = ' +.* {2,}?';         # Regexp for a description line.
***************
*** 333,337 ****
      $Pir_acc = '[A-Z][A-Z0-9]{5,}';  # Regexp for PIR accession number
      $Word    = '[\w_.]+';            # Regexp for a word. Include dot for version.
!     
      $_set_markup = 1;
  }
--- 332,336 ----
      $Pir_acc = '[A-Z][A-Z0-9]{5,}';  # Regexp for PIR accession number
      $Word    = '[\w_.]+';            # Regexp for a word. Include dot for version.
! 
      $_set_markup = 1;
  }
***************
*** 345,349 ****
   Comments  : This is used for converting local database IDs into
             : understandable terms. At present, it only recognizes
!            : databases used locally at SGD. 
  
  See Also   : L<get_html_func()|get_html_func>
--- 344,348 ----
   Comments  : This is used for converting local database IDs into
             : understandable terms. At present, it only recognizes
!            : databases used locally at SGD.
  
  See Also   : L<get_html_func()|get_html_func>
***************
*** 378,383 ****
             : to accomodate reports produced by other servers/sites.
             :
!            : This function is simply a collection of substitution regexps 
!            : that recognize and modify the relevant lines of the Blast report. 
             : All non-header lines of the report are passed through this function,
             : only the ones that match will get modified.
--- 377,382 ----
             : to accomodate reports produced by other servers/sites.
             :
!            : This function is simply a collection of substitution regexps
!            : that recognize and modify the relevant lines of the Blast report.
             : All non-header lines of the report are passed through this function,
             : only the ones that match will get modified.
***************
*** 396,400 ****
             : For the alignment sections in the body of the report:
             :
!            : DB:SEQUENCE_ID  (Back | Top) DESCRIPTION 
             :        DB          = links to the indicated database (if not Gen/Embl/Ddbj).
             :        SEQUENCE_ID = links to GenBank entry for the sequence.
--- 395,399 ----
             : For the alignment sections in the body of the report:
             :
!            : DB:SEQUENCE_ID  (Back | Top) DESCRIPTION
             :        DB          = links to the indicated database (if not Gen/Embl/Ddbj).
             :        SEQUENCE_ID = links to GenBank entry for the sequence.
***************
*** 413,417 ****
             : Parsing HTML-formatted reports is dependent on the specific structure
             : of the HTML and is generally not recommended.
!            : 
             : Note that since URLs can change without notice, links will need updating.
             : The links are obtained from Bio::Tools::WWW.pm updating that module
--- 412,416 ----
             : Parsing HTML-formatted reports is dependent on the specific structure
             : of the HTML and is generally not recommended.
!            :
             : Note that since URLs can change without notice, links will need updating.
             : The links are obtained from Bio::Tools::WWW.pm updating that module
***************
*** 433,448 ****
      local $_ = $$line_ref;
  ##
! ## REGEXPS FOR ALIGNMENT SECTIONS (within the body of the report, 
  ##                                 the text above the list of HSPs).
  ##
  ## If the HSP alignment sections don't start with a '>' we have no way
! ## of finding them. This occurs with reports saved from HTML-formatted 
  ## web pages, which we shouldn't be processing here anyway.
  
  ## To facilitate parsing of HTML-formatted reports by Bio::Tools::Blast.pm,
! ## the <a name=...> anchors should be added at the BEGINNING of the HSP 
  ## alignment section lines and at the END of the description section lines.
  
!     # Removing " ! " addded by GCG. 
      s/ ! / /;
  
--- 432,447 ----
      local $_ = $$line_ref;
  ##
! ## REGEXPS FOR ALIGNMENT SECTIONS (within the body of the report,
  ##                                 the text above the list of HSPs).
  ##
  ## If the HSP alignment sections don't start with a '>' we have no way
! ## of finding them. This occurs with reports saved from HTML-formatted
  ## web pages, which we shouldn't be processing here anyway.
  
  ## To facilitate parsing of HTML-formatted reports by Bio::Tools::Blast.pm,
! ## the <a name=...> anchors should be added at the BEGINNING of the HSP
  ## alignment section lines and at the END of the description section lines.
  
!     # Removing " ! " addded by GCG.
      s/ ! / /;
  
***************
*** 524,528 ****
  ##
  ## Not using bold face to highlight the sequence id's since this can throw off
! ## off formatting of the line when the IDs are different lengths. This lead to 
  ## the scores and P/Expect values not lining up properly.
  
--- 523,527 ----
  ##
  ## Not using bold face to highlight the sequence id's since this can throw off
! ## off formatting of the line when the IDs are different lengths. This lead to
  ## the scores and P/Expect values not lining up properly.
  
***************
*** 569,573 ****
      ## Mike Cherry's markups. SAC note: added back database name to allow
      ## the HTML-formatted version to be parsable by Blast.pm.
!     
    s#^ ?(GB_$Word:)($Word)( *)($Acc)($Descrip)($Int)  ( *$Signif) ( *\d*)$#GenBank\|<a href="$_gi_link$4">$2</A>\|$4 $3$5$6 <a href="\#$2_$4_A">$7</A> $8<a name="$2_$4_H"></A>#o;
  
--- 568,572 ----
      ## Mike Cherry's markups. SAC note: added back database name to allow
      ## the HTML-formatted version to be parsable by Blast.pm.
! 
    s#^ ?(GB_$Word:)($Word)( *)($Acc)($Descrip)($Int)  ( *$Signif) ( *\d*)$#GenBank\|<a href="$_gi_link$4">$2</A>\|$4 $3$5$6 <a href="\#$2_$4_A">$7</A> $8<a name="$2_$4_H"></A>#o;
  
***************
*** 594,598 ****
    s#^ ?(UTR5_SC_[0-9]*:)(\S*)($Descrip)($Int)  ($Signif) ($Int)$#UTR5:$2 $3  $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
  
!   # Hits without a db identifier. 
    s@^ ?($Word)($Descrip)($Int)  ($Signif)(.*)$@$1$2$3  <A href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
  
--- 593,597 ----
    s#^ ?(UTR5_SC_[0-9]*:)(\S*)($Descrip)($Int)  ($Signif) ($Int)$#UTR5:$2 $3  $4 <a href="\#$2_A">$5</a> $6<a name="$2_H"></a>#o;
  
!   # Hits without a db identifier.
    s@^ ?($Word)($Descrip)($Int)  ($Signif)(.*)$@$1$2$3  <A href="\#$1_A">$4</a>$5<a name="$1_H"></a>@o;
  
***************
*** 619,631 ****
  <p>
  <small>
! <b>References:</b> 
  <ol>
! <li>Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990). 
  Basic local alignment search tool.
  <a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=2231712&form=6&db=m&Dopt=r">J. Mol. Biol. 215: 403-10</a>.
! <li>Altschul et al. (1997), Gapped BLAST and PSI-BLAST: 
! a new generation of protein database search programs. 
  <a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">Nucl. Acids Res. 25: 3389-3402</a>.
! <li><b>Program Descriptions</b>: 
  <a href="http://www.ncbi.nlm.nih.gov/BLAST/newblast.html">BLAST2</a> |
  <a href="http://blast.wustl.edu/">WU-BLAST2</a> |
--- 618,630 ----
  <p>
  <small>
! <b>References:</b>
  <ol>
! <li>Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman (1990).
  Basic local alignment search tool.
  <a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=2231712&form=6&db=m&Dopt=r">J. Mol. Biol. 215: 403-10</a>.
! <li>Altschul et al. (1997), Gapped BLAST and PSI-BLAST:
! a new generation of protein database search programs.
  <a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">Nucl. Acids Res. 25: 3389-3402</a>.
! <li><b>Program Descriptions</b>:
  <a href="http://www.ncbi.nlm.nih.gov/BLAST/newblast.html">BLAST2</a> |
  <a href="http://blast.wustl.edu/">WU-BLAST2</a> |
***************
*** 641,645 ****
  
  # Not really a reference for the Blast algorithm itself but an interesting usage.
! #<li>Gish, Warren, and David J. States (1993). Identification of protein coding regions by database similarity search. 
  #<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8485583&form=6&db=m&Dopt=r">Nature Genetics 3:266-72</a>.
  
--- 640,644 ----
  
  # Not really a reference for the Blast algorithm itself but an interesting usage.
! #<li>Gish, Warren, and David J. States (1993). Identification of protein coding regions by database similarity search.
  #<a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8485583&form=6&db=m&Dopt=r">Nature Genetics 3:266-72</a>.
  
***************
*** 661,670 ****
  #------------------
      return << "QQ_GENBANK_QQ";
! <p><b><font color="red">CAUTION: Hits reported on this page may be derived from DNA sequences 
!          that contain more than one gene. 
           </font>To avoid mis-interpretation, always check database entries
!          for any sequence of interest to verify that the similarity 
           occurs within the described sequence. (E.g., A DNA sequence
!          for gene X as reported in GenBank may contain a 5' or 3' 
           fragment of coding sequence for a neighboring gene Y, yet will
           be listed as gene X, since gene Y had not yet been identified). </b>
--- 660,669 ----
  #------------------
      return << "QQ_GENBANK_QQ";
! <p><b><font color="red">CAUTION: Hits reported on this page may be derived from DNA sequences
!          that contain more than one gene.
           </font>To avoid mis-interpretation, always check database entries
!          for any sequence of interest to verify that the similarity
           occurs within the described sequence. (E.g., A DNA sequence
!          for gene X as reported in GenBank may contain a 5' or 3'
           fragment of coding sequence for a neighboring gene Y, yet will
           be listed as gene X, since gene Y had not yet been identified). </b>
***************
*** 687,701 ****
   Comments  : Based on code originally written by Alex Dong Li
             : (ali at genet.sickkids.on.ca).
!            : This method does some Blast-specific stripping 
!            : (adds back a '>' character in front of each HSP 
             : alignment listing).
!            :   
             : THIS METHOD IS HIGHLY ERROR-PRONE!
             :
             : Removal of the HTML tags and accurate reconstitution of the
             : non-HTML-formatted report is highly dependent on structure of
!            : the HTML-formatted version. For example, it assumes that first 
             : line of each alignment section (HSP listing) starts with a
!            : <a name=..> anchor tag. This permits the reconstruction of the 
             : original report in which these lines begin with a ">".
             : This is required for parsing.
--- 686,700 ----
   Comments  : Based on code originally written by Alex Dong Li
             : (ali at genet.sickkids.on.ca).
!            : This method does some Blast-specific stripping
!            : (adds back a '>' character in front of each HSP
             : alignment listing).
!            :
             : THIS METHOD IS HIGHLY ERROR-PRONE!
             :
             : Removal of the HTML tags and accurate reconstitution of the
             : non-HTML-formatted report is highly dependent on structure of
!            : the HTML-formatted version. For example, it assumes that first
             : line of each alignment section (HSP listing) starts with a
!            : <a name=..> anchor tag. This permits the reconstruction of the
             : original report in which these lines begin with a ">".
             : This is required for parsing.
***************
*** 719,726 ****
        #    2) if a tag is split over multiple lines and this method is
        #       used to process one line at a time.
!       
      my $string_ref = shift;
  
!     ref $string_ref eq 'SCALAR' or 
  	croak ("Can't strip HTML: ".
  	       "Argument is should be a SCALAR reference not a ${\ref $string_ref}");
--- 718,725 ----
        #    2) if a tag is split over multiple lines and this method is
        #       used to process one line at a time.
! 
      my $string_ref = shift;
  
!     ref $string_ref eq 'SCALAR' or
  	croak ("Can't strip HTML: ".
  	       "Argument is should be a SCALAR reference not a ${\ref $string_ref}");
***************
*** 729,737 ****
      my $stripped = 0;
  
!     # Removing "<a name =...>" and adding the '>' character for 
      # HSP alignment listings.
      $str =~ s/(\A|\n)<a name ?=[^>]+> ?/>/sgi and $stripped = 1;
  
!     # Removing all "<>" tags. 
      $str =~ s/<[^>]+>|&nbsp//sgi and $stripped = 1;
  
--- 728,736 ----
      my $stripped = 0;
  
!     # Removing "<a name =...>" and adding the '>' character for
      # HSP alignment listings.
      $str =~ s/(\A|\n)<a name ?=[^>]+> ?/>/sgi and $stripped = 1;
  
!     # Removing all "<>" tags.
      $str =~ s/<[^>]+>|&nbsp//sgi and $stripped = 1;
  

Index: HSP.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Blast/HSP.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** HSP.pm	4 Jul 2006 22:23:25 -0000	1.23
--- HSP.pm	24 Sep 2006 15:36:32 -0000	1.24
***************
*** 13,17 ****
  #
  # Copyright (c) 1996-2000 Steve Chervitz. All Rights Reserved.
! #           This module is free software; you can redistribute it and/or 
  #           modify it under the same terms as Perl itself.
  #----------------------------------------------------------------------------
--- 13,17 ----
  #
  # Copyright (c) 1996-2000 Steve Chervitz. All Rights Reserved.
! #           This module is free software; you can redistribute it and/or
  #           modify it under the same terms as Perl itself.
[...1096 lines suppressed...]
*** 1847,1855 ****
                           Query:   285 QNSAPWGLARISHRERLNLGSFNKYLYDDDAG
                                        Q +APWGLARIS       G+ + Y YD+ AG
!                          ^^^^^^^^^^^^^ 
  
!  INHERITED DATA MEMBERS 
  
!  _name          : From Bio::Root::Object.pm. 
  		:
   _parent        : From Bio::Root::Object.pm. This member contains a reference to the
--- 1846,1854 ----
                           Query:   285 QNSAPWGLARISHRERLNLGSFNKYLYDDDAG
                                        Q +APWGLARIS       G+ + Y YD+ AG
!                          ^^^^^^^^^^^^^
  
!  INHERITED DATA MEMBERS
  
!  _name          : From Bio::Root::Object.pm.
  		:
   _parent        : From Bio::Root::Object.pm. This member contains a reference to the



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