2
;; $Id: bioperl.lisp,v 1.28 2003/03/06 03:41:24 lapp Exp $
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(assoc "\\.pl$" auto-mode-alist)
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(setq auto-mode-alist (cons '("\\.pl$" . perl-mode) auto-mode-alist))
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(assoc "\\.pm$" auto-mode-alist)
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(setq auto-mode-alist (cons '("\\.pm$" . perl-mode) auto-mode-alist))
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(defun perl-insert-start ()
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"Places #!..perl at the start of the script"
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(goto-char (point-min))
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(insert "#!/usr/local/bin/perl\n"))
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(defun bioperl-object-start (perl-object-name perl-caretaker-name caretaker-email)
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"Places standard bioperl object notation headers and footers"
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(interactive "sName of Object: \nsName of caretaker: \nsEmail: ")
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(insert "# $Id: bioperl.lisp,v 1.28 2003/03/06 03:41:24 lapp Exp $\n#\n# BioPerl module for " perl-object-name "\n#\n# Cared for by " perl-caretaker-name " <" caretaker-email ">\n#\n# Copyright " perl-caretaker-name "\n#\n# You may distribute this module under the same terms as perl itself\n\n")
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(insert "# POD documentation - main docs before the code\n\n")
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(insert "=head1 NAME\n\n" perl-object-name " - DESCRIPTION of Object\n\n")
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(insert "=head1 SYNOPSIS\n\nGive standard usage here\n\n")
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(insert "=head1 DESCRIPTION\n\nDescribe the object here\n\n")
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(insert "=head1 FEEDBACK\n\n=head2 Mailing Lists\n\n")
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(insert "User feedback is an integral part of the evolution of this and other\nBioperl modules. Send your comments and suggestions preferably to\nthe Bioperl mailing list. Your participation is much appreciated.\n\n")
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(insert " bioperl-l@bioperl.org - General discussion\n http://bioperl.org/MailList.shtml - About the mailing lists\n\n")
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(insert "=head2 Reporting Bugs\n\nReport bugs to the Bioperl bug tracking system to help us keep track\nof the bugs and their resolution. Bug reports can be submitted via\nthe web:\n\n")
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(insert " http://bugzilla.bioperl.org/\n\n")
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(insert "=head1 AUTHOR - " perl-caretaker-name "\n\nEmail " caretaker-email "\n\nDescribe contact details here\n\n")
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(insert "=head1 CONTRIBUTORS\n\nAdditional contributors names and emails here\n\n")
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(insert "=head1 APPENDIX\n\nThe rest of the documentation details each of the object methods.\nInternal methods are usually preceded with a _\n\n=cut\n\n")
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(insert "\n# Let the code begin...\n\n")
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(insert "\npackage " perl-object-name ";\n")
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(insert "use vars qw(@ISA);\n")
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(insert "use strict;\n")
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(insert "\n# Object preamble - inherits from Bio::Root::Root\n")
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(insert "\nuse Bio::Root::Root;\n\n")
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(insert "\n@ISA = qw(Bio::Root::Root );\n\n")
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(insert "=head2 new\n\n Title : new\n Usage : my $obj = new "
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perl-object-name "();\n Function: Builds a new "
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perl-object-name " object \n Returns : an instance of "
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perl-object-name "\n Args :\n\n\n=cut\n\n")
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(insert "sub new {\n my($class,@args) = @_;\n\n my $self = $class->SUPER::new(@args);\n return $self;\n}\n")
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(defun bioperl-interface-start (perl-object-name perl-caretaker-name
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"Places standard bioperl object notation headers and footers"
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(interactive "sName of Object: \nsName of caretaker: \nsEmail: ")
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(insert "# $Id $\n#\n# BioPerl module for " perl-object-name "\n#\n# Cared for by " perl-caretaker-name " <" caretaker-email ">\n#\n# Copyright " perl-caretaker-name "\n#\n# You may distribute this module under the same terms as perl itself\n\n")
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(insert "# POD documentation - main docs before the code\n\n")
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(insert "=head1 NAME\n\n" perl-object-name " - DESCRIPTION of Interface\n\n")
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(insert "=head1 SYNOPSIS\n\nGive standard usage here\n\n")
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(insert "=head1 DESCRIPTION\n\nDescribe the interface here\n\n")
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(insert "=head1 FEEDBACK\n\n=head2 Mailing Lists\n\n")
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(insert "User feedback is an integral part of the evolution of this and other\nBioperl modules. Send your comments and suggestions preferably to\nthe Bioperl mailing list. Your participation is much appreciated.\n\n")
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(insert " bioperl-l@bioperl.org - General discussion\n http://bioperl.org/MailList.shtml - About the mailing lists\n\n")
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(insert "=head2 Reporting Bugs\n\nReport bugs to the Bioperl bug tracking system to help us keep track\nof the bugs and their resolution. Bug reports can be submitted via\nemail or the web:\n\n")
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(insert " http://bugzilla.bioperl.org/\n\n")
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(insert "=head1 AUTHOR - " perl-caretaker-name "\n\nEmail " caretaker-email "\n\nDescribe contact details here\n\n")
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(insert "=head1 CONTRIBUTORS\n\nAdditional contributors names and emails here\n\n")
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(insert "=head1 APPENDIX\n\nThe rest of the documentation details each of the object methods.\nInternal methods are usually preceded with a _\n\n=cut\n\n")
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(insert "\n# Let the code begin...\n\n")
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(insert "\npackage " perl-object-name ";\n")
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(insert "use vars qw(@ISA);\n")
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(insert "use strict;\n\nuse Bio::Root::RootI;\n\n")
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(insert "@ISA = qw( Bio::Root::RootI );")
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(defun bioperl-method (method-name)
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"puts in a bioperl method complete with pod boiler-plate"
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(interactive "smethod name:")
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(insert "=head2 " method-name "\n\n Title : " method-name "\n Usage :\n Function:\n Example :\n Returns : \n Args :\n\n\n=cut\n\n")
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(insert "sub " method-name "{\n my ($self,@args) = @_;\n")
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(defun bioperl-getset (field-name)
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"puts in a bioperl method for a get/set method complete with pod boiler-plate"
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(interactive "sfield name:")
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(insert "=head2 " field-name "\n\n Title : " field-name "\n Usage : $obj->" field-name "($newval)\n Function: \n Example : \n Returns : value of " field-name " (a scalar)\n Args : on set, new value (a scalar or undef, optional)\n\n\n=cut\n\n")
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(insert "sub " field-name "{\n my $self = shift;\n\n return $self->{'" field-name "'} = shift if @_;\n return $self->{'" field-name "'};")
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(defun bioperl-array-getset (field-name class-name)
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"puts in a bioperl method for array get/add/remove methods complete with pod boiler-plate"
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(interactive "sarray base object: \nstype of element: ")
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(insert "=head2 get_" field-name "s\n\n Title : get_" field-name "s\n Usage : @arr = get_" field-name "s()\n Function: Get the list of " field-name "(s) for this object.\n Example :\n Returns : An array of " class-name " objects\n Args :\n\n\n=cut\n\n")
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(insert "sub get_" field-name "s{\n my $self = shift;\n\n return @{$self->{'_" field-name "s'}} if exists($self->{'_" field-name "s'});\n return ();\n}\n\n")
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(insert "=head2 add_" field-name "\n\n Title : add_" field-name "\n Usage :\n Function: Add one or more " field-name "(s) to this object.\n Example :\n Returns : \n Args : One or more " class-name " objects.\n\n\n=cut\n\n")
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(insert "sub add_" field-name "{\n my $self = shift;\n\n $self->{'_" field-name "s'} = [] unless exists($self->{'_" field-name "s'});\n push(@{$self->{'_" field-name "s'}}, @_);\n}\n\n")
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(insert "=head2 remove_" field-name "s\n\n Title : remove_" field-name "s\n Usage :\n Function: Remove all " field-name "s for this class.\n Example :\n Returns : The list of previous " field-name "s as an array of\n " class-name " objects.\n Args :\n\n\n=cut\n\n")
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(insert "sub remove_" field-name "s{\n my $self = shift;\n\n my @arr = $self->get_" field-name "s();\n $self->{'_" field-name "s'} = [];\n return @arr;\n}\n\n"))
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(defun bioperl-abstract-method (method-name)
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"puts in a bioperl abstract method for interface classes"
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(interactive "smethod-name:")
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(insert "=head2 " method-name "\n\n Title : " method-name "\n Usage :\n Function:\n Example :\n Returns : \n Args :\n\n\n=cut\n\n")
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(insert "sub " method-name "{\n my ($self) = @_;\n\n $self->throw(\"Abstract method " method-name " implementing class did not provide method\");\n")
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(define-key perl-mode-map "\C-c\C-h" 'perl-insert-start)
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(define-key perl-mode-map "\C-c\C-b" 'bioperl-object-start)
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(define-key perl-mode-map "\C-c\C-i" 'bioperl-interface-start)
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(define-key perl-mode-map "\C-c\C-v" 'bioperl-getset)
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(define-key perl-mode-map "\C-c\C-r" 'bioperl-arrray-getset)
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(define-key perl-mode-map "\C-c\C-b" 'bioperl-method)
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(define-key perl-mode-map "\C-c\C-a\C-m" 'bioperl-abstract-method)
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(define-key perl-mode-map "\C-c\C-z" 'compile)
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(define-key perl-mode-map [menu-bar] (make-sparse-keymap))
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(define-key perl-mode-map [menu-bar p]
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(cons "BioPerl" (make-sparse-keymap "BioPerl")))
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(define-key perl-mode-map [menu-bar p perl-script-start]
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'("Insert script template" . perl-script-start))
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(define-key perl-mode-map [menu-bar p bioperl-object-start]
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'("bioperl object template" . bioperl-object-start))
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(define-key perl-mode-map [menu-bar p bioperl-interface-start]
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'("bioperl interface template" . bioperl-interface-start))
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(define-key perl-mode-map [menu-bar p bioperl-getset]
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'("bioperl field func" . bioperl-getset))
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(define-key perl-mode-map [menu-bar p bioperl-array-getset]
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'("bioperl array get/add/remove" . bioperl-array-getset))
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(define-key perl-mode-map [menu-bar p bioperl-method]
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'("bioperl method" . bioperl-method))
added
removed
bioperl.lisp
