Bio::CUA module, first commit

fortune9 · Apr 28, 2015 · 3e566b2 · 3e566b2
commit 3e566b2
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diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,18 @@
+Makefile
+Makefile.old
+Build
+Build.bat
+META.*
+MYMETA.*
+.build/
+_build/
+cover_db/
+blib/
+inc/
+.lwpcookies
+.last_cover_stats
+nytprof.out
+pod2htm*.tmp
+pm_to_blib
+Bio-CUA-*
+Bio-CUA-*.tar.gz
diff --git a/Changes b/Changes
@@ -0,0 +1,5 @@
+Revision history for Bio-CUA
+
+0.01    Date/time
+        First version, released on an unsuspecting world.
+
diff --git a/MANIFEST b/MANIFEST
@@ -0,0 +1,11 @@
+Changes
+lib/Bio/CUA.pm
+lib/Bio/CUA/CUB/Builder.pm
+lib/Bio/CUA/CUB/Calculator.pm
+Makefile.PL
+MANIFEST			This list of files
+README
+t/00-load.t
+t/manifest.t
+t/pod-coverage.t
+t/pod.t
diff --git a/Makefile.PL b/Makefile.PL
@@ -0,0 +1,26 @@
+use 5.006;
+use strict;
+use warnings;
+use ExtUtils::MakeMaker;
+
+WriteMakefile(
+    NAME             => 'Bio::CUA::CUB::Builder',
+    AUTHOR           => q{Zhenguo Zhang <zhangz.sci@gmail.com>},
+    VERSION_FROM     => 'lib/Bio/CUA/CUB/Builder.pm',
+    ABSTRACT_FROM    => 'lib/Bio/CUA/CUB/Builder.pm',
+    LICENSE          => 'gpl_3',
+    PL_FILES         => {},
+    MIN_PERL_VERSION => 5.006,
+    CONFIGURE_REQUIRES => {
+        'ExtUtils::MakeMaker' => 0,
+    },
+    BUILD_REQUIRES => {
+        'Test::More' => 0,
+    },
+    PREREQ_PM => {
+        #'ABC'              => 1.6,
+        #'Foo::Bar::Module' => 5.0401,
+    },
+    dist  => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', },
+    clean => { FILES => 'Bio-CUA-*' },
+);
diff --git a/README b/README
@@ -0,0 +1,62 @@
+Bio-CUA
+
+The README is used to introduce the module and provide instructions on
+how to install the module, any machine dependencies it may have (for
+example C compilers and installed libraries) and any other information
+that should be provided before the module is installed.
+
+A README file is required for CPAN modules since CPAN extracts the README
+file from a module distribution so that people browsing the archive
+can use it to get an idea of the module's uses. It is usually a good idea
+to provide version information here so that people can decide whether
+fixes for the module are worth downloading.
+
+
+INSTALLATION
+
+To install this module, run the following commands:
+
+	perl Makefile.PL
+	make
+	make test
+	make install
+
+SUPPORT AND DOCUMENTATION
+
+After installing, you can find documentation for this module with the
+perldoc command.
+
+    perldoc Bio::CUA::CUB::Builder
+
+You can also look for information at:
+
+    RT, CPAN's request tracker (report bugs here)
+        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA
+
+    AnnoCPAN, Annotated CPAN documentation
+        http://annocpan.org/dist/Bio-CUA
+
+    CPAN Ratings
+        http://cpanratings.perl.org/d/Bio-CUA
+
+    Search CPAN
+        http://search.cpan.org/dist/Bio-CUA/
+
+
+LICENSE AND COPYRIGHT
+
+Copyright (C) 2015 Zhenguo Zhang
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see L<http://www.gnu.org/licenses/>.
+
diff --git a/ignore.txt b/ignore.txt
@@ -0,0 +1,18 @@
+Makefile
+Makefile.old
+Build
+Build.bat
+META.*
+MYMETA.*
+.build/
+_build/
+cover_db/
+blib/
+inc/
+.lwpcookies
+.last_cover_stats
+nytprof.out
+pod2htm*.tmp
+pm_to_blib
+Bio-CUA-*
+Bio-CUA-*.tar.gz
diff --git a/lib/Bio/CUA.pm b/lib/Bio/CUA.pm
@@ -0,0 +1,118 @@
+package Bio::CUA;
+
+use 5.006;
+use strict;
+use warnings;
+
+=head1 NAME
+
+Bio::CUA - The great new Bio::CUA!
+
+=head1 VERSION
+
+Version 0.01
+
+=cut
+
+our $VERSION = '0.01';
+
+
+=head1 SYNOPSIS
+
+Quick summary of what the module does.
+
+Perhaps a little code snippet.
+
+    use Bio::CUA;
+
+    my $foo = Bio::CUA->new();
+    ...
+
+=head1 EXPORT
+
+A list of functions that can be exported.  You can delete this section
+if you don't export anything, such as for a purely object-oriented module.
+
+=head1 SUBROUTINES/METHODS
+
+=head2 function1
+
+=cut
+
+sub function1 {
+}
+
+=head2 function2
+
+=cut
+
+sub function2 {
+}
+
+=head1 AUTHOR
+
+Zhenguo Zhang, C<< <zhangz.sci at gmail.com> >>
+
+=head1 BUGS
+
+Please report any bugs or feature requests to C<bug-bio-cua at rt.cpan.org>, or through
+the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-CUA>.  I will be notified, and then you'll
+automatically be notified of progress on your bug as I make changes.
+
+
+
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+    perldoc Bio::CUA
+
+
+You can also look for information at:
+
+=over 4
+
+=item * RT: CPAN's request tracker (report bugs here)
+
+L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA>
+
+=item * AnnoCPAN: Annotated CPAN documentation
+
+L<http://annocpan.org/dist/Bio-CUA>
+
+=item * CPAN Ratings
+
+L<http://cpanratings.perl.org/d/Bio-CUA>
+
+=item * Search CPAN
+
+L<http://search.cpan.org/dist/Bio-CUA/>
+
+=back
+
+
+=head1 ACKNOWLEDGEMENTS
+
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright 2015 Zhenguo Zhang.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see L<http://www.gnu.org/licenses/>.
+
+
+=cut
+
+1; # End of Bio::CUA
diff --git a/lib/Bio/CUA/CUB/Builder.pm b/lib/Bio/CUA/CUB/Builder.pm
@@ -0,0 +1,118 @@
+package Bio::CUA::CUB::Builder;
+
+use 5.006;
+use strict;
+use warnings;
+
+=head1 NAME
+
+Bio::CUA::CUB::Builder - The great new Bio::CUA::CUB::Builder!
+
+=head1 VERSION
+
+Version 0.01
+
+=cut
+
+our $VERSION = '0.01';
+
+
+=head1 SYNOPSIS
+
+Quick summary of what the module does.
+
+Perhaps a little code snippet.
+
+    use Bio::CUA::CUB::Builder;
+
+    my $foo = Bio::CUA::CUB::Builder->new();
+    ...
+
+=head1 EXPORT
+
+A list of functions that can be exported.  You can delete this section
+if you don't export anything, such as for a purely object-oriented module.
+
+=head1 SUBROUTINES/METHODS
+
+=head2 function1
+
+=cut
+
+sub function1 {
+}
+
+=head2 function2
+
+=cut
+
+sub function2 {
+}
+
+=head1 AUTHOR
+
+Zhenguo Zhang, C<< <zhangz.sci at gmail.com> >>
+
+=head1 BUGS
+
+Please report any bugs or feature requests to C<bug-bio-cua at rt.cpan.org>, or through
+the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-CUA>.  I will be notified, and then you'll
+automatically be notified of progress on your bug as I make changes.
+
+
+
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+    perldoc Bio::CUA::CUB::Builder
+
+
+You can also look for information at:
+
+=over 4
+
+=item * RT: CPAN's request tracker (report bugs here)
+
+L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-CUA>
+
+=item * AnnoCPAN: Annotated CPAN documentation
+
+L<http://annocpan.org/dist/Bio-CUA>
+
+=item * CPAN Ratings
+
+L<http://cpanratings.perl.org/d/Bio-CUA>
+
+=item * Search CPAN
+
+L<http://search.cpan.org/dist/Bio-CUA/>
+
+=back
+
+
+=head1 ACKNOWLEDGEMENTS
+
+
+=head1 LICENSE AND COPYRIGHT
+
+Copyright 2015 Zhenguo Zhang.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see L<http://www.gnu.org/licenses/>.
+
+
+=cut
+
+1; # End of Bio::CUA::CUB::Builder