Zoombrowser Ex Tools

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...

Bio::Tools::AlignFactory is a base object for alignment factories. SYNOPSIS You wont be using this as an object, but using a dervied class like Bio::Tools::pSW Holds common Alignment Factory attributes in place.

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...


Platforms: *nix

ex::constant::vars is a Perl pragma to create readonly variables. SYNOPSIS Using the tie() interface: use ex::constant::vars; tie my $pi, ex::constant::vars, 4 * atan2( 1, 1 ); tie my @family, ex::constant::vars, qw( John Jane ); tie my %age, ex::constant::vars, John => 27, Jane => Back...


Platforms: *nix

ex::override is a Perl pragma to override core functions. SYNOPSIS use ex::override ucfirst => sub { # make sure only the first # letter is uppercased ucfirst( lc( shift ) ); }; ucfirst( MAKE THIS RIGHT ); # Make this right no ex::override ucfirst; ucfirst( MAKE THIS RIGHT ); #...


Platforms: *nix

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db...


Platforms: *nix

Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences to an existing model. Parameters: align2model (String) run (String) Run name db (Sequence) Sequences to align (-db) model_file (InFile) Model (-i) pipe:...


Platforms: *nix

Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...


Platforms: *nix

Bio::Tools::Run::PiseApplication::charge is a Perl module. Bio::Tools::Run::PiseApplication::charge Bioperl class for: CHARGE Protein charge plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/charge.html for available values): charge (String) init...


Platforms: *nix

ATA over Ethernet Tools are intended for use in conjunction with an ATA over Ethernet (AoE) driver for a Linux 2.6 kernel. They perform simple tasks like listing available devices, triggering device discovery, and restricting the network interfaces on which AoE is performed. Whats New in This...


Platforms: *nix

The ICMP Hostname Tools for Linux include a responder daemon, a lookup tool, and a nameswitch module to handle ICMP host name functions. The NSS module caches all requests (including failures) and honors the TTL value sent by the responding host. It uses a configuration file called...


Platforms: *nix

Gtk2::Ex::MindMapView::ContentFactory is a maker of standard content. SYNOPSIS use Gtk2::Ex::MindMapView::ContentFactory; This module is internal to Gtk2::Ex::MindMapView. This factory makes content that can be passed to a Gtk2::Ex::MindMapView::Border. This module is called by...


Platforms: *nix

Gtk2::Ex::MindMapView::HotSpot is a base class for grips and toggles. SYNOPSIS use base Gtk2::Ex::MindMapView::HotSpot; This module is internal to Gtk2::Ex::MindMapView. Four Gtk2::Ex::MindMapView::HotSpots are created for each Gtk2::Ex::MindMapView::Item. The hotspots are areas on a mind...


Platforms: *nix

Gtk2::Ex::MindMapView::Layout::Cluster is a vertical layout of view items. HEIRARCHY Gtk2::Ex::MindMapView::Layout::Group +----Gtk2::Ex::MindMapView::Layout::Cluster SYNOPSIS use Gtk2::Ex::MindMapView::Layout::Cluster; INTERFACE new(cluster_no=>$cluster_no) Instantiates an array of...


Platforms: *nix

Gtk2::Ex::MindMapView::Layout::Group is a group of items displayed on canvas. SYNOPSIS use base Gtk2::Ex::MindMapView::Layout::Group; Base class for the layout modules. This module is internal to Gtk2::Ex::MindMapView. INTERFACE new() Instantiates an object and intializes the x, y,...


Platforms: *nix

Gtk2::Ex::MindMapView::HotSpot::Grip::Round is a Perl module to manage a round grip type "hot spot" on a view item. SYNOPSIS use Gtk2::Ex::MindMapView::HotSpot::Grip::Round; The Gtk2::Ex::MindMapView::HotSpot::Grip::Round is a round grip that may be used to resize a...


Platforms: *nix

Gtk2::Ex::MindMapView::HotSpot::Grip::Lentil is a Perl module to manage a lentil shaped grip "hot spot" on a view item. SYNOPSIS use Gtk2::Ex::MindMapView::HotSpot::Grip::Lentil; A LentilGrip hotspot may be used to resize a Gtk2::Ex::MindMapView::Item. Normally, this grip will be used with...


Platforms: *nix

The mjpeg programs are a set of tools that can do recording of videos and playback, simple cut-and-paste editing and the MPEG compression of audio and video under Linux. Recording is supported for the Zoran based cards like the Buz (Iomega), DC10 (MIRO, Pinnacle), Matrox Marvel cards and the...


Platforms: *nix

Cmos password recovery tools decrypts password stored in cmos used to access BIOS SETUP. Works with the following BIOSes: - ACER/IBM BIOS - AMI BIOS - AMI WinBIOS 2.5 - Award 4.5x/4.6x/6.0 - Compaq (1992) - Compaq (New version) - IBM (PS/2, Activa, Thinkpad) - Packard Bell - Phoenix...


Platforms: *nix

Heirloom Development Tools package provides yacc, lex, m4, make, and SCCS as portable derivatives of the utilities released by Sun as part of OpenSolaris. The OpenSolaris utilities were in turn derived from the original Unix versions, and are assumed be conforming implementations of the POSIX...


Platforms: *nix