Free protein structure and function software for linux

XML::Structured is a simple conversion API from XML to perl structures and back.

SYNOPSIS

use XML::Structured;

$dtd = [
element =>
attribute1,
attribute2,
[],
element1,
[ element2 ],
[ element3 =>
...
],
[[ element4 =>
...
]],
];

$hashref = XMLin($dtd, $xmlstring);
$hashref = XMLinfile($dtd, $filename_or_glob);
$xmlstring = XMLout($dtd, $hashref);

The XML::Structured module provides a way to convert xml data into a predefined perl data structure and back to xml. Unlike with modules like XML::Simple it is an error if the xml data does not match the provided skeleton (the "dtd"). Another advantage is that the order of the attributes and elements is taken from the dtd when converting back to xml.

Structured Document Validator project implements a generalized method for validating both the structure and content of structured documents.

Any data format that can be deterministically divided into tags and data is classed as a structured document. This definition applies to a wide array of data formats, including XML, Java properties files, and delimited value files.

The application performs validations based on user-defined Structured Document Definitions (SDDs). It provides an environment for validation, SDD development, and document editing.

CoreLinux++ Function Load Library (libclfll++) takes advantage of the abstract Library Load framework in the CoreLinux libclfw++ library by providing management of loading Linux shared libraries.
Application developers define function objects as wrappers and can then dynamically load the functions. It is very useful for implementing a framework for plug-ins.
Main features:
- Enlist members ( for requirements, analysis, design, and development )
- Formalize conventions for Object Oriented Analysis (OOA) and Design (OOD).
- Formalize standards and conventions for C++ code style.
- Gather requirements. Perform OOA and OOD using UML as the modeling language.
- Implement designs and example drivers.
- Develop utilities and applications for Linux that are CoreLinux++ certified
- Showcase CoreLinux++ certified applications by others

Struct::Compare is a recursive diff for perl structures.

SYNOPSIS

use Struct::Compare;
my $is_different = compare($ref1, $ref2);

Compares two values of any type and structure and returns true if they are the same. It does a deep comparison of the structures, so a hash of a hash of a whatever will be compared correctly.

This is especially useful for writing unit tests for your modules!

PUBLIC FUNCTIONS

$bool = compare($var1, $var2)

Recursively compares $var1 to $var2, returning false if either structure is different than the other at any point. If both are undefined, it returns true as well, because that is considered equal.

Bio::LiveSeq::Translation is a translation class for LiveSeq.

This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate system and eventually its own ranges (protein domains).

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title : new
Usage : $protein = Bio::LiveSeq::Translation->new(-transcript => $transcr);

Function: generates a new Bio::LiveSeq::Translation
Returns : reference to a new object of class Translation
Errorcode -1
Args : reference to an object of class Transcript

get_Transcript

Title : valid
Usage : $transcript = $obj->get_Transcript()
Function: retrieves the reference to the object of class Transcript (if any)
attached to a LiveSeq object
Returns : object reference
Args : none

aa_ranges

Title : aa_ranges
Usage : @proteinfeatures = $translation->aa_ranges()
Function: to retrieve all the LiveSeq AARange objects attached to a
Translation, usually created out of a SwissProt database entry
crossreferenced from an EMBL CDS feature.
Returns : an array
Args : none

PAPI aims to provide the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors.
PAPI enables software engineers to see, in near real time, the relation between software performance and processor events.
The Performance API (PAPI) project specifies a standard application programming interface (API) for accessing hardware performance counters available on most modern microprocessors.
These counters exist as a small set of registers that count Events, occurrences of specific signals related to the processors function. Monitoring these events facilitates correlation between the structure of source/object code and the efficiency of the mapping of that code to the underlying architecture.
This correlation has a variety of uses in performance analysis including hand tuning, compiler optimization, debugging, benchmarking, monitoring and performance modeling. In addition, it is hoped that this information will prove useful in the development of new compilation technology as well as in steering architectural development towards alleviating commonly occurring bottlenecks in high performance computing.
PAPI provides two interfaces to the underlying counter hardware; a simple, high level interface for the acquisition of simple measurements and a fully programmable, low level interface directed towards users with more sophisticated needs.
The low level PAPI interface deals with hardware events in groups called EventSets. EventSets reflect how the counters are most frequently used, such as taking simultaneous measurements of different hardware events and relating them to one another.
For example, relating cycles to memory references or flops to level 1 cache misses can indicate poor locality and memory management. In addition, EventSets allow a highly efficient implementation which translates to more detailed and accurate measurements.
EventSets are fully programmable and have features such as guaranteed thread safety, writing of counter values, multiplexing and notification on threshold crossing, as well as processor specific features. The high level interface simply provides the ability to start, stop and read specific events, one at a time.
PAPI provides portability across different platforms. It uses the same routines with similar argument lists to control and access the counters for every architecture. As part of PAPI, we have predefined a set of events that we feel represents the lowest common denominator of every good counter implementation.
Our intent is that the same source code will count similar and possibly comparable events when run on different platforms. If the programmer chooses to use this set of standardized events, then the source code need not be changed and only a fresh compilation and link is necessary. However, should the developer wish to access machine specific events, the low level API provides access to all available events and counting modes.
If an event or feature does not exist on the current platform, PAPI returns an appropriate error code. This significantly reduces the porting effort of code using PAPI because the semantics of each call to PAPI remains the same, just the argument lists need updating. In addition to the standard set, each PAPI implementation supports all native events through the ability to directly accept platform specific counter numbers. Definitions for most, if not all of these, are included as conditional macros in the header file. In this way, PAPI avoids having inefficient code to translate all events for all platforms into a uniform representation and back again.
This translation is only done for the relatively few events defined in the standardized set. Some processors like those in the POWER series have counter groups. They enable access to specific groups of counters, instead of individual events. This presents a serious portability problem, thus PAPI abstracts hardware counters from their groups with a packed naming scheme. Each counter control value or event is made up of the counter group number and the number of the specific counter in that group.
PAPI can be divided into two layers of software. The upper layer consists of the API and machine independent support functions. The lower layer defines and exports a machine independent interface to machine dependent functions and data structures. These functions access the substrate, which may consist of the operating system, a kernel extension or assembly functions to directly access the processors registers.
PAPI tries to use the most efficient and flexible of the three, depending on what is available. Naturally, the functionality of the upper layers heavily depends on that provided by the substrate. In cases where the substrates do not provide highly desirable features, PAPI attempts to emulate them as described below.
PAPI makes sure the underlying operating system or library guards against overflow of counter values.
Each counter can potentially be incremented multiple times in a single clock cycle. This combined with increasing clock speeds and the small precision of some of the physical counters means that overflow is likely to occur.
One of the more advanced features of PAPI is to provide a portable implementation of asynchronous notification when counters exceed a user specified value.
This functionality provides the basis for PAPIs SVR4 compatible profiling calls, that generate an accurate histogram of performance interrupts based on hardware metrics, not on time. Such functionality provides the basis for all line level performance analysis software, from the antiquated days of AT&Ts prof to SGIs SpeedShop. Thus for any architecture with even the most rudimentary access to hardware performance counters, PAPI provides the foundation for a truly portable, source level, performance analysis tool based on real processor statistics.
Enhancements:
- The API was extended to decouple abstraction layers from hardware support and to provide initial support for different types of performance counters.

Readonly is a Perl module that offers the facility for creating read-only scalars, arrays, hashes.

SYNOPSIS

use Readonly;

# Read-only scalar
Readonly::Scalar $sca => $initial_value;
Readonly::Scalar my $sca => $initial_value;

# Read-only array
Readonly::Array @arr => @values;
Readonly::Array my @arr => @values;

# Read-only hash
Readonly::Hash %has => (key => value, key => value, ...);
Readonly::Hash my %has => (key => value, key => value, ...);
# or:
Readonly::Hash %has => {key => value, key => value, ...};

# You can use the read-only variables like any regular variables:
print $sca;
$something = $sca + $arr[2];
next if $has{$some_key};

# But if you try to modify a value, your program will die:
$sca = 7;
push @arr, seven;
delete $has{key};
# The error message is "Modification of a read-only value
attempted"

# Alternate form (Perl 5.8 and later)
Readonly $sca => $initial_value;
Readonly my $sca => $initial_value;
Readonly @arr => @values;
Readonly my @arr => @values;
Readonly %has => (key => value, key => value, ...);
Readonly my %has => (key => value, key => value, ...);
# Alternate form (for Perls earlier than v5.8)
Readonly $sca => $initial_value;
Readonly my $sca => $initial_value;
Readonly @arr => @values;
Readonly my @arr => @values;
Readonly %has => (key => value, key => value, ...);
Readonly my %has => (key => value, key => value, ...);

This is a facility for creating non-modifiable variables. This is useful for configuration files, headers, etc. It can also be useful as a development and debugging tool, for catching updates to variables that should not be changed.
If any of the values you pass to Scalar, Array, or Hash are references, then those functions recurse over the data structures, marking everything as Readonly. Usually, this is what you want: the entire structure nonmodifiable. If you want only the top level to be Readonly, use the alternate Scalar1, Array1 and Hash1 functions.

Please note that most users of Readonly will also want to install a companion module Readonly::XS. See the "CONS" section below for more details.