dna structure
XML::Structured 1.0
XML::Structured is a simple conversion API from XML to perl structures and back. more>>
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.
Erwin Data Structures 2.1.58633
Erwin Data Structures is a library that is meant to be the ultimate data structure library for mixed usage of C and C++. more>>
Arbitrary key and value types are implemented by template files that dont use C++ templates, but are instantiated by a Perl script.
This way, mixed usage in C and C++ is possible. However, a C++ interface is generated to support the advantages of the C++ language. No templates, no void*.
Erwin contains a number of tools, too, all of them written in Perl. The following list shows the data structures and tools, together with some typical examples.
Memory Structures Library 4.0
Memory Structures Library (MemSL) is a complete data structures/collection classes library with memory tracing. more>>
The project supports single, double, and circular linked lists, AVL balanced and threaded binary trees, dynamic hashing tables, stacks, queues and dequeues (using arrays or linked lists), sets (Pascal implementation, with union, difference, intersection, etc.), bags, tables and dictionaries, priority heaps, priority search queue, and more.
Struct::Compare 1.0.1
Struct::Compare is a recursive diff for perl structures. more>>
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.
DNA Counter 1.0.4
www.dnabaser.com This tool will show the proportions between nucleotides in a DNA sequence. You dont need to install it or unpack it. Just download the program and double click to run it. Other software: DNA Baser is an affordable alternative for assembly of DNA sequences and generation of contigs. File formats supported are abi, scf and seq (or FASTA). Chromatograms of the assembled sequences are displayed in a synchronized format with the generated contig. more>>
DNA Counter - www.dnabaser.com
This tool will show the proportions between nucleotides in a DNA sequence.
You dont need to install it or unpack it. Just download the program and double click to run it.
Other software by HeracleSoftware:
DNA Baser is an affordable alternative for assembly of DNA sequences and generation of contigs. File formats supported are abi, scf and seq (or FASTA). Chromatograms of the assembled sequences are displayed in a synchronized format with the generated contig. Ambiguous bases in the contig are highlighted and corrections are suggested by DNABaser based on Quality Values of the trace files. Minimum input from the user required. Editing of ambiguous bases, including insertion and deletion, is possible. The settings of the assembly engine can be adjusted by the user. The user can personalize the appearance of chromatograms, nucleotides, background. The Quality Values of the trace files are displayed above chromatograms, so that the user can easily decide on the corrections in the final contig. Original chromatogram files are automatically trimmed based on Quality Values. The contig is automatically saved in FASTA format, in the same directory with the original trace files. By using a built-up database of primer and vector sequences, that can be edited/upgraded by the user, DNABaser can be set to automatically trim the vector sequence out of the final contig.
The affordable price is another important feature of DNABaser, at only 490 USD per single license; significant discounts are offered for institutions that order several licenses of DNABaser (see our pricing policy on our web pages).
Enhancements:
Version 1.0.3
better speed
System Requirements:CPU: 100MHz, 16MB RAM, Video 800x600, 0.3MB HDD free space<<less
GraphViz::Data::Structure 0.15
GraphViz::Data::Structure can visualise data structures. more>>
SYNOPSIS
use GraphViz::Data::Structure;
my $gvds = GraphViz:Data::Structure->new($data_structure);
print $gvds->graph()->as_png;
This module makes it easy to visualise data structures, even recursive or circular ones.
It is provided as an alternative to GraphViz::Data::Grapher. Differences:
GraphViz::Data::Structure handles structures of arbitrary depth and complexity, automatically following links using a standard graph traversal algorithm.
GraphViz::Data::Grapher creates graphics of indiividual substructures (arrays, scalars, hashes) which keep the substructure type and data together; GraphViz::Data::Structure does this by shape alone.
GraphViz::Data::Structure encapsulates object info (if any) directly into the node being used to represent the class.
GraphViz::Data::Grapher colors its graphs; GraphViz::Data::Structure doesnt by default.
GraphViz::Data:Structure can parse out globs and CODE references (almost as well as the debugger does).
Generic Data Structures Library 1.4-pl1
Generic Data Structures Library (GDSL) is a collection of routines for generic data structures manipulation. more>>
Generic Data Structures Library is a portable and re-entrant library fully written from scratch in pure ANSI C. It is designed to offer for C programmers common data structures with powerful algorithms, and hidden implementation.
Available structures are lists, queues, stacks, hash tables, binary trees, binary search trees, red-black trees, 2D arrays, and permutations.
GDSL provides a modern Applications Programming Interface (API) for C programmers, while allowing wrappers to be written for very high level languages.
The library covers the following data structures:
- Low-level doubly-linked nodes
- Low-level doubly-linked low-level lists
- Low level binary trees
- Low level binary search trees
- Binary search trees
- Red-black trees
- 2D arrays
- Hash tables
- Lists
- Queues
- Stacks
- Permutations
Enhancements:
- A bug that was introduced in gdsl_hash_insert in the previous release was fixed.
- A missing include in gdsl.h was fixed.
Xephyrus Data Structures Tag Library 1.5
Xephyrus Data Structures Tag Library is a tag library to provide access to common data-structures. more>>
Enhancements:
- The library was polished up.
- Several improvements were made and a few bugs were fixed.
- This version is aimed at Java 5 and JSP 2.0.
GNOME Structured File Library 1.14.5
The GNOME Structured File Library is a utility library for reading and writing structured file formats. more>>
There is also support for document metadata and some initial work on decompressing VBA streams in OLE files for future conversion to other languages.
This library replaces libole2 and is used in gnumeric, mrproject, abiword, libwv2, koffice. It is also part of the AAF format.
Enhancements:
- This release reverts jump to dynamic types, as they arent thread-safe.
- A compilation glitch on Windows has been fixed.
- Problems building without gconf macros installed are avoided.
- Configure breakage with --without-gnome has been fixed.
DNA BASER 2.60
Visit us for updated info: http://www.DNABaser.com DNA Baser Assembler is easy to use software for simple and batch DNA sequence assembly, DNA sequence analysis, contig editing, metadata integration and mutation detection. It also offers a powerful chromatogram viewer/editor. The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page. File formats supported are abi, scf and seq (or FASTA). Features: end clip, export,auto trim... more>>
DNA BASER - Visit us for updated info: http://www.DNABaser.com
DNA Baser Assembler is easy to use software for simple and batch DNA sequence assembly, DNA sequence analysis, contig editing, metadata integration and mutation detection. It also offers a powerful chromatogram viewer/editor. The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page.
Why is DNA Baser Assembler special?
Any software company pretends that their product is the best. But lets see for real if DNA Baser can offer you a better proposition. As you will see below we concentrate on adding automatic and batch functions to our product in order to decrease the time. Additional to this, DNA Baser is available at a "kill your competition" price.
Forget about manually trimming the low quality ends of your sequences. DNA Baser Assembler will do it for you!
Do you think you need weeks to assemble hundreds of contigs? What about doing this in minutes? DNA Baser is the only software that can automatically detect and assemble sequences belonging to the same contig based on their filename.
Do you think that is necessary to spend more than 20 minutes to correct discrepancies and mismatches in every contig? Wrong! DNA Baser is the first software which can make correct suggestions in at least 98% of cases.
Have you ever wondered how others laboratories afford to have sequence assembly software in EVERY computer? Simple! They dont spend thousands of dollars for each license. They use DNA Baser Assembler. DNA Baser is affordable, has no annual maintenance fees, technical support is included in price and you have instant access to your key, right after purchase.
You dont have to fill in and submit forms in order to get a trial version. If you want to try it, you can download and install it in less than one minute. No personal data or registration process is required. The trial version is fully functional.
DNA BASER Assembler offers a smart navigation system that takes you to the location of each sequence ambiguity / mutation with a single click.
Enhancements:
Version 2.60
New: Metadata and batch metadata integration.
New: Button to open Windows Explorer in contigs folder, after sequence assembly.
New: Remove vectors from single chromatograms.
New: SEQUENCE ANALISYS - mark al bases with a confidence level (QV) below a specified threshold, in red.
New: Batch convert from chromatogram to Fasta with vector removal and automatic metadata integration.
New: Resizable chromatograms.
Full support for low quality sample ends editing.
100% compatible with Mac via Parallels/Bootcamp/VMWare.
Improved handling of corrupted/invalid ABI/SCF files.
Improved contig editor.
Improved file association.
Improved Assemble to reference.
Improved log window.
Improved file handling: Before starting the contig, check if all files in the JobList are valid. Invalid samples are automatically removed from Job List so the assembly process can continue without human intervention. Build a list of invalid files and report it.
Improved user interface: new toolbar, improved embedded help, interactive help, workflow...
Improved sample viewer: Mark as trusted/un-trusted can now be used also in Sample viewer window
New: Show error message while trying to open empty/invalid FASTA files
Improved: Correctly handle multiple contigs resulted when assembling to a reference.
Improved: menu Save as Fasta/Seq/Scf was replaced with Save all as... and Save selected as.... Now the user can choose where to save the file.
Version 2.10
Batch assembly. Thousand of contigs can be assembled at once.
System Requirements:CPU: 333MHz, 64MB RAM, Video 1024x768, 2MB HDD free space<<less
MKDoc::Text::Structured::Inline 0.83
MKDoc::Text::Structured::Inline is a Perl module to convert text to HTML without handling block-level tags. more>>
SYNOPSIS
my $text = some_structured_text();
my $this = MKDoc::Text::Structured::Inline::process ($text);
my $that = MKDoc::Text::Structured::Inline::process_entities_only ($text);
IRCTree 0.10
IRCTree is a project which shows a tree representing the structure of an IRC network in ASCII. more>>
Introduction
IRCTree shows a tree in ascii format representing the structure of an
IRC network.
You need netcat (nc) for it to work.
Example uses
$ irctree irc.swipnet.se
Compiling
No need to compile, but you can copy it into /usr/local/bin with make install.
Image::MetaData::JPEG::Structures 0.15
Image::MetaData::JPEG::Structures is a Perl module that describes the structure of a JPEG file. more>>
THE STRUCTURE OF JPEG PICTURES
The JPEG (Joint Photographic Experts Group) ISO standard is a lossy image compression mechanism developed before 1990, designed for compressing colour or gray-scale photo-realistic images (it performs poorly on line-art drawings). The JPEG mechanism is designed to exploit known limitations of the human eye, in particular the fact that colour changes are perceived less accurately than changes in brightness.
Note that although the "baseline" JPEG format is patent-free, there are patents associated with some optional features, namely arithmetic coding and hierarchical storage. For this reason, these optional features are never used on the Web (good job, patent fans ...). JPEG refers only to a class of compression algorithms, not to a specific file format. In order to produce files with embedded JPEG streams, a number of file format (semi-)standards have been adapted or devised, some of which are listed in the format section. The structure of a well formed JPEG file can be described by the following pseudo production rules (for sake of simplicity, some additional constraints between tables and SOF segments are neglected).
JPEG --> (SOI)(misc)*(image)?(EOI)
(image) --> (hierarch.)|(non-hier.)
(hierarch.) --> (DHP)(frame)+
(frame) --> (misc)*(EXP)?(non-hier.)
(non-hier.) --> (SOF)(scan)+
(scan) --> (misc)*(SOS)(data)*(ECS)(DNL)?
(data) --> (ECS)(RST)
(misc) --> (DQT)|(DHT)|(DAC)|(DRI)|(COM)|(APP)
(SOI) = Start Of Image
(EOI) = End Of Image
(SOF) = Start Of Frame header (10 types)
(SOS) = Start Of Scan header
(ECS) = Entropy Coded Segment (row data, not a real segment)
(DNL) = Define Number of Lines segment
(DHP) = Define Hierarchical P??? segment
(EXP) = EXPansion segment
(RST) = ReSTart segment (8 types)
(DQT) = Define Quantisation Table
(DHT) = Define Huffman coding Table
(DAC) = Define Arithmetic coding Table
(DRI) = Define Restart Interval
(COM) = COMment segment
(APP) = APPlication segment
This package does not check that a JPEG file is really correct; it accepts a looser syntax, were segments and ECS blocks are just contiguous (basically, because it does not need to display the image!). All meta-data information is concentrated in the (COM*) and (APP) Segments, exception made for some records in the (SOF*) segment (e.g. image dimensions).
Reference: B< "Digital compression and coding of continuous-tone still
images: requirements and guidelines", CCITT recommend. T.81, 1992,
The International Telegraph and Telephone Consultative Committee,
standard ISO/IEC IS 10918-1 or ITU-T Recommendation T.81 >.
Also: B< "The JPEG still picture compression standard", G.K.Wallace,
1991, IEEE Transactions on Consumer Electronics >.
Structured Document Validator 0.7.9
Structured Document Validator project implements a generalized method for structured documents. more>>
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.
Rubytree 0.2.4
Rubytree is a simple to use general purpose tree data structure implementation in Ruby. more>>
It provides easy access methods for navigating the hierarchy, as well as for accessing the nodes. Rubytree project also provides ability to marshal the entire tree structure.
Enhancements:
- Minor changes were made to the documentation.
