Free suffix trees software for linux

Suffix tree implementation library is a C library, an implementation of the suffix trees algorithm to store/retrieve key/data pairs.
The main advantages are a linear indexing time, little memory usage, and very fast retrieving.
It has been developped on FreeBSD/gcc but should be fairly portable.
The source code "testsfx.c" show an example of how to use the library both for inserting, retrieving, and deleting data. There arent many functions and comments should be enough to give you an idea of how to use the library. (read the header of the source file)
You should edit sfxdisk.h to suit your needs: you can change the alphabet size and the offset type. It should be OK to use "long long" 64 bits ints instead of long, in fact I tested it succesfully but havent gone to the point of filling more than 2 GB of data (needless to say you need a 64 bits filesystem).
Two "tools" come with the library (new with version 1.2): dumpsfx and loadsfx. dumpsfx is used to dump the database: dumpsfx [-s separator] if you want to output the result as readable text or dumpsfx < file.sfx > -h to output it for reloading with loadsfx.
dumpsfx outputs on stdout and loadsfx reads from stdin. loadsfx < suffix tree file to create > < dumped_file
Enhancements:
- removed an useless offset incrementation in STwritenode

glastree application builds live backup trees, with branches for each day. Users directly browse the past to recover older documents or retrieve lost files. Hard links serve to compress out unchanged files, while modified ones are copied verbatim. A prune utility effects a constant, sliding window.

DBIx::OO::Tree is a Perl module to manipulate hierarchical data using the "nested sets" model.

SYNOPSYS

CREATE TABLE Categories (
id INTEGER UNSIGNED AUTO_INCREMENT PRIMARY KEY,
label VARCHAR(255),

-- these columns are required by DBIx::OO::Tree
parent INTEGER UNSIGNED,
lft INTEGER UNSIGNED NOT NULL,
rgt INTEGER UNSIGNED NOT NULL,
mvg TINYINT DEFAULT 0,

INDEX(lft),
INDEX(rgt),
INDEX(mvg),
INDEX(parent)
);

* * *

package Category;
use base DBIx::OO;
use DBIx::OO::Tree;

__PACKAGE__->table(Categories);
__PACKAGE__->columns(P => [ id ],
E => [ label, parent ]);

# note its not necessary to declare lft, rgt, mvg or parent. We
# declare parent simply because it might be useful, but
# DBIx::OO:Tree works with low-level SQL therefore it doesnt
# require that the DBIx::OO object has these fields.

# the code below creates the structure presented in [1]

my $electronics = Category->tree_append({ label => electronics });
my $tvs = $electronics->tree_append({ label => televisions });
my $tube = $tvs->tree_append({ label => tube });
my $plasma = $tvs->tree_append({ label => plasma });
my $lcd = $plasma->tree_insert_before({ label => lcd });
my $portable = $tvs->tree_insert_after({ label => portable electronics });
my $mp3 = $portable->tree_append({ label => mp3 players });
my $flash = $mp3->tree_append({ label => flash });
my $cds = $portable->tree_append({ label => cd players });
my $radios = Category->tree_append($portable->id,
{ label => 2 way radios });

# fetch and display a subtree

my $data = $electronics->tree_get_subtree({
fields => [qw( label lft rgt parent )]
});
my $levels = Category->tree_compute_levels($data);

foreach my $i (@$data) {
print x $levels->{$i->{id}}, $i->{label}, "n";
}

## or, create DBIx::OO objects from returned data:

my $array = Category->init_from_data($data);
print join("n", (map { x $levels->{$_->id} . $_->label } @$array));

# display path info

my $data = $flash->tree_get_path;
print join("n", (map { $_->{label} } @$data));

# move nodes around

$mp3->tree_reparent($lcd->id);
$tvs->tree_reparent($portable->id);
$cds->tree_reparent(undef);

$plasma->tree_move_before($tube->id);
$portable->tree_move_before($electronics->id);

# delete nodes

$lcd->tree_delete;

This module is a complement to DBIx::OO to facilitate storing trees in database using the "nested sets model", presented in [1]. Its main ambition is to be extremely fast at retrieving data (sacrificing for this the performance of UPDATE-s, INSERT-s or DELETE-s). Currently this module requires you to have these columns in the table:

- id: primary key (integer)
- parent: integer, references the parent node (NULL for root nodes)
- lft, rgt: store the node position
- mvg: used only when moving nodes

"parent" and "mvg" are not esentially required by the nested sets model as presented in [1], but they are necessary for this module to work. In particular, "mvg" is only required by functions that move nodes, such as tree_reparent(). If you dont want to move nodes around you can omit "mvg".

Retrieval functions should be very fast (one SQL executed). To further promote speed, they dont return DBIx::OO blessed objects, but an array of hashes instead. Its easy to create DBIx::OO objects from these, if required, by calling DBIx::OO->init_from_data() (see DBIx::OO for more information).

Insert/delete/move functions, however, need to ensure the tree integrity. Heres what happens currently:

- tree_append, tree_insert_before, tree_insert_after -- these execute
one SELECT and two UPDATE-s (that potentially could affect a lot of
rows).

- tree_delete: execute one SELECT, one DELETE and two UPDATE-s.

- tree_reparent -- executes 2 SELECT-s and 7 UPDATE-s. I know, this
sounds horrible--if you have better ideas Id love to hear them.

Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file.

SYNOPSIS

if ( $type =~ /trees/i ) {
$block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose );
}

If a NEXUS block is a Trees Block, this module parses the block and stores the tree data.

METHODS

new

Title : new
Usage : block_object = new Bio::NEXUS::TreesBlock($block_type, $commands, $verbose );
Function: Creates a new Bio::NEXUS::TreesBlock object and automatically reads the file
Returns : Bio::NEXUS::TreesBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)

clone

Title : clone
Usage : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args : none

set_trees

Title : set_trees
Usage : $block->set_trees($trees);
Function: Sets the list of trees (Bio::NEXUS::Tree objects)
Returns : none
Args : ref to array of Bio::NEXUS::Tree objects

add_tree

Title : add_tree
Usage : $block->add_tree($tree);
Function: Add trees (Bio::NEXUS::Tree object)
Returns : none
Args : a Bio::NEXUS::Tree object

add_tree_from_newick

Title : add_tree_from_newick
Usage : $block->add_tree_from_newick($newick_tree, $tree_name);
Function: Add a tree (Bio::NEXUS::Tree object)
Returns : none
Args : a tree string in newick format and a name for the tree (scalars)

get_trees

Title : get_trees
Usage : $block->get_trees();
Function: Gets the list of trees (Bio::NEXUS::Tree objects) and returns it
Returns : ref to array of Bio::NEXUS::Tree objects
Args : none

get_tree

Title : get_tree
Usage : $block->get_tree($treename);
Function: Gets the first tree (Bio::NEXUS::Tree object) that matches the name given or the first tree if $treename is not specified. If no tree matches, returns undef.
Returns : a Bio::NEXUS::Tree object
Args : tree name or none

set_translate

Title : set_translate
Usage : $block->set_translate($translate);
Function: Sets the hash of translates for nodes names
Returns : none
Args : hash of translates

translate

Title : translate
Usage : $self->translate($num);
Function: Translates a number with its associated name.
Returns : integer or string
Args : integer
Method : Returns the name associated with that numbers translated name.
If it cant find an association, returns the number.

reroot_tree

Title : reroot_tree
Usage : $block->reroot_tree($outgroup,$root_position, $treename);
Function: Reroot a tree using an OTU as new outgroup.
Returns : none
Args : outgroup name, the distance before the root position and tree name

reroot_all_trees

Title : reroot_all_trees
Usage : $block->reroot_all_trees($outgroup, $root_position);
Function: Reroot all the trees in the treesblock tree. use an OTU as new outgroup
Returns : none
Args : outgroup name and root position

rename_otus

Title : rename_otus
Usage : $block->rename_otus(%translation);
Function: Renames nodes based on a translation hash
Returns : none
Args : hash containing translation (e.g., { old_name => new_name} )
Comments: nodes not included in translation hash are unaffected

select_otus

Name : select_otus
Usage : $nexus->select_otus(@otunames);
Function: select a subset of OTUs
Returns : a new nexus object
Args : a ref to array of OTU names

select_tree

Name : select_tree
Usage : $nexus->select_tree($treename);
Function: select a tree
Returns : a new nexus object
Args : a tree name

select_subtree

Name : select_subtree
Usage : $nexus->select_subtree($inodename);
Function: select a subtree
Returns : a new nexus object
Args : an internal node name for subtree to be selected

exclude_subtree

Name : exclude_subtree
Usage : $nexus->exclude_subtree($inodename);
Function: remove a subtree
Returns : a new nexus object
Args : an internal node for subtree to be removed

equals

Name : equals
Usage : $nexus->equals($another);
Function: compare if two NEXUS objects are equal
Returns : boolean
Args : a NEXUS object

mod_domaintree is a hostname to filesystem mapper for Apache2. It maps host names like www.example.com to a filesystem tree like $prefix/com/example/www/$suffix.
mod_domaintree module can optionally strip the www prefix of host names.
Enhancements:
- The suexec hook and DomainTreeSuexec directory configuration directive were added.
- "make clean" was fixed.

kdtree project is a simple C library for working with KD-Trees.
Kd-trees are an extension of binary search trees to k-dimensional data. They facilitate very fast searching, and nearest-neighbor queries.
This particular implementation is designed to be efficient and very easy to use. It is completely written in ANSI/ISO C, and thus completely cross-platform.
Enhancements:
- This release fixes both reported bugs, and adds a contributed, more extensive, and well commented example program.

SILC Autodist is a program which is used to manage and create source distributions.

The Autodist is a source distribution management system that allows powerful mechanisms to define what is included in and excluded from a distribution, and what license the distribution is released under. It is also used to create the actual distribution source packages. Autodist allows distribution management in file, directory and file content level. Different distributions may include different portions of files, for example, excluding certain features from certain distributions. It is always guaranteed that anything not defined for the distribution, is removed automatically (files, file content, directories), thus ensuring that nothing is accidentally included in the distribution.

The Autodist creates Makefile.am files from Makefile.ad files and configure.ac file from one or more configure.ad files. Any other file ending with .ad suffix will also be processed. The processed file will have the .ad suffix removed (see Preparing source tree). Autodist also creates and packages the distribution using common GNU distribution creation process, specificly `make dist. Autodist, however, controls this process and during packaging phase the Autodist processes all files in the distribution (other than *.ad files, which has already been processed earlier by Autodist). The resulted package is a processed source distribution package, processed according to the rules specified in the distribution file(s) (see Creating distribution).

Any file in the source tree may use distdefs (distribution defines (see Distdefines)) which are defined in the distributions. When distribution is packaged only the files, directories and file content that is either outside of any distdef, or inside the defined distdefs will be included in the distribution. Any other file, directory or content in the file will be removed. It is guaranteed, if a file, a directory or a piece of file content is not inside a defined distdef it will not be delivered to the distribution.

Any file, Makefile.am, configure.ac, or source file processed with Autodist is always compliant with the tools needed to process them. All files can also be processed with the corresponding tools even before processing them with Autodist. This makes it possible, for example, to compile sources before they have been processed, and undefined lines are removed. The distdefs are respected in source files by the preprocessor.

Autodist is not a binary packaging system. It is specificly used to create source distributions. A binary packaging system, however can be hooked to the distribution creation process, if needed.