Free pipe software for linux

GTK-server enables access for shellscripts & interpreted programming languages to apps using either GTK 1.x or 2.x.

GTK-server project is a standalone binary, which is able to communicate by a 2-way pipe or by a TCP/UDP port. The script invokes this binary, sets up a pipe or a TCP/UDP connection and prints the GTK call in plain text to the pipe or socket. The GTK-server then sends information back which can be used in the program or script.

Below a summary of advantages when using the GTK-server:

- No need to learn C or C++, you can stick to your favorite programming language
- No need to hack the source of existing programming languages to realize GUI programming
- High flexibility in creating GUIs, e.g. not limited to dialogs
- Full GTK API available, the user can extend the gtk-server.cfg file by himself
- Access to both GTK 1.x and GTK 2.x
- Convenient GTK test tool, easy to learn GTK programming.

Fetch and deliver mail is a simple, lightweight replacement for mail fetching, filtering, and delivery programs such as fetchmail and procmail.
It can fetch using POP3, POP3S, IMAP, IMAPS, or stdin, and deliver to a pipe, file, maildir, mbox, or SMTP server, based on a set of regexps.
Fetch and deliver mail can be used for both single user and multiuser setups, and is designed with privilege separation when running as root.
Enhancements:
- Mostly configuration file enhancements and code cleanup were done since 1.2. ifdef/endif blocks and inline shell commands are allowed in the configuration file.
- A built-in string cache using TDB was added.
- Some extra default tags were added. NNTPS fetching was implemented.

alph implements and analyzes historical and traditional ciphers and codes, such as polyalphabetic, susbstitutional, and mixed employing human-reconstructable algorithms.
alph project provides a pipe filter interface in order to encrypt and decrypt block text to acheive transparency.
The program is meant to be used in conjunction with external programs that transfer data, resulting in transparent encryption or decryption of information.
The program can thus be used as a mail filter, IRC filter, IM filter, and so on.
The program can be conjuncted with pipes reulting in transparent en-decrypt: Atbash, Caesar, Vigenere, Playfair, Vernam.
Enhancements:
- Warnings for unstable cyphers have been added as well as the possibility to unscramble words based on a dictionary file.
- The tools section has been altered to accept pipe strings instead of file operations.

Astro::Aladin::LowLevel is a Perl class designed to drive CDS Aladin Application.

SYNOPSIS

my $aladin = new Astro::Aladin::LowLevel( );

Drives the CDS Aladin Application through a anonymous pipe, expects the a copy of the standalone Aladin application to be installed locally and pointed to by the ALADIN_JAR environment variable.

REVISION

$Id: LowLevel.pm,v 1.2 2003/02/24 22:45:56 aa Exp $

METHODS

Constructor

new

Create a new instance from a hash of options

$aladin = new Astro::Aladin::LowLevel( );

returns a reference to an Aladin object.

Accessor Methods

close

Closes the anonymous pipe to the aladin application

$aladin->close();

it should be noted that if you DONT do this after finishing with the object youre going to have zombie Java VM hanging around eating up all your CPU. This is amougst the many reasons why you should use Astro::Aladin rather than Astro::Aladin::LowLevel to drive the Aladin Application.

reopen

Reopen the anonymous pipe to the aladin application

my $status = $aladin->reopen()

returns undef if the pipe if defined and (presumably) already active.

status

Prints out the status of the current stack.

$aladin->status()

sync

Waits until all planes are ready

$aladin->sync()

export

Export a plane to a file

$aladin->sync( $plane_number, $filename )

get

Gets images and catalogues from the server

$aladin->get( $server, @args, $object, $radius );
$aladin->get( $server, $object );

For example

$aladin->get( "aladin", ["DSS1"], $object_name, $radius );
$aladin->get( "aladin", ["DSS1", "LOW"], $object_name, $radius );
$aladin->get( "aladin", [""], $object_name, $radius );

the radius arguement can be omitted

$aladin->get( "aladin", ["DSS1"], $object_name );

or even more simply

$aladin->get( "simbad", $object_name );

always remember to sync after a series of request, or you might end up closing Aladin before its actually finished download the layers.

HTTunnel::Client is a client class for Apache::HTTunnel.

SYNOPSIS

my $hc = new HTTunnel::Client("http://localhost/httunnel") ;
$hc->connect(tcp, $some_host, $some_port) ;

$hc->print(some request) ;
my $some_response = $hc->read(1024) ;

$ch->close() ;

HTTunnel::Client is the client class to Apache::HTTunnel. It allows the creation of a network connection tunnelled through HTTP. All data sent and received during this connection will be transported inside normal HTTP requests.

HTTunnel::Client extends LWP::UserAgent, so all LWP::UserAgent methods are available through HTTunnel::Client.

CONSTRUCTORS

new ( URL, [ARGS] )

Creates an HTTunnel::Client object that will use URL to contact the Apache::HTTunnel server. ARGS are is passed directly to the LWP::UserAgent constructor.

METHODS

connect ( PROTO, HOST, PORT, [TIMEOUT] )

Asks the Apache::HTTunnel server to establish a connection of protocol PROTO to HOST:PORT. An exception is thrown if an error occurs.

Accepted values for PROTO are tcp and udp.

print ( DATA )

Asks the Apache::HTTunnel server to write DATA to the established remote connection. An exception is thrown if an error occurs.
DATA can be a scalar or a list, in which case the list items are concatenated together.

read ( LEN, [TIMEOUT], [LIFELINE], [LIFELINE_CUT_ACTION] )

Asks the Apache::HTTunnel server to read up to LEN bytes from the established remote connection. An exception is thrown if an error occurs.

When trying to read, HTTunnel::Client will establish an HTTP connection to the Apache::HTTunnel server asking that LEN bytes be read. If no data is available after TIMEOUT seconds (the default value is 15 seconds), the HTTP connection is closed by the server and the read method will establish a new one. This will go on until some data or EOF is returned.

Therefore read will return only when some (or no more) data is available to be read (like the regular read).

LIFELINE can be any valid filehandle from which one can read. If used, read will interrupt its connection loop and execute LIFELINE_CUT_ACTION when data (or EOF) is available to be read from LIFELINE. It will then return undef.
LIFELINE_CUT_ACTION wust be a CODE ref. The default value is

sub {die("lifeline cutn")}

These features can be used if you want fork and to start a process that does nothing but reads and returns the data via a pipe. You can then use a second pipe to make sure the reader process terminates when the master process terminates.

Here is an example:

my $lifeline = new IO::Pipe() ;
my $reader = new IO::Pipe() ;
my $pid = fork() ;
if ($pid){
$reader->reader() ;
$lifeline->writer() ;

# Read data from $reader...
}
else {
$reader->writer() ;
$reader->autoflush(1) ;
$lifeline->reader() ;

while (1){
my $data = $hc->read(1024, 15, $lifeline, sub {exit()}) ;
exit() unless defined($data) ;
print $reader $data ;
}
}
close ( )

Asks the Apache::HTTunnel server to close a previously established connection.
get_peer_info ( )

The get_peer_info method returns information about the remote connection. A string containing the IP address and port number, separated by a colon (:) is returned. This method can be useful with UDP connections to validate the sender of each packet.

request_callback ( REQUEST )

The request_callback method is a callback method that can be used to access the HTTP::Request object just before it is sent. The default implementation does nothing.

response_callback ( RESPONSE )

The response_callback method is a callback method that can be used to access the HTTP::Response object just after it is received. The default implementation does nothing.

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 (Excl)
Nucleotid Database

break_long (Integer)
Break long library sequences into blocks (-N)

ktup (Integer)
ktup : sensitivity and speed of the search (protein:2, DNA:6)

optcut (Integer)
OPTCUT : the threshold for optimization. (-c)

gapinit (Integer)
Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f)

gapext (Integer)
Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g)

high_expect (Float)
Maximal expectation value threshold for displaying scores and alignments (-E)

low_expect (Float)
Minimal expectation value threshold for displaying scores and alignments (-F)

nucleotid_match (Integer)
Reward for a nucleotid match (-r)

nucleotid_mismatch (Integer)
Penalty for a nucleotid mismatch (-r)

matrix (Excl)
Scoring matrix file (-s)

X_penalty (Integer)
Penalty for a match to X (independently of the PAM matrix) (-x)

frameshift (Integer)
Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h)

frameshift_within (Integer)
Penalty for frameshift within a codon (fasty/tfasty)(-j)

threeframe (Switch)
Search only the three forward frames (tfasta) (-3)

invert (Switch)
Reverse complement the query sequence (all tfasta) (-i)

genetic_code (Excl)
Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)

band (Integer)
band-width used for optimization (-y)

swalig (Switch)
unlimited Smith-Waterman alignment for DNA (-A)

noopt (Switch)
no limited optimization (-o)

stat (Excl)
Specify statistical calculation. (-z)

random (Switch)
Estimate stat parameters from shuffled copies of each library sequence (-z)

histogram (Switch)
No histogram (-H)

scores (Integer)
number of similarity scores to be shown (-b)

alns (Integer)
number of alignments to be shown (-d)

html_output (Switch)
HTML output (-m)

markx (Excl)
Alternate display of matches and mismatches in alignments

init1 (Switch)
sequences ranked by the z-score based on the init1 score (-1)

z_score_out (Excl)
Show normalize score as (-B)

showall (Switch)
both sequences are shown in their entirety in alignments (fasta only) (-a)

linlen (Integer)
output line length for sequence alignments (max. 200) (-w)

offsets (String)
Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X)

info (Switch)
Display more information about the library sequence in the alignment (-L)

statfile (OutFile)
Write out the sequence identifier, superfamily number, and similarity scores to this file (-R)

filter (Switch)
Lower case filtering (-S)

outfile (OutFile)
pipe: mview_input

html_outfile (OutFile)