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Biskit
Package Biskit :: Package Mod :: Module AlignerMaster :: Class AlignerMaster
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Class AlignerMaster

source code

Instance Methods [hide private]
  __init__(self, hosts, folders, pdbFolder=None, fastaTemplates=None, fastaSequences=None, fastaTarget=None, ferror=None, verbose=1, **kw)
  __dir_or_none(self, folder, filename)
{{str}} setupJobs(self)
Prepare the job dictionnary for 'AlignerSlave'
{param:value} getInitParameters(self, slave_tid)
Hand over parameters to slave once.
  cleanup(self)
Called after exit.
  done(self)
Called by finish() after exit(), cleanup(), and reportProgress(), but before thread notification (notifyAll() ) and before executing the callBack method.

Inherited from PVM.TrackingJobMaster.TrackingJobMaster: calculateResult, finish, getResult, getRst, hostnameFromTID, is_valid_slave, job_done, mark_slow_slaves, notifyAll, reportProgress, saveRst, setCallback, setRst, start_job

Inherited from PVM.dispatcher.JobMaster: bindMessages, get_slave_chunk, initializationDone, spawn, spawnAll, start

Inherited from PVM.PVMThread.PVMMasterSlave: exit, initialize, messageLoopIsUp, startMessageLoop

Inherited from PVM.PVMThread.PVMThread: bind, getBindings, getMessageLoopDelay, getParent, getPingTimeout, getTID, getTasks, isStopped, log, messageLoopIsStopped, nicknameFromTID, ping, post, post_execute_method, post_message_received, post_message_sent, rm_log, run, send, sendToAll, send_primitive, setMessageLoopDelay, setPingTimeout, stop, stopMessageLoop, unbind

Inherited from PVM.PVMThread.PVMThread (private): _ping

Inherited from threading.Thread: __repr__, getName, isAlive, isDaemon, join, setDaemon, setName

Inherited from threading.Thread (private): _set_daemon

Inherited from threading._Verbose (private): _note

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __str__


Class Variables [hide private]
  slave_script = projectRoot()+ '/Biskit/Mod/AlignerSlave.py'

Properties [hide private]

Inherited from object: __class__


Method Details [hide private]

__init__(self, hosts, folders, pdbFolder=None, fastaTemplates=None, fastaSequences=None, fastaTarget=None, ferror=None, verbose=1, **kw)
(Constructor)

source code 
Parameters:
  • hosts ([str]) - list of host-names
  • folders ([str]) - list of project directories (path)
  • pdbFolder (str) - pdb directory (*.alpha for Aligner)
  • fastaTemplates (str) - path to find 'templates.fasta'
  • fastaSequences (str) - path to find 'nr.fasta'
  • fastaTarget (str) - path to find 'target.fasta'
  • ferror (str) - filename to output errors from the Slave
  • verbose (1|0) - verbosity level (default: 1)
  • kw (param=value) - additional TrackingJobMaster arguments: 
       chunk_size   - int, number of items that are processed per job
   niceness     - {str_host-name: int_niceness}
   slave_script - str, absolute path to slave-script
   show_output  - 1|0, display one xterm per slave [0]
   add_hosts    - 1|0, add hosts to PVM before starting [1]
Overrides: PVM.TrackingJobMaster.TrackingJobMaster.__init__

__dir_or_none(self, folder, filename)

source code 

setupJobs(self)

source code 

Prepare the job dictionnary for 'AlignerSlave'
Returns: {{str}}
input informations for aligner for each project

getInitParameters(self, slave_tid)

source code 

Hand over parameters to slave once.
Parameters:
  • slave_tid (int) - slave task id
Returns: {param:value}
dictionary with init parameters
Overrides: PVM.dispatcher.JobMaster.getInitParameters

cleanup(self)

source code 

Called after exit. Override.
Overrides: PVM.TrackingJobMaster.TrackingJobMaster.cleanup
(inherited documentation)

done(self)

source code 

Called by finish() after exit(), cleanup(), and reportProgress(), but before thread notification (notifyAll() ) and before executing the callBack method. Override.
Overrides: PVM.TrackingJobMaster.TrackingJobMaster.done
(inherited documentation)

Class Variable Details [hide private]

slave_script

Value:
projectRoot()+ '/Biskit/Mod/AlignerSlave.py'

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