edu.mssm.crover.ims.tasks.engines
Class MaskSequenceTaskEngine

java.lang.Object
  |
  +--edu.mssm.crover.ims.tasks.engines.MaskSequenceTaskEngine
All Implemented Interfaces:
TaskEngine

public class MaskSequenceTaskEngine
extends java.lang.Object
implements TaskEngine

This engine masks FASTA sequences from a file using the scylla command.


Constructor Summary
MaskSequenceTaskEngine()
           
 
Method Summary
 void copy(java.io.File from, java.io.File dest)
           
 void copy(java.io.InputStream is, java.io.File dest)
           
 boolean installed(java.lang.String cmdPath, java.lang.String execName)
          Checks if the command is installed on this machine.
 void process(TaskControl task, TaskData data)
          Each TaskEngine implements this method to define how to process a type of task.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MaskSequenceTaskEngine

public MaskSequenceTaskEngine()
Method Detail

process

public void process(TaskControl task,
                    TaskData data)
Description copied from interface: TaskEngine
Each TaskEngine implements this method to define how to process a type of task.

Specified by:
process in interface TaskEngine

installed

public boolean installed(java.lang.String cmdPath,
                         java.lang.String execName)
Checks if the command is installed on this machine. Check to see if /home/icb/softs/blast/megablast (or blast.executable.path/megablast.executable.name)

Returns:
True when megablast is installed on the machine, False otherwise.

copy

public void copy(java.io.InputStream is,
                 java.io.File dest)

copy

public void copy(java.io.File from,
                 java.io.File dest)


Copyright @ 2003 Mount Sinai School of Medicine. All Rights Reserved.