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

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

public class MegablastTaskEngine
extends java.lang.Object
implements TaskEngine

This engine performs a MegaBLAST operation on the FileTaskData (which contains sequence(s)).


Constructor Summary
MegablastTaskEngine()
           
 
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.
 void process(TaskControl task, TaskData data, TaskManagerRMIServer tm)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MegablastTaskEngine

public MegablastTaskEngine()
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

process

public void process(TaskControl task,
                    TaskData data,
                    TaskManagerRMIServer tm)

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.