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)