org.genepi.means
Class TinaShell

java.lang.Object
  extended by org.genepi.Task
      extended by org.genepi.means.TinaShell
All Implemented Interfaces:
FeatureHandler
Direct Known Subclasses:
Blastp, Blastx, FastRna, ProkovCds, ProkovCds2, ProkovLearn, ProkovOrf, RbsFinder, Termit

public abstract class TinaShell
extends Task
implements FeatureHandler


Field Summary
protected  geno.core.util.tasks.GCTinaCommand cmd
           
protected  boolean isFramed
           
protected  java.util.Iterator itResults
           
protected  java.lang.String progName
           
protected  HSequence seqMother
           
protected  java.lang.String shellCommand
           
 
Fields inherited from class org.genepi.Task
inputs, outputs
 
Constructor Summary
TinaShell()
           
 
Method Summary
 void execute()
          Implementation du comportement du moyen.
protected abstract  void extractRecords()
           
 void featureReady(int from, int to, boolean sens, java.util.Hashtable annot)
          Cette methode est appelee par le parser pour recevoir le feature.
protected abstract  void prepare()
           
protected abstract  void setScriptName()
           
 
Methods inherited from class org.genepi.Task
afterExec, beforeExec, flush, getConfiguration, getInputs, getOutputs, getOwningKS, message, process, setConfiguration, setInputs, setOwningKS
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

shellCommand

protected java.lang.String shellCommand

progName

protected java.lang.String progName

cmd

protected geno.core.util.tasks.GCTinaCommand cmd

itResults

protected java.util.Iterator itResults

seqMother

protected HSequence seqMother

isFramed

protected boolean isFramed
Constructor Detail

TinaShell

public TinaShell()
Method Detail

execute

public void execute()
             throws MeanException
Description copied from class: Task
Implementation du comportement du moyen.

Specified by:
execute in class Task
Throws:
MeanException

featureReady

public void featureReady(int from,
                         int to,
                         boolean sens,
                         java.util.Hashtable annot)
Description copied from interface: FeatureHandler
Cette methode est appelee par le parser pour recevoir le feature.

Specified by:
featureReady in interface FeatureHandler

prepare

protected abstract void prepare()

extractRecords

protected abstract void extractRecords()

setScriptName

protected abstract void setScriptName()