org.genepi.means
Class TinaShell
java.lang.Object
org.genepi.Task
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
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 |
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
TinaShell
public TinaShell()
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()