apollo.analysis
Class GenericProgramHandler

java.lang.Object
  apollo.analysis.GenericProgramHandler

All Implemented Interfaces:

ProgramHandlerI

Direct Known Subclasses:

BlastHandler

public class GenericProgramHandler
extends java.lang.Object
implements ProgramHandlerI

Constructor Summary

GenericProgramHandler()

Method Summary

java.lang.String	createUnixShellCommand(SeqAnalysisLocal seqAnalysis) different analysis programs require different ways of running them assumes a command line is made by programPath programParams inputSequence [datasourcePath]
CurationSet	parseAnalysisResults(SeqAnalysisI seqAnalysis) different programs must be parsed differently implementations may also choose to also filter the results in some configurable way.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenericProgramHandler

public GenericProgramHandler()

Method Detail

createUnixShellCommand

public java.lang.String createUnixShellCommand(SeqAnalysisLocal seqAnalysis)

different analysis programs require different ways of running them assumes a command line is made by programPath programParams inputSequence [datasourcePath]

Specified by:

createUnixShellCommand in interface ProgramHandlerI

parseAnalysisResults

public CurationSet parseAnalysisResults(SeqAnalysisI seqAnalysis)

different programs must be parsed differently implementations may also choose to also filter the results in some configurable way. it is up to the individual implementations to respect these

Specified by:

parseAnalysisResults in interface ProgramHandlerI