apollo.dataadapter.genbank
Class GenbankValidator

java.lang.Object
  apollo.dataadapter.genbank.GenbankValidator

public class GenbankValidator
extends java.lang.Object

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

GenbankValidator()

Method Summary

java.lang.String	addNote(java.lang.String except, PeptideNote patch)
void	checkCuration(CurationSet curation, java.io.DataOutputStream report) Writing G
protected java.lang.String	checkFeature(FeatureSetI fs, java.lang.String type, java.lang.String prefix)
java.lang.String	getDatabase()
java.lang.String	getException(Transcript transcript)
int	getExceptPos(PeptideNote patch)
java.lang.String	getGenotype()
java.lang.String	getOrganism()
java.lang.String	getTech()
protected java.lang.String	getTranslExcept(Transcript transcript, int offset)
java.util.Vector	getXrefs()
java.lang.String	patchPeptideCheck(AnnotatedFeatureI gene, Transcript transcript, java.lang.String header, java.io.DataOutputStream report)
protected java.lang.String	sameName(SeqFeatureI sf, SeqFeatureI test, java.lang.String prefix)
protected boolean	sameName(java.lang.String name, SeqFeatureI test)
boolean	setValidationFile(java.lang.String valid_filename)

Methods inherited from class java.lang.Object

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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

GenbankValidator

public GenbankValidator()

Method Detail

setValidationFile

public boolean setValidationFile(java.lang.String valid_filename)

getDatabase

public java.lang.String getDatabase()

getXrefs

public java.util.Vector getXrefs()

getTech

public java.lang.String getTech()

getOrganism

public java.lang.String getOrganism()

getGenotype

public java.lang.String getGenotype()

checkCuration

public void checkCuration(CurationSet curation,
                          java.io.DataOutputStream report)

Writing G

checkFeature

protected java.lang.String checkFeature(FeatureSetI fs,
                                        java.lang.String type,
                                        java.lang.String prefix)

sameName

protected boolean sameName(java.lang.String name,
                           SeqFeatureI test)

sameName

protected java.lang.String sameName(SeqFeatureI sf,
                                    SeqFeatureI test,
                                    java.lang.String prefix)

patchPeptideCheck

public java.lang.String patchPeptideCheck(AnnotatedFeatureI gene,
                                          Transcript transcript,
                                          java.lang.String header,
                                          java.io.DataOutputStream report)

addNote

public java.lang.String addNote(java.lang.String except,
                                PeptideNote patch)

getExceptPos

public int getExceptPos(PeptideNote patch)

getTranslExcept

protected java.lang.String getTranslExcept(Transcript transcript,
                                           int offset)

getException

public java.lang.String getException(Transcript transcript)