apollo.config
Class TigrSybilNameAdapter

java.lang.Object
  apollo.config.DefaultNameAdapter
      apollo.config.TigrSybilNameAdapter

All Implemented Interfaces:

ApolloNameAdapterI

public class TigrSybilNameAdapter
extends DefaultNameAdapter

TIGR-specific apollo name adapter for Chado. It appears to be necessary to have one of these in order to link to outside URLs from the genes/transcripts in Apollo (despite the specification of a gene URL in the tiers file.) Annotated features appear to be handled differently than computed features (called "Results" in Apollo) in this respect.

Version:

$Revision: 1.2 $ $Date: 2007-01-03 13:50:07 $ $Author: jcrabtree $

Author:

Jonathan Crabtree

Field Summary

protected java.util.regex.Pattern	geneIdPattern Regular expression pattern used to parse a gene's ID from the chado uniquename.
protected static org.apache.log4j.Logger	logger

Constructor Summary

TigrSybilNameAdapter()

Method Summary

java.lang.String

generateURL(AnnotatedFeatureI g)

Methods inherited from class apollo.config.DefaultNameAdapter

addSynonym, checkFormat, checkName, generateAnnotSplitName, generateChadoCdsIdFromTranscriptId, generateChadoCdsNameFromTranscriptName, generateExonId, generateId, generateName, generateName, generateNewExonId, generateNewId, generatePeptideIdFromTranscriptId, generatePeptideNameFromTranscriptName, getNewIdFromTypeChange, getSuffixDelimiter, getTransactionManager, getTranscriptNamePattern, idAndNameHaveSameFormat, isTemp, isTemp, match, nameIsId, nextAnnotNumber, setAnnotId, setAnnotName, setDataAdapter, setId, setName, setTransactionManager, setTranscriptId, setTranscriptName, setTranscriptNameFromAnnot, skipUsedTempNum, suffixInUse, typeChangeCausesIdChange, updateExonId

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

geneIdPattern

protected java.util.regex.Pattern geneIdPattern

Regular expression pattern used to parse a gene's ID from the chado uniquename.

Constructor Detail

TigrSybilNameAdapter

public TigrSybilNameAdapter()

Method Detail

generateURL

public java.lang.String generateURL(AnnotatedFeatureI g)