apollo.config
Class SimpleNameAdapter

java.lang.Object
  apollo.config.DefaultNameAdapter
      apollo.config.SimpleNameAdapter

All Implemented Interfaces:

ApolloNameAdapterI

public class SimpleNameAdapter
extends DefaultNameAdapter

This adapter just uses the name of the result to name the annot. In other words the annots are pre named. So its really not much of a name adapter. This is simpler than DefaultNameAdapter, and perhaps this should be Default(?). Not sure if SimpleNameAdapter is a good name for this - PreNamedNameAdapter? UseResultNameAdapter? ResultNameAdapter? ...? OneLevelNameAdapter? i think this is prtty much for 1 level annots

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

SimpleNameAdapter()

Method Summary

java.lang.String	generateName(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI feature) this is a workaround until we actually have 1-level annots.
java.lang.String	generateName(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI feature, java.util.Vector resultFeats) Generates name for a given feature.

Methods inherited from class apollo.config.DefaultNameAdapter

addSynonym, checkFormat, checkName, generateAnnotSplitName, generateChadoCdsIdFromTranscriptId, generateChadoCdsNameFromTranscriptName, generateExonId, generateId, 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

Constructor Detail

SimpleNameAdapter

public SimpleNameAdapter()

Method Detail

generateName

public java.lang.String generateName(StrandedFeatureSetI annots,
                                     java.lang.String curation_name,
                                     SeqFeatureI feature,
                                     java.util.Vector resultFeats)

Description copied from interface: ApolloNameAdapterI

Generates name for a given feature. May or may not use associated vector of exon results used to make the annot

Specified by:

generateName in interface ApolloNameAdapterI

Overrides:

generateName in class DefaultNameAdapter

generateName

public java.lang.String generateName(StrandedFeatureSetI annots,
                                     java.lang.String curation_name,
                                     SeqFeatureI feature)

this is a workaround until we actually have 1-level annots. for annots that should be 1 level but still have transcripts, name the transcript with the gene name. the transcript name is what shows up in the main window, without this you would see a temp name

Specified by:

generateName in interface ApolloNameAdapterI

Overrides:

generateName in class DefaultNameAdapter