apollo.config
Interface ApolloNameAdapterI

All Known Implementing Classes:

ChadoJdbcNameAdapter, DefaultNameAdapter, FlyNameAdapter, GmodNameAdapter, ParameciumNameAdapter, RiceNameAdapter, SimpleNameAdapter, TigrAnnotNameAdapter, TigrSybilNameAdapter

public interface ApolloNameAdapterI

Method Summary

boolean	checkFormat(SeqFeatureI feat, java.lang.String id) Returns true if id jibes with seq feature's ID format.
boolean	checkName(java.lang.String name, java.lang.Class featureClass)
java.lang.String	generateAnnotSplitName(SeqFeatureI annot, StrandedFeatureSetI annotParent, java.lang.String curationName) Generate a name for a gene split
java.lang.String	generateChadoCdsIdFromTranscriptId(java.lang.String transcriptId)
java.lang.String	generateChadoCdsNameFromTranscriptName(java.lang.String transcriptName) Generate a CDS name given a transcript name.
java.lang.String	generateExonId(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI exon, java.lang.String geneId)
java.lang.String	generateId(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI feature)
java.lang.String	generateName(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI feature)
java.lang.String	generateName(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI feature, java.util.Vector exonResults) Generates name for a given feature.
java.lang.String	generateNewExonId(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI exon, java.lang.String geneId)
java.lang.String	generateNewId(StrandedFeatureSetI annots, java.lang.String curation_name, SeqFeatureI feature)
java.lang.String	generatePeptideIdFromTranscriptId(java.lang.String transcriptId)
java.lang.String	generatePeptideNameFromTranscriptName(java.lang.String transcriptName) Generate a peptide name given a transcript name.
java.lang.String	getNewIdFromTypeChange(java.lang.String oldId, java.lang.String oldType, java.lang.String newType)
java.lang.String	getSuffixDelimiter()
java.lang.String	getTranscriptNamePattern() Returns expected pattern (if any) for transcript names
boolean	idAndNameHaveSameFormat(SeqFeatureI feat, java.lang.String id, java.lang.String name) Return true if id and name have same format
boolean	isTemp(java.lang.String idOrName) Returns true if id/name String is a temp id/name.
boolean	nameIsId(SeqFeatureI feature)
CompoundTransaction	setAnnotId(AnnotatedFeatureI annot, java.lang.String id) Set annots id to id.
CompoundTransaction	setAnnotName(AnnotatedFeatureI annot, java.lang.String newName) Set name for top level annot.
void	setDataAdapter(ApolloDataAdapterI dataAdapter)
void	setTransactionManager(TransactionManager tm) A name adapter needs a TransactionManager.
CompoundTransaction	setTranscriptId(SeqFeatureI trans, java.lang.String id) Sets transcript id, may also set peptide id
CompoundTransaction	setTranscriptName(AnnotatedFeatureI trans, java.lang.String name) Sets transcripts name.
CompoundTransaction	setTranscriptNameFromAnnot(AnnotatedFeatureI transcript, AnnotatedFeatureI gene) Sets the name of a transcript based upon its annot parent.
boolean	suffixInUse(java.util.Vector transcripts, java.lang.String suffix, int t_index)
boolean	typeChangeCausesIdChange(java.lang.String oldType, java.lang.String newType) Returns true if changing type from oldType to newType will cause a change in feature ID, i.e.
void	updateExonId(ExonI exon) This method is used by some adapters/databases to update the exon's id to reflect its new coordinates any time the exon's location is updated.

Method Detail

generateName

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

generateName

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

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

generateAnnotSplitName

java.lang.String generateAnnotSplitName(SeqFeatureI annot,
                                        StrandedFeatureSetI annotParent,
                                        java.lang.String curationName)

Generate a name for a gene split

generateId

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

generateNewId

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

generateExonId

java.lang.String generateExonId(StrandedFeatureSetI annots,
                                java.lang.String curation_name,
                                SeqFeatureI exon,
                                java.lang.String geneId)

generateNewExonId

java.lang.String generateNewExonId(StrandedFeatureSetI annots,
                                   java.lang.String curation_name,
                                   SeqFeatureI exon,
                                   java.lang.String geneId)

updateExonId

void updateExonId(ExonI exon)

This method is used by some adapters/databases to update the exon's id to reflect its new coordinates any time the exon's location is updated.

getSuffixDelimiter

java.lang.String getSuffixDelimiter()

checkName

boolean checkName(java.lang.String name,
                  java.lang.Class featureClass)

setAnnotName

CompoundTransaction setAnnotName(AnnotatedFeatureI annot,
                                 java.lang.String newName)

Set name for top level annot. may set synonym and transcript names as well depending on subclass

setTranscriptName

CompoundTransaction setTranscriptName(AnnotatedFeatureI trans,
                                      java.lang.String name)

Sets transcripts name. may also set peptide & cdna seq accession

setTranscriptId

CompoundTransaction setTranscriptId(SeqFeatureI trans,
                                    java.lang.String id)

Sets transcript id, may also set peptide id

setTranscriptNameFromAnnot

CompoundTransaction setTranscriptNameFromAnnot(AnnotatedFeatureI transcript,
                                               AnnotatedFeatureI gene)

Sets the name of a transcript based upon its annot parent. May also set exon names. May also set peptide accession

nameIsId

boolean nameIsId(SeqFeatureI feature)

suffixInUse

boolean suffixInUse(java.util.Vector transcripts,
                    java.lang.String suffix,
                    int t_index)

checkFormat

boolean checkFormat(SeqFeatureI feat,
                    java.lang.String id)

Returns true if id jibes with seq feature's ID format. This can be used for both ids and names that mirror the id

idAndNameHaveSameFormat

boolean idAndNameHaveSameFormat(SeqFeatureI feat,
                                java.lang.String id,
                                java.lang.String name)

Return true if id and name have same format

getTranscriptNamePattern

java.lang.String getTranscriptNamePattern()

Returns expected pattern (if any) for transcript names

typeChangeCausesIdChange

boolean typeChangeCausesIdChange(java.lang.String oldType,
                                 java.lang.String newType)

Returns true if changing type from oldType to newType will cause a change in feature ID, i.e. the ID prefix will change to reflect the new type

getNewIdFromTypeChange

java.lang.String getNewIdFromTypeChange(java.lang.String oldId,
                                        java.lang.String oldType,
                                        java.lang.String newType)

setTransactionManager

void setTransactionManager(TransactionManager tm)

A name adapter needs a TransactionManager. Has to make sure new temp id isnt in log.

setAnnotId

CompoundTransaction setAnnotId(AnnotatedFeatureI annot,
                               java.lang.String id)

Set annots id to id. May set annot subparts ids as well. Returns a CompoundTransaction of all the transactions that have occurred.

isTemp

boolean isTemp(java.lang.String idOrName)

Returns true if id/name String is a temp id/name. Default is to look for "temp" in id or name.

generatePeptideNameFromTranscriptName

java.lang.String generatePeptideNameFromTranscriptName(java.lang.String transcriptName)

Generate a peptide name given a transcript name.

generatePeptideIdFromTranscriptId

java.lang.String generatePeptideIdFromTranscriptId(java.lang.String transcriptId)

generateChadoCdsNameFromTranscriptName

java.lang.String generateChadoCdsNameFromTranscriptName(java.lang.String transcriptName)

Generate a CDS name given a transcript name. Used only by the chado adapter.

generateChadoCdsIdFromTranscriptId

java.lang.String generateChadoCdsIdFromTranscriptId(java.lang.String transcriptId)

setDataAdapter

void setDataAdapter(ApolloDataAdapterI dataAdapter)