apollo.config
Class ParameciumNameAdapter

java.lang.Object
  apollo.config.ParameciumNameAdapter

All Implemented Interfaces:

ApolloNameAdapterI

public class ParameciumNameAdapter
extends java.lang.Object
implements ApolloNameAdapterI

Field Summary

protected static org.apache.log4j.Logger	logger
protected java.util.regex.Pattern	validBaseNamePattern
protected java.util.regex.Pattern	validCurationNamePattern
protected java.util.regex.Pattern	validNamePattern
protected java.util.regex.Pattern	validPrefixPattern

Constructor Summary

ParameciumNameAdapter()

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)
protected UpdateTransaction	setId(SeqFeatureI annot, java.lang.String newId)
protected UpdateTransaction	setName(AnnotatedFeatureI annFeat, java.lang.String newName)
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 current, AnnotatedFeatureI parent) 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.

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

validCurationNamePattern

protected java.util.regex.Pattern validCurationNamePattern

validNamePattern

protected java.util.regex.Pattern validNamePattern

validBaseNamePattern

protected java.util.regex.Pattern validBaseNamePattern

validPrefixPattern

protected java.util.regex.Pattern validPrefixPattern

Constructor Detail

ParameciumNameAdapter

public ParameciumNameAdapter()

Method Detail

setDataAdapter

public void setDataAdapter(ApolloDataAdapterI dataAdapter)

Specified by:

setDataAdapter in interface ApolloNameAdapterI

generateName

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

Specified by:

generateName in interface ApolloNameAdapterI

generateName

public 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

Specified by:

generateName in interface ApolloNameAdapterI

generateAnnotSplitName

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

Generate a name for a gene split

Specified by:

generateAnnotSplitName in interface ApolloNameAdapterI

generateId

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

Specified by:

generateId in interface ApolloNameAdapterI

generateNewId

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

Specified by:

generateNewId in interface ApolloNameAdapterI

generateExonId

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

Specified by:

generateExonId in interface ApolloNameAdapterI

generateNewExonId

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

Specified by:

generateNewExonId in interface ApolloNameAdapterI

updateExonId

public 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.

Specified by:

updateExonId in interface ApolloNameAdapterI

getSuffixDelimiter

public java.lang.String getSuffixDelimiter()

Specified by:

getSuffixDelimiter in interface ApolloNameAdapterI

checkName

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

Specified by:

checkName in interface ApolloNameAdapterI

setAnnotName

public 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

Specified by:

setAnnotName in interface ApolloNameAdapterI

setTranscriptName

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

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

Specified by:

setTranscriptName in interface ApolloNameAdapterI

setTranscriptId

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

Sets transcript id, may also set peptide id

Specified by:

setTranscriptId in interface ApolloNameAdapterI

setTranscriptNameFromAnnot

public CompoundTransaction setTranscriptNameFromAnnot(AnnotatedFeatureI current,
                                                      AnnotatedFeatureI parent)

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

Specified by:

setTranscriptNameFromAnnot in interface ApolloNameAdapterI

nameIsId

public boolean nameIsId(SeqFeatureI feature)

Specified by:

nameIsId in interface ApolloNameAdapterI

suffixInUse

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

Specified by:

suffixInUse in interface ApolloNameAdapterI

checkFormat

public 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

Specified by:

checkFormat in interface ApolloNameAdapterI

idAndNameHaveSameFormat

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

Return true if id and name have same format

Specified by:

idAndNameHaveSameFormat in interface ApolloNameAdapterI

getTranscriptNamePattern

public java.lang.String getTranscriptNamePattern()

Returns expected pattern (if any) for transcript names

Specified by:

getTranscriptNamePattern in interface ApolloNameAdapterI

typeChangeCausesIdChange

public 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

Specified by:

typeChangeCausesIdChange in interface ApolloNameAdapterI

getNewIdFromTypeChange

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

Specified by:

getNewIdFromTypeChange in interface ApolloNameAdapterI

setTransactionManager

public void setTransactionManager(TransactionManager tm)

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

Specified by:

setTransactionManager in interface ApolloNameAdapterI

setAnnotId

public 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.

Specified by:

setAnnotId in interface ApolloNameAdapterI

isTemp

public 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.

Specified by:

isTemp in interface ApolloNameAdapterI

generatePeptideNameFromTranscriptName

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

Generate a peptide name given a transcript name.

Specified by:

generatePeptideNameFromTranscriptName in interface ApolloNameAdapterI

generatePeptideIdFromTranscriptId

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

Specified by:

generatePeptideIdFromTranscriptId in interface ApolloNameAdapterI

generateChadoCdsNameFromTranscriptName

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

Description copied from interface: ApolloNameAdapterI

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

Specified by:

generateChadoCdsNameFromTranscriptName in interface ApolloNameAdapterI

generateChadoCdsIdFromTranscriptId

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

Specified by:

generateChadoCdsIdFromTranscriptId in interface ApolloNameAdapterI

setName

protected UpdateTransaction setName(AnnotatedFeatureI annFeat,
                                    java.lang.String newName)

setId

protected UpdateTransaction setId(SeqFeatureI annot,
                                  java.lang.String newId)