apollo.dataadapter.chado.jdbc
Class ParameciumDBChadoInstance

java.lang.Object
  apollo.dataadapter.chado.jdbc.ParameciumDBChadoInstance

All Implemented Interfaces:

ChadoInstance, java.lang.Cloneable

public class ParameciumDBChadoInstance
extends java.lang.Object

Implementation of AbstractChadoInstance for ParameciumDB.

Version:

$Revision: 1.10 $ $Date: 2009-02-24 16:51:15 $ $Author: gk_fan $

Author:

Olivier Arnaiz

Field Summary

protected static org.apache.log4j.Logger

logger

Constructor Summary

ParameciumDBChadoInstance()

Method Summary

boolean	cacheAnalysisTable()
void	checkForLocation(DataInput dataInput) If dataInputs type is configured as a location, then change dataInput to be a location - is there a better way to do this?
protected void	clear()
ChadoInstance	cloneInstance()
java.lang.String	getAnalysisType(long analysisId, java.lang.String program, java.lang.String programversion, java.lang.String sourcename) Returns type string as program:sourcename; override if this is not what your database requires.
protected void	getAnnotations(java.sql.Connection conn, SequenceI refSeq, StrandedFeatureSet sfs, apollo.dataadapter.chado.jdbc.FeatureLocImplementation featLocImp, boolean getFeatProps, boolean getSynonyms, boolean getDbXRefs, ChadoAdapter adapter)
StrandedFeatureSet	getAnnotStrandedFeatSet()
java.lang.String	getCdsSql(apollo.dataadapter.chado.jdbc.FeatureLocImplementation featLocImp) Return an SQL query that will retrieve all CDS features within a specified range.
java.lang.String	getCdsTransRelationTerm()
JdbcChadoAdapter	getChadoAdapter()
java.util.List	getChadoTransMacros() This is the beginning of trying to get chado-adapter.xml and transactionXMLTemplate non-redundant, so you dont have to configure the same things twice.
java.lang.String	getCommentPropertyTerm()
protected java.sql.Connection	getConnection()
boolean	getCopyGeneModelsIntoResultTier()
CurationSet	getCurationSet(ChadoAdapter adapter, java.lang.String seqType, java.lang.String topFeatName) Retrieve all the curation data (gene models, gene predictions, search results, etc.) for a single chado feature/sequence.
CurationSet	getCurationSetInRange(ChadoAdapter adapter, java.lang.String seqType, Region region) Retrieve all the curation data (gene models, gene predictions, search results, etc.) for a given region on a single chado feature/sequence.
java.lang.String	getExonTransRelationTerm()
java.lang.String	getFeatureCreateDatePropertyTerm()
java.lang.String	getFeatureCVName() Flybases feature cv is SO
protected java.lang.Long	getFeatureCVTermId(java.lang.String name) calls JdbcChadoAdapter -> cvterms should have its own class
java.lang.String	getFeatureOwnerPropertyTerm()
java.lang.String	getFeatureType(java.lang.String alignType, java.lang.String program, java.lang.String programversion, java.lang.String targetSp, java.lang.String sourcename, java.lang.String featProp) Flybase does feature type "program:sourcename", the rest of the params are ignored (used by tigr feat type)
java.lang.String	getGeneNameField() Return the column in the chado feature table where the gene name can be found.
ChadoProgram[]	getGenePredictionPrograms() Return array for all the gene prediction programs.
SeqType	getLocationSeqType() Assumes theres only 1 location seq type - returns first it finds
java.lang.String	getLogDirectory()
java.util.List	getOneLevelAnnotTypes() Get a list of annotation types that are saved in Chado db as one level features from a list of types.
ChadoProgram[]	getOneLevelResultPrograms() for simple results that are only 1 level deep
java.lang.String	getPartOfCvTerm() return string for part of relationship (tigr part_of, fb partof)
java.lang.String	getPolypeptideCdsRelationTerm()
protected java.lang.Long	getPolypeptideCVTermId()
java.lang.String	getPolypeptideTransRelationTerm()
java.lang.String	getPolypeptideType() Old SO/SOFA uses "protein", new uses "polypeptide" (default)
java.lang.String	getPredictedCdsSql(apollo.dataadapter.chado.jdbc.FeatureLocImplementation featLocImp, ChadoProgram[] chadoPrgs) Returns only the cds linked to a transcript predicted by a program of chadoPrgs which isRetrieveCDS is true
protected java.lang.Long	getProducedByCVTermId()
java.lang.String	getPropertyTypeCVName()
boolean	getPureJDBCCopyOnWrite()
boolean	getPureJDBCNoCommit()
boolean	getPureJDBCUseCDS()
boolean	getPureJDBCWriteMode()
boolean	getQueryFeatureIdWithName()
boolean	getQueryFeatureIdWithUniquename()
java.lang.String	getRelationshipCVName()
protected java.lang.Long	getRelationshipCVTermId(java.lang.String name)
StrandedFeatureSet	getResultStrandedFeatSet()
ChadoProgram[]	getSearchHitPrograms() Return array of strings for all the hit programs.
java.lang.String	getSeqDescriptionCVName()
java.lang.String	getSeqDescriptionTerm()
SeqType	getSeqType(int i) Return ith SeqType
SeqType	getSeqType(java.lang.String name) SeqType for name
int	getSeqTypesSize() Return number of seq types for instance
java.lang.String	getSynonymPropertyTerm()
java.lang.String	getSyntenyRelationshipType()
java.lang.String	getTargetName(java.lang.String chadoName, java.lang.String species, java.lang.String alignType) just returns chadoName - cant add species as fb doesnt record species of target
java.util.List	getThreeLevelAnnotTypes() Get a list of features that are stored in the chado db as three level features (gene-namedFeaure-exon).
apollo.dataadapter.chado.jdbc.FeatureLocImplementation	getTopFeatLoc()
java.lang.String	getTopLevelFeatType() Top level feature type is needed for saving back to chado.
java.lang.Long	getTranscriptCvTermId()
java.lang.String	getTranscriptName(FeatureSet tfs, java.lang.String program)
java.lang.String	getTranscriptNameField() Return the column in the chado feature table where the transcript name can be found.
java.lang.String	getTranscriptTerm()
java.lang.String	getTransGeneRelationTerm()
java.lang.String	getTransProtRelationTerm()
boolean	getUseSynonyms()
java.lang.String	getWritebackTemplateFile()
boolean	searchHitsHaveFeatLocs() returns true if search hits have feature locs.
void	setCacheAnalysisTable(boolean cache)
void	setCdsTransRelationTerm(java.lang.String term) Need to set (from chado-adapter.xml) if diff from default
void	setChadoAdapter(JdbcChadoAdapter jdbcAdapter)
void	setCommentPropertyTerm(java.lang.String commentTerm)
void	setCopyGeneModelsIntoResultTier(boolean copyModels)
void	setExonTransRelationTerm(java.lang.String term) Need to set (from chado-adapter.xml) if diff from default
void	setFeatureCreateDatePropertyTerm(java.lang.String dateTerm)
void	setFeatureCVName(java.lang.String featCV)
void	setFeatureOwnerPropertyTerm(java.lang.String ownerTerm)
void	setGenePredictionPrograms(ChadoProgram[] genePredictionPrograms)
void	setId(java.lang.String id)
void	setLogDirectory(java.lang.String path)
void	setOneLevelAnnotTypes(java.util.List features) Set a list of annotation types that are saved in the Chado database as one-level features.
void	setOneLevelResultPrograms(ChadoProgram[] oneLevelResults)
void	setPartOfCvTerm(java.lang.String term)
void	setPolypeptideCdsRelationTerm(java.lang.String term) Need to set (from chado-adapter.xml) if diff from default
void	setPolypeptideTransRelationTerm(java.lang.String term) Need to set (from chado-adapter.xml) if diff from default
void	setPolypeptideType(java.lang.String polypeptideType) Old SO/SOFA uses "protein", new uses "polypeptide" (default)
void	setPropertyTypeCVName(java.lang.String cv)
void	setPureJDBCCopyOnWrite(boolean copyOnWrite)
void	setPureJDBCNoCommit(boolean noCommit)
void	setPureJDBCUseCDS(boolean useCDS)
void	setPureJDBCWriteMode(boolean writeMode)
void	setQueryFeatureIdWithName(boolean newVal)
void	setQueryFeatureIdWithUniquename(boolean newVal)
void	setRelationshipCVName(java.lang.String relCV)
void	setRetrieveAnnotations(boolean retrieveAnnotations)
void	setSearchHitPrograms(ChadoProgram[] searchHitPrograms)
void	setSearchHitsHaveFeatLocs(boolean haveFeatLocs)
void	setSeqDescriptionCVName(java.lang.String cvName)
void	setSeqDescriptionTerm(java.lang.String term)
void	setSeqTypeList(java.util.List seqTypes)
void	setSynonymPropertyTerm(java.lang.String synonymPropertyTerm)
void	setSyntenyRelationshipType(java.lang.String syntenyRelationshipType)
void	setThreeLevelAnnotTypes(java.util.List features) Set a list of features that are saved in the chado db as three-level features.
void	setTransGeneRelationTerm(java.lang.String term) Need to set (from chado-adapter.xml) if diff from default
void	setTranslationStartAndStop(FeatureSet trans, apollo.dataadapter.chado.jdbc.ChadoCds cds) Using ChadoCds set the start and stop of translation for a FeatureSet (i.e.
void	setTranslationStartAndStop(Transcript trans, apollo.dataadapter.chado.jdbc.ChadoCds cds) Just set start of translation, let apollo calculate stop.
void	setTransProtRelationTerm(java.lang.String term) Need to set (from chado-adapter.xml) if diff from default
void	setUseSynonyms(boolean useSynonyms)
void	setWritebackTemplateFile(java.lang.String templateFile)
boolean	typeHasStartAndEnd(java.lang.String typeName) Does type require start & end data

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

ParameciumDBChadoInstance

public ParameciumDBChadoInstance()

Method Detail

getPolypeptideTransRelationTerm

public java.lang.String getPolypeptideTransRelationTerm()

Specified by:

getPolypeptideTransRelationTerm in interface ChadoInstance

getTransGeneRelationTerm

public java.lang.String getTransGeneRelationTerm()

Specified by:

getTransGeneRelationTerm in interface ChadoInstance

getTranscriptTerm

public java.lang.String getTranscriptTerm()

Specified by:

getTranscriptTerm in interface ChadoInstance

getTranscriptCvTermId

public java.lang.Long getTranscriptCvTermId()

Specified by:

getTranscriptCvTermId in interface ChadoInstance

getCdsSql

public java.lang.String getCdsSql(apollo.dataadapter.chado.jdbc.FeatureLocImplementation featLocImp)
                           throws apollo.dataadapter.chado.jdbc.RelationshipCVException

Description copied from interface: ChadoInstance

Return an SQL query that will retrieve all CDS features within a specified range. The way that CDS and protein/polypeptide features are stored in different chado instances is sufficiently different that the entire SQL query must be returned. The SQL result set must contain (at least) the following fields:

• fmin
• fmax
• strand
• cds_name
• transcript_uniquename
• transcript_seq
• protein_name
• protein_seq

Parameters:

featLocImp - The region whose CDS features the SQL query should retrieve.

Returns:

A string containing a valid SQL query.

Throws:

apollo.dataadapter.chado.jdbc.RelationshipCVException

getPredictedCdsSql

public java.lang.String getPredictedCdsSql(apollo.dataadapter.chado.jdbc.FeatureLocImplementation featLocImp,
                                           ChadoProgram[] chadoPrgs)
                                    throws apollo.dataadapter.chado.jdbc.RelationshipCVException

Returns only the cds linked to a transcript predicted by a program of chadoPrgs which isRetrieveCDS is true

Parameters:

featLocImp -

chadoPrgs - array of chadoProgram

Returns:

an sql query as a string, null if no predicted CDSs wanted (ChadoProgram.retrieveCDS)

Throws:

RelationshipCVException

See Also:

getCdsSql(FeatureLocImplementation)

getGeneNameField

public java.lang.String getGeneNameField()

Description copied from interface: ChadoInstance

Return the column in the chado feature table where the gene name can be found. The adapter will call setName() on each new gene using the value in this field.

Returns:

The name of a field/column in the chado "feature" table.

getTranscriptNameField

public java.lang.String getTranscriptNameField()

Description copied from interface: ChadoInstance

Return the column in the chado feature table where the transcript name can be found. The adapter will call setName() on each new transcript using the value in this field.

Returns:

The name of a field/column in the chado "feature" table.

getTargetName

public java.lang.String getTargetName(java.lang.String chadoName,
                                      java.lang.String species,
                                      java.lang.String alignType)

just returns chadoName - cant add species as fb doesnt record species of target

Parameters:

chadoName - chado feature.uniquename of the feature/sequence

species - organism name generated by JdbcChadoAdapter.getOrganismFullName

alignType - cv.name for the leaf alignment/search hit object

Returns:

The string that will be used to name the target Sequence in the search hit.

getFeatureType

public java.lang.String getFeatureType(java.lang.String alignType,
                                       java.lang.String program,
                                       java.lang.String programversion,
                                       java.lang.String targetSp,
                                       java.lang.String sourcename,
                                       java.lang.String featProp)

Flybase does feature type "program:sourcename", the rest of the params are ignored (used by tigr feat type)

Parameters:

alignType - cv.name for the leaf alignment/search hit object

program - value from analysis.program for the search hit

programversion - value from analysis.programversion for the searc

targetSp - organism name generated by JdbcChadoAdapter.getOrganismFullName

featProp - optional featureprop value associated with the search hit

Returns:

A string containing the type of the specified search hit feature.

getFeatureCVName

public java.lang.String getFeatureCVName()

Flybases feature cv is SO

Specified by:

getFeatureCVName in interface ChadoInstance

Returns:

Name of the chado CV from which to draw feature terms.

getCurationSetInRange

public CurationSet getCurationSetInRange(ChadoAdapter adapter,
                                         java.lang.String seqType,
                                         Region region)

Description copied from interface: ChadoInstance

Retrieve all the curation data (gene models, gene predictions, search results, etc.) for a given region on a single chado feature/sequence.

Parameters:

adapter - ChadoAdapter on whose behalf the database accesses are to be performed.

seqType - cvterm.name that corresponds to the sequence identified by location

region - The region for which to retrieve data.

Returns:

a CurationSet containing all the features in the region given by location

getCurationSet

public CurationSet getCurationSet(ChadoAdapter adapter,
                                  java.lang.String seqType,
                                  java.lang.String topFeatName)

Description copied from interface: ChadoInstance

Retrieve all the curation data (gene models, gene predictions, search results, etc.) for a single chado feature/sequence.

Parameters:

adapter - ChadoAdapter on whose behalf the database accesses are to be performed.

seqType - cvterm type_id of the sequence identified by featName

topFeatName - Chado feature name of the sequence to be displayed/annotated in Apollo. Name correlates with seqType.

Returns:

a CurationSet containing all the features on seqId

setTranslationStartAndStop

public void setTranslationStartAndStop(Transcript trans,
                                       apollo.dataadapter.chado.jdbc.ChadoCds cds)

Just set start of translation, let apollo calculate stop. This mimics the game adapter. Can the stop be different than the calculated stop and if so how does chado represent that? This will do for now i think. I believe the end of the cds is the protein is one less than the translation stop

Parameters:

trans - Transcript whose start and stop should be set.

cds - CDS used to determine start and stop

setTranslationStartAndStop

public void setTranslationStartAndStop(FeatureSet trans,
                                       apollo.dataadapter.chado.jdbc.ChadoCds cds)

Description copied from interface: ChadoInstance

Using ChadoCds set the start and stop of translation for a FeatureSet (i.e. predicted transcript).

Parameters:

trans - Transcript whose start and stop should be set.

cds - CDS used to determine start and stop

getTranscriptName

public java.lang.String getTranscriptName(FeatureSet tfs,
                                          java.lang.String program)

Specified by:

getTranscriptName in interface ChadoInstance

cloneInstance

public ChadoInstance cloneInstance()

Specified by:

cloneInstance in interface ChadoInstance

setId

public void setId(java.lang.String id)

Specified by:

setId in interface ChadoInstance

setChadoAdapter

public void setChadoAdapter(JdbcChadoAdapter jdbcAdapter)

Specified by:

setChadoAdapter in interface ChadoInstance

getChadoAdapter

public JdbcChadoAdapter getChadoAdapter()

Specified by:

getChadoAdapter in interface ChadoInstance

getConnection

protected java.sql.Connection getConnection()

setWritebackTemplateFile

public void setWritebackTemplateFile(java.lang.String templateFile)

Specified by:

setWritebackTemplateFile in interface ChadoInstance

getWritebackTemplateFile

public java.lang.String getWritebackTemplateFile()

Specified by:

getWritebackTemplateFile in interface ChadoInstance

setPureJDBCWriteMode

public void setPureJDBCWriteMode(boolean writeMode)

Specified by:

setPureJDBCWriteMode in interface ChadoInstance

getPureJDBCWriteMode

public boolean getPureJDBCWriteMode()

Specified by:

getPureJDBCWriteMode in interface ChadoInstance

setPureJDBCCopyOnWrite

public void setPureJDBCCopyOnWrite(boolean copyOnWrite)

Specified by:

setPureJDBCCopyOnWrite in interface ChadoInstance

getPureJDBCCopyOnWrite

public boolean getPureJDBCCopyOnWrite()

Specified by:

getPureJDBCCopyOnWrite in interface ChadoInstance

setPureJDBCNoCommit

public void setPureJDBCNoCommit(boolean noCommit)

Specified by:

setPureJDBCNoCommit in interface ChadoInstance

getPureJDBCNoCommit

public boolean getPureJDBCNoCommit()

Specified by:

getPureJDBCNoCommit in interface ChadoInstance

setPureJDBCUseCDS

public void setPureJDBCUseCDS(boolean useCDS)

Specified by:

setPureJDBCUseCDS in interface ChadoInstance

getPureJDBCUseCDS

public boolean getPureJDBCUseCDS()

Specified by:

getPureJDBCUseCDS in interface ChadoInstance

setLogDirectory

public void setLogDirectory(java.lang.String path)

Specified by:

setLogDirectory in interface ChadoInstance

getLogDirectory

public java.lang.String getLogDirectory()

Specified by:

getLogDirectory in interface ChadoInstance

setGenePredictionPrograms

public void setGenePredictionPrograms(ChadoProgram[] genePredictionPrograms)

Specified by:

setGenePredictionPrograms in interface ChadoInstance

getUseSynonyms

public boolean getUseSynonyms()

Specified by:

getUseSynonyms in interface ChadoInstance

setUseSynonyms

public void setUseSynonyms(boolean useSynonyms)

Specified by:

setUseSynonyms in interface ChadoInstance

getGenePredictionPrograms

public ChadoProgram[] getGenePredictionPrograms()

Return array for all the gene prediction programs. This comes from xml configuration

Specified by:

getGenePredictionPrograms in interface ChadoInstance

Returns:

an array of ChadoProgram

setSearchHitPrograms

public void setSearchHitPrograms(ChadoProgram[] searchHitPrograms)

Specified by:

setSearchHitPrograms in interface ChadoInstance

getSearchHitPrograms

public ChadoProgram[] getSearchHitPrograms()

Return array of strings for all the hit programs. This comes from xml configuration

Specified by:

getSearchHitPrograms in interface ChadoInstance

setOneLevelResultPrograms

public void setOneLevelResultPrograms(ChadoProgram[] oneLevelResults)

Specified by:

setOneLevelResultPrograms in interface ChadoInstance

getOneLevelResultPrograms

public ChadoProgram[] getOneLevelResultPrograms()

Description copied from interface: ChadoInstance

for simple results that are only 1 level deep

Specified by:

getOneLevelResultPrograms in interface ChadoInstance

getOneLevelAnnotTypes

public java.util.List getOneLevelAnnotTypes()

Get a list of annotation types that are saved in Chado db as one level features from a list of types.

Specified by:

getOneLevelAnnotTypes in interface ChadoInstance

Returns:

setOneLevelAnnotTypes

public void setOneLevelAnnotTypes(java.util.List features)

Description copied from interface: ChadoInstance

Set a list of annotation types that are saved in the Chado database as one-level features.

Specified by:

setOneLevelAnnotTypes in interface ChadoInstance

Parameters:

features - a list of chado cvterm.name

getThreeLevelAnnotTypes

public java.util.List getThreeLevelAnnotTypes()

Get a list of features that are stored in the chado db as three level features (gene-namedFeaure-exon).

Specified by:

getThreeLevelAnnotTypes in interface ChadoInstance

Returns:

setThreeLevelAnnotTypes

public void setThreeLevelAnnotTypes(java.util.List features)

Description copied from interface: ChadoInstance

Set a list of features that are saved in the chado db as three-level features. (gene-namedFeature-exon).

Specified by:

setThreeLevelAnnotTypes in interface ChadoInstance

Parameters:

features - a list of feature names.

searchHitsHaveFeatLocs

public boolean searchHitsHaveFeatLocs()

returns true if search hits have feature locs. Hits are the feature sets that hold the leaf/hsps. The leaves always have feat-locs, but the featSet/hits dont always have feat locs, which makes it impractical to retrieve out of range leaves/hsps. Currently rice has hit feat locs, fly & tigr dont

Specified by:

searchHitsHaveFeatLocs in interface ChadoInstance

setSearchHitsHaveFeatLocs

public void setSearchHitsHaveFeatLocs(boolean haveFeatLocs)

Specified by:

setSearchHitsHaveFeatLocs in interface ChadoInstance

getRelationshipCVTermId

protected java.lang.Long getRelationshipCVTermId(java.lang.String name)

setRelationshipCVName

public void setRelationshipCVName(java.lang.String relCV)

Specified by:

setRelationshipCVName in interface ChadoInstance

getRelationshipCVName

public java.lang.String getRelationshipCVName()

Specified by:

getRelationshipCVName in interface ChadoInstance

Returns:

Name of the chado CV from which to draw relationship terms.

getPartOfCvTerm

public java.lang.String getPartOfCvTerm()

return string for part of relationship (tigr part_of, fb partof)

Specified by:

getPartOfCvTerm in interface ChadoInstance

setPartOfCvTerm

public void setPartOfCvTerm(java.lang.String term)

Specified by:

setPartOfCvTerm in interface ChadoInstance

getTransProtRelationTerm

public java.lang.String getTransProtRelationTerm()

Specified by:

getTransProtRelationTerm in interface ChadoInstance

setTransProtRelationTerm

public void setTransProtRelationTerm(java.lang.String term)

Need to set (from chado-adapter.xml) if diff from default

Specified by:

setTransProtRelationTerm in interface ChadoInstance

setTransGeneRelationTerm

public void setTransGeneRelationTerm(java.lang.String term)

Need to set (from chado-adapter.xml) if diff from default

Specified by:

setTransGeneRelationTerm in interface ChadoInstance

getExonTransRelationTerm

public java.lang.String getExonTransRelationTerm()

Specified by:

getExonTransRelationTerm in interface ChadoInstance

setExonTransRelationTerm

public void setExonTransRelationTerm(java.lang.String term)

Need to set (from chado-adapter.xml) if diff from default

Specified by:

setExonTransRelationTerm in interface ChadoInstance

getCdsTransRelationTerm

public java.lang.String getCdsTransRelationTerm()

Specified by:

getCdsTransRelationTerm in interface ChadoInstance

setCdsTransRelationTerm

public void setCdsTransRelationTerm(java.lang.String term)

Need to set (from chado-adapter.xml) if diff from default

Specified by:

setCdsTransRelationTerm in interface ChadoInstance

getPolypeptideCdsRelationTerm

public java.lang.String getPolypeptideCdsRelationTerm()

Specified by:

getPolypeptideCdsRelationTerm in interface ChadoInstance

setPolypeptideCdsRelationTerm

public void setPolypeptideCdsRelationTerm(java.lang.String term)

Need to set (from chado-adapter.xml) if diff from default

Specified by:

setPolypeptideCdsRelationTerm in interface ChadoInstance

setPolypeptideTransRelationTerm

public void setPolypeptideTransRelationTerm(java.lang.String term)

Need to set (from chado-adapter.xml) if diff from default

Specified by:

setPolypeptideTransRelationTerm in interface ChadoInstance

getProducedByCVTermId

protected java.lang.Long getProducedByCVTermId()
                                        throws apollo.dataadapter.chado.jdbc.AbstractChadoInstance.ProducedByException

Throws:

apollo.dataadapter.chado.jdbc.AbstractChadoInstance.ProducedByException

setFeatureCVName

public void setFeatureCVName(java.lang.String featCV)

Specified by:

setFeatureCVName in interface ChadoInstance

setPolypeptideType

public void setPolypeptideType(java.lang.String polypeptideType)

Old SO/SOFA uses "protein", new uses "polypeptide" (default)

Specified by:

setPolypeptideType in interface ChadoInstance

getPolypeptideType

public java.lang.String getPolypeptideType()

Description copied from interface: ChadoInstance

Old SO/SOFA uses "protein", new uses "polypeptide" (default)

Specified by:

getPolypeptideType in interface ChadoInstance

setSyntenyRelationshipType

public void setSyntenyRelationshipType(java.lang.String syntenyRelationshipType)

Specified by:

setSyntenyRelationshipType in interface ChadoInstance

getSyntenyRelationshipType

public java.lang.String getSyntenyRelationshipType()

Specified by:

getSyntenyRelationshipType in interface ChadoInstance

setFeatureOwnerPropertyTerm

public void setFeatureOwnerPropertyTerm(java.lang.String ownerTerm)

Specified by:

setFeatureOwnerPropertyTerm in interface ChadoInstance

getFeatureOwnerPropertyTerm

public java.lang.String getFeatureOwnerPropertyTerm()

Specified by:

getFeatureOwnerPropertyTerm in interface ChadoInstance

setFeatureCreateDatePropertyTerm

public void setFeatureCreateDatePropertyTerm(java.lang.String dateTerm)

Specified by:

setFeatureCreateDatePropertyTerm in interface ChadoInstance

getFeatureCreateDatePropertyTerm

public java.lang.String getFeatureCreateDatePropertyTerm()

Specified by:

getFeatureCreateDatePropertyTerm in interface ChadoInstance

setCommentPropertyTerm

public void setCommentPropertyTerm(java.lang.String commentTerm)

Specified by:

setCommentPropertyTerm in interface ChadoInstance

getCommentPropertyTerm

public java.lang.String getCommentPropertyTerm()

Specified by:

getCommentPropertyTerm in interface ChadoInstance

getSynonymPropertyTerm

public java.lang.String getSynonymPropertyTerm()

Specified by:

getSynonymPropertyTerm in interface ChadoInstance

setSynonymPropertyTerm

public void setSynonymPropertyTerm(java.lang.String synonymPropertyTerm)

Specified by:

setSynonymPropertyTerm in interface ChadoInstance

getSeqDescriptionCVName

public java.lang.String getSeqDescriptionCVName()

Specified by:

getSeqDescriptionCVName in interface ChadoInstance

setSeqDescriptionCVName

public void setSeqDescriptionCVName(java.lang.String cvName)

Specified by:

setSeqDescriptionCVName in interface ChadoInstance

getSeqDescriptionTerm

public java.lang.String getSeqDescriptionTerm()

Specified by:

getSeqDescriptionTerm in interface ChadoInstance

setSeqDescriptionTerm

public void setSeqDescriptionTerm(java.lang.String term)

Specified by:

setSeqDescriptionTerm in interface ChadoInstance

getPolypeptideCVTermId

protected java.lang.Long getPolypeptideCVTermId()

getFeatureCVTermId

protected java.lang.Long getFeatureCVTermId(java.lang.String name)

calls JdbcChadoAdapter -> cvterms should have its own class

setPropertyTypeCVName

public void setPropertyTypeCVName(java.lang.String cv)

Specified by:

setPropertyTypeCVName in interface ChadoInstance

getPropertyTypeCVName

public java.lang.String getPropertyTypeCVName()

Specified by:

getPropertyTypeCVName in interface ChadoInstance

Returns:

Name of the chado CV from which to draw property type terms.

getAnalysisType

public java.lang.String getAnalysisType(long analysisId,
                                        java.lang.String program,
                                        java.lang.String programversion,
                                        java.lang.String sourcename)

Returns type string as program:sourcename; override if this is not what your database requires.

Specified by:

getAnalysisType in interface ChadoInstance

Parameters:

analysisId - chado analysis.analysis_id

program - chado analysis.program

programversion - chado analysis.programversion

sourcename - chado analysis.sourcename

Returns:

The Apollo type to be used for all features from this analysis.

setCacheAnalysisTable

public void setCacheAnalysisTable(boolean cache)

Specified by:

setCacheAnalysisTable in interface ChadoInstance

cacheAnalysisTable

public boolean cacheAnalysisTable()

Specified by:

cacheAnalysisTable in interface ChadoInstance

setRetrieveAnnotations

public void setRetrieveAnnotations(boolean retrieveAnnotations)

Specified by:

setRetrieveAnnotations in interface ChadoInstance

setCopyGeneModelsIntoResultTier

public void setCopyGeneModelsIntoResultTier(boolean copyModels)

Specified by:

setCopyGeneModelsIntoResultTier in interface ChadoInstance

getCopyGeneModelsIntoResultTier

public boolean getCopyGeneModelsIntoResultTier()

Specified by:

getCopyGeneModelsIntoResultTier in interface ChadoInstance

setQueryFeatureIdWithUniquename

public void setQueryFeatureIdWithUniquename(boolean newVal)

Specified by:

setQueryFeatureIdWithUniquename in interface ChadoInstance

getQueryFeatureIdWithUniquename

public boolean getQueryFeatureIdWithUniquename()

Specified by:

getQueryFeatureIdWithUniquename in interface ChadoInstance

setQueryFeatureIdWithName

public void setQueryFeatureIdWithName(boolean newVal)

Specified by:

setQueryFeatureIdWithName in interface ChadoInstance

getQueryFeatureIdWithName

public boolean getQueryFeatureIdWithName()

Specified by:

getQueryFeatureIdWithName in interface ChadoInstance

getAnnotations

protected void getAnnotations(java.sql.Connection conn,
                              SequenceI refSeq,
                              StrandedFeatureSet sfs,
                              apollo.dataadapter.chado.jdbc.FeatureLocImplementation featLocImp,
                              boolean getFeatProps,
                              boolean getSynonyms,
                              boolean getDbXRefs,
                              ChadoAdapter adapter)

getChadoTransMacros

public java.util.List getChadoTransMacros()

This is the beginning of trying to get chado-adapter.xml and transactionXMLTemplate non-redundant, so you dont have to configure the same things twice. A bunch of the preamble macros can be figured now from chado-adpter.xml config and dont need to be in the template

Specified by:

getChadoTransMacros in interface ChadoInstance

setSeqTypeList

public void setSeqTypeList(java.util.List seqTypes)

Specified by:

setSeqTypeList in interface ChadoInstance

getSeqTypesSize

public int getSeqTypesSize()

Description copied from interface: ChadoInstance

Return number of seq types for instance

Specified by:

getSeqTypesSize in interface ChadoInstance

getSeqType

public SeqType getSeqType(int i)

Description copied from interface: ChadoInstance

Return ith SeqType

Specified by:

getSeqType in interface ChadoInstance

getLocationSeqType

public SeqType getLocationSeqType()

Assumes theres only 1 location seq type - returns first it finds

Specified by:

getLocationSeqType in interface ChadoInstance

getTopLevelFeatType

public java.lang.String getTopLevelFeatType()

Top level feature type is needed for saving back to chado. Also for querying locations from the command line (where type isnt given). This is configured in chado-adapter cfg file under with true. If top level is not configged tries to gleen from seq types - if theres any seqTypes with start&end, uses that, if no locs then just looks for 'chromosome' in type name, and if all that fails just sets to "chromosome".

Specified by:

getTopLevelFeatType in interface ChadoInstance

checkForLocation

public void checkForLocation(DataInput dataInput)

If dataInputs type is configured as a location, then change dataInput to be a location - is there a better way to do this?

Specified by:

checkForLocation in interface ChadoInstance

getSeqType

public SeqType getSeqType(java.lang.String name)

Description copied from interface: ChadoInstance

SeqType for name

Specified by:

getSeqType in interface ChadoInstance

typeHasStartAndEnd

public boolean typeHasStartAndEnd(java.lang.String typeName)

Description copied from interface: ChadoInstance

Does type require start & end data

Specified by:

typeHasStartAndEnd in interface ChadoInstance

getResultStrandedFeatSet

public StrandedFeatureSet getResultStrandedFeatSet()

Specified by:

getResultStrandedFeatSet in interface ChadoInstance

getAnnotStrandedFeatSet

public StrandedFeatureSet getAnnotStrandedFeatSet()

Specified by:

getAnnotStrandedFeatSet in interface ChadoInstance

clear

protected void clear()

getTopFeatLoc

public apollo.dataadapter.chado.jdbc.FeatureLocImplementation getTopFeatLoc()

Specified by:

getTopFeatLoc in interface ChadoInstance