apollo.datamodel
Class CurationSet

java.lang.Object
  apollo.datamodel.Range
      apollo.datamodel.GenomicRange
          apollo.datamodel.CurationSet

All Implemented Interfaces:

ApolloDataI, RangeI, java.io.Serializable, java.lang.Cloneable

public class CurationSet
extends GenomicRange
implements java.io.Serializable, ApolloDataI

I am the central holder of renderable data - results, annotations etc. I am a composite - I can contain instances of myself. In this case, these "child" curation sets can be retrieved by name. This is the way that the species-specific (and compara-) curation sets are passed around for the Synteny case.

In the case that I have no children, my get... methods will act on the (only) Results, Annotations etc that I have. If I _do_ have children, then the get... methods will blow up when invoked.

My feeling is that CurationSet should not be composite, but just be for one species. There should be a new object for the multi-species scene: MultiSpeciesDataHolder or something like that. It would hold CurationSets and LinkSets. This would mean changing DataLoader to be able to return more than just CurationSets.

See Also:

Serialized Form

Field Summary

protected java.util.Hashtable	sequence_hash
protected java.util.Vector	sequence_vect

Fields inherited from class apollo.datamodel.GenomicRange

chromosome

Fields inherited from class apollo.datamodel.Range

high, low, name, refSeq, strand, type

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Constructor Summary

CurationSet()

CurationSet(StrandedFeatureSetI results, StrandedFeatureSetI annots, java.lang.String region)

Method Summary

void	accept(Visitor visitor) General implementation of Visitor pattern.
void	addCurationSet(java.lang.Object key, CurationSet curationSet)
SequenceI	addSequence(SequenceI seq)
boolean	contains(RangeI sf) Overrides Range.contains.
FeatureList	getAnalysisFeatureList(java.lang.String analysisName) Returns a FeatureList for both strands of an analysis, the first item in list is forward strand, 2nd is rev strand.
StrandedFeatureSetI	getAnnots() A CurationSet has a dangling reference that needs to be cleaned up when a new curation set is loaded to replace this one, otherwise it will persist as a memory leak.
java.lang.String	getAssemblyType()
java.util.HashMap	getChildCurationSets()
java.util.Vector	getChildSetOrderedNames()
CompositeDataHolder	getCompositeDataHolder()
CurationSet	getCurationSet() if isCurationSet returns true than a real curation set would be returned here.
CurationSet	getCurationSet(java.lang.Object key)
java.lang.String	getInputFilename()
StrandedFeatureSetI	getResults()
SequenceI	getSequence(java.lang.String id)
java.util.Vector	getSequences()
TransactionManager	getTransactionManager()
boolean	hasTransactionManager()
boolean	hasTransactions()
boolean	isChromosomeArmUsed() A rather strange implemenation.
boolean	isCompositeDataHolder()
boolean	isCurationSet() ApolloDataI
boolean	isMultiSpecies() Temporary method until all synteny stuff uses CompositeDataHolder rename isComposite?
boolean	overlaps(RangeI sf) Overrides Range.overlaps.
void	removeSequence(SequenceI seq)
void	setAnnots(StrandedFeatureSetI annots)
void	setAssemblyType(java.lang.String type)
void	setChildSetOrderedNames(java.util.Vector setNames)
void	setInputFilename(java.lang.String file)
void	setRefSequence(SequenceI seq) Set the SequenceI that this feature annotates.
void	setResults(StrandedFeatureSetI results)
void	setTransactionManager(TransactionManager tranManager)
java.lang.String	toString() In the single-curation set case, this toString method is good for GAME fly data, but * for Ensembl data, the range already has all the info, so the title ends up something like "2 from Chr 2 200000 4000000:20000-4000000"

Methods inherited from class apollo.datamodel.GenomicRange

getChromosome, getOrganism, setChromosome, setOrganism

Methods inherited from class apollo.datamodel.Range

canHaveChildren, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getEnd, getEndAsString, getFeatureType, getHigh, getLeftOverlap, getLow, getName, getRangeClone, getRefSequence, getResidues, getRightOverlap, getStart, getStartAsString, getStrand, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, rangeIsUnassigned, sameRange, setEnd, setFeatureType, setHigh, setLow, setName, setStart, setStrand

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface apollo.datamodel.ApolloDataI

getName

Field Detail

sequence_vect

protected java.util.Vector sequence_vect

sequence_hash

protected java.util.Hashtable sequence_hash

Constructor Detail

CurationSet

public CurationSet()

CurationSet

public CurationSet(StrandedFeatureSetI results,
                   StrandedFeatureSetI annots,
                   java.lang.String region)

Method Detail

getChildCurationSets

public java.util.HashMap getChildCurationSets()

setChildSetOrderedNames

public void setChildSetOrderedNames(java.util.Vector setNames)

getChildSetOrderedNames

public java.util.Vector getChildSetOrderedNames()

addCurationSet

public void addCurationSet(java.lang.Object key,
                           CurationSet curationSet)

getCurationSet

public CurationSet getCurationSet(java.lang.Object key)

setRefSequence

public void setRefSequence(SequenceI seq)

Description copied from interface: RangeI

Set the SequenceI that this feature annotates.

Specified by:

setRefSequence in interface RangeI

Overrides:

setRefSequence in class Range

Parameters:

seq - the new parent SequenceI

getAnnots

public StrandedFeatureSetI getAnnots()

A CurationSet has a dangling reference that needs to be cleaned up when a new curation set is loaded to replace this one, otherwise it will persist as a memory leak. The dangling reference is that if its ref seq is an AbstractLazySequence, ALS's LazyLoadControlledObject is a listener to the Controller. ALS.LLCO has to get a signal to remove itself as a listener when a new curation set is loaded and this is pase, thus this method.

getResults

public StrandedFeatureSetI getResults()

setResults

public void setResults(StrandedFeatureSetI results)

getAssemblyType

public java.lang.String getAssemblyType()

setAssemblyType

public void setAssemblyType(java.lang.String type)

getInputFilename

public java.lang.String getInputFilename()

setInputFilename

public void setInputFilename(java.lang.String file)

setAnnots

public void setAnnots(StrandedFeatureSetI annots)

addSequence

public SequenceI addSequence(SequenceI seq)

getSequences

public java.util.Vector getSequences()

getSequence

public SequenceI getSequence(java.lang.String id)

removeSequence

public void removeSequence(SequenceI seq)

toString

public java.lang.String toString()

In the single-curation set case, this toString method is good for GAME fly data, but * for Ensembl data, the range already has all the info, so the title ends up something like "2 from Chr 2 200000 4000000:20000-4000000"

For a composite case, the toString is the concatentation of all toString's on the children nodes.

Overrides:

toString in class Range

accept

public void accept(Visitor visitor)

General implementation of Visitor pattern. (see apollo.util.Visitor).

contains

public boolean contains(RangeI sf)

Overrides Range.contains. The only difference is that CurationSet does not consider strand in its contains method, where Range does. CurationSets are usually forward stranded (since there start is less than their start - see Range constructor), but they hold reverse as well as forwards stranded features. Without this override all of the reverse stranded features fail the contains test with their CurationSet.

Specified by:

contains in interface RangeI

Overrides:

contains in class Range

overlaps

public boolean overlaps(RangeI sf)

Overrides Range.overlaps. Took out strand comparison.

Specified by:

overlaps in interface RangeI

Overrides:

overlaps in class Range

See Also:

contains

isCurationSet

public boolean isCurationSet()

ApolloDataI

Specified by:

isCurationSet in interface ApolloDataI

getCurationSet

public CurationSet getCurationSet()

Description copied from interface: ApolloDataI

if isCurationSet returns true than a real curation set would be returned here. This method should be used after testing isCurationSet()==true

Specified by:

getCurationSet in interface ApolloDataI

isCompositeDataHolder

public boolean isCompositeDataHolder()

Specified by:

isCompositeDataHolder in interface ApolloDataI

getCompositeDataHolder

public CompositeDataHolder getCompositeDataHolder()

Specified by:

getCompositeDataHolder in interface ApolloDataI

isMultiSpecies

public boolean isMultiSpecies()

Temporary method until all synteny stuff uses CompositeDataHolder rename isComposite?

Specified by:

isMultiSpecies in interface ApolloDataI

getAnalysisFeatureList

public FeatureList getAnalysisFeatureList(java.lang.String analysisName)

Returns a FeatureList for both strands of an analysis, the first item in list is forward strand, 2nd is rev strand. analysisName is what is called resulttype in the tiers file - its the name for the analysis in the data itself - not the name of the tier that it maps to in the gui (via the tiers file)

hasTransactions

public boolean hasTransactions()

hasTransactionManager

public boolean hasTransactionManager()

getTransactionManager

public TransactionManager getTransactionManager()

Returns:

Returns the tranManager.

setTransactionManager

public void setTransactionManager(TransactionManager tranManager)

Parameters:

tranManager - The tranManager to set.

isChromosomeArmUsed

public boolean isChromosomeArmUsed()

A rather strange implemenation. This method is based on GAMESave.writeGenomePosition(CurationSet).