apollo.datamodel
Class Protein

java.lang.Object
  apollo.datamodel.Range
      apollo.datamodel.SeqFeature
          apollo.datamodel.FeatureSet
              apollo.datamodel.AnnotatedFeature
                  apollo.datamodel.Protein

All Implemented Interfaces:

AnnotatedFeatureI, Comparable, FeatureSetI, RangeI, SeqFeatureI, TranslationI, java.io.Serializable, java.lang.Cloneable

public class Protein
extends AnnotatedFeature

See Also:

Serialized Form

Field Summary

Fields inherited from class apollo.datamodel.AnnotatedFeature

annotationRoot, logger, owner

Fields inherited from class apollo.datamodel.FeatureSet

features, flags, genericReadThroughStopResidue, hitSequence, minus1_frameshift, missing_3prime, missing_5prime, plus1_frameshift, POLYA_REMOVED, readthrough_stop, standard_start_codon, start_codon, trans_spliced

Fields inherited from class apollo.datamodel.SeqFeature

biotype, edit_offset_adjust, id, phase, properties, ref_features, refFeature, refId, score, scores

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

Protein(SeqFeatureI protFeat, Transcript transcript)

Protein(Transcript transcript)

Method Summary

int	getEnd() so the end is rather controversial.
java.lang.String	getFeatureType() Returns "polypeptide" as that is the SO term for proteins
java.lang.String	getId() for now just a wrapper for prot seq - eventually id will migrate here
java.lang.String	getName() In the case where the range is chromosomal the name is the chromosome name
SequenceI	getPeptideSequence() transcripts peptide sequence should be moved here eventually
SequenceI	getRefSequence() Retrieve the SequenceI that this feature annotates.
int	getStart()
boolean	hasTranslationEnd() well this is actually controversial - translation end is just beyond the protien - this should either be refactored or just be in transcript - need to think about this...
boolean	hasTranslationStart() should this just be hasStart? translation is implicit now isnt it?
boolean	isProtein()
boolean	isProteinCodingGene() this better be true considering we are a protein
void	setId(java.lang.String id)
void	setName(java.lang.String name)
void	setStart(int start) Theres 2 situations for setting start - one is when initially building the datamodel and the exons havent been read in yet so you are not yet ready to calculate the translation, the other is the transcript is in place so setting start should cause a translate recalc to get a new end - for now just doing former(for game adapters sake) - for the latter i think there should be a 2nd setStart with a recalc flag or vice versa - or is setting start a result of the translate process rather than a trigger?

Methods inherited from class apollo.datamodel.AnnotatedFeature

accept, addComment, addComment, addEvidence, addEvidence, addEvidence, addEvidence, addSynonym, addSynonym, addSynonym, clearComments, clearSynonyms, clone, cloneAnnot, deleteComment, deleteComment, deleteEvidence, deleteSynonym, deleteSynonym, get_cDNASequence, getAnnotatedFeature, getAnnotChild, getCommentIndex, getComments, getDescription, getEvidence, getEvidenceFinder, getNonConsensusAcceptorNum, getNonConsensusDonorNum, getOwner, getSynonym, getSynonyms, getSynonyms, getSynonymSize, hasAnnotatedFeature, hasSynonym, isAnnotTop, isFinished, isProblematic, nonConsensusSplicingOkay, nonConsensusSplicingOkay, setDescription, setEvidenceFinder, setIsProblematic, setOwner, toString

Methods inherited from class apollo.datamodel.FeatureSet

addFeature, addFeature, adjustEdges, adjustEdges, beforeFivePrimeEnd, buildEditList, buildORFEditList, calcTranslationStartForLongestPeptide, canHaveChildren, clearKids, deleteFeature, deleteFeatureAt, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByHitName, findFeaturesByName, findFeaturesByName, flipFlop, get_cDNA, get_ORF, get_ORF, getFeatureAt, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatures, getGenomicPosForPeptidePos, getGenomicPosition, getHitSequence, getIndexContaining, getLastBaseOfStopCodon, getLeafFeatsOver, getNumberOfDescendents, getPeptidePosForGenomicPos, getPositionFrom, getScore, getSequencingErrorAtPosition, getSplicedLength, getSplicedLength, getSplicedTranscript, getStartAA, getStartCodon, getTranslation, getTranslationEnd, getTranslationRange, getTranslationStart, hasDescendents, hasNameBeenSet, hasReadThroughStop, hasTranslation, insertFeatureAt, isFlagSet, isMissing3prime, isMissing5prime, isSequencingErrorPosition, isTransSpliced, minus1FrameShiftPosition, pastThreePrimeEnd, plus1FrameShiftPosition, rangeIsUnassigned, readThroughStopPosition, readThroughStopResidue, setFlag, setHitSequence, setMinus1FrameShiftPosition, setMissing3prime, setMissing5prime, setPeptideValidity, setPhases, setPlus1FrameShiftPosition, setProteinCodingGene, setReadThroughStop, setReadThroughStop, setRefSequence, setTranslationEnd, setTranslationEndFromStart, setTranslationEndNoPhase, setTranslationStart, setTranslationStart, size, sort, sort, translate, unConventionalStart, withinCDS

Methods inherited from class apollo.datamodel.SeqFeature

addDbXref, addProperty, addRefFeature, addScore, addScore, addScore, addScore, alignmentIsPeptide, amend_RNA, buildmRNAEditList, clearProperties, cloneFeature, compareTo, descendsFrom, getAlignment, getAnalogousOppositeStrandFeature, getCigar, getCloneSource, getCodingDNA, getCodingProperties, getDatabase, getDbXref, getDbXrefs, getEndPhase, getExplicitAlignment, getFeatureSequence, getFrame, getGenomicErrors, getHend, getHhigh, getHitFeature, getHlow, getHname, getHstart, getHstrand, getIdentifier, getNumberOfChildren, getParent, getPhase, getPrimaryDbXref, getProgramName, getProperties, getPropertiesMulti, getProperty, getPropertyMulti, getProteinFeat, getRefFeature, getRefFeature, getRefId, getScore, getScores, getStrandedFeatSetAncestor, getSubSequence, getSyntenyLinkInfo, getTopLevelType, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasCigar, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, haveExplicitAlignment, haveRealAlignment, initWithSeqFeat, isAncestorOf, isAnnot, isClone, isCodon, isExon, isSameFeat, isSequencingError, isTranscript, main, merge, na2aa, numberOfGenerations, parseCigar, removeProperty, replaceProperty, setAlignment, setAnalogousOppositeStrandFeature, setCigar, setDatabase, setExplicitAlignment, setIdentifier, setPhase, setProgramName, setQueryFeature, setRefFeature, setScore, setSyntenyLinkInfo, setTopLevelType, setUserObject

Methods inherited from class apollo.datamodel.Range

contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getEndAsString, getHigh, getLeftOverlap, getLow, getRangeClone, getResidues, getRightOverlap, getStartAsString, getStrand, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, sameRange, setEnd, setFeatureType, setHigh, setLow, setStrand

Methods inherited from class java.lang.Object

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

Methods inherited from interface apollo.datamodel.AnnotatedFeatureI

getIdentifier, setIdentifier

Methods inherited from interface apollo.datamodel.FeatureSetI

adjustEdges, adjustEdges, buildEditList, deleteFeature, deleteFeatureAt, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByHitName, findFeaturesByName, findFeaturesByName, getHitSequence, getIndexContaining, getPositionFrom, getSequencingErrorAtPosition, getSplicedLength, getStartAA, getStartCodon, hasDescendents, hasNameBeenSet, hasReadThroughStop, isFlagSet, isSequencingErrorPosition, minus1FrameShiftPosition, plus1FrameShiftPosition, readThroughStopPosition, readThroughStopResidue, setFlag, setHitSequence, setMinus1FrameShiftPosition, setPlus1FrameShiftPosition, setProteinCodingGene, setReadThroughStop, setReadThroughStop, sort, sort, unConventionalStart, withinCDS

Methods inherited from interface apollo.datamodel.SeqFeatureI

addDbXref, addFeature, addFeature, addProperty, addScore, addScore, addScore, addScore, alignmentIsPeptide, clearKids, clearProperties, cloneFeature, compareTo, descendsFrom, flipFlop, get_cDNA, getAlignment, getAnalogousOppositeStrandFeature, getCigar, getCloneSource, getCodingDNA, getCodingProperties, getDatabase, getDbXref, getDbXrefs, getEndPhase, getExplicitAlignment, getFeatureAt, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatures, getFeatureSequence, getFrame, getGenomicErrors, getGenomicPosForPeptidePos, getGenomicPosition, getHend, getHhigh, getHitFeature, getHlow, getHname, getHstart, getHstrand, getLeafFeatsOver, getNumberOfChildren, getNumberOfDescendents, getParent, getPhase, getProgramName, getProperties, getPropertiesMulti, getProperty, getPropertyMulti, getProteinFeat, getRefFeature, getRefId, getScore, getScore, getScores, getStrandedFeatSetAncestor, getSyntenyLinkInfo, getTopLevelType, getTranslation, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, isAncestorOf, isAnnot, isClone, isCodon, isExon, isSameFeat, isSequencingError, isTranscript, merge, numberOfGenerations, parseCigar, removeProperty, replaceProperty, setAlignment, setAnalogousOppositeStrandFeature, setCigar, setDatabase, setExplicitAlignment, setPhase, setProgramName, setQueryFeature, setRefFeature, setScore, setSyntenyLinkInfo, setTopLevelType, setUserObject, size, translate

Methods inherited from interface apollo.datamodel.RangeI

canHaveChildren, contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getHigh, getLeftOverlap, getLow, getRangeClone, getResidues, getRightOverlap, getStrand, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, rangeIsUnassigned, sameRange, setEnd, setFeatureType, setHigh, setLow, setRefSequence, setStrand

Methods inherited from interface apollo.datamodel.TranslationI

calcTranslationStartForLongestPeptide, getLastBaseOfStopCodon, getTranslationEnd, getTranslationRange, getTranslationStart, isMissing3prime, isMissing5prime, setMissing3prime, setMissing5prime, setPeptideValidity, setTranslationEnd, setTranslationEndFromStart, setTranslationStart, setTranslationStart

Constructor Detail

Protein

public Protein(Transcript transcript)

Protein

public Protein(SeqFeatureI protFeat,
               Transcript transcript)

Method Detail

isProtein

public boolean isProtein()

Specified by:

isProtein in interface SeqFeatureI

Overrides:

isProtein in class SeqFeature

isProteinCodingGene

public boolean isProteinCodingGene()

this better be true considering we are a protein

Specified by:

isProteinCodingGene in interface FeatureSetI

Specified by:

isProteinCodingGene in interface SeqFeatureI

Overrides:

isProteinCodingGene in class AnnotatedFeature

See Also:

FeatureSet.setProteinCodingGene(boolean)

getRefSequence

public SequenceI getRefSequence()

Description copied from interface: RangeI

Retrieve the SequenceI that this feature annotates.

Specified by:

getRefSequence in interface RangeI

Overrides:

getRefSequence in class Range

Returns:

the current parent SequenceI

getPeptideSequence

public SequenceI getPeptideSequence()

transcripts peptide sequence should be moved here eventually

Specified by:

getPeptideSequence in interface SeqFeatureI

Overrides:

getPeptideSequence in class SeqFeature

getId

public java.lang.String getId()

for now just a wrapper for prot seq - eventually id will migrate here

Specified by:

getId in interface SeqFeatureI

Overrides:

getId in class SeqFeature

setId

public void setId(java.lang.String id)

Specified by:

setId in interface SeqFeatureI

Overrides:

setId in class SeqFeature

setName

public void setName(java.lang.String name)

Specified by:

setName in interface RangeI

Overrides:

setName in class Range

getName

public java.lang.String getName()

Description copied from interface: RangeI

In the case where the range is chromosomal the name is the chromosome name

Specified by:

getName in interface RangeI

Overrides:

getName in class FeatureSet

getFeatureType

public java.lang.String getFeatureType()

Returns "polypeptide" as that is the SO term for proteins

Specified by:

getFeatureType in interface RangeI

Overrides:

getFeatureType in class Range

getStart

public int getStart()

Specified by:

getStart in interface RangeI

Overrides:

getStart in class Range

setStart

public void setStart(int start)

Theres 2 situations for setting start - one is when initially building the datamodel and the exons havent been read in yet so you are not yet ready to calculate the translation, the other is the transcript is in place so setting start should cause a translate recalc to get a new end - for now just doing former(for game adapters sake) - for the latter i think there should be a 2nd setStart with a recalc flag or vice versa - or is setting start a result of the translate process rather than a trigger?

Specified by:

setStart in interface RangeI

Overrides:

setStart in class Range

getEnd

public int getEnd()

so the end is rather controversial. transcript.getTranslationEnd() is actually the first base of the stop - the last base of the protein is in fact the base before this - so the question is do we use the translation end or the last base of the protein (as chado does for their proteins) which is in fact getTranslationEnd() +/- 1??? i think we should go with real prot end not trans stop

Specified by:

getEnd in interface RangeI

Overrides:

getEnd in class Range

hasTranslationStart

public boolean hasTranslationStart()

should this just be hasStart? translation is implicit now isnt it?

Specified by:

hasTranslationStart in interface TranslationI

Overrides:

hasTranslationStart in class FeatureSet

hasTranslationEnd

public boolean hasTranslationEnd()

well this is actually controversial - translation end is just beyond the protien - this should either be refactored or just be in transcript - need to think about this...

Specified by:

hasTranslationEnd in interface TranslationI

Overrides:

hasTranslationEnd in class FeatureSet