apollo.datamodel
Class Link

java.lang.Object
  apollo.datamodel.Link

public class Link
extends java.lang.Object

Constructor Summary

Link(FeaturePairI wrappedFeatPair)

Link(SeqFeatureI link1Feature, SeqFeatureI link2Feature, boolean hasSpec, boolean hasPercentIdentity)

Method Summary

int	getHigh1()
int	getHigh2()
SeqFeatureI	getLinkedSpeciesFeature(SeqFeatureI feat) If feat is not part of link - neither species1 nor species2 feature - then return null.
int	getLow1()
int	getLow2()
java.lang.String	getName1()
java.lang.String	getName2()
double	getPercentIdentity()
SeqFeatureI	getSpeciesFeature1()
SeqFeatureI	getSpeciesFeature2()
int	getStrand1()
int	getStrand2()
java.lang.String	getType() return null if no type
boolean	hasNames() Returns true if query and hit have names
boolean	hasPercentIdentity() Return false if species feat has no score or if its score is no perc id
boolean	hasSpeciesFeatures()
boolean	isForwardStrand1()
boolean	isForwardStrand2()
void	setSpeciesFeature1(SeqFeatureI species1) set species1 feature if different than link1 feature (often they are the same)
void	setSpeciesFeature2(SeqFeatureI species2)
void	setTypeIsFeat1(boolean state) If state is true use species feature 1 for type, false use spec feat 2 link type is used by gui for color/vis

Methods inherited from class java.lang.Object

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

Constructor Detail

Link

public Link(SeqFeatureI link1Feature,
            SeqFeatureI link2Feature,
            boolean hasSpec,
            boolean hasPercentIdentity)

Link

public Link(FeaturePairI wrappedFeatPair)

Method Detail

setSpeciesFeature1

public void setSpeciesFeature1(SeqFeatureI species1)

set species1 feature if different than link1 feature (often they are the same)

setSpeciesFeature2

public void setSpeciesFeature2(SeqFeatureI species2)

setTypeIsFeat1

public void setTypeIsFeat1(boolean state)

If state is true use species feature 1 for type, false use spec feat 2 link type is used by gui for color/vis

getType

public java.lang.String getType()

return null if no type

getName1

public java.lang.String getName1()

getName2

public java.lang.String getName2()

hasNames

public boolean hasNames()

Returns true if query and hit have names

getLow1

public int getLow1()

getHigh1

public int getHigh1()

getLow2

public int getLow2()

getHigh2

public int getHigh2()

getStrand1

public int getStrand1()

isForwardStrand1

public boolean isForwardStrand1()

getStrand2

public int getStrand2()

isForwardStrand2

public boolean isForwardStrand2()

getPercentIdentity

public double getPercentIdentity()

hasPercentIdentity

public boolean hasPercentIdentity()

Return false if species feat has no score or if its score is no perc id

hasSpeciesFeatures

public boolean hasSpeciesFeatures()

getSpeciesFeature1

public SeqFeatureI getSpeciesFeature1()

getSpeciesFeature2

public SeqFeatureI getSpeciesFeature2()

getLinkedSpeciesFeature

public SeqFeatureI getLinkedSpeciesFeature(SeqFeatureI feat)

If feat is not part of link - neither species1 nor species2 feature - then return null. If part of link return the feature it links to