Package | Description |
---|---|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
org.biopax.paxtools.model.level2 |
This package contains the interfaces that maps to the BioPAX level 2 specification.
|
Modifier and Type | Method and Description |
---|---|
physicalEntityParticipant |
ConversionScore.getMatch(physicalEntityParticipant pep1) |
Modifier and Type | Method and Description |
---|---|
Set<physicalEntityParticipant> |
ConversionScore.getMatchedPEPs() |
Modifier and Type | Method and Description |
---|---|
Object |
ReusedPEPHelper.fixReusedPEP(physicalEntityParticipant pep,
BioPAXElement bpe) |
physicalEntityParticipant |
ConversionScore.getMatch(physicalEntityParticipant pep1) |
Constructor and Description |
---|
ConversionScore(conversion conv1,
conversion conv2,
Double score,
Map<physicalEntityParticipant,physicalEntityParticipant> pepMap,
boolean reverseMatch) |
ConversionScore(conversion conv1,
conversion conv2,
Double score,
Map<physicalEntityParticipant,physicalEntityParticipant> pepMap,
boolean reverseMatch) |
Modifier and Type | Interface and Description |
---|---|
interface |
sequenceParticipant |
Modifier and Type | Method and Description |
---|---|
physicalEntityParticipant |
experimentalForm.getPARTICIPANT() |
Modifier and Type | Method and Description |
---|---|
Set<physicalEntityParticipant> |
catalysis.getCOFACTOR() |
Set<physicalEntityParticipant> |
complex.getCOMPONENTS() |
Set<physicalEntityParticipant> |
control.getCONTROLLER() |
Set<physicalEntityParticipant> |
conversion.getLEFT() |
Set<physicalEntityParticipant> |
conversion.getRIGHT() |
Set<physicalEntityParticipant> |
physicalEntity.isPHYSICAL_ENTITYof() |
Modifier and Type | Method and Description |
---|---|
void |
catalysis.setCOFACTOR(Set<physicalEntityParticipant> COFACTOR) |
void |
complex.setCOMPONENTS(Set<physicalEntityParticipant> COMPONENTS) |
void |
control.setCONTROLLER(Set<physicalEntityParticipant> CONTROLLER) |
void |
conversion.setLEFT(Set<physicalEntityParticipant> LEFT) |
void |
conversion.setRIGHT(Set<physicalEntityParticipant> RIGHT) |
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