public class PhysicalEntityChain extends Object
Modifier and Type | Class and Description |
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static class |
PhysicalEntityChain.Activity
Values for activity.
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Modifier and Type | Field and Description |
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protected static PathAccessor |
PE2FEAT
Accessor to the modification term.
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protected static PathAccessor |
PE2TERM
Accessor to the modification term.
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PhysicalEntity[] |
pes
Array that links two ends of the chain.
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Constructor and Description |
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PhysicalEntityChain(PhysicalEntity small,
PhysicalEntity big)
Constructor with endpoints.
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Modifier and Type | Method and Description |
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PhysicalEntityChain.Activity |
checkActivityLabel()
Checks if the chain has a member with an activity label.
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protected PhysicalEntity[] |
fillArray(PhysicalEntity parent,
PhysicalEntity target,
int depth,
int dir)
Creates the chain that links the given endpoints.
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Set<String> |
getCellularLocations()
Retrieves the cellular location of the PhysicalEntity.
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Set<ModificationFeature> |
getModifications()
Collects modifications from the elements of the chain.
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boolean |
intersects(PhysicalEntityChain rpeh)
Checks if two chains intersect without ignoring endpoint intersection.
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boolean |
intersects(PhysicalEntityChain rpeh,
boolean ignoreEndPoints)
Checks if two chains intersect.
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public PhysicalEntity[] pes
protected static final PathAccessor PE2TERM
protected static final PathAccessor PE2FEAT
public PhysicalEntityChain(PhysicalEntity small, PhysicalEntity big)
small
- member end of the chainbig
- complex end of the chainLinkedPE
protected PhysicalEntity[] fillArray(PhysicalEntity parent, PhysicalEntity target, int depth, int dir)
parent
- current elementtarget
- target at the member enddepth
- current depthdir
- current direction to traverse homologiespublic Set<String> getCellularLocations()
public boolean intersects(PhysicalEntityChain rpeh)
rpeh
- second chainpublic boolean intersects(PhysicalEntityChain rpeh, boolean ignoreEndPoints)
rpeh
- second chainignoreEndPoints
- flag to ignore intersections at the endpoints of the chainspublic PhysicalEntityChain.Activity checkActivityLabel()
public Set<ModificationFeature> getModifications()
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