org.phenotips.matchingnotification.match

Interface PatientInMatch

public interface PatientInMatch

The interface is used for unified access to reference and matched patients. It calculate the content of the column for each patient in the match and gives a simpler access for their details (these two concerns could potentially be handled in different classes, but for now are handled together).

The advantage of using this interface over a direct access to the match can be seen in comparing these two code blocks:

 
     PatientInMatch pim = condition ? PatientMatch.getReference() : patientMatch.getMatched();
     pim.getPatientId();
     pim.getServerId();
     pim.getGenes();
 compared to
     if (condition) {
        patientMatch.getReferencePatientId(),
        patientMatch.getReferenceServerId(),
        patientMatch.getReferenceGenes() (see comment)
     } else {
        patientMatch.getMatchedPatientId(),
        patientMatch.getMatchedServerId(),
        patientMatch.getMatchedGenes() (see comment)
     }
 
 

See DefaultAdminPatientMatchEmail for some actual usage examples.

Comment: getMatchedGenes()/getReferenceGenes() do not exist - the code serves as an example why it's not a good idea. The access to genes is via PatientInMatch as in the first example.

Version:

$Id: 7d3aded9317c539e6c5b5547797ec36db85caadc $

Method Summary

Modifier and Type	Method and Description
org.phenotips.data.permissions.AccessLevel	getAccess()
String	getAgeOfOnset()
Set<String>	getCandidateGenes()
org.phenotips.data.ContactInfo	getContactInfo()
org.json.JSONObject	getDetailsColumnJSON()
Collection<String>	getEmails()
String	getExternalId()
String	getGenesStatus()
String	getHref()
Set<String>	getMatchedExomeGenes()
Collection<String>	getModeOfInheritance()
org.phenotips.data.Patient	getPatient()
String	getPatientId()
PhenotypesMap	getPhenotypes()
String	getServerId()
boolean	hasExomeData()
boolean	isLocal()
org.json.JSONObject	toJSON()

Method Detail

getPatientId

String getPatientId()

Returns:

id of patient.

getExternalId

String getExternalId()

Returns:

external id of patient.

getServerId

String getServerId()

Returns:

id of server where patient is found. Null if local.

getCandidateGenes

Set<String> getCandidateGenes()

Returns:

a set of candidate genes for patient.

getMatchedExomeGenes

Set<String> getMatchedExomeGenes()

Returns:

a set of matched exome genes for patient.

getPhenotypes

PhenotypesMap getPhenotypes()

Returns:

phenotypes map

toJSON

org.json.JSONObject toJSON()

Returns:

JSON representation of object

isLocal

boolean isLocal()

Returns:

true if patient is local

getEmails

Collection<String> getEmails()

Returns:

a collection of email addresses associated with the patient. If the patient is local, this collection will contain the patient's owner's address, addresses of people from project the patient is part of, etc. If the patient is remote, the collection will contain only an href taken from the match.

getDetailsColumnJSON

org.json.JSONObject getDetailsColumnJSON()

Returns:

the content of details columns for the patient in the match table

getModeOfInheritance

Collection<String> getModeOfInheritance()

Returns:

mode of inheritance

getAgeOfOnset

String getAgeOfOnset()

Returns:

age of onset

getPatient

org.phenotips.data.Patient getPatient()

Returns:

patient if patient is local and exists or null otherwise.

getHref

String getHref()

Returns:

patient href.

hasExomeData

boolean hasExomeData()

Returns:

true if patient has exome data.

getAccess

org.phenotips.data.permissions.AccessLevel getAccess()

Returns:

What type of access does the user have to this patient profile.

getGenesStatus

String getGenesStatus()

Returns:

status of genes (solved or candidate) stored in PatientGenotype class, or null if patient does not have genotype or genotype status is unknown.

getContactInfo

org.phenotips.data.ContactInfo getContactInfo()

Returns:

patient contact information.