Index (PhenoTips - Patient Network - Matching Notification

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A

addNote(Long, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Saves note for a match that has the given matchId internal ID.
addNote(PatientMatch, String) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Saves a note to a match.

C

createAdminEmailsToLocalUsers(List<PatientMatch>, Map<Long, List<String>>) - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotifier: Build a list of emails based on the given matches.
createUserEmail(PatientMatch, String, String, String, String) - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotifier: Generates a email to be sent from the current user to the owner of the subjectPatientId on subjectServerId describing the given match.

D

DATA_SPACE - Static variable in interface org.phenotips.matchingnotification.match.PatientMatch: The space where matches data is stored.
deleteMatchesForLocalPatient(String) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Deletes all matches (including those that users have been notified about, and MME matches) for the given local patient (e.g.

F

findMatches(List<String>, Set<String>, boolean) - Method in interface org.phenotips.matchingnotification.finder.MatchFinder: Finds matches for all patients.
findMatches(Patient, String) - Method in interface org.phenotips.matchingnotification.finder.MatchFinder: Finds matches for a given patient.
findMatchesForAllPatients(Set<String>, boolean) - Method in interface org.phenotips.matchingnotification.finder.MatchFinderManager: Finds matches for all local patients on the selected servers.
findMatchesForPatient(Patient, String) - Method in interface org.phenotips.matchingnotification.finder.MatchFinderManager: Finds matches for a local patient on the selected server.

G

getAccess() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getAccessType() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getAgeOfOnset() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getCandidateGenes() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getComments() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getContactInfo() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getDetailsColumnJSON() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getDisorders() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getEmail() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchEmail: Get email data (body, subject, recipients) in a JSON format.
getEmails() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getErrorMessage() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotificationResponse
getExternalId() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getFeatureMatchesJSON() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getFoundTimestamp() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getGenesStatus() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getGenotypeScore() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getGenotypeSimilarityJSON() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getHref() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getHref() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getId() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getLastMatchUpdateStatus(String) - Method in interface org.phenotips.matchingnotification.finder.MatchFinderManager: Returns a JSON object containing last matches update details for a provided patientId patient for all servers (local matches or MME matches).
getLastUpdatedDateForServerForPatient(String, String) - Method in interface org.phenotips.matchingnotification.finder.MatchFinder: Finds last matches update status for a provided patientId patient for the selected server.
getMatch(Long) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Returns a match that has the given matchId internal ID.
getMatched() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getMatchedDetails() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getMatchedExomeGenes() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getMatchedPatientId() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getMatchedServerId() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getMatches() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchEmail
getModeOfInheritance() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getNote() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getNotes() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getNotificationHistory() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getNumberOfRemoteMatches() - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Calculates the number of matches that were found by all remote outgoing/incoming requests where at least one patient in the match is remote.
getPatient() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getPatientId() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getPatientMatches() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotificationResponse
getPhenotypes() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getPhenotypeScore() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getPriority() - Method in interface org.phenotips.matchingnotification.finder.MatchFinder
getReference() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getReferenceDetails() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getReferencePatientId() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getReferenceServerId() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getScore() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getServerId() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
getStatus() - Method in interface org.phenotips.matchingnotification.match.PatientMatch
getStatus() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchEmail
getSubjectPatientId() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchEmail
getSupportedServerIdList() - Method in interface org.phenotips.matchingnotification.finder.MatchFinder
getUserEmailContent(Long, String, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Returns the contents of the email that will be send as a notification for match with the given id, with the recipient being the owner of the given patient on the given server.

H

hasExomeData() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
hasSameMatchData(PatientMatch) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Checks that matches are equivalent (see isEquivalent()) and that the match data is the same, meaning that scores are the same, phenotype/genotype is the same, etc.

I

isEquivalent(PatientMatch) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Checks if other is equivalent to this.
isIncoming() - Method in interface org.phenotips.matchingnotification.match.PatientMatch: See PatientMatch.isLocal().
isLocal() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
isLocal() - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Checks if a request is local.
isMatched(String, String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Checks if the patient given in parameter is the matched patient of the match.
isOutgoing() - Method in interface org.phenotips.matchingnotification.match.PatientMatch: See PatientMatch.isLocal().
isReference(String, String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Checks if the patient given in parameter is the reference patient of the match.
isRejected() - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Deprecated.
use PatientMatch.getStatus() instead
isSuccessul() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotificationResponse

L

loadMatches(String, double, double, double, boolean, Timestamp, Timestamp) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Loads matches filtered by the parameters.
loadMatchesByIds(Set<Long>) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Load all matches with ids in matchesIds.

M

MATCHES - Static variable in class org.phenotips.matchingnotification.export.PatientMatchExport: Key for matches array.
MatchFinder - Interface in org.phenotips.matchingnotification.finder
MatchFinderManager - Interface in org.phenotips.matchingnotification.finder
MatchingNotificationManager - Interface in org.phenotips.matchingnotification
MatchStorageManager - Interface in org.phenotips.matchingnotification.storage

N

notify(PatientMatchEmail) - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotifier: Sends notification for an email.

O

onEvent(Event, Object, Object) - Method in class org.phenotips.matchingnotification.events.PatientMatchesRemover
org.phenotips.matchingnotification - package org.phenotips.matchingnotification
org.phenotips.matchingnotification.events - package org.phenotips.matchingnotification.events
org.phenotips.matchingnotification.export - package org.phenotips.matchingnotification.export
org.phenotips.matchingnotification.finder - package org.phenotips.matchingnotification.finder
org.phenotips.matchingnotification.match - package org.phenotips.matchingnotification.match
org.phenotips.matchingnotification.notification - package org.phenotips.matchingnotification.notification
org.phenotips.matchingnotification.storage - package org.phenotips.matchingnotification.storage

P

PatientInMatch - Interface in org.phenotips.matchingnotification.match: The interface is used for unified access to reference and matched patients.
PatientMatch - Interface in org.phenotips.matchingnotification.match: Encapsulates a match between a reference patient and a matched patient.
PatientMatchEmail - Interface in org.phenotips.matchingnotification.notification
PatientMatchesRemover - Class in org.phenotips.matchingnotification.events: Removes local matches from database for the patient that was deleted.
PatientMatchesRemover() - Constructor for class org.phenotips.matchingnotification.events.PatientMatchesRemover: Default constructor, sets up the listener name and the list of events to subscribe to.
PatientMatchExport - Class in org.phenotips.matchingnotification.export
PatientMatchExport() - Constructor for class org.phenotips.matchingnotification.export.PatientMatchExport
PatientMatchNotificationResponse - Interface in org.phenotips.matchingnotification.notification: Response to a notification.
PatientMatchNotifier - Interface in org.phenotips.matchingnotification.notification: Send a notification per patient.

S

saveComment(Long, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Saves comment for a match that has the given matchId internal ID.
saveComment(PatientMatch, String) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Saves comment to a match.
saveIncomingMatches(List<? extends PatientSimilarityView>, String, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Saves a list of matches that were found by a remote incoming request.
saveLocalMatches(Collection<? extends PatientSimilarityView>, String) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Saves a list of local matches.
saveOutgoingMatches(List<? extends PatientSimilarityView>, String, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Saves a list of matches that were found by a remote outgoing request.
saveRemoteMatches(Collection<? extends PatientSimilarityView>, String, String, boolean) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Saves a list of matches that were found by a remote outgoing/incoming request.
send() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchEmail: Send the email.
sendAdminNotificationsToLocalUsers(Map<Long, List<String>>) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Sends notification to the owner of every match with id in matchesId, then marks match as notified.
sendUserNotification(Long, String, String, String, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Sends notification to the owner of the suvbjectpatientId about the given match.
setComments(JSONArray) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Sets match comments.
setExternallyContacted(boolean) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Add a record to the notification history in case user contacted regarding this match outside of PhenomeCentral.
setFoundTimestamp(Timestamp) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set the timestamp when the match was found.
setGenotypeScore(Double) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set genotype the score.
setMatchedDetails(String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set matched details.
setMatchedPatientInMatch(PatientInMatch) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set the matched patient in match.
setNotes(JSONArray) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Sets match notes as a JSON object, in the following format:
setNotificationHistory(JSONObject) - Method in interface org.phenotips.matchingnotification.match.PatientMatch
setPatientMatches(Collection<PatientMatch>) - Method in interface org.phenotips.matchingnotification.notification.PatientMatchNotificationResponse
setPhenotypeScore(Double) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set the phenotype score.
setReferenceDetails(String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set the reference details.
setReferencePatientInMatch(PatientInMatch) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set the reference patient in match when the match was found.
setScore(Double) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Set the match score.
setStatus(String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Marks status property of match (saved, rejected or uncategorized).
setStatus(Long, String) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Sets status for a match that has the given matchId internal ID.
setStatus(PatientMatch, String) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Sets status to a match.
setUserContacted(Long, boolean) - Method in interface org.phenotips.matchingnotification.MatchingNotificationManager: Marks all matches with ids in matchesIds as user-contacted or not.
setUserContacted(PatientMatch, boolean) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Marks a match as user-contacted or not.

T

toJSON(List<PatientMatch>) - Method in class org.phenotips.matchingnotification.export.PatientMatchExport
toJSON() - Method in interface org.phenotips.matchingnotification.match.PatientInMatch
toJSON() - Method in interface org.phenotips.matchingnotification.match.PatientMatch

U

updateComments(String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Updates match comments JSON log string property with new comment.
updateNotes(String) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Updates a notes JSON with new note record.
updateNotes(PatientMatch, String) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Updates match notes string property with new note record.
updateNotificationHistory(JSONObject) - Method in interface org.phenotips.matchingnotification.match.PatientMatch: Updates a notification history JSON log string property with new notification record.
updateNotificationHistory(PatientMatch, JSONObject) - Method in interface org.phenotips.matchingnotification.storage.MatchStorageManager: Updates a notification history JSON log string with new notification record.

W

wasSent() - Method in interface org.phenotips.matchingnotification.notification.PatientMatchEmail

A C D F G H I L M N O P S T U W