Public

delete

update

countAll

getByAc

Fetches the annotations using its parent AC.

getByParentAc

persist

List

Updating database using SQL prepared statement

A thread is a thread of execution in a program. The Java Virtual Machine allows
an application to ha

java.lang.Thread

ArrayList is an implementation of List, backed by an array. All optional
operations including adding

java.util.ArrayList

An object that executes submitted Runnable tasks. This interface provides a way
of decoupling task s

java.util.concurrent.Executor

An ExecutorService that executes each submitted task using one of possibly
several pooled threads, n

java.util.concurrent.ThreadPoolExecutor

Basic implementation of javax.sql.DataSource that is configured via JavaBeans
properties. This is no

org.apache.commons.dbcp.BasicDataSource

This is the main interface of a Quartz Scheduler. A Scheduler maintains a registry of org.quartz.Job

org.quartz.Scheduler

scheduleAtFixedRate

Return the original filename in the client's filesystem.This may contain path
information depending 

getOriginalFilename

addToBackStack

/**
     * Delete hidden annotations for each cv given in the collection
     */

/**
     * Update the proteins with no uniprot cross references and the proteins with uniprot cross references set to 'uniprot-removed-ac'
     * @throws ProteinUpdateException
     */

// create a new file where the results are stored in

"annotation no_uniprot_update removed from the annotations of "

"caution removed from the annotations of "

"Processing the update of the proteins in Intact"

//UpdateReportHandler reportHandler = new FileReportHandler(new File("target"));

//ProteinUpdateProcessorConfig configUpdate = new ProteinUpdateProcessorConfig(reportHandler);

//ProteinUpdateProcessor protUpdateProcessor = new ProteinUpdateProcessor(configUpdate);

//ProteinUpdateProcessor protUpdateProcessor = new ProteinUpdateProcessor();

//protUpdateProcessor.updateByACs(accessionsToUpdate);

"There is a problem when executing the protein update strategy. Check the protein contexts."

/**
     * Add an annotation in a CvObject if it is not in there yet.
     * <p/>
     * The CvTopic and the text of the annotation are given as parameters so the methods is flexible.
     *
     * @param experiment the CvObject in which we want to add the annotation
     * @param topic      the topic of the annotation. must not be null.
     * @param text       the text of the annotation. Can be null.
     */

"ERROR - You must give a non null topic when updating term "

// We allow only one annotation to carry the given topic,

//   > if one if found, we update the text,

//   > if more than one, we delete the excess.

// select all annotation of that object filtered by topic

// first, check if the annotation we want to have in that CvObject is already in

// found it, then we just remove it from the list and we are done.

// not found, we recycle an existing annotation and delete all others

// remove it from the list as we are going to delete all other

// if any annotation left, delete them as we want a unique one.

// update/persist xrefs. Don't call delete because of annotation orphanRemoval = true which is detaching the xref

// update/persist aliases. Don't call delete because of annotation orphanRemoval = true which is detaching the aliases

How to use deletemethodin uk.ac.ebi.intact.core.persistence.dao.AnnotationDao

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How to use
delete
method
in
uk.ac.ebi.intact.core.persistence.dao.AnnotationDao