Public

getId

createAttribute

Creates a new ConceptAccession with the given accession, the information which
DataSource it belongs

createConceptAccession

Creates a new ConceptName with the given name and the information if this name
is preferred. Then ad

createConceptName

getOfType

getConceptAccessions

Returns the DataSource, which this AbstractConcept belongs to.

getElementOf

Returns the parser id of this instance of AbstractConcept.

getPID

Returns all ConceptNames contained in the list of ConceptNames.

getConceptNames

getAttribute

Returns a ConceptName or null if unsuccessful for a given name or null if
unsuccessful.

getConceptName

Returns the annotation of this instance of AbstractConcept.

getAnnotation

addTag

Returns the description of this instance of AbstractConcept.

getDescription

getAttributes

getTags

getEvidence

Sets the annotation of this instance of AbstractConcept.

setAnnotation

Returns a ConceptAccession or null if unsuccessful for a given accession and
DataSource or null if u

getConceptAccession

Sets the description of this instance of AbstractConcept.

setDescription

ONDEXConcept

Finding current android device location

A FileInputStream obtains input bytes from a file in a file system. What files
are available depends

java.io.FileInputStream

A specialized Reader that reads from a file in the file system. All read
requests made by calling me

java.io.FileReader

An exception that indicates a failed JDBC operation. It provides the following
information about pro

java.sql.SQLException

A counting semaphore. Conceptually, a semaphore maintains a set of permits. Each
#acquire blocks if 

java.util.concurrent.Semaphore

An int value that may be updated atomically. See the java.util.concurrent.atomic
package specificati

java.util.concurrent.atomic.AtomicInteger

Operations on java.lang.String that arenull safe.

 * IsEmpty/IsBlank - checks if a String contains 

org.apache.commons.lang.StringUtils

addToBackStack

getSharedPreferences

Return the FragmentManager for interacting with fragments associated with this
activity.

getSupportFragmentManager

/**
	 * 
	 * @see net.sourceforge.ondex.core.ONDEXGraph#deleteConcept(java.lang.Integer)
	 */

// check for null concept, happens only for invalid id

// remove from possible tag, avoid concurrent

// modification exception by converting to array

// delete associate relations of concept, avoid concurrent

/**
	 * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
	 */

// add new EvidenceType or modify list of Evidences

// this is a pre-filter step if a DataSource was given

// start at a root concept of given concept class

/**
	 * filters on a subset of a graph rather than the whole
	 * 
	 * @param conceptSubset
	 * @param relationsSubset
	 */

// filter only within given concept classes

// if concept is actually a tag for some other concept

// remove concept from all other concept tag lists

// remove concept from all other relation tag lists

" concepts because they are used as tag."

/**
	 * Removes all contexts from the graph and assigns the correct pathway
	 * contexts. Only works for KEGG(graph must be compatible to version at
	 * 12.08.09) Used in Lysenko et. al. (2009)
	 * 
	 * @param viewer
	 *            - ovtk viewer
	 */

/*
		 * String[][] pattern = new String[][]{ new String[]{"Path"}, new
		 * String[]{"m_isp"}, new String[]{"Reaction"}, new
		 * String[]{"pd_by","cs_by","ca_by","cat_c"}, new
		 * String[]{"Comp","Enzyme","EC"}, new
		 * String[]{"part_of","in_by","ac_by","bi_to","is_a"}, new
		 * String[]{"Protcmplx","Protein"} }; List<Subgraph> subs =
		 * StandardFunctions.getSubgraphMatch(graph, pattern);
		 * System.err.println("Found subnetworks: "+subs.size()); ConceptClass
		 * path = graph.getMetaData().getConceptClass("Path"); for(Subgraph sub
		 * :subs){ Set<ONDEXConcept> ms =sub.getConcepts(); while(ms.hasNext()){
		 * ONDEXConcept m = ms.next(); if(m.getOfType().equals(path)){
		 * sub.addContext(m); break; } } ms.close(); }
		 */

/**
     * Runs a Filter producer on the input graph and applies results and there
     * tag dependencies to the output graph
     *
     * @param filter  the filter to run
     * @param args  the arguments to run with
     * @param graphInput  the graph to apply the filter on
     * @param graphOutput the graph to write results to (cloned from input graph)
     * @throws Exception  if the filter fails
     */

"Can not run plugin with a null graphInput"

"filter.getVisibleRelations() returns null after start"

"filter.getVisibleConcepts() returns null after start"

" filter complete cloning returned concept from "

// delete all not found concepts in the graph

" filter complete removing non matching concepts from original graph as GraphInput is the same as GraphOutput"

"Identifying Tag dependencies on Relations "

//				explicitly delete relations on deleted concepts (for safety)

How to use removeTagmethodin net.sourceforge.ondex.core.ONDEXConcept

Best Java code snippets using net.sourceforge.ondex.core.ONDEXConcept.removeTag (Showing top 6 results out of 315)

How to use
removeTag
method
in
net.sourceforge.ondex.core.ONDEXConcept