diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
index fdc6a03e96acdaf28b633a5a2ce2a574633be64c..ab1810dd4e548f66bcafe189f74b559d73a908fa 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
@@ -4,7 +4,7 @@ import java.util.ArrayList;
import java.util.List;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -21,7 +21,7 @@ public class ImproperAnnotations implements ProblematicAnnotation {
/**
* Object improperly annotated.
*/
- private AnnotatedObject object;
+ private BioEntity object;
/**
* Wrong miriam data.
@@ -29,7 +29,7 @@ public class ImproperAnnotations implements ProblematicAnnotation {
private List<MiriamData> wrongAnnotations = new ArrayList<>();
/**
- * Constructor that initializes the data with {@link #object annotated object}
+ * Constructor that initializes the data with {@link #object bioEntity}
* and list of improper {@link MiriamData}.
*
* @param list
@@ -37,7 +37,7 @@ public class ImproperAnnotations implements ProblematicAnnotation {
* @param object
* annotated object
*/
- public ImproperAnnotations(AnnotatedObject object, List<MiriamData> list) {
+ public ImproperAnnotations(BioEntity object, List<MiriamData> list) {
if (list.size() == 0) {
throw new InvalidArgumentException("List of improper annotations cannot be null");
}
@@ -54,7 +54,7 @@ public class ImproperAnnotations implements ProblematicAnnotation {
* @param object
* annotated object
*/
- public ImproperAnnotations(AnnotatedObject object, MiriamData miriamData) {
+ public ImproperAnnotations(BioEntity object, MiriamData miriamData) {
this.object = object;
wrongAnnotations.add(miriamData);
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
index fa0918a2489fa67575473a3ac473f0eb86dafeb7..64aa9a4bc144eb9929a04c835a26ed11576d88a4 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.services;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -15,7 +15,7 @@ public class MissingAnnotation implements ProblematicAnnotation {
/**
* Object improperly annotated.
*/
- private AnnotatedObject object;
+ private BioEntity object;
/**
* Constructor that initializes the data with {@link #object annotated object}
@@ -24,7 +24,7 @@ public class MissingAnnotation implements ProblematicAnnotation {
* @param object
* annotated object that miss annotation
*/
- public MissingAnnotation(AnnotatedObject object) {
+ public MissingAnnotation(BioEntity object) {
this.object = object;
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
index 8d42181bf0de7b2f1847d73505f444b6960bbe0e..c6a40a2e92f5e24e502ac300aaefd66d7d0acbe6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
@@ -5,7 +5,7 @@ import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -22,7 +22,7 @@ public class MissingRequiredAnnotations implements ProblematicAnnotation {
/**
* Object improperly annotated.
*/
- private AnnotatedObject object;
+ private BioEntity object;
/**
* Required miriam type.
@@ -38,7 +38,7 @@ public class MissingRequiredAnnotations implements ProblematicAnnotation {
* @param object
* annotated object
*/
- public MissingRequiredAnnotations(AnnotatedObject object, Collection<MiriamType> list) {
+ public MissingRequiredAnnotations(BioEntity object, Collection<MiriamType> list) {
if (list.size() == 0) {
throw new InvalidArgumentException("List of improper annotations cannot be null");
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index f7f3cc8d51e9d2f27f4802df75328b7d9a76581b..9808ebd014b966acec5a64d4c7f9a14290e65fa0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -27,7 +27,7 @@ import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.annotation.services.annotators.UniprotAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -289,7 +289,7 @@ public class ModelAnnotator {
}
// annotate all reactions
- for (AnnotatedObject element : model.getReactions()) {
+ for (BioEntity element : model.getReactions()) {
List<ElementAnnotator> list = null;
if (annotators != null) {
list = annotators.get(element.getClass());
@@ -336,7 +336,7 @@ public class ModelAnnotator {
* @return list of improper annotations
*/
public Collection<ImproperAnnotations> findImproperAnnotations(Model m, IProgressUpdater updater,
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> validAnnotations) {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations) {
if (validAnnotations == null) {
logger.warn("List of valid annotations is missing. Using default.");
validAnnotations = getDefaultValidClasses();
@@ -375,10 +375,10 @@ public class ModelAnnotator {
* where we look for improper annotations
* @param validClasses
* list of {@link MiriamType miriam types} that are valid for a given
- * {@link AnnotatedObject}
+ * {@link BioEntity}
* @return list of improper annotations
*/
- protected List<ImproperAnnotations> findImproperAnnotations(AnnotatedObject element, Collection<MiriamType> validClasses) {
+ protected List<ImproperAnnotations> findImproperAnnotations(BioEntity element, Collection<MiriamType> validClasses) {
List<ImproperAnnotations> result = new ArrayList<>();
for (MiriamData md : element.getMiriamData()) {
boolean valid = false;
@@ -406,7 +406,7 @@ public class ModelAnnotator {
*
* @return list of all elements that miss annotation
*/
- public Collection<ProblematicAnnotation> findMissingAnnotations(Model m, Map<Class<? extends AnnotatedObject>, Set<MiriamType>> requestedAnnotations) {
+ public Collection<ProblematicAnnotation> findMissingAnnotations(Model m, Map<Class<? extends BioEntity>, Set<MiriamType>> requestedAnnotations) {
if (requestedAnnotations == null) {
logger.warn("List of requested annotations is missing. Using default.");
requestedAnnotations = getDefaultRequiredClasses();
@@ -428,7 +428,7 @@ public class ModelAnnotator {
}
/**
- * Checks if {@link AnnotatedObject} is properly annotated and if not return
+ * Checks if {@link BioEntity} is properly annotated and if not return
* info about missing annotation.
*
* @param element
@@ -440,7 +440,7 @@ public class ModelAnnotator {
* miriam
* @return list of containing improper annotations about element
*/
- private List<ProblematicAnnotation> findMissing(AnnotatedObject element, Collection<MiriamType> requestedAnnotations) {
+ private List<ProblematicAnnotation> findMissing(BioEntity element, Collection<MiriamType> requestedAnnotations) {
List<ProblematicAnnotation> result = new ArrayList<>();
// if there are no requested annotations then don't check
if (requestedAnnotations == null) {
@@ -567,14 +567,14 @@ public class ModelAnnotator {
/**
* Returns map with informations about default valid {@link MiriamType miriam
- * types } for {@link AnnotatedObject} class type.
+ * types } for {@link BioEntity} class type.
*
* @return map with informations about valid {@link MiriamType miriam types }
- * for {@link AnnotatedObject} class type
+ * for {@link BioEntity} class type
*/
@SuppressWarnings("unchecked")
- public Map<Class<? extends AnnotatedObject>, Set<MiriamType>> getDefaultValidClasses() {
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> result = new HashMap<Class<? extends AnnotatedObject>, Set<MiriamType>>();
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultValidClasses() {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> result = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
ElementUtils eu = new ElementUtils();
ClassTreeNode tree = eu.getAnnotatedElementClassTree();
@@ -583,7 +583,7 @@ public class ModelAnnotator {
while (!nodes.isEmpty()) {
ClassTreeNode node = nodes.poll();
Set<MiriamType> set = new HashSet<MiriamType>();
- Class<? extends AnnotatedObject> clazz = (Class<? extends AnnotatedObject>) node.getClazz();
+ Class<? extends BioEntity> clazz = (Class<? extends BioEntity>) node.getClazz();
for (MiriamType mt : MiriamType.values()) {
for (Class<?> clazz2 : mt.getValidClass()) {
if (clazz2.isAssignableFrom(clazz)) {
@@ -601,14 +601,14 @@ public class ModelAnnotator {
/**
* Returns map with informations about default required {@link MiriamType
- * miriam types } for {@link AnnotatedObject} class type.
+ * miriam types } for {@link BioEntity} class type.
*
* @return map with informations about required {@link MiriamType miriam types
- * * } for {@link AnnotatedObject} class type
+ * * } for {@link BioEntity} class type
*/
@SuppressWarnings("unchecked")
- public Map<Class<? extends AnnotatedObject>, Set<MiriamType>> getDefaultRequiredClasses() {
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> result = new HashMap<>();
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultRequiredClasses() {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> result = new HashMap<>();
ElementUtils eu = new ElementUtils();
ClassTreeNode tree = eu.getAnnotatedElementClassTree();
@@ -617,7 +617,7 @@ public class ModelAnnotator {
while (!nodes.isEmpty()) {
ClassTreeNode node = nodes.poll();
Set<MiriamType> set = null;
- Class<? extends AnnotatedObject> clazz = (Class<? extends AnnotatedObject>) node.getClazz();
+ Class<? extends BioEntity> clazz = (Class<? extends BioEntity>) node.getClazz();
if ((Boolean) (node.getData())) {
set = new HashSet<>();
for (MiriamType mt : MiriamType.values()) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index 01d78102f9331a535045bbcaf87213f97e24c86c..de59bb3bcf6876d82dc9165e801f8319cc342696 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -29,7 +29,7 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Protein;
@@ -297,7 +297,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
}
@Override
- public void annotateElement(AnnotatedObject element) throws AnnotatorException {
+ public void annotateElement(BioEntity element) throws AnnotatorException {
if (isAnnotatable(element)) {
try {
String annotationString = getAnnotation(new MiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
index bc37df5ec1c44ffb2ede277f415182e3039bc308..a95985e33938f17feadd1366c4d683bb82a491dd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
@@ -20,7 +20,7 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -76,7 +76,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
private static final int NAME_PREFIX_LENGTH = NAME_PREFIX.length();
/**
- * Class used for some simple operations on {@link AnnotatedObject} elements.
+ * Class used for some simple operations on {@link BioEntity} elements.
*/
private ElementUtils elementUtils = new ElementUtils();
@@ -438,7 +438,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(AnnotatedObject element) throws AnnotatorException {
+ public void annotateElement(BioEntity element) throws AnnotatorException {
if (isAnnotatable(element)) {
try {
String warnPrefix = elementUtils.getElementTag(element, this);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index b47160d555d02ecbc1638af6d05e7646e0cde918..dde647a3bf294e8e2aaeeb1e3744ae451ee458c8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -10,7 +10,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -19,7 +19,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * Interface that allows to annotate {@link AnnotatedObject elements} in the
+ * Interface that allows to annotate {@link BioEntity elements} in the
* system. Different implementation use different resources to perform
* annotation. They can annotate different types of elements.
*
@@ -37,7 +37,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* List of classes that can be annotated by this {@link IElementAnnotator
* annotator}.
*/
- private final List<Class<? extends AnnotatedObject>> validClasses = new ArrayList<>();
+ private final List<Class<? extends BioEntity>> validClasses = new ArrayList<>();
/**
* Should be this annotator used as a default annotatior.
@@ -58,11 +58,11 @@ public abstract class ElementAnnotator extends CachableInterface {
public ElementAnnotator(Class<? extends CachableInterface> clazz, Class<?>[] validClasses, boolean isDefault) {
super(clazz);
for (Class<?> validClass : validClasses) {
- if (AnnotatedObject.class.isAssignableFrom(validClass)) {
- addValidClass((Class<? extends AnnotatedObject>) validClass);
+ if (BioEntity.class.isAssignableFrom(validClass)) {
+ addValidClass((Class<? extends BioEntity>) validClass);
} else {
throw new InvalidArgumentException(
- "Cannot pass class of type: " + validClass + ". Only classes extending " + AnnotatedObject.class + " are accepted.");
+ "Cannot pass class of type: " + validClass + ". Only classes extending " + BioEntity.class + " are accepted.");
}
}
this.isDefault = isDefault;
@@ -77,14 +77,14 @@ public abstract class ElementAnnotator extends CachableInterface {
* thrown when there is a problem with annotating not related to
* data
*/
- public abstract void annotateElement(AnnotatedObject element) throws AnnotatorException;
+ public abstract void annotateElement(BioEntity element) throws AnnotatorException;
/**
* Returns a list of all classes that can be annotated using this annotator.
*
* @return a list of all classes that can be annotated using this annotator
*/
- public List<Class<? extends AnnotatedObject>> getValidClasses() {
+ public List<Class<? extends BioEntity>> getValidClasses() {
return validClasses;
}
@@ -97,7 +97,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @return <code>true</code> if object can be annotated by this annotator,
* <code>false</code> otherwise
*/
- public boolean isAnnotatable(AnnotatedObject object) {
+ public boolean isAnnotatable(BioEntity object) {
Class<?> clazz = object.getClass();
for (Class<?> validClazz : getValidClasses()) {
if (validClazz.isAssignableFrom(clazz)) {
@@ -113,7 +113,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param clazz
* class to add
*/
- private void addValidClass(Class<? extends AnnotatedObject> clazz) {
+ private void addValidClass(Class<? extends BioEntity> clazz) {
validClasses.add(clazz);
}
@@ -167,7 +167,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setSymbol(AnnotatedObject element, String symbol, String prefix) {
+ protected void setSymbol(BioEntity element, String symbol, String prefix) {
if (element.getSymbol() == null || element.getSymbol().equals("") || element.getSymbol().equals(symbol)) {
element.setSymbol(symbol);
} else {
@@ -188,7 +188,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setSynonyms(AnnotatedObject element, Collection<String> synonyms, String prefix) {
+ protected void setSynonyms(BioEntity element, Collection<String> synonyms, String prefix) {
if (element.getSynonyms() == null || element.getSynonyms().size() == 0) {
List<String> sortedSynonyms = new ArrayList<>();
sortedSynonyms.addAll(synonyms);
@@ -219,14 +219,14 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Adds description to {@link AnnotatedObject#getNotes()}.
+ * Adds description to {@link BioEntity#getNotes()}.
*
* @param element
* element where annotation should be added
* @param description
* value to set
*/
- protected void setDescription(AnnotatedObject element, String description) {
+ protected void setDescription(BioEntity element, String description) {
if (element.getNotes() == null || element.getNotes().equals("") || element.getNotes().equals(description)) {
element.setNotes(description);
} else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
@@ -242,7 +242,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addHmdbMiriam(AnnotatedObject element, String value) {
+ protected void addHmdbMiriam(BioEntity element, String value) {
element.addMiriamData(new MiriamData(MiriamType.HMDB, value));
}
@@ -311,7 +311,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addChebiMiriam(AnnotatedObject element, String value) {
+ protected void addChebiMiriam(BioEntity element, String value) {
if (!value.startsWith("CHEBI:")) {
value = "CHEBI:" + value;
}
@@ -346,7 +346,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addPubchemMiriam(AnnotatedObject element, String value) {
+ protected void addPubchemMiriam(BioEntity element, String value) {
element.addMiriamData(new MiriamData(MiriamType.PUBCHEM, value));
}
@@ -358,7 +358,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addCogMiriam(AnnotatedObject element, String value) {
+ protected void addCogMiriam(BioEntity element, String value) {
element.addMiriamData(new MiriamData(MiriamType.COG, value));
}
@@ -388,7 +388,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addEcMiriam(AnnotatedObject element, String value) {
+ protected void addEcMiriam(BioEntity element, String value) {
element.addMiriamData(new MiriamData(MiriamType.EC, value));
}
@@ -403,7 +403,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void addKeggMiriam(AnnotatedObject element, String value, String prefix) {
+ protected void addKeggMiriam(BioEntity element, String value, String prefix) {
if (value.startsWith("C")) {
MiriamData md = new MiriamData(MiriamType.KEGG_COMPOUND, value);
element.addMiriamData(md);
@@ -419,7 +419,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Sets {@link AnnotatedObject#getFormula()}.
+ * Sets {@link BioEntity#getFormula()}.
*
* @param element
* element where annotation should be added
@@ -428,7 +428,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setFormula(AnnotatedObject element, String value, String prefix) {
+ protected void setFormula(BioEntity element, String value, String prefix) {
if (element.getFormula() == null || element.getFormula().isEmpty() || element.getFormula().equals(value)) {
element.setFormula(value);
} else {
@@ -437,7 +437,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
- * Sets {@link AnnotatedObject#getAbbreviation()}.
+ * Sets {@link BioEntity#getAbbreviation()}.
*
* @param element
* element where annotation should be added
@@ -446,7 +446,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setAbbreviation(AnnotatedObject element, String value, String prefix) {
+ protected void setAbbreviation(BioEntity element, String value, String prefix) {
if (element.getAbbreviation() == null || element.getAbbreviation().isEmpty() || element.getAbbreviation().equals(value)) {
element.setAbbreviation(value);
} else if (!element.getAbbreviation().contains(value)) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index 3aed48d5ade5967e51e61645b485c19666f6ed8b..61233cb0aca326d933b0f12e53c571a93a0f3c09 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -17,7 +17,7 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Element;
@@ -153,7 +153,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- public void annotateElement(AnnotatedObject element) throws AnnotatorException {
+ public void annotateElement(BioEntity element) throws AnnotatorException {
if (isAnnotatable(element)) {
ElementUtils eu = new ElementUtils();
String prefix = eu.getElementTag(element);
@@ -186,7 +186,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
* @throws AnnotatorException
* thrown when there is a problem with annotating element
*/
- private void annotateElement(AnnotatedObject annotatedObject, MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
+ private void annotateElement(BioEntity annotatedObject, MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
String query = REST_SERVICE_URL + entrezMiriamData.getResource() + URL_SUFFIX;
try {
String content = getWebPageContent(query);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 350037bf732740228ad0b218de248ea7fc18d281..7b61647b9fdeb7cfae84b2bf6196f5e7b436fe53 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -23,7 +23,7 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -148,7 +148,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public void annotateElement(AnnotatedObject element) throws AnnotatorException {
+ public void annotateElement(BioEntity element) throws AnnotatorException {
if (isAnnotatable(element)) {
ElementUtils eu = new ElementUtils();
String prefix = eu.getElementTag(element);
@@ -181,7 +181,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
* @throws AnnotatorException
* thrown when there is a problem with annotating element
*/
- private void annotateElement(AnnotatedObject element, MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
+ private void annotateElement(BioEntity element, MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
EntrezData data = getEntrezForMiriamData(entrezMiriamData, prefix);
if (data != null) {
setSymbol(element, data.getSymbol(), prefix);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index a6ac2d4c677287f051a86f57f2918858abe94ac4..c740c3f3fa0e9fae5d47100b87491e9eb4935292 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -21,7 +21,7 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.MiriamConnector;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -95,7 +95,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
}
@Override
- public void annotateElement(AnnotatedObject object) throws AnnotatorException {
+ public void annotateElement(BioEntity object) throws AnnotatorException {
if (isAnnotatable(object)) {
MiriamData goTerm = null;
for (MiriamData md : object.getMiriamData()) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index fdff86ed88f2bc45e5644258ff899841c8624bf8..c4e5cb7b25e514eaadeaea0a43e33c695fe6c45b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -109,7 +109,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(AnnotatedObject element) throws AnnotatorException {
+ public void annotateElement(BioEntity element) throws AnnotatorException {
if (isAnnotatable(element)) {
ElementUtils eu = new ElementUtils();
String prefix = eu.getElementTag(element);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 5de318adf208d089b93ccbaacf15389b3ae24ab2..3e26f3006a7d190ec35450ba5f9c388cc2d4e8af 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -19,7 +19,7 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.Element;
@@ -46,7 +46,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
private static final String REACTION_ANNOTATION_URL_PREFIX = "http://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
/**
- * Class used for some simple operations on {@link AnnotatedObject} elements.
+ * Class used for some simple operations on {@link BioEntity} elements.
*/
private ElementUtils elementUtils = new ElementUtils();
@@ -111,7 +111,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(AnnotatedObject annotatedObject) throws AnnotatorException {
+ public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
if (isAnnotatable(annotatedObject)) {
String id = annotatedObject.getAbbreviation();
if (id == null || id.isEmpty()) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 583e80f30fff80189050710ff0d9a8c6bb33e35e..997494bd6562f088eb1fd2a0ce46aa3f15912f6b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -17,7 +17,7 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Gene;
@@ -49,7 +49,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
private Pattern uniprotToEntrez = Pattern.compile("DR[\\ ]+GeneID;\\ ([^;\\ ]+)");
/**
- * Class used for some simple operations on {@link AnnotatedObject} elements.
+ * Class used for some simple operations on {@link BioEntity} elements.
*/
private ElementUtils elementUtils = new ElementUtils();
@@ -85,7 +85,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- public void annotateElement(AnnotatedObject object) throws AnnotatorException {
+ public void annotateElement(BioEntity object) throws AnnotatorException {
if (isAnnotatable(object)) {
String uniprotId = object.getName();
boolean uniprotFound = false;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java
index 7df99e6f7ed0b4feeec931a5fbd38804895840c8..ceb28e626080993f73fc4ae22ff0fce947b9f343 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/package-info.java
@@ -1,6 +1,6 @@
/**
* This package contains classes that can annotate
- * {@link lcsb.mapviewer.model.map.AnnotatedObject} objects. General annotation
+ * {@link lcsb.mapviewer.model.map.BioEntity} objects. General annotation
* interface is defined in
* {@link lcsb.mapviewer.annotation.services.annotators.ElementAnnotator} class.
*
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index 77ef6574e8b9626ac64086e7b79847cb65c0d3c4..17af451888c1984d054a889e30c2e2757e48333f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -30,7 +30,7 @@ import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ReconAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -287,7 +287,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
public void testFindMissingAnnotations2() throws Exception {
try {
Model model = getModelForFile("testFiles/annotation/missingAnnotations.xml", false);
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> requestedAnnotations = new HashMap<>();;
+ Map<Class<? extends BioEntity>, Set<MiriamType>> requestedAnnotations = new HashMap<>();;
requestedAnnotations.put(GenericProtein.class, new HashSet<>());
Collection<? extends ProblematicAnnotation> results = modelAnnotator.findMissingAnnotations(model, requestedAnnotations);
assertEquals(1, results.size());
@@ -318,7 +318,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetDefaultRequired() throws Exception {
try {
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> map1 = modelAnnotator.getDefaultRequiredClasses();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map1 = modelAnnotator.getDefaultRequiredClasses();
assertNotNull(map1);
} catch (Exception e) {
@@ -330,7 +330,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetDefaultValid() throws Exception {
try {
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> map2 = modelAnnotator.getDefaultValidClasses();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map2 = modelAnnotator.getDefaultValidClasses();
assertNotNull(map2);
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
index 133858707a7c91f191df75a2d20faec745b40b85..a02974da7d865847f035cc1e0541374f4a667b8d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
@@ -11,7 +11,7 @@ import org.junit.Test;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
@@ -25,7 +25,7 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
}
@Override
- public void annotateElement(AnnotatedObject element) throws AnnotatorException {
+ public void annotateElement(BioEntity element) throws AnnotatorException {
}
@Override
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
index e7068cb3fa9d81aaac56c1addad712e834859c3d..78fe4d4a99c7f8b02e0467cf0fdd345543fc140e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
@@ -25,7 +25,7 @@ import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Ion;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
@@ -161,11 +161,11 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAnnotateUnknownElement() throws Exception {
try {
- AnnotatedObject obj = Mockito.mock(AnnotatedObject.class);
+ BioEntity obj = Mockito.mock(BioEntity.class);
when(obj.getName()).thenReturn("O16G2e");
ReconAnnotator tweakedReconAnnotator = Mockito.spy(reconAnnotator);
- doReturn(true).when(tweakedReconAnnotator).isAnnotatable(any(AnnotatedObject.class));
+ doReturn(true).when(tweakedReconAnnotator).isAnnotatable(any(BioEntity.class));
tweakedReconAnnotator.annotateElement(obj);
assertEquals(1, getWarnings().size());
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index f9ec3e0770b7e80ca0f178a8dded4d8d3aa8dcf8..0f045c0b3955b66629c5acc5b9b050e8a7bf4dcf 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.converter.model.celldesigner.annotation;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -18,37 +18,37 @@ public enum NoteField {
/**
* List of {@link MiriamType#HGNC} identifiers.
*/
- HGNC("HGNC_ID", AnnotatedObject.class, MiriamType.HGNC), //
+ HGNC("HGNC_ID", BioEntity.class, MiriamType.HGNC), //
/**
* List of {@link MiriamType#REFSEQ} identifiers.
*/
- REFSEQ("RefSeq_ID", AnnotatedObject.class, MiriamType.REFSEQ), //
+ REFSEQ("RefSeq_ID", BioEntity.class, MiriamType.REFSEQ), //
/**
* List of {@link MiriamType#ENTREZ} identifiers.
*/
- ENTREZ("EntrezGene_ID", AnnotatedObject.class, MiriamType.ENTREZ), //
+ ENTREZ("EntrezGene_ID", BioEntity.class, MiriamType.ENTREZ), //
/**
* List of {@link MiriamType#REACTOME} identifiers.
*/
- REACTOME("Reactome_ID", AnnotatedObject.class, MiriamType.REACTOME), //
+ REACTOME("Reactome_ID", BioEntity.class, MiriamType.REACTOME), //
/**
* List of {@link MiriamType#PUBMED} identifiers.
*/
- PUBMED("Pubmed_ID", AnnotatedObject.class, MiriamType.PUBMED), //
+ PUBMED("Pubmed_ID", BioEntity.class, MiriamType.PUBMED), //
/**
* List of {@link MiriamType#KEGG_GENES} identifiers.
*/
- KEGG_GENES("KEGG_ID", AnnotatedObject.class, MiriamType.KEGG_GENES), //
+ KEGG_GENES("KEGG_ID", BioEntity.class, MiriamType.KEGG_GENES), //
/**
* List of {@link MiriamType#PANTHER} identifiers.
*/
- PANTHER("PANTHER", AnnotatedObject.class, MiriamType.PANTHER), //
+ PANTHER("PANTHER", BioEntity.class, MiriamType.PANTHER), //
/**
* {@link Element#symbol}.
@@ -63,7 +63,7 @@ public enum NoteField {
/**
* {@link Element#notes} or {@link Reaction#notes} .
*/
- DESCRIPTION("Description", AnnotatedObject.class, null), //
+ DESCRIPTION("Description", BioEntity.class, null), //
/**
* {@link Element#formerSymbols}.
@@ -73,12 +73,12 @@ public enum NoteField {
/**
* {@link Element#synonyms} or {@link Reaction#synonyms}.
*/
- SYNONYMS("Synonyms", AnnotatedObject.class, null), //
+ SYNONYMS("Synonyms", BioEntity.class, null), //
/**
* {@link Element#abbreviation} or {@link Reaction#abbreviation}.
*/
- ABBREVIATION("Abbreviation", AnnotatedObject.class, null), //
+ ABBREVIATION("Abbreviation", BioEntity.class, null), //
/**
* {@link Reaction#formula}.
@@ -123,7 +123,7 @@ public enum NoteField {
/**
* {@link Element#getSemanticZoomLevelVisibility()}.
*/
- SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", AnnotatedObject.class, null); //
+ SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", BioEntity.class, null); //
/**
* Name used in the notes to distinguish fields.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index ccec089ae552859c1d2c1d97aabab79ff12d9676..6838b61339f23be0e3c976b672d5e1f3dc713b94 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -24,7 +24,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -58,7 +58,7 @@ public class RestAnnotationParser extends XmlParser {
private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
/**
- * Class used for some simple operations on {@link AnnotatedObject} elements.
+ * Class used for some simple operations on {@link BioEntity} elements.
*/
private ElementUtils elementUtils = new ElementUtils();
@@ -319,7 +319,7 @@ public class RestAnnotationParser extends XmlParser {
* @param element
* where the structural data should be put
*/
- public void processNotes(Node node, AnnotatedObject element) {
+ public void processNotes(Node node, BioEntity element) {
String notes = getNotes(node);
processNotes(notes, element);
}
@@ -360,7 +360,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setSynonyms(AnnotatedObject element, String annotationString) {
+ private void setSynonyms(BioEntity element, String annotationString) {
List<String> synonyms = getSynonyms(annotationString);
if (synonyms.size() == 0) {
return;
@@ -433,7 +433,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setAbbreviation(AnnotatedObject element, String annotationString) {
+ private void setAbbreviation(BioEntity element, String annotationString) {
StringComparator stringComparator = new StringComparator();
String abbreviation = getParamByPrefix(annotationString, NoteField.ABBREVIATION.getCommonName() + ":");
if (abbreviation == null) {
@@ -499,7 +499,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setFormula(AnnotatedObject element, String annotationString) {
+ private void setFormula(BioEntity element, String annotationString) {
StringComparator stringComparator = new StringComparator();
String formula = getParamByPrefix(annotationString, NoteField.FORMULA.getCommonName() + ":");
if (formula == null) {
@@ -618,7 +618,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setSymbol(AnnotatedObject element, String annotationString) {
+ private void setSymbol(BioEntity element, String annotationString) {
String symbol = getParamByPrefix(annotationString, NoteField.SYMBOL.getCommonName() + ":");
if (symbol == null) {
return;
@@ -638,7 +638,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setSemanticZoomLevelVisibility(AnnotatedObject element, String annotationString) {
+ private void setSemanticZoomLevelVisibility(BioEntity element, String annotationString) {
String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
if (zoomLevelVisibility == null) {
return;
@@ -663,7 +663,7 @@ public class RestAnnotationParser extends XmlParser {
* @param annotationString
* notes string
*/
- private void setNotes(AnnotatedObject element, String annotationString) {
+ private void setNotes(BioEntity element, String annotationString) {
String description = getParamByPrefix(annotationString, NoteField.DESCRIPTION.getCommonName() + ":");
if (description == null) {
return;
@@ -685,7 +685,7 @@ public class RestAnnotationParser extends XmlParser {
* @param object
* where the structural data should be put
*/
- public void processNotes(String notes, AnnotatedObject object) {
+ public void processNotes(String notes, BioEntity object) {
StringBuilder annotations = new StringBuilder();
String[] string = notes.split("\n");
@@ -747,7 +747,7 @@ public class RestAnnotationParser extends XmlParser {
* @throws InvalidXmlSchemaException
* thrown when there is a problem with xml
*/
- void processRdfDescription(AnnotatedObject element) throws InvalidXmlSchemaException {
+ void processRdfDescription(BioEntity element) throws InvalidXmlSchemaException {
String notes = element.getNotes();
Matcher nodeMatcher = rdfNodePattern.matcher(notes);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index 6cca1af6e56bd8d559e4375b6f6ca2a69282bba5..0195858815d730bba0c0f50d7c2d40e07ac64ff0 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -23,7 +23,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -343,7 +343,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
try {
RestAnnotationParser parser = new RestAnnotationParser();
Document node = getXmlDocumentFromFile("testFiles/xmlNodeTestExamples/notes4.xml");
- parser.processNotes(node.getFirstChild(), new AnnotatedObject() {
+ parser.processNotes(node.getFirstChild(), new BioEntity() {
/**
*
*/
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index 18ddccbf22573d7029c07b0229f6f48059ca165c..eaa090e2966932c54e93380b2f1844dd52f5217c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -10,7 +10,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
@@ -25,14 +25,14 @@ import lcsb.mapviewer.model.map.species.Species;
/**
* This interface defines what operations should be possible to convert
- * {@link AnnotatedObject} into a graphics on Graphics2D object.
+ * {@link BioEntity} into a graphics on Graphics2D object.
*
* @author Piotr Gawron
*
* @param <T>
* class of alias to convert
*/
-public abstract class BioEntityConverter<T extends AnnotatedObject> {
+public abstract class BioEntityConverter<T extends BioEntity> {
/**
* Default class logger.
@@ -50,7 +50,7 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
* This function draw representation of the alias on the graphics object.
*
* @param bioEntity
- * {@link AnnotatedObject} that should be drawn
+ * {@link BioEntity} that should be drawn
* @param graphics
* where we want to draw bioEntity
* @param params
@@ -67,7 +67,7 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
* This function draw representation of the alias on the graphics object.
*
* @param bioEntity
- * {@link AnnotatedObject} that should be drawn
+ * {@link BioEntity} that should be drawn
* @param graphics
* where we want to draw bioEntity
* @param params
@@ -144,7 +144,7 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
}
/**
- * Checks if {@link AnnotatedObject} is visible according to visualization
+ * Checks if {@link BioEntity} is visible according to visualization
* given in params.
*
* @param bioEntity
@@ -153,7 +153,7 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
* visualization params
* @return true if object is visible
*/
- protected boolean isVisible(AnnotatedObject bioEntity, ConverterParams params) {
+ protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
if (params.isSemanticZoomingOn()) {
boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
if (bioEntity instanceof Element) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index bb68987a1ce1d12af1161f848bfea2622930a5ce..6f71c865dce77931cf7c3ebb27c619d3c464a177 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -30,7 +30,7 @@ import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SBGNNucleicAc
import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeConverter;
import lcsb.mapviewer.converter.graphics.bioEntity.element.species.UnknownConverter;
import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
@@ -64,7 +64,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
* @author Piotr Gawron
*
*/
-public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject> {
+public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
/**
* Default class logger.
@@ -82,7 +82,7 @@ public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject>
* object that helps to convert overlay values into colors
* @return converter that can be applied for the given element
*/
- private BioEntityConverter<? extends AnnotatedObject> getConverterForElement(AnnotatedObject element, ColorExtractor colorExtractor) {
+ private BioEntityConverter<? extends BioEntity> getConverterForElement(BioEntity element, ColorExtractor colorExtractor) {
if (element == null) {
throw new InvalidArgumentException("element cannot be null");
}
@@ -151,7 +151,7 @@ public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject>
* @param sbgnFormat
* boolean value indicating if SBGN display format should be used
*/
- public BioEntityConverterImpl(final AnnotatedObject element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
+ public BioEntityConverterImpl(final BioEntity element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
// If element is a nucleic acid feature to be displayed in SBGN
if (sbgnFormat && (element instanceof AntisenseRna || element instanceof Rna || element instanceof Gene)) {
@@ -181,7 +181,7 @@ public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject>
@SuppressWarnings("unchecked")
@Override
- public void drawText(final AnnotatedObject element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ public void drawText(final BioEntity element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
if (isVisible(element, params)) {
elementConverter.drawText(element, graphics, params);
}
@@ -189,7 +189,7 @@ public class BioEntityConverterImpl extends BioEntityConverter<AnnotatedObject>
@SuppressWarnings("unchecked")
@Override
- public void draw(AnnotatedObject element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ public void draw(BioEntity element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
if (isVisible(element, params)) {
elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
index 128760d664f8f39309c72c3a0713eb13dcd171fc..1c4360d0749df0ae0248cac73a0c7c67045c0798 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
@@ -1,5 +1,5 @@
/**
- * Provides classes that draws {@link lcsb.mapviewer.model.map.AnnotatedObject
+ * Provides classes that draws {@link lcsb.mapviewer.model.map.BioEntity
* BioEntites} on the Graphics2D object.
*/
package lcsb.mapviewer.converter.graphics.bioEntity;
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index 427c7f77216e77e1ae31c62cef008510adeec1f4..ceb5a31f734b0982f775f65472e8d96966e24a1b 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -12,7 +12,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -56,7 +56,7 @@ public class ColorModelCommand extends ModelCommand {
private ColorExtractor colorExtractor;
/**
- * Util class for all {@link AnnotatedObject} elements.
+ * Util class for all {@link BioEntity} elements.
*/
private ElementUtils eu = new ElementUtils();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
similarity index 90%
rename from model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
rename to model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index 2a9ec585d0e782d016f3e629837005049d058213..eb2f82d237feca3a737cbd430daa07b20f32b919 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -5,12 +5,12 @@ import java.util.Collection;
import java.util.List;
/**
- * Interface that describes object that can be annotated.
+ * Interface that describes bio entity on the map (like Protein or Reaction).
*
* @author Piotr Gawron
*
*/
-public interface AnnotatedObject extends Serializable {
+public interface BioEntity extends Serializable {
/**
* Returns list of {@link MiriamData annotations} for the object.
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index ad34aaa372a8ca9fffa6143da14fe2232cc100e1..cd8b930f1703058b08f2138e4688354fc45bfa4a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -306,7 +306,7 @@ public enum MiriamType {
PUBMED("PubMed", //
"http://www.ncbi.nlm.nih.gov/PubMed/", //
new String[] { "urn:miriam:pubmed" }, //
- new Class<?>[] { AnnotatedObject.class }, "MIR:00000015", //
+ new Class<?>[] { BioEntity.class }, "MIR:00000015", //
new Class<?>[] { Reaction.class }), //
/**
@@ -447,13 +447,13 @@ public enum MiriamType {
/**
* Classes that can be annotated by this resource.
*/
- private List<Class<? extends AnnotatedObject>> validClass = new ArrayList<>();
+ private List<Class<? extends BioEntity>> validClass = new ArrayList<>();
/**
* When class from this list is marked as "require at least one annotation"
* then annotation of this type is valid.
*/
- private List<Class<? extends AnnotatedObject>> requiredClass = new ArrayList<>();
+ private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
/**
* Constructor that initialize enum object.
@@ -496,10 +496,10 @@ public enum MiriamType {
this.uris.add(string);
}
for (Class<?> clazz : classes) {
- this.validClass.add((Class<? extends AnnotatedObject>) clazz);
+ this.validClass.add((Class<? extends BioEntity>) clazz);
}
for (Class<?> clazz : requiredClasses) {
- this.requiredClass.add((Class<? extends AnnotatedObject>) clazz);
+ this.requiredClass.add((Class<? extends BioEntity>) clazz);
}
this.registryIdentifier = registryIdentifier;
}
@@ -542,7 +542,7 @@ public enum MiriamType {
*
* @return {@link #validClass}
*/
- public List<Class<? extends AnnotatedObject>> getValidClass() {
+ public List<Class<? extends BioEntity>> getValidClass() {
return validClass;
}
@@ -584,7 +584,7 @@ public enum MiriamType {
* @return the requiredClass
* @see #requiredClass
*/
- public List<Class<? extends AnnotatedObject>> getRequiredClass() {
+ public List<Class<? extends BioEntity>> getRequiredClass() {
return requiredClass;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 9d1b4cc137cdbca7d1bfa5ebb43e06fb669e3199..aaf297002e8a2e1a9384d7197db32e0da71c02d0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -6,7 +6,7 @@ import java.util.List;
import java.util.Set;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -323,7 +323,7 @@ public interface Model {
* {@link MiriamData}
* @return list of elements
*/
- Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData);
+ Set<BioEntity> getElementsByAnnotation(MiriamData miriamData);
/**
* Returns list of elements with given name.
@@ -622,10 +622,10 @@ public interface Model {
void setId(int id);
/**
- * Return list od all {@link AnnotatedObject} in the map. This includes all
+ * Return list od all {@link BioEntity} in the map. This includes all
* {@link Reaction reactions} and {@link Element elements}.
*
- * @return list od all {@link AnnotatedObject} in the map
+ * @return list od all {@link BioEntity} in the map
*/
- List<AnnotatedObject> getAnnotatedObjects();
+ List<BioEntity> getAnnotatedObjects();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 86704ddf5d3d08fad3746d8c9a99427343b307da..0877d492b83416bb75085572d566e7fea65123a4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -14,7 +14,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewImageLink;
@@ -312,8 +312,8 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Set<AnnotatedObject> getElementsByAnnotation(MiriamData miriamData) {
- Set<AnnotatedObject> result = new HashSet<>();
+ public Set<BioEntity> getElementsByAnnotation(MiriamData miriamData) {
+ Set<BioEntity> result = new HashSet<>();
for (Element element : getElements()) {
for (MiriamData md : element.getMiriamData()) {
if (md.equals(miriamData)) {
@@ -660,8 +660,8 @@ public class ModelFullIndexed implements Model {
}
@Override
- public List<AnnotatedObject> getAnnotatedObjects() {
- List<AnnotatedObject> result = new ArrayList<>();
+ public List<BioEntity> getAnnotatedObjects() {
+ List<BioEntity> result = new ArrayList<>();
result.addAll(getElements());
result.addAll(getReactions());
return result;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index c1eb4a094427f36cfe14e5d45f7f4061489c688e..6a2fafcf6bb5a2aca158bbbe0b628a33c065461a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -38,7 +38,7 @@ import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.LineTransformation;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -74,7 +74,7 @@ import lcsb.mapviewer.model.map.species.Element;
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(name = "reaction_type_db", discriminatorType = DiscriminatorType.STRING)
@DiscriminatorValue("GENERIC_REACTION")
-public class Reaction implements AnnotatedObject {
+public class Reaction implements BioEntity {
/**
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 8cfbc8cc39b3c7dd6745a6ba03ecc18fafd6e91a..01688104f11e53210eee5b9d377ef7f33ae4e006 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -38,7 +38,7 @@ import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.IndexColumn;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -61,7 +61,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(name = "element_type_db", discriminatorType = DiscriminatorType.STRING)
@DiscriminatorValue("GENERIC_ALIAS")
-public abstract class Element implements AnnotatedObject, Serializable {
+public abstract class Element implements BioEntity, Serializable {
/**
*
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 99b971e2745b8e1ff764ecf73401a343781c03b3..5b6b011b97016f9ec03ed6457c50f6f19c4dca74 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -12,12 +12,12 @@ import org.apache.log4j.Logger;
import org.reflections.Reflections;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
/**
- * Class with some util method for {@link AnnotatedObject} objects.
+ * Class with some util method for {@link BioEntity} objects.
*
* @author Piotr Gawron
*
@@ -25,7 +25,7 @@ import lcsb.mapviewer.model.map.species.Element;
public final class ElementUtils {
/**
- * This object contains inheritance tree for {@link AnnotatedObject}
+ * This object contains inheritance tree for {@link BioEntity}
* interface.
*/
private static ClassTreeNode annotatedObjectTree = null;
@@ -49,19 +49,19 @@ public final class ElementUtils {
private final Logger logger = Logger.getLogger(ElementUtils.class);
/**
- * This method return tag that identifies {@link AnnotatedObject}. This tag
+ * This method return tag that identifies {@link BioEntity}. This tag
* should be used in warning messages.
*
* @param element
* tag for this element is created
* @return tag that identifies element
*/
- public String getElementTag(AnnotatedObject element) {
+ public String getElementTag(BioEntity element) {
return getElementTag(element, null);
}
/**
- * This method return tag that identifies {@link AnnotatedObject}. This tag
+ * This method return tag that identifies {@link BioEntity}. This tag
* should be used in warning messages.
*
* @param element
@@ -71,7 +71,7 @@ public final class ElementUtils {
* null (in such situation it will be skipped in the tag)
* @return tag that identifies element
*/
- public String getElementTag(AnnotatedObject element, Object annotator) {
+ public String getElementTag(BioEntity element, Object annotator) {
String id = null;
if (element instanceof Element) {
id = ((Element) element).getElementId();
@@ -95,14 +95,14 @@ public final class ElementUtils {
public ClassTreeNode getAnnotatedElementClassTree() {
if (annotatedObjectTree == null) {
Reflections reflections = new Reflections("lcsb.mapviewer.model.map");
- Set<Class<? extends AnnotatedObject>> classes = reflections.getSubTypesOf(AnnotatedObject.class);
+ Set<Class<? extends BioEntity>> classes = reflections.getSubTypesOf(BioEntity.class);
- annotatedObjectTree = new ClassTreeNode(AnnotatedObject.class);
+ annotatedObjectTree = new ClassTreeNode(BioEntity.class);
annotatedObjectTree.setData(false);
Map<Class<?>, ClassTreeNode> map = new HashMap<Class<?>, ClassTreeNode>();
map.put(Object.class, annotatedObjectTree);
- for (Class<? extends AnnotatedObject> class1 : classes) {
+ for (Class<? extends BioEntity> class1 : classes) {
if (map.get(class1) == null) {
ClassTreeNode node = new ClassTreeNode(class1);
// set information if the class annotation should be required
@@ -114,7 +114,7 @@ public final class ElementUtils {
map.put(class1, node);
}
}
- for (Class<? extends AnnotatedObject> class1 : classes) {
+ for (Class<? extends BioEntity> class1 : classes) {
ClassTreeNode parent = map.get(class1.getSuperclass());
ClassTreeNode child = map.get(class1);
parent.getChildren().add(child);
@@ -123,7 +123,7 @@ public final class ElementUtils {
// set information if the class annotation should be required for children
// classes (if not explicitly set in child then inherit it from parent)
- for (Class<? extends AnnotatedObject> class1 : classes) {
+ for (Class<? extends BioEntity> class1 : classes) {
ClassTreeNode child = map.get(class1);
Boolean value = (Boolean) child.getData();
if (value == null) {
@@ -207,12 +207,12 @@ public final class ElementUtils {
}
/**
- * Returns a {@link Class} that extends {@link AnnotatedObject} for a given
+ * Returns a {@link Class} that extends {@link BioEntity} for a given
* name.
*
* @param name
* name of the class
- * @return {@link Class} that extends {@link AnnotatedObject} for a given name
+ * @return {@link Class} that extends {@link BioEntity} for a given name
*/
public Class<?> getClassByName(String name) {
if (elementClasses == null) {
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
index 2a844090f0a35b97bb28de3f68ada623460ac276..e52647e90139d59b653daf348aa3d93c84f86339 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/RequireAnnotationMap.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.modelutils.map;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Chemical;
@@ -12,7 +12,7 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
/**
- * List of {@link AnnotatedObject} that must be annototed with at least one
+ * List of {@link BioEntity} that must be annototed with at least one
* {@link lcsb.mapviewer.model.map.MiriamData}.
*
* @author Piotr Gawron
@@ -68,7 +68,7 @@ public enum RequireAnnotationMap {
/**
* Class which should be annotated.
*/
- private Class<? extends AnnotatedObject> clazz;
+ private Class<? extends BioEntity> clazz;
/**
* Default constructor.
@@ -76,7 +76,7 @@ public enum RequireAnnotationMap {
* @param clazz
* {@link #clazz}
*/
- RequireAnnotationMap(Class<? extends AnnotatedObject> clazz) {
+ RequireAnnotationMap(Class<? extends BioEntity> clazz) {
this.clazz = clazz;
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index 10f5c549e4928cc43711882ce381f4666a370b5b..869ff766de94364416a4059f520014eb71347199 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -22,7 +22,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
@@ -525,7 +525,7 @@ public class ModelFullIndexedTest {
reaction.addMiriamData(new MiriamData(MiriamType.CAS, "C"));
model.addReaction(reaction);
- Set<AnnotatedObject> objects = model.getElementsByAnnotation(new MiriamData());
+ Set<BioEntity> objects = model.getElementsByAnnotation(new MiriamData());
assertEquals(0, objects.size());
objects = model.getElementsByAnnotation(new MiriamData(MiriamType.CAS, "C"));
assertTrue(objects.contains(reaction));
@@ -850,7 +850,7 @@ public class ModelFullIndexedTest {
Species protein = new GenericProtein("2");
model.addElement(protein);
- Collection<AnnotatedObject> obj = model.getAnnotatedObjects();
+ Collection<BioEntity> obj = model.getAnnotatedObjects();
assertEquals(2, obj.size());
} catch (Exception e) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
index 93808c4c64e2db5db1e88aa2abeeeeb7fbe97d3e..2d3078e3dabb80aa22a6b7fc6ac3ce4d12dc2a88 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java
@@ -14,7 +14,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -124,10 +124,10 @@ public class ModelTest {
try {
model = createModel();
- Set<AnnotatedObject> elements = model.getElementsByAnnotation(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
+ Set<BioEntity> elements = model.getElementsByAnnotation(new MiriamData(MiriamRelationType.BQ_MODEL_IS, MiriamType.CHEMBL_TARGET, "CHEMBL12345"));
assertNotNull(elements);
assertEquals(1, elements.size());
- AnnotatedObject element = elements.iterator().next();
+ BioEntity element = elements.iterator().next();
assertTrue(element instanceof Species);
Species species = (Species) element;
assertEquals("s5", species.getName());
diff --git a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
index 41ef01ea86d0a4a452f137da1d9a85bdc1e3401c..2d2432d1860c8ee912a04003a5b180cf6128c4f0 100644
--- a/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
+++ b/model/src/test/java/lcsb/mapviewer/modelutils/map/ElementUtilsTest.java
@@ -19,7 +19,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -99,7 +99,7 @@ public class ElementUtilsTest {
try {
ElementUtils elementUtils = new ElementUtils();
- AnnotatedObject element = Mockito.mock(AnnotatedObject.class);
+ BioEntity element = Mockito.mock(BioEntity.class);
assertNotNull(elementUtils.getElementTag(element));
fail("Exception expected");
} catch (NotImplementedException e) {
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 83355856444bdb59b0bf7e60f3623c537831ca1c..577b87b38f60aed91f21f62a5277ce5d0e854c65 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -10,7 +10,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
@@ -591,7 +591,7 @@ public class ModelToGPML {
gpml.append(getComparments(model));
gpml.append(groups);
Set<MiriamData> set = new HashSet<>();
- for (AnnotatedObject element : model.getAnnotatedObjects()) {
+ for (BioEntity element : model.getAnnotatedObjects()) {
set.addAll(element.getMiriamData());
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
index f8bb0ad229124dd544d300037d99778d8c4263fe..e348315d22d4d56c6e77f73b7da2c1be4ef3756f 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ElementUtil.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Element;
@@ -33,7 +33,7 @@ public class ElementUtil {
* element to be identified
* @return human readable id of the element from paramter
*/
- public String getElementTag(AnnotatedObject element) {
+ public String getElementTag(BioEntity element) {
return new ElementUtils().getElementTag(element);
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
index e73db35d17601f3e32b4b1cba9f838c53166f31d..6618c911d6866f220f3ae3b839acfc455e03031a 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeQueryUtil.java
@@ -18,7 +18,7 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -92,7 +92,7 @@ public class ReactomeQueryUtil {
* element for which we want id string.
* @return human readable id of element
*/
- public String getElementTag(AnnotatedObject element) {
+ public String getElementTag(BioEntity element) {
return new ElementUtils().getElementTag(element);
}
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
index a7bf80f52d8a5a4cae417dc6464164a3f0304eeb..1d907e1c4c65268108b9d6606815ab36c539fe25 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
+++ b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/comparators/ANodeComparator.java
@@ -8,7 +8,7 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -239,7 +239,7 @@ public abstract class ANodeComparator<T extends Element, U extends ReactomeDatab
* element to be transformed into string id
* @return short string description identifing element
*/
- public String getElementTag(AnnotatedObject element) {
+ public String getElementTag(BioEntity element) {
return new ElementUtils().getElementTag(element);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 13560acbd52a8bae567b3f1569c863f27a9e795b..7d5a66c649974cef99f0cad3037a7f4be34cd375 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -21,7 +21,7 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.modelutils.map.ClassTreeNode;
@@ -145,9 +145,9 @@ public class ConfigurationRestImpl {
if (!Modifier.isAbstract(clazz.getClazz().getModifiers())) {
try {
if (elementClass.isAssignableFrom(Reaction.class)) {
- result.add(((AnnotatedObject) (clazz.getClazz().getDeclaredConstructor().newInstance())).getStringType());
+ result.add(((BioEntity) (clazz.getClazz().getDeclaredConstructor().newInstance())).getStringType());
} else {
- result.add(((AnnotatedObject) (clazz.getClazz().getDeclaredConstructor(String.class).newInstance("id"))).getStringType());
+ result.add(((BioEntity) (clazz.getClazz().getDeclaredConstructor(String.class).newInstance("id"))).getStringType());
}
} catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException | NoSuchMethodException
| java.lang.SecurityException e) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index 93febcd23ce73b14718a5d89729b5655bf027431..44ae84835382be992117fef7e7045b8c42972988 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -172,7 +172,7 @@ public class ChemicalRestImpl {
List<Map<String, Object>> targetedObjects = new ArrayList<>();
for (Model model : models) {
- for (AnnotatedObject object : model.getAnnotatedObjects()) {
+ for (BioEntity object : model.getAnnotatedObjects()) {
if (elementMatcher.elementMatch(target, object)) {
Map<String, Object> elementMapping = new HashMap<>();
@@ -189,7 +189,7 @@ public class ChemicalRestImpl {
return result;
}
- private String getType(AnnotatedObject object) {
+ private String getType(BioEntity object) {
if (object instanceof Reaction) {
return ElementIdentifierType.REACTION.getJsName();
} else if (object instanceof Element) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index 75f01d1125cadac9bd7edb37bcf0020f62d3f3d4..2e779e826199aba1ba677284b1277ef132789c8e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -166,7 +166,7 @@ public class DrugRestImpl {
List<Map<String, Object>> targetedObjects = new ArrayList<>();
for (Model model : models) {
- for (AnnotatedObject object : model.getAnnotatedObjects()) {
+ for (BioEntity object : model.getAnnotatedObjects()) {
if (elementMatcher.elementMatch(target, object)) {
Map<String, Object> elementMapping = new HashMap<>();
@@ -183,7 +183,7 @@ public class DrugRestImpl {
return result;
}
- private String getType(AnnotatedObject object) {
+ private String getType(BioEntity object) {
if (object instanceof Reaction) {
return ElementIdentifierType.REACTION.getJsName();
} else if (object instanceof Element) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
index c597bcd68931634f9d310ddddc3f1e30e3ece4a8..8ef791e3adbc2e1f57977edf1ab946276804db74 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -159,7 +159,7 @@ public class MiRnaRestImpl {
List<Map<String, Object>> targetedObjects = new ArrayList<>();
for (Model model : models) {
- for (AnnotatedObject object : model.getAnnotatedObjects()) {
+ for (BioEntity object : model.getAnnotatedObjects()) {
if (elementMatcher.elementMatch(target, object)) {
Map<String, Object> elementMapping = new HashMap<>();
@@ -176,7 +176,7 @@ public class MiRnaRestImpl {
return result;
}
- private String getType(AnnotatedObject object) {
+ private String getType(BioEntity object) {
if (object instanceof Reaction) {
return ElementIdentifierType.REACTION.getJsName();
} else if (object instanceof Element) {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
index 599e6256c9b24ea6b8d26662db1a7b60bdcf5043..b2b1dd3884d242331786a8c1349ff2f8cf9142f6 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -10,7 +10,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
@@ -61,7 +61,7 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
Model submodel = model.getSubmodelById(modelId);
- List<AnnotatedObject> elements = searchService.getClosestElements(submodel, coordinates, count, perfectMatch.equalsIgnoreCase("true"));
+ List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count, perfectMatch.equalsIgnoreCase("true"));
for (Object object : elements) {
Map<String, Object> result = createMinifiedSearchResult(object);
resultMap.add(result);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index 50f9b691892db89ac0941f0c54abe744bf448191..23184a3296e13b26ce6e4b3f4407006d9eb1a6e3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -16,7 +16,7 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -52,13 +52,13 @@ public class PublicationsRestImpl extends BaseRestImpl {
@Autowired
private OverviewImageViewFactory factory;
- public SortedMap<MiriamData, List<AnnotatedObject>> getPublications(List<Model> models) {
- SortedMap<MiriamData, List<AnnotatedObject>> publications = new TreeMap<>();
+ public SortedMap<MiriamData, List<BioEntity>> getPublications(List<Model> models) {
+ SortedMap<MiriamData, List<BioEntity>> publications = new TreeMap<>();
for (Model modelData : models) {
for (Element element : modelData.getElements()) {
for (MiriamData md : element.getMiriamData()) {
if (md.getDataType().equals(MiriamType.PUBMED)) {
- List<AnnotatedObject> list = publications.get(md);
+ List<BioEntity> list = publications.get(md);
if (list == null) {
list = new ArrayList<>();
publications.put(md, list);
@@ -70,7 +70,7 @@ public class PublicationsRestImpl extends BaseRestImpl {
for (Reaction reaction : modelData.getReactions()) {
for (MiriamData md : reaction.getMiriamData()) {
if (md.getDataType().equals(MiriamType.PUBMED)) {
- List<AnnotatedObject> list = publications.get(md);
+ List<BioEntity> list = publications.get(md);
if (list == null) {
list = new ArrayList<>();
publications.put(md, list);
@@ -159,16 +159,16 @@ public class PublicationsRestImpl extends BaseRestImpl {
Integer start = Math.max(0, Integer.valueOf(startString));
List<Map<String, Object>> resultList = new ArrayList<>();
- SortedMap<MiriamData, List<AnnotatedObject>> publications = getPublications(models);
+ SortedMap<MiriamData, List<BioEntity>> publications = getPublications(models);
int index = 0;
Set<String> columns = new HashSet<>();
columns.add("id");
columns.add("type");
columns.add("modelid");
- for (Map.Entry<MiriamData, List<AnnotatedObject>> entry : publications.entrySet()) {
+ for (Map.Entry<MiriamData, List<BioEntity>> entry : publications.entrySet()) {
if (index >= start && index < start + length) {
List<Object> elements = new ArrayList<>();
- for (AnnotatedObject object : entry.getValue()) {
+ for (BioEntity object : entry.getValue()) {
elements.add(createMinifiedSearchResult(object));
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 212e7360c7dcd0c7e1849862b1e3126a30c488ac..272848fa2a2ec240be53102dc03b3324ae30c15b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -58,7 +58,7 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
import lcsb.mapviewer.model.log.LogType;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.graph.DataMining;
@@ -1328,8 +1328,8 @@ public class ProjectService implements IProjectService {
ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> validMiriam = modelAnnotator.getDefaultValidClasses();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> requiredMiriam = modelAnnotator.getDefaultRequiredClasses();
Queue<ClassTreeNode> nodes = new LinkedList<ClassTreeNode>();
nodes.add(top);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index c99199d01ec1d90b8a2dab61a7a043c89c63cc04..fdc2a74e6e9a2a25c748e886872c4ce04f9891bc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -18,7 +18,7 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.SearchIndex;
@@ -494,7 +494,7 @@ public class SearchService implements ISearchService {
*/
private List<IHeavyView> searchByMiriam(Model model, MiriamData md, int limit) {
List<IHeavyView> result = new ArrayList<>();
- for (AnnotatedObject obj : model.getElementsByAnnotation(md)) {
+ for (BioEntity obj : model.getElementsByAnnotation(md)) {
if (result.size() >= limit) {
break;
}
@@ -527,8 +527,8 @@ public class SearchService implements ISearchService {
}
@Override
- public List<AnnotatedObject> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
- List<AnnotatedObject> result = new ArrayList<>();
+ public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
+ List<BioEntity> result = new ArrayList<>();
// probably this could be improved algorithmitically, right now all objects
// are sorted by distance, and numberOfElements closest are chosen as a list
@@ -566,7 +566,7 @@ public class SearchService implements ISearchService {
/**
* Reference to the object.
*/
- private AnnotatedObject reference;
+ private BioEntity reference;
/**
* Distance between the object and some point.
@@ -628,7 +628,7 @@ public class SearchService implements ISearchService {
* @return the reference
* @see #reference
*/
- public AnnotatedObject getReference() {
+ public BioEntity getReference() {
return reference;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
index ba82510d70903606ce9591c699d1ca28d2ccb9a4..c32dee9143c6f6679fa01f3d4db39b377d09b23f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -5,7 +5,7 @@ import java.util.List;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -296,7 +296,7 @@ public interface ISearchService {
* how many closest elements should be returned
* @return list of the closest elements
*/
- List<AnnotatedObject> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit);
+ List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit);
/**
* Returns list of autocomplete strings for the partial query.
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
index fef2d1af65f0924fdeae09801d0bb3cbf691b8dd..5e51b690b28c99ef45a207110bcd44f35c4163ea 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -9,7 +9,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Complex;
@@ -47,7 +47,7 @@ public class ElementMatcher {
* @return <code>true</code> if drug target can target element,
* <code>false</code> otherwise
*/
- public boolean elementMatch(TargetView target, AnnotatedObject element) {
+ public boolean elementMatch(TargetView target, BioEntity element) {
if (target.getType().equals(TargetType.COMPLEX_PROTEIN.getCommonName())) {
MiriamData targetAnnotation = annotationViewFactory.viewToObject(target.getAnnotation());
if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
index fcc8cc04e4aeaf50c82daf4e6882dd1cf0c57cd3..994ca460ecfda84f5d97e85cf72090e226a41314 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/TargetViewFactory.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -87,7 +87,7 @@ public class TargetViewFactory extends AbstractViewFactory<Target, TargetView> {
GeneRow geneRow = new GeneRow();
geneRow.setAnnotation(annotationViewFactory.create(md));
if (model != null) {
- Set<AnnotatedObject> list = new HashSet<>();
+ Set<BioEntity> list = new HashSet<>();
list.addAll(model.getElementsByName(md.getResource()));
list.addAll(model.getElementsByAnnotation(md));
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
index 388ff0ed7fef61006d0650c28ed475c224352608..aae39c5c6b7e4d48593404b40418877713d16378 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/chemical/ChemicalService.java
@@ -23,7 +23,7 @@ import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -302,7 +302,7 @@ public class ChemicalService implements IChemicalService {
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
- for (AnnotatedObject element : model.getAnnotatedObjects()) {
+ for (BioEntity element : model.getAnnotatedObjects()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
index 9ba9d56733aee9dad7aecf116c7b9e0e65d00d52..5de463996711e732d30fbbbfde34609654e0ac2e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/drug/DrugService.java
@@ -20,7 +20,7 @@ import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -384,7 +384,7 @@ public class DrugService implements IDrugService {
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
- for (AnnotatedObject element : model.getAnnotatedObjects()) {
+ for (BioEntity element : model.getAnnotatedObjects()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
index 4f3359b694b2a017645fdb6851b655750abb7525..525e4d1529a7353a7a2fe7a74fb15e55a84bb21a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAService.java
@@ -20,7 +20,7 @@ import lcsb.mapviewer.annotation.services.MiRNASearchException;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.HgncAnnotator;
import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -218,7 +218,7 @@ public class MiRNAService implements IMiRNAService {
models.add(originalModel);
models.addAll(originalModel.getSubmodels());
for (Model model : models) {
- for (AnnotatedObject element : model.getAnnotatedObjects()) {
+ for (BioEntity element : model.getAnnotatedObjects()) {
for (MiriamData md : element.getMiriamData()) {
if (MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
targetMiriams.add(md);
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
index 21df2ed92d971e0160604b9b9f9b859b8075fdcf..4e1f886cb2e823d2b72e509be84bcc940dcc3d0a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -17,7 +17,7 @@ import org.apache.commons.io.IOUtils;
import org.primefaces.model.TreeNode;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
import lcsb.mapviewer.services.view.AuthenticationToken;
@@ -151,13 +151,13 @@ public class CreateProjectParams {
* Map that contains information which {@link MiriamType miriam types} are
* valid for which class.
*/
- private Map<Class<? extends AnnotatedObject>, Set<MiriamType>> validAnnotations = null;
+ private Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations = null;
/**
* Map that contains information which {@link MiriamType miriam types} are
* obigatory for which class.
*/
- private Map<Class<? extends AnnotatedObject>, Set<MiriamType>> requiredAnnotations = null;
+ private Map<Class<? extends BioEntity>, Set<MiriamType>> requiredAnnotations = null;
/**
* @param projectId
@@ -534,7 +534,7 @@ public class CreateProjectParams {
*/
@SuppressWarnings("unchecked")
public void validAnnotations(TreeNode annotatorsTree) {
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> map = new HashMap<Class<? extends AnnotatedObject>, Set<MiriamType>>();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
Queue<TreeNode> queue = new LinkedList<TreeNode>();
queue.add(annotatorsTree);
while (!queue.isEmpty()) {
@@ -546,7 +546,7 @@ public class CreateProjectParams {
set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getValidAnnotations());
parent = parent.getParent();
}
- map.put((Class<? extends AnnotatedObject>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
+ map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
for (TreeNode node2 : node.getChildren()) {
queue.add(node2);
@@ -564,7 +564,7 @@ public class CreateProjectParams {
*/
@SuppressWarnings("unchecked")
public void requiredAnnotations(TreeNode annotatorsTree) {
- Map<Class<? extends AnnotatedObject>, Set<MiriamType>> map = new HashMap<Class<? extends AnnotatedObject>, Set<MiriamType>>();
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
Queue<TreeNode> queue = new LinkedList<TreeNode>();
queue.add(annotatorsTree);
while (!queue.isEmpty()) {
@@ -583,7 +583,7 @@ public class CreateProjectParams {
if (!valid) {
set = null;
}
- map.put((Class<? extends AnnotatedObject>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
+ map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
for (TreeNode node2 : node.getChildren()) {
queue.add(node2);
@@ -597,7 +597,7 @@ public class CreateProjectParams {
*
* @return {@link #validAnnotations}.
*/
- public Map<Class<? extends AnnotatedObject>, Set<MiriamType>> getValidAnnotations() {
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getValidAnnotations() {
return validAnnotations;
}
@@ -606,7 +606,7 @@ public class CreateProjectParams {
*
* @return {@link #requiredAnnotations}.
*/
- public Map<Class<? extends AnnotatedObject>, Set<MiriamType>> getRequiredAnnotations() {
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getRequiredAnnotations() {
return requiredAnnotations;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
index 4be94f326962a66a8fa68b3323854055c3abe7a8..fa8eb02646c17c36ee7132dbf92ee9940d0ce041 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsView.java
@@ -6,7 +6,7 @@ import java.util.List;
import lcsb.mapviewer.annotation.data.Article;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
@@ -91,7 +91,7 @@ public class PubmedAnnotatedElementsView extends AbstractView<MiriamData> {
* @param annotatedObject
* object to add
*/
- public void addElement(AnnotatedObject annotatedObject) {
+ public void addElement(BioEntity annotatedObject) {
if (annotatedObject instanceof Element) {
Element alias = (Element) annotatedObject;
elements.add(new Pair<String, String>(alias.getName(), SearchService.SPECIES_SEARCH_PREFIX + ":" + alias.getElementId()));
@@ -101,7 +101,7 @@ public class PubmedAnnotatedElementsView extends AbstractView<MiriamData> {
new Pair<>(
SearchService.REACTION_SEARCH_PREFIX + ":" + reaction.getIdReaction(), SearchService.REACTION_SEARCH_PREFIX + ":" + reaction.getIdReaction()));
} else {
- throw new InvalidStateException("Unknown subtype of " + AnnotatedObject.class.getName() + ": " + annotatedObject.getClass().getName());
+ throw new InvalidStateException("Unknown subtype of " + BioEntity.class.getName() + ": " + annotatedObject.getClass().getName());
}
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
index 54dc5b2e7b5a03891c2d3a24c47165108c220341..f743b95b3ac9b74d1284b818d9985452187c9da7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/PubmedAnnotatedElementsViewFactory.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.annotation.services.PubmedSearchException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
@@ -66,11 +66,11 @@ public class PubmedAnnotatedElementsViewFactory extends AbstractViewFactory<Miri
*/
public PubmedAnnotatedElementsView create(MiriamData miriamData, Model model) {
PubmedAnnotatedElementsView result = create(miriamData);
- Set<AnnotatedObject> elements = model.getElementsByAnnotation(miriamData);
+ Set<BioEntity> elements = model.getElementsByAnnotation(miriamData);
for (Model submodel : model.getSubmodels()) {
elements.addAll(submodel.getElementsByAnnotation(miriamData));
}
- for (AnnotatedObject annotatedObject : elements) {
+ for (BioEntity annotatedObject : elements) {
result.addElement(annotatedObject);
}
return result;
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 95aea93365d9a3ebd6ddeea571a5516af7d50482..93ed9e8c1cee784cc0bc7683ee084bc414aec1ee 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -35,7 +35,7 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
@@ -468,7 +468,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
- assertEquals(AnnotatedObject.class, dataNode.getClazz());
+ assertEquals(BioEntity.class, dataNode.getClazz());
Queue<TreeNode> nodes = new LinkedList<TreeNode>();
nodes.add(tree);
@@ -504,7 +504,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
- assertEquals(AnnotatedObject.class, dataNode.getClazz());
+ assertEquals(BioEntity.class, dataNode.getClazz());
Queue<TreeNode> nodes = new LinkedList<TreeNode>();
nodes.add(tree);
@@ -543,7 +543,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
- assertEquals(AnnotatedObject.class, dataNode.getClazz());
+ assertEquals(BioEntity.class, dataNode.getClazz());
Queue<TreeNode> nodes = new LinkedList<>();
nodes.add(tree);
@@ -581,7 +581,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
- assertEquals(AnnotatedObject.class, dataNode.getClazz());
+ assertEquals(BioEntity.class, dataNode.getClazz());
Queue<TreeNode> nodes = new LinkedList<TreeNode>();
nodes.add(tree);
@@ -622,7 +622,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
- assertEquals(AnnotatedObject.class, dataNode.getClazz());
+ assertEquals(BioEntity.class, dataNode.getClazz());
Queue<TreeNode> nodes = new LinkedList<>();
nodes.add(tree);
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index 64ff5dc2de7f86973ef15604b34035dd5a409e9c..a86d4ede01b97e957a9c920cb5e5d6f181c5f5b9 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -18,7 +18,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
@@ -232,7 +232,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosest() throws Exception {
try {
model = getModelForFile("testFiles/graph_path_example3.xml", true);
- List<AnnotatedObject> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
+ List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(5, elements.size());
assertTrue(elements.get(0) instanceof Species);
@@ -280,12 +280,12 @@ public class SearchServiceTest extends ServiceTestFunctions {
protein3.setY(0);
model.addElement(protein3);
- List<AnnotatedObject> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false);
+ List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false);
assertNotNull(elements);
assertEquals(3, elements.size());
- AnnotatedObject sAlias = elements.get(0);
+ BioEntity sAlias = elements.get(0);
assertEquals("s2", sAlias.getName());
- AnnotatedObject reaction = elements.get(1);
+ BioEntity reaction = elements.get(1);
assertEquals("s1", reaction.getName());
sAlias = elements.get(2);
assertEquals("s3", sAlias.getName());
@@ -300,7 +300,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosestWithEmptyModel() throws Exception {
try {
model = new ModelFullIndexed(null);
- List<AnnotatedObject> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
+ List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(0, elements.size());