From 4e1f117323193485a66854a2f8bd35e18b651af2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 26 Jun 2017 11:59:02 +0200
Subject: [PATCH] javadoc update of for BioEntity rename
---
.../services/ImproperAnnotations.java | 26 +++++++++----------
.../services/MissingAnnotation.java | 17 ++++++------
.../services/MissingRequiredAnnotations.java | 20 +++++++-------
.../annotation/services/ModelAnnotator.java | 6 ++---
4 files changed, 34 insertions(+), 35 deletions(-)
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 ab1810dd4e..4337be731d 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
@@ -19,9 +19,9 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
public class ImproperAnnotations implements ProblematicAnnotation {
/**
- * Object improperly annotated.
+ * {@link BioEntity} improperly annotated.
*/
- private BioEntity object;
+ private BioEntity bioEntity;
/**
* Wrong miriam data.
@@ -29,39 +29,39 @@ public class ImproperAnnotations implements ProblematicAnnotation {
private List<MiriamData> wrongAnnotations = new ArrayList<>();
/**
- * Constructor that initializes the data with {@link #object bioEntity}
- * and list of improper {@link MiriamData}.
+ * Constructor that initializes the data with {@link #bioEntity bioEntity} and
+ * list of improper {@link MiriamData}.
*
* @param list
* list of improper {@link MiriamData}
- * @param object
- * annotated object
+ * @param bioEntity
+ * bioentity
*/
- public ImproperAnnotations(BioEntity object, List<MiriamData> list) {
+ public ImproperAnnotations(BioEntity bioEntity, List<MiriamData> list) {
if (list.size() == 0) {
throw new InvalidArgumentException("List of improper annotations cannot be null");
}
- this.object = object;
+ this.bioEntity = bioEntity;
wrongAnnotations.addAll(list);
}
/**
- * Constructor that initializes the data with {@link #object annotated object}
+ * Constructor that initializes the data with {@link #bioEntity bio entity}
* and improper {@link MiriamData}.
*
* @param miriamData
* invalid {@link MiriamData}
- * @param object
+ * @param bioEntity
* annotated object
*/
- public ImproperAnnotations(BioEntity object, MiriamData miriamData) {
- this.object = object;
+ public ImproperAnnotations(BioEntity bioEntity, MiriamData miriamData) {
+ this.bioEntity = bioEntity;
wrongAnnotations.add(miriamData);
}
@Override
public String getMessage() {
- StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(object));
+ StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
result.append("contains invalid annotations: ");
for (MiriamData miriamData : wrongAnnotations) {
result.append(miriamData.getDataType().getCommonName() + "(" + miriamData.getResource() + "), ");
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 64aa9a4bc1..d981d5a1ba 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
@@ -13,24 +13,23 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
public class MissingAnnotation implements ProblematicAnnotation {
/**
- * Object improperly annotated.
+ * BioEntity improperly annotated.
*/
- private BioEntity object;
+ private BioEntity bioEntity;
/**
- * Constructor that initializes the data with {@link #object annotated object}
- * .
+ * Constructor that initializes the data with {@link #bioEntity bioEntity} .
*
- * @param object
- * annotated object that miss annotation
+ * @param bioEntity
+ * bioEntity that misses annotation
*/
- public MissingAnnotation(BioEntity object) {
- this.object = object;
+ public MissingAnnotation(BioEntity bioEntity) {
+ this.bioEntity = bioEntity;
}
@Override
public String getMessage() {
- return new ElementUtils().getElementTag(object) + "misses annotations.";
+ return new ElementUtils().getElementTag(bioEntity) + "misses annotations.";
}
@Override
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 c6a40a2e92..c2ba975f0e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* Defines problem with element annotation when there are some required
- * annotations,but none of them can be found in the element.
+ * annotations, but none of them can be found in the element.
*
* @author Piotr Gawron
*
@@ -20,9 +20,9 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
public class MissingRequiredAnnotations implements ProblematicAnnotation {
/**
- * Object improperly annotated.
+ * BioEntity improperly annotated.
*/
- private BioEntity object;
+ private BioEntity bioEntity;
/**
* Required miriam type.
@@ -30,25 +30,25 @@ public class MissingRequiredAnnotations implements ProblematicAnnotation {
private List<MiriamType> requiredMiriamType = new ArrayList<>();
/**
- * Constructor that initializes the data with {@link #object annotated object}
- * and list of improper {@link MiriamData}.
+ * Constructor that initializes the data with {@link #bioEntity bioEntity} and
+ * list of improper {@link MiriamData}.
*
* @param list
* list of missing but required {@link MiriamType}
- * @param object
- * annotated object
+ * @param bioEntity
+ * {@link BioEntity}
*/
- public MissingRequiredAnnotations(BioEntity object, Collection<MiriamType> list) {
+ public MissingRequiredAnnotations(BioEntity bioEntity, Collection<MiriamType> list) {
if (list.size() == 0) {
throw new InvalidArgumentException("List of improper annotations cannot be null");
}
- this.object = object;
+ this.bioEntity = bioEntity;
requiredMiriamType.addAll(list);
}
@Override
public String getMessage() {
- StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(object));
+ StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
result.append("misses one of the following annotations: ");
for (MiriamType type : requiredMiriamType) {
result.append(type.getCommonName());
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 9808ebd014..fb21e1e31b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -428,8 +428,8 @@ public class ModelAnnotator {
}
/**
- * Checks if {@link BioEntity} is properly annotated and if not return
- * info about missing annotation.
+ * Checks if {@link BioEntity} is properly annotated and if not return info
+ * about missing annotation.
*
* @param element
* object to be checked
@@ -604,7 +604,7 @@ public class ModelAnnotator {
* miriam types } for {@link BioEntity} class type.
*
* @return map with informations about required {@link MiriamType miriam types
- * * } for {@link BioEntity} class type
+ * } for {@link BioEntity} class type
*/
@SuppressWarnings("unchecked")
public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultRequiredClasses() {
--
GitLab