From dbc3e6c8435af505e5f09fb4e19586402f1a3952 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 24 Jul 2017 13:40:48 +0200
Subject: [PATCH] mirna view structure removed
---
.../lcsb/mapviewer/annotation/data/MiRNA.java | 21 +++
.../api/projects/mirnas/MiRnaRestImpl.java | 8 -
.../search/db/mirna/MiRNAService.java | 2 +-
.../services/search/db/mirna/MiRNAView.java | 154 ------------------
4 files changed, 22 insertions(+), 163 deletions(-)
delete mode 100644 service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAView.java
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
index c26622b7af..faef1dd19c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/data/MiRNA.java
@@ -3,10 +3,12 @@ package lcsb.mapviewer.annotation.data;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.Comparator;
import java.util.List;
import javax.xml.bind.annotation.XmlRootElement;
+import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.model.map.MiriamData;
/**
@@ -108,4 +110,23 @@ public class MiRNA implements Serializable, TargettingStructure {
return new ArrayList<>();
}
+ /**
+ * Comparator of the objects by their name.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class NameComparator implements Comparator<MiRNA> {
+ /**
+ * Default string comparator.
+ */
+ private StringComparator stringComparator = new StringComparator();
+
+ @Override
+ public int compare(MiRNA arg0, MiRNA arg1) {
+ return stringComparator.compare(arg0.getName(), arg1.getName());
+ }
+
+ }
+
}
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 35f4873cd3..1d9f8fc7e6 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
@@ -1,7 +1,6 @@
package lcsb.mapviewer.api.projects.mirnas;
import java.util.ArrayList;
-import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -13,25 +12,18 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.annotation.data.Target;
import lcsb.mapviewer.annotation.services.TaxonomyBackend;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
-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;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.search.ElementMatcher;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
-import lcsb.mapviewer.services.search.db.GeneRow;
-import lcsb.mapviewer.services.search.db.TargetView;
import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
-import lcsb.mapviewer.services.search.db.mirna.MiRNAView;
import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
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 9d2b1b10da..57ccbb24e6 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
@@ -167,7 +167,7 @@ public class MiRNAService implements IMiRNAService {
removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
}
- Collections.sort(mirnaList, new MiRNAView.NameComparator());
+ Collections.sort(mirnaList, new MiRNA.NameComparator());
return mirnaList;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAView.java b/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAView.java
deleted file mode 100644
index 833fd40e36..0000000000
--- a/service/src/main/java/lcsb/mapviewer/services/search/db/mirna/MiRNAView.java
+++ /dev/null
@@ -1,154 +0,0 @@
-package lcsb.mapviewer.services.search.db.mirna;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.annotation.data.MiRNA;
-import lcsb.mapviewer.common.comparator.StringComparator;
-import lcsb.mapviewer.services.search.ISearchResultView;
-import lcsb.mapviewer.services.search.db.TargetView;
-import lcsb.mapviewer.services.view.AbstractView;
-
-/**
- * Data of the MiRNA from external database to be visualized in the client side.
- *
- * @author Ayan Rota
- *
- */
-public class MiRNAView extends AbstractView<MiRNA> implements Serializable, ISearchResultView {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(MiRNAView.class);
-
- /**
- * Name of the miRNA.
- */
- private String name;
-
- /**
- * Is the MiRNA selected by the client or not.
- */
- private boolean selected = false;
-
- /**
- * List of targets for the MiRNA.
- */
- private List<TargetView> targetRows = new ArrayList<>();
-
- /***
- * Constructor that initialize the data with information from the
- * parameter*object.
- **
- * @param miRna
- * original MiRNA from which the data will be initialized
- */
- protected MiRNAView(MiRNA miRna) {
- // MiRNA is not db entity so don't pass it to super constructor
- super(null);
- }
-
- /**
- * Default constructor. Should be used only for deserialization.
- */
- protected MiRNAView() {
- }
-
- /**
- * Default constructor that creates a copy.
- *
- * @param original
- * origianl object that should be copied
- */
- public MiRNAView(MiRNAView original) {
- super(null);
- name = original.getName();
- selected = original.isSelected();
- targetRows.addAll(original.getTargetRows());
- }
-
- /**
- * Comparator of the objects by their name.
- *
- * @author Piotr Gawron
- *
- */
- public static class NameComparator implements Comparator<MiRNA> {
- /**
- * Default string comparator.
- */
- private StringComparator stringComparator = new StringComparator();
-
- @Override
- public int compare(MiRNA arg0, MiRNA arg1) {
- return stringComparator.compare(arg0.getName(), arg1.getName());
- }
-
- }
-
- /**
- * @return the selected
- */
- public boolean isSelected() {
- return selected;
- }
-
- /**
- * @param selected
- * the selected to set
- */
- public void setSelected(boolean selected) {
- this.selected = selected;
- }
-
- /**
- * @return the targetRows
- */
- public List<TargetView> getTargetRows() {
- return targetRows;
- }
-
- /**
- * @param targetRows
- * the targetRows to set
- */
- public void setTargetRows(List<TargetView> targetRows) {
- this.targetRows = targetRows;
- }
-
- /**
- * @return the mirBase id
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * mirBase id
- */
- public void setName(String name) {
- this.name = name;
- }
-
- @Override
- public String getUniqueId() {
- return name;
- }
-
- @Override
- public void setUniqueId(String uniqueId) {
- this.name = uniqueId;
- }
-
-}
--
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