From fa1e013ffd2fdcce685c56f5726bb49dd9a64906 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 24 Jul 2017 11:46:32 +0200
Subject: [PATCH] switch statement fixed after refactoring
---
.../services/search/ElementMatcher.java | 128 +++++++++---------
1 file changed, 63 insertions(+), 65 deletions(-)
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 e42dd90ee7..44ba848aa0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/ElementMatcher.java
@@ -24,20 +24,19 @@ import lcsb.mapviewer.services.search.db.TargetView;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
public class ElementMatcher {
-
+
/**
* Default class logger.
*/
- private final Logger logger = Logger.getLogger(ElementMatcher.class);
+ private final Logger logger = Logger.getLogger(ElementMatcher.class);
/**
* Factory object used for creation of
* {@link lcsb.mapviewer.services.view.AnnotationView} elements.
*/
@Autowired
- private AnnotationViewFactory annotationViewFactory;
-
-
+ private AnnotationViewFactory annotationViewFactory;
+
/**
* Check if the target should be applied to the element.
*
@@ -125,82 +124,81 @@ public class ElementMatcher {
}
public boolean elementMatch(Target target, BioEntity element) {
- if (target.getType().equals(TargetType.COMPLEX_PROTEIN.getCommonName())) {
- MiriamData targetAnnotation = target.getSource();
- if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
- if (element.getMiriamData().contains(targetAnnotation)) {
- return true;
+ MiriamData targetAnnotation = target.getSource();
+ switch (target.getType()) {
+ case COMPLEX_PROTEIN:
+ if (MiriamType.CHEMBL_TARGET.equals(targetAnnotation.getDataType())) {
+ if (element.getMiriamData().contains(targetAnnotation)) {
+ return true;
+ }
}
- }
- Collection<String> ids = new HashSet<String>();
- for (MiriamData row : target.getGenes()) {
- ids.add(row.getResource());
- }
-
- if (element instanceof Complex) {
- Complex complex = (Complex) element;
- Set<Species> speciesSet = complex.getAllSimpleChildren();
- if (speciesSet.size() != ids.size()) {
- return false;
+ Collection<String> ids = new HashSet<String>();
+ for (MiriamData row : target.getGenes()) {
+ ids.add(row.getResource());
}
- for (Element id : speciesSet) {
- if (!ids.contains(id.getName())) {
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ Set<Species> speciesSet = complex.getAllSimpleChildren();
+ if (speciesSet.size() != ids.size()) {
return false;
}
- }
- return true;
- }
- return false;
- } else if (target.getType().equals(TargetType.SINGLE_PROTEIN.getCommonName())) {
- MiriamData targetAnnotation = null;
- if (target.getSource() != null) {
- targetAnnotation = target.getSource();
- } else if (target.getGenes().size() > 0) {
- targetAnnotation = target.getGenes().get(0);
- } else {
- logger.warn("Invalid target found: " + target);
- }
- if (targetAnnotation != null && element.getMiriamData().contains(targetAnnotation)) {
- return true;
- }
- if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
- if (target.getGenes().size() > 0) {
- String hgncId = target.getGenes().get(0).getResource();
- if (element.getName().equalsIgnoreCase(hgncId)) {
- return true;
+
+ for (Element id : speciesSet) {
+ if (!ids.contains(id.getName())) {
+ return false;
+ }
}
- }
- }
- return false;
- } else if (target.getType().equals(TargetType.PROTEIN_FAMILY.getCommonName())) {
- if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
- String hgncId = target.getGenes().get(0).getResource();
- if (element.getName().equalsIgnoreCase(hgncId)) {
return true;
- } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
+ }
+ return false;
+ case SINGLE_PROTEIN:
+ if (target.getSource() != null) {
+ targetAnnotation = target.getSource();
+ } else if (target.getGenes().size() > 0) {
+ targetAnnotation = target.getGenes().get(0);
+ } else {
+ logger.warn("Invalid target found: " + target);
+ }
+ if (targetAnnotation != null && element.getMiriamData().contains(targetAnnotation)) {
return true;
}
- for (MiriamData protein : target.getGenes()) {
- hgncId = protein.getResource();
+ if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
+ if (target.getGenes().size() > 0) {
+ String hgncId = target.getGenes().get(0).getResource();
+ if (element.getName().equalsIgnoreCase(hgncId)) {
+ return true;
+ }
+ }
+ }
+ return false;
+ case PROTEIN_FAMILY:
+ if (element instanceof Protein || element instanceof Rna || element instanceof Gene) {
+ String hgncId = target.getGenes().get(0).getResource();
if (element.getName().equalsIgnoreCase(hgncId)) {
return true;
} else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
return true;
}
+ for (MiriamData protein : target.getGenes()) {
+ hgncId = protein.getResource();
+ if (element.getName().equalsIgnoreCase(hgncId)) {
+ return true;
+ } else if (element.getMiriamData().contains(new MiriamData(MiriamType.HGNC_SYMBOL, hgncId))) {
+ return true;
+ }
+ }
}
- }
- return false;
- } else if (target.getType().equals(TargetType.OTHER.getCommonName())) {
- // in other case just compare names
- String name = target.getGenes().get(0).getResource();
- return element.getName().equalsIgnoreCase(name);
- } else {
- throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
+ return false;
+ case OTHER:
+ // in other case just compare names
+ String name = target.getGenes().get(0).getResource();
+ return element.getName().equalsIgnoreCase(name);
+ default:
+ throw new InvalidArgumentException("Unknown drug target type: " + target.getType());
}
}
-
/**
* @return the annotationViewFactory
* @see #annotationViewFactory
@@ -209,9 +207,9 @@ public class ElementMatcher {
return annotationViewFactory;
}
-
/**
- * @param annotationViewFactory the annotationViewFactory to set
+ * @param annotationViewFactory
+ * the annotationViewFactory to set
* @see #annotationViewFactory
*/
public void setAnnotationViewFactory(AnnotationViewFactory annotationViewFactory) {
--
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