From 3515a9bc7a43e907c178285dd04ac36daa55e9a5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 19 Mar 2019 09:25:58 +0100
Subject: [PATCH] miriam data comparator implemented
---
.../model/map/MiriamDataComparator.java | 40 +++++++++++++++++
.../map/reaction/ReactionComparator.java | 27 +++++------
.../model/map/species/ElementComparator.java | 45 ++++---------------
.../map/reaction/ReactionComparatorTest.java | 14 ++++++
4 files changed, 73 insertions(+), 53 deletions(-)
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/MiriamDataComparator.java
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamDataComparator.java
new file mode 100644
index 0000000000..d4a5240ea1
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamDataComparator.java
@@ -0,0 +1,40 @@
+package lcsb.mapviewer.model.map;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+/**
+ * Comparator of {@link MiriamData} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class MiriamDataComparator extends Comparator<MiriamData> {
+
+ /**
+ * Default constructor.
+ */
+ public MiriamDataComparator() {
+ super(MiriamData.class);
+ }
+
+ @Override
+ protected int internalCompare(MiriamData arg0, MiriamData arg1) {
+ StringComparator stringComparator = new StringComparator();
+ if (stringComparator.compare(arg0.getResource(), arg1.getResource()) != 0) {
+ return stringComparator.compare(arg0.getResource(), arg1.getResource());
+ }
+ if (arg0.getDataType() != arg1.getDataType()) {
+ return -1;
+ }
+ if (arg0.getRelationType() != arg1.getRelationType()) {
+ return -1;
+ }
+ if (arg0.getAnnotator() != arg1.getAnnotator()) {
+ return -1;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index 2bb9e00ea2..91900fa4e9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -10,10 +10,12 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringListComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
/**
@@ -129,23 +131,14 @@ public class ReactionComparator extends Comparator<Reaction> {
return stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms());
}
- Set<String> hashCode1 = new HashSet<String>();
- Set<String> hashCode2 = new HashSet<String>();
+ SetComparator<MiriamData> miriamDataSetComparator = new SetComparator<>(new MiriamDataComparator());
- for (MiriamData md : arg0.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode1.add(hash);
- }
-
- for (MiriamData md : arg1.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode2.add(hash);
- }
-
- StringSetComparator stringSetComparator = new StringSetComparator();
- if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
- logger.debug("Miriam dataset different");
- return stringSetComparator.compare(hashCode1, hashCode2);
+ int status = miriamDataSetComparator.compare(arg0.getMiriamData(), arg1.getMiriamData());
+ if (status != 0) {
+ logger.debug("miriam data different");
+ logger.debug(arg0.getMiriamData());
+ logger.debug(arg1.getMiriamData());
+ return status;
}
if (arg0.getNodes().size() != arg1.getNodes().size()) {
@@ -155,7 +148,7 @@ public class ReactionComparator extends Comparator<Reaction> {
for (int i = 0; i < arg0.getNodes().size(); i++) {
AbstractNode node0 = arg0.getNodes().get(i);
- int status = -1;
+ status = -1;
for (int j = 0; j < arg1.getNodes().size(); j++) {
int tmpStatus = aNodeComparator.compare(node0, arg1.getNodes().get(j));
if (tmpStatus == 0) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index aef04ac56d..e02724a703 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -1,18 +1,16 @@
package lcsb.mapviewer.model.map.species;
-import java.util.HashSet;
-import java.util.Set;
-
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.ColorComparator;
import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringListComparator;
-import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
@@ -149,7 +147,6 @@ public class ElementComparator extends Comparator<Element> {
return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
}
- StringSetComparator stringSetComparator = new StringSetComparator();
StringListComparator stringListComparator = new StringListComparator();
if (stringListComparator.compare(arg0.getSynonyms(), arg1.getSynonyms()) != 0) {
@@ -162,38 +159,14 @@ public class ElementComparator extends Comparator<Element> {
return stringListComparator.compare(arg0.getFormerSymbols(), arg1.getFormerSymbols());
}
- Set<String> hashCode1 = new HashSet<>();
- Set<String> hashCode2 = new HashSet<>();
-
- if (arg0.getMiriamData().size() != arg1.getMiriamData().size()) {
- logger.debug(
- "different number of annotations: " + arg0.getMiriamData().size() + ", " + arg1.getMiriamData().size());
- return ((Integer) arg0.getMiriamData().size()).compareTo(arg1.getMiriamData().size());
- }
-
- for (MiriamData md : arg0.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode1.add(hash);
- }
-
- for (MiriamData md : arg1.getMiriamData()) {
- String hash = md.getRelationType() + " " + md.getDataType() + " " + md.getResource();
- hashCode2.add(hash);
- }
-
- if (stringSetComparator.compare(hashCode1, hashCode2) != 0) {
- logger.debug("different annotations: ");
- logger.debug("A:");
- for (String string : hashCode1) {
- logger.debug("|" + string + "|");
- }
- logger.debug("B:");
- for (String string : hashCode2) {
- logger.debug("|" + string + "|");
- }
- logger.debug("--");
- return stringSetComparator.compare(hashCode1, hashCode2);
+ SetComparator<MiriamData> miriamDataSetComparator = new SetComparator<>(new MiriamDataComparator());
+ status = miriamDataSetComparator.compare(arg0.getMiriamData(), arg1.getMiriamData());
+ if (status != 0) {
+ logger.debug("miriam data different");
+ logger.debug(arg0.getMiriamData());
+ logger.debug(arg1.getMiriamData());
+ return status;
}
return 0;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index 271edc6538..689f253e07 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -295,4 +295,18 @@ public class ReactionComparatorTest {
assertTrue(comparator.compare(reaction1, reaction2) != 0);
assertTrue(comparator.compare(reaction2, reaction1) != 0);
}
+
+ @Test
+ public void testDifferentMiriamData() {
+ Reaction reaction1 = createReaction();
+ Reaction reaction2 = createReaction();
+
+ reaction1.addMiriamData(new MiriamData(MiriamType.HGNC, "SNCA"));
+ assertTrue(comparator.compare(reaction1, reaction2) != 0);
+ assertTrue(comparator.compare(reaction2, reaction1) != 0);
+
+ reaction2.addMiriamData(new MiriamData(MiriamType.HGNC, "SNCA"));
+ assertEquals(0, comparator.compare(reaction1, reaction2));
+ assertEquals(0, comparator.compare(reaction2, reaction1));
+ }
}
--
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