From 3f3fd7fd0952613bc5fe00cb52c291f5efb872b2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 13 Feb 2018 17:40:31 +0100
Subject: [PATCH] fix on matching reactions
---
.../mapviewer/commands/ColorModelCommand.java | 8 ++--
.../commands/ColorModelCommandTest.java | 46 +++++++++++++++++++
2 files changed, 50 insertions(+), 4 deletions(-)
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 f6ff490e8d..43df86700d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -137,16 +137,16 @@ public class ColorModelCommand extends ModelCommand {
if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
- if (reaction.getMiriamData().contains(md)) {
- return true;
+ if (!reaction.getMiriamData().contains(md)) {
+ return false;
}
}
for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
if (pair.getRight() != null && !pair.getRight().equals("")) {
MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (reaction.getMiriamData().contains(md)) {
- return true;
+ if (!reaction.getMiriamData().contains(md)) {
+ return false;
}
}
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index d240a93b7c..b8d977f446 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -17,6 +17,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
@@ -363,6 +364,51 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
+ @Test
+ public void testReactionMatchWithProteinMiriamData() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setGeneralIdentifier(MiriamType.HGNC_SYMBOL.getCommonName()+":SNCA");
+
+ Reaction reaction = new Reaction();
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertFalse(factory.match(reaction, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testReactionMatchWithMiriamData() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setGeneralIdentifier(MiriamType.PUBMED.getCommonName()+":1234");
+
+ Reaction reaction = new Reaction();
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(reaction, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
@Test
public void testReactionColoringWithModelNotMatching() throws Exception {
try {
--
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