From 3f95ee99cc72fa6bd89520e1141228b078d59d00 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 31 Jul 2018 11:18:35 +0200
Subject: [PATCH] selecting element by annotation type doesn't include
annotator from which it was selected
---
.../mapviewer/commands/ColorModelCommand.java | 9 ++-
.../commands/ColorModelCommandTest.java | 55 +++++++++++++++++++
2 files changed, 63 insertions(+), 1 deletion(-)
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 dc51d7bd73..0604eb7b48 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -221,7 +221,14 @@ public class ColorModelCommand extends ModelCommand {
}
}
for (MiriamData md : schema.getMiriamData()) {
- if (!element.getMiriamData().contains(md)) {
+ boolean found = false;
+ for (MiriamData elementMiriamData : element.getMiriamData()) {
+ if (elementMiriamData.getDataType().equals(md.getDataType())
+ && elementMiriamData.getResource().equals(md.getResource())) {
+ found = true;
+ }
+ }
+ if (!found) {
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 7d0d731afd..a7e8702c8f 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -360,6 +360,61 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
+ @Test
+ public void testSpeciesMatchWithMiriamData() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setName("s1");
+ colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ GenericColorSchema colorSchema2 = new GenericColorSchema();
+ colorSchema2.setName("s1");
+ colorSchema2.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
+
+ GenericProtein species = new GenericProtein("id");
+ species.setName("s1");
+ species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(species, colorSchema));
+ assertFalse(factory.match(species, colorSchema2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSpeciesMatchWithMiriamDataDifferentAnnotator() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setName("s1");
+ colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ GenericProtein species = new GenericProtein("id");
+ species.setName("s1");
+ species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA", Object.class));
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(species, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
@Test
public void testReactionMatchWithProteinMiriamData() throws Exception {
try {
--
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