From 2ae42db37f49969e762c42adcbc64b3314ab00c1 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 7 May 2019 19:17:41 +0200
Subject: [PATCH] when parsing sbgn file z-index is automatically assigned
---
.../model/sbgnml/SbgnmlXmlParser.java | 3 ++
.../model/sbgnml/SbgnmlXmlParserTest2.java | 37 ++++++++++++++-----
2 files changed, 30 insertions(+), 10 deletions(-)
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 0808b4ec81..2161a4a2ea 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -24,6 +24,7 @@ import org.sbgn.bindings.Sbgn;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
@@ -185,6 +186,8 @@ public class SbgnmlXmlParser {
}
}
}
+
+ new ZIndexPopulator().populateZIndex(model);
return model;
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
index 1bdffa18e7..1c8a70fb12 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
@@ -43,16 +43,33 @@ public class SbgnmlXmlParserTest2 {
@Test
public void createModelWithCompartmentsTest() throws Exception {
try {
- Converter converter = new SbgnmlXmlConverter();
-
- Model model = converter
- .createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));
- Complex complexInsideCompartment = model.getElementByElementId("csa1830");
- assertNotNull("Complex inside compartment has undefined compartment", complexInsideCompartment.getCompartment());
- Complex complexOutsideCompartment = model.getElementByElementId("csa1831");
- assertNull("Complex outside compartment has not null compartment",complexOutsideCompartment.getCompartment());
- Compartment compartment = model.getElementByElementId("ca107");
- assertNull("Top compartment has not null compartment", compartment.getCompartment());
+ Converter converter = new SbgnmlXmlConverter();
+
+ Model model = converter
+ .createModel(new ConverterParams()
+ .filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));
+ Complex complexInsideCompartment = model.getElementByElementId("csa1830");
+ assertNotNull("Complex inside compartment has undefined compartment", complexInsideCompartment.getCompartment());
+ Complex complexOutsideCompartment = model.getElementByElementId("csa1831");
+ assertNull("Complex outside compartment has not null compartment", complexOutsideCompartment.getCompartment());
+ Compartment compartment = model.getElementByElementId("ca107");
+ assertNull("Top compartment has not null compartment", compartment.getCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void createModelWithZIndex() throws Exception {
+ try {
+ Converter converter = new SbgnmlXmlConverter();
+
+ Model model = converter
+ .createModel(new ConverterParams()
+ .filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));
+ Complex complex = model.getElementByElementId("csa1830");
+ assertNotNull(complex.getZ());
} catch (Exception e) {
e.printStackTrace();
throw e;
--
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