From 3131738400461b3147c2ac4ddba6016d9f6270d3 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 28 Jun 2017 15:55:35 +0200
Subject: [PATCH] parent compartment is assigned properly when processing
compartments
---
.../alias/AliasCollectionXmlParser.java | 1 +
.../CellDesignerXmlParserTest.java | 24 ++++
.../annotation/RestAnnotationParserTest.java | 1 -
...ested_compartments_in_few_compartments.xml | 105 ++++++++++++++++++
4 files changed, 130 insertions(+), 1 deletion(-)
create mode 100644 converter-CellDesigner/testFiles/compartment/nested_compartments_in_few_compartments.xml
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
index 688f761cfe..e80d09ae7a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
@@ -215,6 +215,7 @@ public class AliasCollectionXmlParser extends XmlParser {
}
if (parent != nullParent) {
child.setCompartment(parent);
+ parent.addElement(child);
}
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 445722f272..5ebeb1ae3a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -29,6 +29,7 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
@@ -991,4 +992,27 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testCompartmentWithSubcompartments() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/compartment/nested_compartments_in_few_compartments.xml"));
+ Compartment c3 = model.getElementByElementId("ca3");
+ Compartment c4 = model.getElementByElementId("ca4");
+ Compartment c1 = model.getElementByElementId("ca1");
+ Compartment c2 = model.getElementByElementId("ca2");
+ assertEquals("ca1", c3.getCompartment().getElementId());
+ assertEquals("ca2", c4.getCompartment().getElementId());
+
+ assertEquals(1, c1.getElements().size());
+ assertEquals(1, c2.getElements().size());
+ assertEquals(0, c3.getElements().size());
+ assertEquals(0, c4.getElements().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index 0195858815..f396388cca 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -289,7 +289,6 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
element.addFormerSymbol(former2);
element.setCharge(1);
String str = rap.createAnnotationString(element, true);
- logger.debug(str);
assertTrue(str.contains(former1));
assertTrue(str.contains(former2));
diff --git a/converter-CellDesigner/testFiles/compartment/nested_compartments_in_few_compartments.xml b/converter-CellDesigner/testFiles/compartment/nested_compartments_in_few_compartments.xml
new file mode 100644
index 0000000000..8ca2988a0d
--- /dev/null
+++ b/converter-CellDesigner/testFiles/compartment/nested_compartments_in_few_compartments.xml
@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="35.0" y="77.0" w="171.0" h="179.0"/>
+<celldesigner:namePoint x="98.5" y="153.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca2" compartment="c2">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="316.0" y="110.0" w="248.0" h="149.0"/>
+<celldesigner:namePoint x="432.5" y="222.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca3" compartment="c3">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="64.0" y="144.0" w="105.0" h="68.0"/>
+<celldesigner:namePoint x="109.0" y="175.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca4" compartment="c3">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="351.0" y="180.0" w="86.0" h="33.0"/>
+<celldesigner:namePoint x="386.5" y="184.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases/>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c2" id="c2" name="c2" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c2</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c3" id="c3" name="c3" size="1" units="volume" outside="c2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c3</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+</model>
+</sbml>
--
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