conversion of top and left compartment fixed

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java

@@ -113,12 +113,14 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
           if (result instanceof BottomSquareCompartment) {
             result.setY(XmlParser.getNodeAttr("y", node));
           } else if (result instanceof LeftSquareCompartment) {
-            result.setX(XmlParser.getNodeAttr("x", node));
+            result.setWidth(XmlParser.getNodeAttr("x", node));
+            result.setX(0.0);
           } else if (result instanceof RightSquareCompartment) {
             result.setX(XmlParser.getNodeAttr("x", node));
             result.setWidth(result.getWidth() - result.getX());
           } else if (result instanceof TopSquareCompartment) {
-            result.setY(XmlParser.getNodeAttr("y", node));
+            result.setHeight(XmlParser.getNodeAttr("y", node));
+            result.setY(0.0);
           } else {
             throw new InvalidXmlSchemaException(
                 "Don't know what to do with celldesigner:point for class: " + result.getClass());

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java

 package lcsb.mapviewer.converter.model.celldesigner.compartment;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.*;
 
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 
 public class CompartmentParserTests extends CellDesignerTestFunctions {
@@ -23,6 +26,11 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
   @Test
   public void testParseCompartmensBottom() throws Exception {
     Model model = getModelForFile("testFiles/compartment/bottom_compartment.xml");
+    Compartment c = model.getElementByElementId("ca4");
+    assertTrue(c.getY() > 0);
+    assertTrue(c.getWidth() > 0);
+    assertTrue(c.getHeight() > 0);
+    assertEquals(0, c.getX(), Configuration.EPSILON);
 
     assertEquals(1, model.getElements().size());
   }
@@ -31,19 +39,33 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
   public void testParseCompartmensTop() throws Exception {
     Model model = getModelForFile("testFiles/compartment/top_compartment.xml");
 
+    Compartment c = model.getElementByElementId("ca3");
+    assertEquals(0, c.getX(), Configuration.EPSILON);
+    assertEquals(0, c.getY(), Configuration.EPSILON);
+    assertTrue(c.getWidth() > 0);
+    assertTrue(c.getHeight() < model.getHeight());
     assertEquals(1, model.getElements().size());
   }
 
   @Test
   public void testParseCompartmensRight() throws Exception {
     Model model = getModelForFile("testFiles/compartment/right_compartment.xml");
-
+    Compartment c = model.getElementByElementId("ca2");
+    assertTrue(c.getX() > 0);
+    assertTrue(c.getWidth() > 0);
+    assertTrue(c.getHeight() > 0);
+    assertEquals(0, c.getY(), Configuration.EPSILON);
     assertEquals(1, model.getElements().size());
   }
 
   @Test
   public void testParseCompartmensLeft() throws Exception {
     Model model = getModelForFile("testFiles/compartment/left_compartment.xml");
+    Compartment c = model.getElementByElementId("ca1");
+    assertEquals(0, c.getX(), Configuration.EPSILON);
+    assertEquals(0, c.getY(), Configuration.EPSILON);
+    assertTrue(c.getWidth() < model.getWidth());
+    assertTrue(c.getHeight() > 0);
 
     assertEquals(1, model.getElements().size());
   }