Resolve "export form GPML to CellDesigner"

Closes #1146 (closed)

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

@@ -14,6 +14,8 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.compartment.*;
 import lcsb.mapviewer.model.map.model.Model;
 
@@ -25,11 +27,13 @@ import lcsb.mapviewer.model.map.model.Model;
  */
 public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartment> {
 
+  private final static double MIN_INNER_WIDTH = 1.0;
+
   /**
    * Default class logger.
    */
   @SuppressWarnings("unused")
-  private Logger logger = LogManager.getLogger(CompartmentAliasXmlParser.class.getName());
+  private Logger logger = LogManager.getLogger();
 
   /**
    * Model for which we are parsing aliases.
@@ -210,10 +214,7 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
     sb.append("x=\"" + compartment.getNamePoint().getX() + "\" ");
     sb.append("y=\"" + compartment.getNamePoint().getY() + "\"/>\n");
 
-    sb.append("<celldesigner:doubleLine ");
-    sb.append("thickness=\"" + compartment.getThickness() + "\" ");
-    sb.append("outerWidth=\"" + compartment.getOuterWidth() + "\" ");
-    sb.append("innerWidth=\"" + compartment.getInnerWidth() + "\"/>\n");
+    sb.append(getDoubleLineNode(compartment));
 
     sb.append("<celldesigner:paint ");
     sb.append("color=\"" + XmlParser.colorToString(compartment.getFillColor()) + "\" scheme=\"Color\"/>\n");
@@ -223,4 +224,41 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
     return sb.toString();
   }
 
+  private String getDoubleLineNode(Compartment compartment) {
+    StringBuilder result = new StringBuilder();
+    result.append("<celldesigner:doubleLine ");
+    double innerWidth = getInnerWidth(compartment);
+    if (innerWidth != compartment.getInnerWidth()) {
+      logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, compartment),
+          "CellDesigner requires innerWidth to be at least: " + innerWidth);
+    }
+    double outerWidth = getOuterWidth(compartment);
+    if (outerWidth != compartment.getOuterWidth()) {
+      logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, compartment),
+          "CellDesigner requires outerWidth to be at least: " + outerWidth);
+    }
+    double thickness = getThickness(compartment);
+    if (thickness != compartment.getThickness()) {
+      logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, compartment),
+          "CellDesigner requires thickness to be at least: " + thickness);
+    }
+    result.append("thickness=\"" + thickness + "\" ");
+    result.append("outerWidth=\"" + outerWidth + "\" ");
+    result.append("innerWidth=\"" + innerWidth + "\"/>\n");
+
+    return result.toString();
+  }
+
+  private double getInnerWidth(Compartment compartment) {
+    return Math.max(MIN_INNER_WIDTH, compartment.getInnerWidth());
+  }
+
+  private double getOuterWidth(Compartment compartment) {
+    return Math.max(getInnerWidth(compartment) + 1, compartment.getOuterWidth());
+  }
+
+  private double getThickness(Compartment compartment) {
+    return Math.max((getInnerWidth(compartment) + getOuterWidth(compartment)) / 2 + 1, compartment.getThickness());
+  }
+
 }