font color is properly encoded and compartments properly handle fill color

CHANGELOG

@@ -4,6 +4,10 @@ minerva (15.1.0) unstable; urgency=medium
   * Small improvement: plugin API allows to add/remove data overlays (#1153)
   * Small improvement: logged user can change password (#1119)
   * Small improvement: possibility to reset password added (#275)
+  * Small improvement: import SBML uses render:fill color for compartment
+    (#1254)
+  * Small improvement: in SBML render stroke color for glyphs is used for
+    defining font color
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Jun 2020 16:00:00 +0200
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java

@@ -15,10 +15,6 @@ import lcsb.mapviewer.model.map.species.Element;
 public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.jsbml.Symbol>
     extends SbmlBioEntityExporter<T, S> {
 
-  /**
-   * Default class logger.
-   */
-  @SuppressWarnings("unused")
   private static Logger logger = LogManager.getLogger();
 
   public SbmlElementExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
@@ -58,35 +54,37 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
       LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
       LocalStyle style = new LocalStyle();
       style.getIDList().add(textGlyph.getId());
-      style.setGroup(new RenderGroup());
-      style.getGroup().setVTextAnchor(VTextAnchor.MIDDLE);
-      style.getGroup().setTextAnchor(HTextAnchor.MIDDLE);
+      RenderGroup group = new RenderGroup();
+      style.setGroup(group);
+      group.setVTextAnchor(VTextAnchor.MIDDLE);
+      group.setTextAnchor(HTextAnchor.MIDDLE);
       switch (element.getNameHorizontalAlign()) {
       case CENTER:
-        style.getGroup().setTextAnchor(HTextAnchor.MIDDLE);
+        group.setTextAnchor(HTextAnchor.MIDDLE);
         break;
       case LEFT:
-        style.getGroup().setTextAnchor(HTextAnchor.START);
+        group.setTextAnchor(HTextAnchor.START);
         x = element.getNamePoint().getX();
         break;
       case RIGTH:
-        style.getGroup().setTextAnchor(HTextAnchor.END);
+        group.setTextAnchor(HTextAnchor.END);
         width = element.getNamePoint().getX() - x;
         break;
       }
       switch (element.getNameVerticalAlign()) {
       case BOTTOM:
-        style.getGroup().setVTextAnchor(VTextAnchor.BOTTOM);
+        group.setVTextAnchor(VTextAnchor.BOTTOM);
         height = element.getNamePoint().getY() - y;
         break;
       case MIDDLE:
-        style.getGroup().setVTextAnchor(VTextAnchor.MIDDLE);
+        group.setVTextAnchor(VTextAnchor.MIDDLE);
         break;
       case TOP:
-        style.getGroup().setVTextAnchor(VTextAnchor.TOP);
+        group.setVTextAnchor(VTextAnchor.TOP);
         y = element.getNamePoint().getY();
         break;
       }
+      group.setStroke(getColorDefinition(element.getFontColor()).getId());
       renderInformation.addLocalStyle(style);
     }
     textGlyph.setBoundingBox(createBoundingBox(x, y, element.getZ() + 1, width, height));

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java

@@ -18,7 +18,6 @@ import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.HorizontalAlign;
 import lcsb.mapviewer.model.graphics.VerticalAlign;
-import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.species.Element;
 
 public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends SbmlBioEntityParser {
@@ -99,7 +98,12 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
 
     for (Pair<String, AbstractReferenceGlyph> idGlyphPair : getGlyphs()) {
       String id = idGlyphPair.getLeft();
-      Element source = getAnyElementBySbmlElementId(id);
+
+      Element source = getMinervaModel().getElementByElementId(idGlyphPair.getRight().getId());
+      if (source == null) {
+        source = getAnyElementBySbmlElementId(id);
+      }
+
       if (source == null) {
         throw new InvalidInputDataExecption("Layout contains invalid Species id: " + idGlyphPair.getLeft());
       }
@@ -152,6 +156,10 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
                     group.getTextAnchor() + " text alignment is not supported");
               }
             }
+            if (group.isSetStroke()) {
+              Color fontColor = getColorByColorDefinition(group.getStroke());
+              source.setFontColor(fontColor);
+            }
           }
           source.setNamePoint(new Point2D.Double(x, y));
         }
@@ -199,10 +207,13 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
     if (style.getGroup().isSetFill()) {
       Color backgroundColor = getColorByColorDefinition(style.getGroup().getFill());
       elementWithLayout.setFillColor(backgroundColor);
-      if (elementWithLayout instanceof Compartment) {
-        elementWithLayout.setBorderColor(backgroundColor);
-      }
     }
+    if (style.getGroup().isSetStroke()) {
+      Color borderColor = getColorByColorDefinition(style.getGroup().getStroke());
+      elementWithLayout.setBorderColor(borderColor);
+      elementWithLayout.setFontColor(borderColor);
+    }
+
     if (style.getGroup().isSetFontSize()) {
       elementWithLayout.setFontSize(style.getGroup().getFontSize());
     }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java

@@ -73,12 +73,10 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
 
   @Override
   protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
+    super.applyStyleToElement(elementWithLayout, style);
     if (!style.getGroup().isSetFill() && style.getGroup().isSetStroke()) {
       Color backgroundColor = getColorByColorDefinition(style.getGroup().getStroke());
       elementWithLayout.setFillColor(backgroundColor);
-      if (elementWithLayout instanceof Compartment) {
-        elementWithLayout.setBorderColor(backgroundColor);
-      }
     }
   }