Merge branch '744-sbml-reaction-color-coding' into 'devel_12.2.x'

Resolve "color coding for reaction in sbml is improperly used (Copasi doesn't reaction colors provided by minerva)"

See merge request minerva/core!718

CHANGELOG

+minerva (12.2.1) stable; urgency=medium
+  * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
+    read colors properly) (#744) 
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200
+
 minerva (12.2.0) stable; urgency=medium
   * Feature: bug report utility
   * Feature: url GET parameters support all kind of search and selected overlays

commons/src/main/java/lcsb/mapviewer/common/comparator/FloatComparator.java

+package lcsb.mapviewer.common.comparator;
+
+import java.util.Comparator;
+
+import lcsb.mapviewer.common.Configuration;
+
+/**
+ * Comparator used for {@link Float} class.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class FloatComparator implements Comparator<Float> {
+
+  /**
+   * Epsilon value used for comparison of doubles.
+   */
+  private double epsilon;
+
+  /**
+   * Default constructor.
+   */
+  public FloatComparator() {
+    this(Configuration.EPSILON);
+  }
+
+  /**
+   * Constructor that requires {@link #epsilon} parameter.
+   * 
+   * @param epsilon
+   *          {@link #epsilon}
+   */
+  public FloatComparator(double epsilon) {
+    this.epsilon = epsilon;
+  }
+
+  @Override
+  public int compare(Float arg0, Float arg1) {
+    if (arg0 == null) {
+      if (arg1 == null) {
+        return 0;
+      } else {
+        return 1;
+      }
+
+    } else if (arg1 == null) {
+      return -1;
+    }
+    if (Math.abs(arg0 - arg1) < epsilon) {
+      return 0;
+    } else {
+      return arg0.compareTo(arg1);
+    }
+  }
+
+}

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -293,10 +293,10 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     LocalStyle style = new LocalStyle();
     style.setGroup(new RenderGroup());
     renderInformation.addLocalStyle(style);
-    style.getGroup().setStroke(node.getLine().getType().name());
     ColorDefinition color = getColorDefinition(node.getLine().getColor());
-    style.getGroup().setStrokeWidth(node.getLine().getWidth());
+    style.getGroup().setStroke(color.getId());
     style.getGroup().setFill(color.getId());
+    style.getGroup().setStrokeWidth(node.getLine().getWidth());
     style.getGroup().setStrokeDashArray(strokeToArray(node.getLine().getType().getStroke()));
 
     return style;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -30,6 +30,7 @@ import org.sbml.jsbml.ext.render.LocalStyle;
 import org.sbml.jsbml.ext.render.RenderGroup;
 import org.w3c.dom.Node;
 
+import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
@@ -247,21 +248,16 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
 
   private void applyStyleToReactionNode(ReactionNode modifier, LocalStyle style, boolean reverse) {
     RenderGroup group = style.getGroup();
-    if (group.isSetFill()) {
-      Color color = getColorByColorDefinition(group.getFill());
+    if (group.isSetStroke()) {
+      Color color = getColorByColorDefinition(group.getStroke());
       modifier.getLine().setColor(color);
     }
     if (group.isSetStrokeWidth()) {
       modifier.getLine().setWidth(group.getStrokeWidth());
     }
-    if (group.isSetStroke()) {
-      try {
-        LineType type = LineType.valueOf(group.getStroke());
-        modifier.getLine().setType(type);
-      } catch (Exception e) {
-        logger.warn(new ElementUtils().getElementTag(modifier.getReaction()) + "Problematic line type: "
-            + group.getStroke(), e);
-      }
+    if (group.isSetStrokeDashArray()) {
+      LineType type = LineType.getTypeByDashArray(group.getStrokeDashArray());
+      modifier.getLine().setType(type);
     }
     if (group.isSetEndHead()) {
       try {
@@ -413,8 +409,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
 
   public void applyStyleToReaction(Reaction reactionWithLayout, LocalStyle style) {
     RenderGroup group = style.getGroup();
-    if (group.getFill() != null) {
-      Color color = getColorByColorDefinition(group.getFill());
+    if (group.isSetStroke()) {
+      Color color = getColorByColorDefinition(group.getStroke());
       for (AbstractNode node : reactionWithLayout.getNodes()) {
         node.getLine().setColor(color);
       }
@@ -424,15 +420,10 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
         node.getLine().setWidth(group.getStrokeWidth());
       }
     }
-    if (group.isSetStroke()) {
-      try {
-        LineType type = LineType.valueOf(group.getStroke());
-        for (AbstractNode node : reactionWithLayout.getNodes()) {
-          node.getLine().setType(type);
-        }
-      } catch (Exception e) {
-        logger.warn(new ElementUtils().getElementTag(reactionWithLayout) + "Problematic line type: "
-            + group.getStroke(), e);
+    if (group.isSetStrokeDashArray()) {
+      LineType type = LineType.getTypeByDashArray(group.getStrokeDashArray());
+      for (AbstractNode node : reactionWithLayout.getNodes()) {
+        node.getLine().setType(type);
       }
     }
     if (group.isSetEndHead()) {

model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java

@@ -2,7 +2,9 @@ package lcsb.mapviewer.model.graphics;
 
 import java.awt.BasicStroke;
 import java.awt.Stroke;
+import java.util.List;
 
+import lcsb.mapviewer.common.comparator.FloatComparator;
 import lcsb.mapviewer.common.geometry.CompositeStroke;
 
 /**
@@ -21,7 +23,7 @@ public enum LineType {
    * Solid bold line.
    */
   SOLID_BOLD(3),
-  
+
   /**
    * Dash-dot-dot line:
    * 
@@ -30,7 +32,7 @@ public enum LineType {
    * </pre>
    */
   DASH_DOT_DOT(1, new float[] { 11.0f, 3.0f, 1.0f, 3.0f, 1.0f, 3.0f }),
-  
+
   /**
    * Dash-dot line:
    * 
@@ -132,4 +134,25 @@ public enum LineType {
   public Stroke getStroke() {
     return stroke;
   }
+
+  public static LineType getTypeByDashArray(List<Short> strokeDashArray) {
+    FloatComparator doubleComparator = new FloatComparator();
+    for (LineType type : LineType.values()) {
+      if (type.getStroke() instanceof BasicStroke) {
+        BasicStroke basicStroke = (BasicStroke) type.getStroke();
+        if (basicStroke.getDashArray() != null && strokeDashArray.size() == basicStroke.getDashArray().length) {
+          boolean match = true;
+          for (int i = 0; i < strokeDashArray.size(); i++) {
+            if (doubleComparator.compare(basicStroke.getDashArray()[i], (float) strokeDashArray.get(i)) != 0) {
+              match = false;
+            }
+          }
+          if (match) {
+            return type;
+          }
+        }
+      }
+    }
+    return LineType.SOLID;
+  }
 }