export of z index for reactions added

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java

@@ -269,7 +269,7 @@ public class ModelToGPML {
 
   /**
    * This function transform Compartments into Shapes (Oval or Rectangle) from
-   * PathVisio. 
+   * PathVisio.
    * 
    * @param model
    *          model where compartments are placed
@@ -338,7 +338,10 @@ public class ModelToGPML {
     interaction.append("  <Interaction GraphId=\"" + getNewId() + "\">\n");
     interaction.append("    <Attribute Key=\"org.pathvisio.core.ds\" Value=\"\"/>\n");
     interaction.append("    <Attribute Key=\"org.pathvisio.core.id\" Value=\"\"/>\n");
-    interaction.append("    <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
+    interaction.append("    <Graphics "
+        + "ConnectorType=\"Segmented\" "
+        + "ZOrder=\"" + rn.getReaction().getZ() + "\" "
+        + "LineThickness=\"" + rn.getLine().getWidth() + "\">\n");
 
     if (rn instanceof Reactant) {
       for (Point2D p2d : line.getPoints()) {
@@ -514,11 +517,10 @@ public class ModelToGPML {
 
       interactions.append("  <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
       interactions.append(biopaxParser.toReferenceXml(reaction.getMiriamData()));
-      // interactions.append(" <Attribute Key=\"org.pathvisio.core.ds\"
-      // Value=\"\"/>\n");
-      // interactions.append(" <Attribute Key=\"org.pathvisio.core.id\"
-      // Value=\"\"/>\n");
-      interactions.append("    <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
+      interactions.append("    <Graphics "
+          + "ConnectorType=\"Segmented\" "
+          + "ZOrder=\"" + reaction.getZ() + "\" "
+          + "LineThickness=\"" + reaction.getLine().getWidth() + "\">\n");
 
       /** Start and End **/
       Reactant start = reaction.getReactants().get(0);
@@ -608,7 +610,7 @@ public class ModelToGPML {
 
     return gpml.toString();
   }
-  
+
   private String colorToString(Color color) {
     return colorParser.colorToHtml(color).substring(1);
   }