diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java index 581ae12c704802b16b91741ff9b8b33f92b69324..ffc86624258d3625c019e9c343faf3f08215cce0 100644 --- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java +++ b/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); }