From 6eda7ed1458ac0637a6657a813d2bce66839d94e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 31 Oct 2019 12:00:25 +0100
Subject: [PATCH] export of z index for reactions added
---
.../mapviewer/wikipathway/XML/ModelToGPML.java | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
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 581ae12c70..ffc8662425 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);
}
--
GitLab