From f289d1e80060606cd03ed9111f6f893d519c8a51 Mon Sep 17 00:00:00 2001
From: sherzinger <sascha.herzinger@uni.lu>
Date: Tue, 19 Feb 2019 08:53:12 +0100
Subject: [PATCH] fixed pathvisio module tests

---
 .../ComplexReactionToModelTest.java           |  6 +-
 .../wikipathway/GPMLToModelTest.java          | 46 ++++++------
 .../wikipathway/ReactionElbowsTest.java       | 48 ++++++-------
 .../ReactionGpmlInputToModelTest.java         | 64 ++++++++---------
 .../ReactionGpmlOutputToModelTest.java        | 64 ++++++++---------
 .../wikipathway/ReactionGpmlToModelTest.java  | 70 +++++++++----------
 .../mapviewer/wikipathway/XML/BugTest.java    |  2 +-
 7 files changed, 150 insertions(+), 150 deletions(-)

diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index d75e6ef106..cce59fd6a8 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -100,7 +100,7 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
 			Model model1 = new GPMLToModel().getModel(fileName);
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -124,7 +124,7 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
 			Model model1 = new GPMLToModel().getModel(fileName);
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -148,7 +148,7 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
 			Model model1 = new GPMLToModel().getModel(fileName);
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 188a815136..0baa17ed73 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -47,7 +47,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
 
       assertEquals(22, getWarnings().size());
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -69,7 +69,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
 
       assertEquals(22, getWarnings().size());
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -92,7 +92,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
 
       assertEquals(15, getWarnings().size());
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -115,7 +115,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(16, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -138,7 +138,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(3, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -161,7 +161,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(38, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -185,7 +185,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(41, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -209,7 +209,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(22, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -233,7 +233,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(0, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
 
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -258,7 +258,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(0, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
 
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -283,7 +283,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(0, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
 
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -307,7 +307,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(3, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
 
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -331,7 +331,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(3, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
 
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -447,7 +447,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       Model model1 = new GPMLToModel().getModel(fileName);
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -477,7 +477,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       Model model1 = new GPMLToModel().getModel(fileName);
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -498,7 +498,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       Model model1 = new GPMLToModel().getModel(fileName);
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -519,7 +519,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       Model model1 = new GPMLToModel().getModel(fileName);
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -538,7 +538,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       Model model1 = new GPMLToModel().getModel(fileName);
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -561,7 +561,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(2, protein.getModificationResidues().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1, false);
+      String xml = parser.model2Xml(model1, false);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -585,7 +585,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(2, protein.getModificationResidues().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1, false);
+      String xml = parser.model2Xml(model1, false);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -629,7 +629,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(1, model1.getReactions().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -653,7 +653,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals(1, getWarnings().size());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
@@ -676,7 +676,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
       assertEquals("GTP", protein.getStructuralState());
 
       CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xml = parser.toXml(model1);
+      String xml = parser.model2Xml(model1);
       InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
       Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
index cf795f8e45..83c2151349 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
@@ -52,7 +52,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -87,7 +87,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -122,7 +122,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -157,7 +157,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -192,7 +192,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -227,7 +227,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -262,7 +262,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -297,7 +297,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -332,7 +332,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -367,7 +367,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -402,7 +402,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -437,7 +437,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -472,7 +472,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -507,7 +507,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -542,7 +542,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -577,7 +577,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -612,7 +612,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -647,7 +647,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -682,7 +682,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -717,7 +717,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -752,7 +752,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -787,7 +787,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -822,7 +822,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -857,7 +857,7 @@ public class ReactionElbowsTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
index 27d7f4d35a..66c2f6952d 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
@@ -68,7 +68,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -111,7 +111,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -154,7 +154,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -197,7 +197,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -241,7 +241,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -284,7 +284,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -327,7 +327,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -370,7 +370,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -413,7 +413,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -456,7 +456,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -499,7 +499,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -542,7 +542,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -585,7 +585,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -628,7 +628,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -671,7 +671,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -714,7 +714,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -757,7 +757,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -800,7 +800,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -844,7 +844,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -887,7 +887,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -930,7 +930,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -973,7 +973,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1016,7 +1016,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1059,7 +1059,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1102,7 +1102,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1145,7 +1145,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1188,7 +1188,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1231,7 +1231,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1274,7 +1274,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1317,7 +1317,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1360,7 +1360,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1403,7 +1403,7 @@ public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
index 18048170e3..e57e374678 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
@@ -66,7 +66,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -110,7 +110,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -154,7 +154,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -198,7 +198,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -242,7 +242,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -286,7 +286,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -330,7 +330,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -374,7 +374,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -418,7 +418,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -462,7 +462,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -506,7 +506,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -550,7 +550,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -594,7 +594,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -638,7 +638,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -682,7 +682,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -726,7 +726,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(0, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -770,7 +770,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -814,7 +814,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(1, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -858,7 +858,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -902,7 +902,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -946,7 +946,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -990,7 +990,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1034,7 +1034,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1078,7 +1078,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1122,7 +1122,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1166,7 +1166,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1210,7 +1210,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1254,7 +1254,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1298,7 +1298,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1342,7 +1342,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1386,7 +1386,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
@@ -1430,7 +1430,7 @@ public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
 
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
index 8bc873568a..e4e077d702 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
@@ -50,7 +50,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -80,7 +80,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -109,7 +109,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -138,7 +138,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -168,7 +168,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -199,7 +199,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(2, reaction.getReactants().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -228,7 +228,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -257,7 +257,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -286,7 +286,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -315,7 +315,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -344,7 +344,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -373,7 +373,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -402,7 +402,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -431,7 +431,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -460,7 +460,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -489,7 +489,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -518,7 +518,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -547,7 +547,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -576,7 +576,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -606,7 +606,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -636,7 +636,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -665,7 +665,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -694,7 +694,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -723,7 +723,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -752,7 +752,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -781,7 +781,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -810,7 +810,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -839,7 +839,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertTrue(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -868,7 +868,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -897,7 +897,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -926,7 +926,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -955,7 +955,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -984,7 +984,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -1013,7 +1013,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertFalse(reaction.isReversible());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
@@ -1038,7 +1038,7 @@ public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
 			assertEquals(4, getWarnings().size());
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index 85cd00bac4..0eb9608a2b 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -53,7 +53,7 @@ public class BugTest extends WikipathwaysTestFunctions {
 			assertEquals("Invalid number of complexes", 1, complexes);
 
 			CellDesignerXmlParser parser = new CellDesignerXmlParser();
-			String xml = parser.toXml(model1);
+			String xml = parser.model2Xml(model1);
 			InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
 
 			Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-- 
GitLab