fixing sbml converter tests

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java

@@ -19,7 +19,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -49,7 +49,7 @@ public class CellDesignerToMultiExportTest {
   @Test
   public void createModelTest() throws Exception {
     try {
-      IConverter converter = new CellDesignerXmlParser();
+      Converter converter = new CellDesignerXmlParser();
 
       Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
       model.setName(null);

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java

@@ -16,7 +16,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.model.map.model.Model;
 
 @RunWith(Parameterized.class)
@@ -44,11 +44,11 @@ public class CopasiImportTest extends SbmlTestFunctions{
   @Test
   public void createModelTest() throws Exception {
     try {
-      IConverter converter = new SbmlParser();
+      Converter converter = new SbmlParser();
 
       Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
       assertNotNull(model);
-      converter.exportModelToInputStream(model);
+      converter.model2InputStream(model);
 
     } catch (Exception e) {
       e.printStackTrace();

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java

@@ -21,7 +21,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
 import lcsb.mapviewer.converter.graphics.PngImageGenerator;
@@ -61,7 +61,7 @@ public class GenericSbmlParserTest {
     try {
       String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
 
-      IConverter converter = new SbmlParser();
+      Converter converter = new SbmlParser();
 
       Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
       model.setName(null);
@@ -77,7 +77,7 @@ public class GenericSbmlParserTest {
       // Desktop.getDesktop().open(new File(pngFilePath));
 
       CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
-      String xmlString = cellDesignerXmlParser.toXml(model);
+      String xmlString = cellDesignerXmlParser.model2Xml(model);
 
       InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java

@@ -19,7 +19,6 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
 
@@ -65,7 +64,7 @@ public class GenericSbmlToXmlParserTest {
       String pathWithouExtension = dir + "/"
           + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
       String xmlFilePath = pathWithouExtension.concat(".xml");
-      converter.exportModelToFile(model, xmlFilePath);
+      converter.model2File(model, xmlFilePath);
 
       Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
       model2.setName(null);

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java

@@ -21,7 +21,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
 import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
 import lcsb.mapviewer.converter.graphics.PngImageGenerator;
@@ -56,7 +56,7 @@ public class MultiParserTest {
     try {
       String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
 
-      IConverter converter = new SbmlParser();
+      Converter converter = new SbmlParser();
 
       Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
       model.setName(null);
@@ -72,7 +72,7 @@ public class MultiParserTest {
       // Desktop.getDesktop().open(new File(pngFilePath));
 
       CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
-      String xmlString = cellDesignerXmlParser.toXml(model);
+      String xmlString = cellDesignerXmlParser.model2Xml(model);
 
       InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java

@@ -36,7 +36,7 @@ public class SbmlExporterFromCellDesignerTest extends SbmlTestFunctions {
 
       model.setName(originalModel.getName());
 
-      String cellDesignerXml = cellDesignerXmlParser.toXml(model);
+      String cellDesignerXml = cellDesignerXmlParser.model2Xml(model);
       ByteArrayInputStream stream = new ByteArrayInputStream(cellDesignerXml.getBytes("UTF-8"));
 
       assertEquals(0, comparator.compare(model, originalModel));

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -239,7 +239,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
     Model model = converter.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
     model.setName(null);
 
-    converter.exportModelToFile(model, tempFilename);
+    converter.model2File(model, tempFilename);
 
     Model model2 = converter.createModel(new ConverterParams().filename(tempFilename));
     model2.setName(null);
@@ -258,7 +258,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
 
     Model model = createEmptyModel();
 
-    converter.exportModelToFile(model, tempFilename);
+    converter.model2File(model, tempFilename);
 
     Model model2 = converter.createModel(new ConverterParams().filename(tempFilename));
 
@@ -666,7 +666,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
         .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/boolean_logic_gate.xml"));
     Model model = getModelAfterSerializing(originalModel);
 
-    new CellDesignerXmlParser().toXml(model);
+    new CellDesignerXmlParser().model2Xml(model);
     List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
     List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java

@@ -16,7 +16,7 @@ import org.junit.runners.Parameterized;
 import org.junit.runners.Parameterized.Parameters;
 
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 
 @RunWith(Parameterized.class)
@@ -44,7 +44,7 @@ public class SbmlPareserForInvalidReactionTest {
   @Test
   public void createModelTest() throws Exception {
     try {
-      IConverter converter = new SbmlParser();
+      Converter converter = new SbmlParser();
 
       converter.createModel(new ConverterParams().filename(filePath.toString()));
       fail("Exception expected when parsing file: " + filePath.toString());

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java

@@ -113,7 +113,7 @@ public class SbmlReactionExportArrowType {
     model.addReaction(reaction);
 
     CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
-    String xmlString = cellDesignerXmlParser.toXml(model);
+    String xmlString = cellDesignerXmlParser.model2Xml(model);
     Model modelAfterSerialization = cellDesignerXmlParser
         .createModel(new ConverterParams().inputStream(new ByteArrayInputStream(xmlString.getBytes())));
     return modelAfterSerialization;