diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
index a4f69ebc8e2b35d142e2f37b3167ee16d0f0c6eb..3b691a55b7d4836a72a426b1168cd857cabc0c1f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
@@ -5,8 +5,10 @@ import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
/**
* Class responsible for providing identifiers of structures inside multi
@@ -70,19 +72,20 @@ public final class MultiPackageNamingUtils {
return featureTypeId.startsWith(MINERVA_POSITION_TO_COMPARTMENT_PREFIX);
}
- public static String getModificationFeatureId(Species species, Class<? extends ModificationResidue> class1) {
- return MINERVA_MODIFICATION_TYPE_PREFIX + species.getClass().getSimpleName() + "_" + class1.getSimpleName();
- }
-
- public static String getModificationFeatureId(Species species, Class<? extends ModificationResidue> class1,
- ModificationState state) {
- String stateName = "null";
- if (state != null) {
- stateName = state.name();
+ public static String getModificationFeatureId(ModificationResidue mr) {
+ String stateSuffix = "";
+ if (mr instanceof AbstractSiteModification) {
+ if (((AbstractSiteModification) mr).getState() != null) {
+ stateSuffix = "_" + ((AbstractSiteModification) mr).getState().name();
+ } else {
+ stateSuffix = "_null";
+ }
+ } else if (mr instanceof TranscriptionSite) {
+ stateSuffix = "_" + ((TranscriptionSite) mr).getActive() + "_" + ((TranscriptionSite) mr).getDirection();
}
-
- return MINERVA_MODIFICATION_TYPE_PREFIX + species.getClass().getSimpleName() + "_" + class1.getSimpleName() + "_"
- + stateName;
+
+ return MINERVA_MODIFICATION_TYPE_PREFIX + mr.getSpecies().getClass().getSimpleName() + "_"
+ + mr.getClass().getSimpleName() + stateSuffix;
}
public static boolean isModificationFeatureId(String featureTypeString) {
@@ -103,4 +106,26 @@ public final class MultiPackageNamingUtils {
return null;
}
+ public static Boolean getTranscriptionFactorActiveStateFromFeatureTypeName(String featureTypeString) {
+ String tmp[] = featureTypeString.split("_");
+ Boolean result = null;
+ if (tmp.length >= 2) {
+ if (tmp[tmp.length - 2].equalsIgnoreCase("TRUE")) {
+ result = true;
+ } else if (tmp[tmp.length - 2].equalsIgnoreCase("FALSE")) {
+ result = false;
+ }
+ }
+ return result;
+ }
+
+ public static String getTranscriptionFactorDirectionStateFromFeatureTypeName(String featureTypeString) {
+ String tmp[] = featureTypeString.split("_");
+ String result = null;
+ if (tmp.length >= 1) {
+ result = tmp[tmp.length - 1];
+ }
+ return result;
+ }
+
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index 670c655dbc548660877cc1b995a479600597597e..fe1c72781d56f3bd2e093bec5785abc2db4fd062 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -120,15 +120,15 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
PossibleSpeciesFeatureValue value;
if (mr instanceof BindingRegion) {
- feature = getBindingRegionFeature(mr.getSpecies(), speciesType);
+ feature = getBindingRegionFeature((BindingRegion) mr, speciesType);
} else if (mr instanceof CodingRegion) {
- feature = getCodingRegionFeature(mr.getSpecies(), speciesType);
+ feature = getCodingRegionFeature((CodingRegion) mr, speciesType);
} else if (mr instanceof ProteinBindingDomain) {
- feature = getProteinBindingDomainFeature(mr.getSpecies(), speciesType);
+ feature = getProteinBindingDomainFeature((ProteinBindingDomain) mr, speciesType);
} else if (mr instanceof RegulatoryRegion) {
- feature = getRegulatoryRegionFeature(mr.getSpecies(), speciesType);
+ feature = getRegulatoryRegionFeature((RegulatoryRegion) mr, speciesType);
} else if (mr instanceof TranscriptionSite) {
- feature = getTranscriptionSiteFeature(mr.getSpecies(), speciesType);
+ feature = getTranscriptionSiteFeature((TranscriptionSite) mr, speciesType);
} else if (mr instanceof ModificationSite) {
feature = getModificationSiteFeature((ModificationSite) mr, speciesType);
} else if (mr instanceof Residue) {
@@ -142,40 +142,42 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
- private SpeciesFeatureType getCodingRegionFeature(Species species, MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, CodingRegion.class);
+ private SpeciesFeatureType getCodingRegionFeature(CodingRegion mr, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(mr);
String featureName = "Coding region";
return getOrCreateFeatureById(featureId, featureName, speciesType);
}
- private SpeciesFeatureType getBindingRegionFeature(Species species, MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, BindingRegion.class);
+ private SpeciesFeatureType getBindingRegionFeature(BindingRegion bindingRegion, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(bindingRegion);
String featureName = "Binding region";
return getOrCreateFeatureById(featureId, featureName, speciesType);
}
- private SpeciesFeatureType getProteinBindingDomainFeature(Species species, MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, ProteinBindingDomain.class);
+ private SpeciesFeatureType getProteinBindingDomainFeature(ProteinBindingDomain proteinBindingDomain,
+ MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(proteinBindingDomain);
String featureName = "Protein binding domain";
return getOrCreateFeatureById(featureId, featureName, speciesType);
}
- private SpeciesFeatureType getRegulatoryRegionFeature(Species species, MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, RegulatoryRegion.class);
+ private SpeciesFeatureType getRegulatoryRegionFeature(RegulatoryRegion regulatoryRegion,
+ MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(regulatoryRegion);
String featureName = "Regulatory region";
return getOrCreateFeatureById(featureId, featureName, speciesType);
}
- private SpeciesFeatureType getTranscriptionSiteFeature(Species species, MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, TranscriptionSite.class);
+ private SpeciesFeatureType getTranscriptionSiteFeature(TranscriptionSite transcriptionSite,
+ MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(transcriptionSite);
String featureName = "Transcription site";
return getOrCreateFeatureById(featureId, featureName, speciesType);
}
private SpeciesFeatureType getModificationSiteFeature(ModificationSite modificationSite,
MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(modificationSite.getSpecies(),
- ModificationSite.class, modificationSite.getState());
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(modificationSite);
String featureName = "";
if (modificationSite.getState() != null) {
featureName = modificationSite.getState().getFullName();
@@ -184,8 +186,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
private SpeciesFeatureType getResidueFeature(Residue residue, MultiSpeciesType speciesType) {
- String featureId = MultiPackageNamingUtils.getModificationFeatureId(residue.getSpecies(), Residue.class,
- residue.getState());
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(residue);
String featureName = "";
if (residue.getState() != null) {
featureName = residue.getState().getFullName();
@@ -401,11 +402,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private void createModificationGlyph(ModificationResidue mr, org.sbml.jsbml.Species sbmlSpecies) {
MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
SpeciesFeature feature = null;
- String featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr.getSpecies(), mr.getClass());
- if (mr instanceof AbstractSiteModification) {
- featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr.getSpecies(), mr.getClass(),
- ((AbstractSiteModification) mr).getState());
- }
+ String featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr);
for (SpeciesFeature existingFeature : speciesExtension.getListOfSpeciesFeatures()) {
if (existingFeature.getSpeciesFeatureType().equals(featureTypeId)) {
feature = existingFeature;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index 4fb0cf872e70171ca46f853ac62ffd1f7d6175d3..1bdf6ff54812ec2cdedad74d3811bf493579f2c8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -210,7 +210,10 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, TranscriptionSite.class)) {
mr = new TranscriptionSite();
if (minervaElement instanceof SpeciesWithTranscriptionSite) {
- ((SpeciesWithTranscriptionSite) minervaElement).addTranscriptionSite((TranscriptionSite) mr);
+ TranscriptionSite transcriptionSite = (TranscriptionSite) mr;
+ transcriptionSite.setActive(MultiPackageNamingUtils.getTranscriptionFactorActiveStateFromFeatureTypeName(featureTypeString));
+ transcriptionSite.setDirection(MultiPackageNamingUtils.getTranscriptionFactorDirectionStateFromFeatureTypeName(featureTypeString));
+ ((SpeciesWithTranscriptionSite) minervaElement).addTranscriptionSite(transcriptionSite);
} else {
logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index 70b980e09dfe35cbe3e06c5b02fced7278e40a74..1bc8fc0a77a511d0ec8615a3cfd6436665ff8bdf 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -12,7 +12,8 @@ import lcsb.mapviewer.converter.model.sbml.species.AllSbmlSpeciesTests;
AllSbmlSpeciesTests.class,
GenericSbmlParserTest.class,
GenericSbmlToXmlParserTest.class,
- MultiSbmlParserTest.class,
+ CellDesignerToMultiExportTest.class,
+ MultiParserTest.class,
SbmlBioEntityExporterTest.class,
SbmlExporterTest.class,
SbmlExporterFromCellDesignerTest.class,
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
index 7cb74fe6152ad221a9d21b13ab0ce1e1baa68e48..7c22d4b924e2583b143e6bf2c22f6553a4365fb1 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
@@ -4,7 +4,6 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import java.io.ByteArrayInputStream;
-import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.file.Files;
@@ -13,7 +12,6 @@ import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Collection;
-import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import org.junit.Test;
import org.junit.runner.RunWith;
@@ -22,9 +20,6 @@ import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
-import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
-import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
-import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -43,7 +38,7 @@ public class CellDesignerToMultiExportTest {
@Parameters(name = "{index} : {0}")
public static Collection<Object[]> data() throws IOException {
Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/multi")).forEach(fPath -> {
+ Files.walk(Paths.get("testFiles/cd_for_multi")).forEach(fPath -> {
if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
data.add(new Object[] { fPath });
}
@@ -54,40 +49,23 @@ public class CellDesignerToMultiExportTest {
@Test
public void createModelTest() throws Exception {
try {
- String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
-
- IConverter converter = new SbmlParser();
+ IConverter converter = new CellDesignerXmlParser();
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
- // Create and display image of parsed map
- AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
- .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
- NormalImageGenerator nig = new PngImageGenerator(params);
- String pathWithouExtension = dir + "/"
- + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
- String pngFilePath = pathWithouExtension.concat(".png");
- nig.saveToFile(pngFilePath);
- // Desktop.getDesktop().open(new File(pngFilePath));
-
- CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- String xmlString = cellDesignerXmlParser.toXml(model);
+ SbmlExporter sbmlExporter = new SbmlExporter();
+ SbmlParser sbmlParser = new SbmlParser();
+ String xmlString = sbmlExporter.toXml(model);
InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
- Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params().height(model2.getHeight())
- .width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
- NormalImageGenerator nig2 = new PngImageGenerator(params2);
- String pngFilePath2 = pathWithouExtension.concat("_2.png");
- nig2.saveToFile(pngFilePath2);
+ Model model2 = sbmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ model2.setName(null);
assertNotNull(model2);
ModelComparator comparator = new ModelComparator(1.0);
assertEquals(0, comparator.compare(model, model2));
- FileUtils.deleteDirectory(new File(dir));
} catch (Exception e) {
// TODO Auto-generated catch block
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index f9e8649a5ae70a6e55361d44a92daf70db95c901..10843990e94ec0bbd610c4e67b643ff68eba32c0 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -22,7 +22,6 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
@RunWith(Parameterized.class)
public class GenericSbmlToXmlParserTest {
@@ -66,7 +65,7 @@ public class GenericSbmlToXmlParserTest {
+ filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
String xmlFilePath = pathWithouExtension.concat(".xml");
converter.exportModelToFile(model, xmlFilePath);
-
+
Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
model2.setName(null);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..9636bdb54b4c1a4e069e0502ef8cfa6086f2e8b7
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
@@ -0,0 +1,99 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+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.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+
+@RunWith(Parameterized.class)
+public class MultiParserTest {
+
+ static Logger logger = Logger.getLogger(MultiParserTest.class.getName());
+
+ private Path filePath;
+
+ public MultiParserTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/multi")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void createModelTest() throws Exception {
+ try {
+ String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
+
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+ model.setName(null);
+
+ // Create and display image of parsed map
+ AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
+ .width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
+ NormalImageGenerator nig = new PngImageGenerator(params);
+ String pathWithouExtension = dir + "/"
+ + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
+ String pngFilePath = pathWithouExtension.concat(".png");
+ nig.saveToFile(pngFilePath);
+ // Desktop.getDesktop().open(new File(pngFilePath));
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+ String xmlString = cellDesignerXmlParser.toXml(model);
+
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+
+ AbstractImageGenerator.Params params2 = new AbstractImageGenerator.Params().height(model2.getHeight())
+ .width(model2.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model2);
+ NormalImageGenerator nig2 = new PngImageGenerator(params2);
+ String pngFilePath2 = pathWithouExtension.concat("_2.png");
+ nig2.saveToFile(pngFilePath2);
+
+ assertNotNull(model2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+ FileUtils.deleteDirectory(new File(dir));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiSbmlParserTest.java
deleted file mode 100644
index d5345cfce8997888dac9530b4f76f98dd6936a17..0000000000000000000000000000000000000000
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiSbmlParserTest.java
+++ /dev/null
@@ -1,77 +0,0 @@
-package lcsb.mapviewer.converter.model.sbml;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import org.apache.log4j.Logger;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-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.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-
-@RunWith(Parameterized.class)
-public class MultiSbmlParserTest {
-
- static Logger logger = Logger.getLogger(MultiSbmlParserTest.class.getName());
-
- private Path filePath;
-
- public MultiSbmlParserTest(Path filePath) {
- this.filePath = filePath;
- }
-
- @Parameters(name = "{index} : {0}")
- public static Collection<Object[]> data() throws IOException {
- Collection<Object[]> data = new ArrayList<Object[]>();
- Files.walk(Paths.get("testFiles/cd_for_multi")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- return data;
- }
-
- @Test
- public void createModelTest() throws Exception {
- try {
- IConverter converter = new CellDesignerXmlParser();
-
- Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
- model.setName(null);
-
- SbmlExporter sbmlExporter = new SbmlExporter();
- SbmlParser sbmlParser = new SbmlParser();
- String xmlString = sbmlExporter.toXml(model);
-
- InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
-
- Model model2 = sbmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- model2.setName(null);
-
- assertNotNull(model2);
- ModelComparator comparator = new ModelComparator(1.0);
- assertEquals(0, comparator.compare(model, model2));
-
- } catch (Exception e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 1a6733fff5661640f0fedf4dfee8a79ca2536727..92b27dcc63168fdc6cb9c1343ad978ef264bcfb0 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -534,7 +534,6 @@ public class SbmlExporterTest {
@Test
public void testMultiExtensionTypeDefinition() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = new GenericProtein("id");
element.setName("test name");
@@ -595,17 +594,17 @@ public class SbmlExporterTest {
Residue mr = new Residue("x1");
mr.setName("217U");
mr.setState(ModificationState.PHOSPHORYLATED);
- mr.setPosition(new Point2D.Double(10,11));
+ mr.setPosition(new Point2D.Double(10, 11));
element.addResidue(mr);
mr = new Residue("Y");
mr.setName("218");
mr.setState(ModificationState.PHOSPHORYLATED);
- mr.setPosition(new Point2D.Double(10,12));
+ mr.setPosition(new Point2D.Double(10, 12));
element.addResidue(mr);
mr = new Residue("Z");
mr.setName("219");
mr.setState(ModificationState.UBIQUITINATED);
- mr.setPosition(new Point2D.Double(10,13));
+ mr.setPosition(new Point2D.Double(10, 13));
element.addResidue(mr);
model.addElement(element);
Model deserializedModel = getModelAfterSerializing(model);
diff --git a/converter-sbml/testFiles/multi/bionetgen.xml b/converter-sbml/testFiles/multi/bionetgen.xml.jsbml-issue
similarity index 100%
rename from converter-sbml/testFiles/multi/bionetgen.xml
rename to converter-sbml/testFiles/multi/bionetgen.xml.jsbml-issue