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Commit 79cbd71a authored by Piotr Gawron's avatar Piotr Gawron
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acceptance test for import export featers into multi

parent ff3c5cb0
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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!560Resolve "add support for modifications and states in sbml export/import"
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converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiSbmlParserTest.java
+ 7
− 29
View file @ 79cbd71a
......@@ -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 MultiSbmlParserTest {
@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 MultiSbmlParserTest {
@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
......
converter-sbml/testFiles/cd_for_multi/coding_sites.xml 0 → 100644
+ 158
− 0
View file @ 79cbd71a
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="untitled" id="untitled">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
<celldesigner:listOfCompartmentAliases/>
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<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
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<unit metaid="CDMT00001" kind="mole"/>
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<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00004" kind="metre"/>
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<unitDefinition metaid="time" id="time" name="time">
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</model>
</sbml>
converter-sbml/testFiles/cd_for_multi/complex.xml 0 → 100644
+ 338
− 0
View file @ 79cbd71a
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="untitled" id="untitled">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
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<head>
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<celldesigner:annotation>
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<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
<celldesigner:protein id="pr2" name="s3" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00001" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00002" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00003" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00004" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00005" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>s1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>s4</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>s7</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
converter-sbml/testFiles/cd_for_multi/modification_residues.xml 0 → 100644
+ 232
− 0
View file @ 79cbd71a
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="untitled" id="untitled">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s4">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="86.0" y="81.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="193.0" y="79.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
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</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa3" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="194.0" y="151.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa4" species="s5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="88.0" y="152.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
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<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa5" species="s3">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="287.0" y="79.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein id="pr1" name="s1" type="GENERIC">
<celldesigner:listOfModificationResidues>
<celldesigner:modificationResidue angle="3.14" id="rs1" name="n2" side="none"/>
<celldesigner:modificationResidue angle="1.64" id="rs2" name="n1" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
<celldesigner:protein id="pr3" name="s3" type="GENERIC"/>
<celldesigner:protein id="pr2" name="s2" type="GENERIC">
<celldesigner:listOfModificationResidues>
<celldesigner:modificationResidue angle="3.141592653589793" id="rs1" name="x" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00001" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00002" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00003" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00004" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00005" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s4" id="s4" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs2" state="phosphorylated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs1" state="acetylated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s5" id="s5" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs1" state="ubiquitinated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
converter-sbml/testFiles/cd_for_multi/structural_state.xml 0 → 100644
+ 195
− 0
View file @ 79cbd71a
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
<model metaid="untitled" id="untitled">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="109.0" y="53.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
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</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa2" species="s3">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="108.0" y="113.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:structuralState angle="1.5707963267948966"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
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</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa3" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="203.0" y="53.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
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<celldesigner:structuralState angle="1.5707963267948966"/>
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<celldesigner:boxSize width="80.0" height="40.0"/>
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<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
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<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa4" species="s4">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="202.0" y="112.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:structuralState angle="1.5707963267948966"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
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<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
<celldesigner:protein id="pr2" name="s4" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00001" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00002" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00003" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00004" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00005" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s2" id="s2" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfStructuralStates>
<celldesigner:structuralState structuralState="xyz"/>
</celldesigner:listOfStructuralStates>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3" id="s3" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfStructuralStates>
<celldesigner:structuralState structuralState="open"/>
</celldesigner:listOfStructuralStates>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfStructuralStates>
<celldesigner:structuralState structuralState="xxx"/>
</celldesigner:listOfStructuralStates>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
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