Skip to content

GitLab

Commit ef19828d authored by Piotr Gawron's avatar Piotr Gawron
Browse files

export of the modification coordinates is handled in the same ways as import

parent 0f27d2d2
Hide whitespace changes
Inline Side-by-side
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
View file @ ef19828d
......@@ -15,6 +15,7 @@ import org.sbgn.bindings.Map;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.PolylineData;
......@@ -205,7 +206,7 @@ public class SbgnmlXmlExporter {
glyph.setState(state);
Bbox bbox = new Bbox();
float width = structuralState.getWidth().floatValue();
float height = structuralState.getHeight().floatValue();
bbox.setH(height);
......@@ -400,32 +401,28 @@ public class SbgnmlXmlExporter {
glyph.setId(mr.getIdModificationResidue());
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
double width = SpeciesConverter.DEFAULT_MODIFICATION_DIAMETER;
double height = SpeciesConverter.DEFAULT_MODIFICATION_DIAMETER;
if (mr instanceof AbstractSiteModification) {
AbstractSiteModification modification = (AbstractSiteModification) mr;
Glyph.State state = new Glyph.State();
state.setVariable(mr.getName());
glyph.setState(state);
if (modification.getState() != null) {
Glyph.State state = new Glyph.State();
state.setValue(modification.getState().getAbbreviation());
state.setVariable(mr.getName());
glyph.setState(state);
}
} else if (mr instanceof AbstractRegionModification) {
width = ((AbstractRegionModification) mr).getWidth();
height = ((AbstractRegionModification) mr).getHeight();
}
Bbox bbox = new Bbox();
final float filledWidth = 70.0f;
final float filledHeight = 28.0f;
final float emptyWidth = 20.0f;
final float emptyHeight = 22.0f;
if (glyph.getState() != null) {
bbox.setH(filledHeight);
bbox.setW(filledWidth);
} else {
bbox.setH(emptyHeight);
bbox.setW(emptyWidth);
}
bbox.setH((float) width);
bbox.setW((float) height);
bbox.setX((float) mr.getPosition().getX());
bbox.setY((float) mr.getPosition().getY());
bbox.setX((float) (mr.getPosition().getX() - width / 2));
bbox.setY((float) (mr.getPosition().getY() - height / 2));
glyph.setBbox(bbox);
......
converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
View file @ ef19828d
......@@ -3,21 +3,29 @@ package lcsb.mapviewer.converter.model.sbgnml;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.awt.Color;
import java.io.File;
import java.io.FileInputStream;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.*;
import lcsb.mapviewer.common.comparator.SetComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.StructuralStateComparator;
import lcsb.mapviewer.modelutils.map.ElementUtils;
......@@ -114,4 +122,35 @@ public class CellDesignerToSbgnTest extends SbgnmlTestFunctions {
assertEquals(0, comparator.compare(protein1.getStructuralState(), protein2.getStructuralState()));
}
@Test
public void testModifications() throws Exception {
Converter converter = new CellDesignerXmlParser();
Converter converter2 = new SbgnmlXmlConverter();
Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/modifications.xml"));
String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
converter2.model2File(model, output);
Model model2 = converter2.createModel(new ConverterParams().filename(output).sizeAutoAdjust(false));
Set<String> set1 = new HashSet<>();
Set<String> set2 = new HashSet<>();
for (ModificationResidue region : ((Protein)model.getElementByElementId("sa3988")).getModificationResidues()) {
set1.add(region.toString());
}
for (ModificationResidue region : ((Protein)model2.getElementByElementId("sa3988")).getModificationResidues()) {
set2.add(region.toString());
}
SetComparator<String> comparator = new SetComparator<>(new StringComparator());
assertEquals(0, comparator.compare(set1, set2));
new File(output).delete();
}
}
converter-SBGNML/testFiles/cellDesigner/modifications.xml 0 → 100644
View file @ ef19828d
<?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="A_comprehensive_Parkinsons_disease_map" id="A_comprehensive_Parkinsons_disease_map">
<listOfUnitDefinitions>
<unitDefinition id="substance" name="substance" >
<listOfUnits>
<unit kind="mole" scale="0" exponent="1" multiplier="1.0" />
</listOfUnits>
</unitDefinition><unitDefinition id="length" name="length" >
<listOfUnits>
<unit kind="metre" scale="0" exponent="1" multiplier="1.0" />
</listOfUnits>
</unitDefinition><unitDefinition id="time" name="time" >
<listOfUnits>
<unit kind="second" scale="0" exponent="1" multiplier="1.0" />
</listOfUnits>
</unitDefinition><unitDefinition id="volume" name="volume" >
<listOfUnits>
<unit kind="litre" scale="0" exponent="1" multiplier="1.0" />
</listOfUnits>
</unitDefinition><unitDefinition id="area" name="area" >
<listOfUnits>
<unit kind="metre" scale="0" exponent="2" multiplier="1.0" />
</listOfUnits>
</unitDefinition></listOfUnitDefinitions>
<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body></body></html></notes><annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="2203" sizeY="1269"/>
<celldesigner:listOfIncludedSpecies>
<celldesigner:species id="s_id_sa3987" name="NFKBIA"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_id_sa3987">
</rdf:Description>
</rdf:RDF>
</body></html></celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s_id_csa553</celldesigner:complexSpecies>
<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p_s_id_sa3987</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs1" state="phosphorylated"> </celldesigner:modification>
<celldesigner:modification residue="rs2" state="phosphorylated"> </celldesigner:modification>
</celldesigner:listOfModifications>
</celldesigner:state>
<celldesigner:name>NFKBIA</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s_id_sa3989" name="NFKB1"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_id_sa3989">
</rdf:Description>
</rdf:RDF>
</body></html></celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s_id_csa553</celldesigner:complexSpecies>
<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p_s_id_sa3989</celldesigner:proteinReference>
<celldesigner:name>NFKB1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
<celldesigner:species id="s_id_sa3988" name="RELA"><celldesigner:notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_id_sa3988">
</rdf:Description>
</rdf:RDF>
</body></html></celldesigner:notes>
<celldesigner:annotation>
<celldesigner:complexSpecies>s_id_csa553</celldesigner:complexSpecies>
<celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>p_s_id_sa3988</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
</celldesigner:listOfModifications>
</celldesigner:state>
<celldesigner:name>RELA</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:annotation>
</celldesigner:species>
</celldesigner:listOfIncludedSpecies>
<celldesigner:listOfCompartmentAliases>
</celldesigner:listOfCompartmentAliases>
<celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias id="csa553" species="s_id_csa553" >
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="171.72326936217178" y="638.1046227966417" w="190.0" h="120.0" />
<celldesigner:font size="12"/><celldesigner:view state="usual"/>
<celldesigner:usualView><celldesigner:innerPosition x="171.72326936217178" y="638.1046227966417"/><celldesigner:boxSize width="190.0" height="120.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFF7F7F7" scheme="Color"/></celldesigner:usualView>
<celldesigner:briefView><celldesigner:innerPosition x="171.72326936217178" y="638.1046227966417"/><celldesigner:boxSize width="190.0" height="120.0"/><celldesigner:singleLine width="190.0"/><celldesigner:paint color="FFF7F7F7" scheme="Color"/></celldesigner:briefView>
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa3988" species="s_id_sa3988" complexSpeciesAlias="csa553" >
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="268.056818181818" y="696.545454545454" w="80.0" h="40.0" />
<celldesigner:font size="12"/><celldesigner:view state="usual"/>
<celldesigner:usualView><celldesigner:innerPosition x="268.056818181818" y="696.545454545454"/><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="268.056818181818" y="696.545454545454"/><celldesigner:boxSize width="80.0" height="40.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFCCFFCC" scheme="Color"/></celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa3989" species="s_id_sa3989" complexSpeciesAlias="csa553" >
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="181.80681818181802" y="696.545454545454" w="80.0" h="40.0" />
<celldesigner:font size="12"/><celldesigner:view state="usual"/>
<celldesigner:usualView><celldesigner:innerPosition x="181.80681818181802" y="696.545454545454"/><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="181.80681818181802" y="696.545454545454"/><celldesigner:boxSize width="80.0" height="40.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFCCFFCC" scheme="Color"/></celldesigner:briefView>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa3987" species="s_id_sa3987" complexSpeciesAlias="csa553" >
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="226.067170457276" y="645.3546227966417" w="80.0" h="40.0" />
<celldesigner:font size="12"/><celldesigner:view state="usual"/>
<celldesigner:usualView><celldesigner:innerPosition x="226.067170457276" y="645.3546227966417"/><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="226.067170457276" y="645.3546227966417"/><celldesigner:boxSize width="80.0" height="40.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFCCFFCC" scheme="Color"/></celldesigner:briefView>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfProteins><celldesigner:protein id="p_s_id_sa3988" name="RELA" type="GENERIC">
<celldesigner:listOfModificationResidues><celldesigner:modificationResidue id="rs1" name="S276" angle="3.8682226504929313"></celldesigner:modificationResidue><celldesigner:modificationResidue id="rs2" name="S529" angle="2.3550214342198026"></celldesigner:modificationResidue></celldesigner:listOfModificationResidues>
</celldesigner:protein>
<celldesigner:protein id="p_s_id_sa3989" name="NFKB1" type="GENERIC">
</celldesigner:protein>
<celldesigner:protein id="p_s_id_sa3987" name="NFKBIA" type="GENERIC">
<celldesigner:listOfModificationResidues><celldesigner:modificationResidue id="rs1" name="S32" angle="3.87729847927592"></celldesigner:modificationResidue><celldesigner:modificationResidue id="rs2" name="S36" angle="2.4376765858046574"></celldesigner:modificationResidue><celldesigner:modificationResidue id="rs4" angle="-1.5001322409935126E-12"></celldesigner:modificationResidue></celldesigner:listOfModificationResidues>
</celldesigner:protein>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes></celldesigner:listOfGenes>
<celldesigner:listOfRNAs></celldesigner:listOfRNAs>
<celldesigner:listOfAntisenseRNAs></celldesigner:listOfAntisenseRNAs>
<celldesigner:listOfLayers><celldesigner:layer id ="1" name ="Layout annotation" locked ="false" visible ="false">
<celldesigner:listOfTexts>
<celldesigner:layerSpeciesAlias><celldesigner:layerNotes>
Inflammation Signalling
</celldesigner:layerNotes><celldesigner:paint color="FF000000"/><celldesigner:bounds x="207.16666666666606" y="142.0" w="1825.0" h="985.0"/><celldesigner:font size="11"/></celldesigner:layerSpeciesAlias>
</celldesigner:listOfTexts>
<celldesigner:listOfSquares>
</celldesigner:listOfSquares>
<celldesigner:listOfFreeLines>
</celldesigner:listOfFreeLines>
</celldesigner:layer>
</celldesigner:listOfLayers>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#A_comprehensive_Parkinsons_disease_map">
<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfCompartments>
<compartment metaid="default" id="default" name="" size="1" units="volume" >
<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
</body></html></notes>
<annotation>
<celldesigner:extension>
<celldesigner:name></celldesigner:name>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#default">
<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies><species name="NFkappaB:IkappaB" id="s_id_csa553" metaid="s_id_csa553" initialAmount="0.0" hasOnlySubstanceUnits="false" constant="false" boundaryCondition="false" compartment="default"><annotation><celldesigner:extension><celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment><celldesigner:speciesIdentity><celldesigner:class>COMPLEX</celldesigner:class>
<celldesigner:name>NFkappaB:IkappaB</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_id_csa553">
<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
</model></sbml>
\ No newline at end of file
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
View file @ ef19828d
......@@ -47,7 +47,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
/**
* Default diameter of the modification residues.
*/
protected static final int DEFAULT_MODIFICATION_DIAMETER = 15;
public static final int DEFAULT_MODIFICATION_DIAMETER = 15;
/**
* How far from the original shape should the activity border be drawn.
*/
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment