diff --git a/CHANGELOG b/CHANGELOG
index 64ccace37428560e78ff59b6c9d27a1b74172ebd..4c2cfd9bd370302675b61362a25b0b36dd5365d4 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+minerva (15.0.0~alpha.0) stable; urgency=medium
+ * Bug fix: position of structural state is preserved on upload CellDesigner
+ file (#671)
+
minerva (14.0.3) stable; urgency=medium
* Bug fix: default zoom level on main map works even when x or y are
undefined (#993)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index bfdabc42923e68d275393f892641752655325ba3..259a5e75bef4e2532aa82d9ec9c9433bd291a557 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -107,14 +107,18 @@ public class CellDesignerElementCollection {
regions.addAll(asGene.getModificationResidues());
} else if (modelElement instanceof Protein) {
Protein asProtein = ((Protein) modelElement);
- modifications = asProtein.getStructuralState();
+ if (asProtein.getStructuralState() != null) {
+ modifications = asProtein.getStructuralState().getValue();
+ }
regions.addAll(asProtein.getModificationResidues());
} else if (modelElement instanceof Rna) {
Rna asRna = ((Rna) modelElement);
regions.addAll(asRna.getRegions());
} else if (modelElement instanceof Complex) {
Complex asComplex = ((Complex) modelElement);
- modifications = asComplex.getStructuralState();
+ if (asComplex.getStructuralState() != null) {
+ modifications = asComplex.getStructuralState().getValue();
+ }
}
for (ModificationResidue region : regions) {
if (region instanceof AbstractSiteModification) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
index c70a43f7a53a0f5aaef4f122e70ec156619df22f..db1a38bcbada679280da60e109b0626ee2eacc61 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AbstractAliasXmlParser.java
@@ -7,7 +7,10 @@ import org.w3c.dom.*;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
/**
* Generic abstract interface for parsing CellDesigner xml nodes with species
@@ -87,4 +90,20 @@ public abstract class AbstractAliasXmlParser<T extends Element> {
return "<celldesigner:font size=\"" + alias.getFontSize().intValue() + "\"/>";
}
+ protected String createStructuralStateTag(Species species) {
+ StructuralState structuralState = null;
+ if (species instanceof Protein) {
+ structuralState = ((Protein) species).getStructuralState();
+ }
+ if (species instanceof Complex) {
+ structuralState = ((Complex) species).getStructuralState();
+ }
+ if (structuralState != null) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(species, false);
+ double angle = converter.getAngleForPoint(species, structuralState.getCenter());
+ return "<celldesigner:structuralState angle=\"" + angle + "\"/>";
+ }
+ return "";
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
index ee84daedd66d96f37b405104bee40903f6f71d54..8c11c5182f25088c1d613d3c67fc520451d741be 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
@@ -120,8 +120,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
// not handled
continue;
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- // not handled
- continue;
+ species.setStructuralStateAngle(Double.parseDouble(XmlParser.getNodeAttr("angle", node)));
} else {
throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
}
@@ -163,21 +162,22 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
parents.put(result.getElementId(), complexSpeciesAliasId);
}
complexAliasesMapById.put(result.getElementId(), result);
+ species.updateModelElementAfterLayoutAdded(result);
return result;
}
@Override
- public String toXml(Complex alias) {
+ public String toXml(Complex complex) {
Compartment ca = null;
- // we have to exclude artifitial compartment aliases, becuase they aren't
+ // we have to exclude artificial compartment aliases, because they aren't
// exported to CellDesigner file
- if (alias.getCompartment() != null && !(alias.getCompartment() instanceof PathwayCompartment)) {
- ca = alias.getCompartment();
- } else if (alias.getComplex() == null) {
- ModelData modelData = alias.getModelData();
+ if (complex.getCompartment() != null && !(complex.getCompartment() instanceof PathwayCompartment)) {
+ ca = complex.getCompartment();
+ } else if (complex.getComplex() == null) {
+ ModelData modelData = complex.getModelData();
if (modelData != null) {
for (Compartment cAlias : modelData.getModel().getCompartments()) {
- if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(alias)) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(complex)) {
if (ca == null) {
ca = cAlias;
} else if (ca.getSize() > cAlias.getSize()) {
@@ -188,7 +188,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
}
}
- Complex complexAlias = alias.getComplex();
+ Complex complexAlias = complex.getComplex();
String compartmentAliasId = null;
if (ca != null) {
@@ -196,8 +196,8 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
}
StringBuilder sb = new StringBuilder("");
sb.append("<celldesigner:complexSpeciesAlias ");
- sb.append("id=\"" + alias.getElementId() + "\" ");
- sb.append("species=\"" + elements.getElementId(alias) + "\" ");
+ sb.append("id=\"" + complex.getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(complex) + "\" ");
if (compartmentAliasId != null) {
sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
}
@@ -206,8 +206,8 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
}
sb.append(">\n");
- if (alias.getActivity() != null) {
- if (alias.getActivity()) {
+ if (complex.getActivity() != null) {
+ if (complex.getActivity()) {
sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
} else {
sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
@@ -215,28 +215,29 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
}
sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + alias.getX() + "\" ");
- sb.append("y=\"" + alias.getY() + "\" ");
- sb.append("w=\"" + alias.getWidth() + "\" ");
- sb.append("h=\"" + alias.getHeight() + "\" ");
+ sb.append("x=\"" + complex.getX() + "\" ");
+ sb.append("y=\"" + complex.getY() + "\" ");
+ sb.append("w=\"" + complex.getWidth() + "\" ");
+ sb.append("h=\"" + complex.getHeight() + "\" ");
sb.append("/>\n");
- sb.append(createFontTag(alias));
+ sb.append(createFontTag(complex));
sb.append("<celldesigner:view state=\"usual\"/>\n");
sb.append("<celldesigner:usualView>");
- sb.append("<celldesigner:innerPosition x=\"" + alias.getX() + "\" y=\"" + alias.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + alias.getWidth() + "\" height=\"" + alias.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + alias.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("<celldesigner:innerPosition x=\"" + complex.getX() + "\" y=\"" + complex.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + complex.getWidth() + "\" height=\"" + complex.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + complex.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(complex.getColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:usualView>\n");
sb.append("<celldesigner:briefView>");
- sb.append("<celldesigner:innerPosition x=\"" + alias.getX() + "\" y=\"" + alias.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + alias.getWidth() + "\" height=\"" + alias.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + alias.getWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(alias.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("<celldesigner:innerPosition x=\"" + complex.getX() + "\" y=\"" + complex.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + complex.getWidth() + "\" height=\"" + complex.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + complex.getWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(complex.getColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:briefView>\n");
+ sb.append(createStructuralStateTag(complex));
sb.append("</celldesigner:complexSpeciesAlias>\n");
return sb.toString();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index 88744fd1d07afa4b4dc02ec1d7fea103a9833e41..eb6732861b5a0a78a43082cad9f4a29d035775a3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -14,8 +14,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.*;
/**
* Parser of CellDesigner xml used for parsing SpeciesAlias.
@@ -98,8 +97,10 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
processAliasState(node, result);
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- // not handled
- continue;
+ if (species instanceof CellDesignerProtein) {
+ ((CellDesignerProtein<?>) species)
+ .setStructuralStateAngle(Double.parseDouble(XmlParser.getNodeAttr("angle", node)));
+ }
} else {
throw new InvalidXmlSchemaException(
errorPrefix + "Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
@@ -231,6 +232,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
+ species.getStateLabel() + "\"/>\n");
}
+ sb.append(createStructuralStateTag(species));
sb.append("</celldesigner:speciesAlias>\n");
return sb.toString();
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
index 2a815be82acd526c74db1b11a6ce801ae50ac20b..b3e924533aaf224d55dd56e7b3afd1394d129a2c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerComplexSpecies.java
@@ -9,6 +9,7 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Class representing CellDesigner {@link Complex}.
@@ -38,6 +39,8 @@ public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
*/
private String structuralState = null;
+ private Double structuralStateAngle = null;
+
/**
* Default constructor.
*/
@@ -46,8 +49,8 @@ public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
}
/**
- * Constructor that initiale the complex with the data from the object passed as
- * an argument.
+ * Constructor that initialize the complex with the data from the object passed
+ * as an argument.
*
* @param original
* object used for initializing data
@@ -90,11 +93,15 @@ public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
if (elements.size() > 0) {
throw new NotImplementedException();
}
- result.setStructuralState(structuralState);
return result;
}
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ ((Complex) element).setStructuralState(createStructuralState(element, structuralState, structuralStateAngle));
+ }
+
/**
* Adds element to the complex.
*
@@ -169,4 +176,12 @@ public class CellDesignerComplexSpecies extends CellDesignerSpecies<Complex> {
this.elements = elements;
}
+ public Double getStructuralStateAngle() {
+ return structuralStateAngle;
+ }
+
+ public void setStructuralStateAngle(Double structuralStateAngle) {
+ this.structuralStateAngle = structuralStateAngle;
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index 70e447b3712aa2140a4240da0f586efaff38cf2b..f970c873ae21b0b44e0629e25193448f6ff67d77 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -37,6 +37,8 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
*/
private String structuralState = null;
+ private Double structuralStateAngle = null;
+
/**
* List of modifications for the Protein.
*/
@@ -94,7 +96,6 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
@Override
protected void setModelObjectFields(T result) {
super.setModelObjectFields(result);
- result.setStructuralState(structuralState);
}
@Override
@@ -110,6 +111,7 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
throw new InvalidArgumentException("Cannot add modification residue to element: " + mr.getClass());
}
}
+ protein.setStructuralState(createStructuralState(species, structuralState, structuralStateAngle));
}
/**
@@ -167,4 +169,12 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
this.modificationResidues = modificationResidues;
}
+ public Double getStructuralStateAngle() {
+ return structuralStateAngle;
+ }
+
+ public void setStructuralStateAngle(Double structuralStateAngle) {
+ this.structuralStateAngle = structuralStateAngle;
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
index 35f6b92423cf3873fcc70fad6025929cd29a17e5..6bb922034175ea7aee9cb0ae621c66f5c473e2b4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerSpecies.java
@@ -1,15 +1,20 @@
package lcsb.mapviewer.converter.model.celldesigner.structure;
+import java.awt.*;
+import java.awt.geom.Point2D;
+
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
/**
* Generic CellDesigner element.
@@ -26,6 +31,14 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
*/
private static final long serialVersionUID = 1L;
+ private static final int STRUCTURAL_STATE_FONT_SIZE = 10;
+
+ private static final double MIN_STRUCTURAL_STATE_WIDTH = 60;
+
+ private static final int TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC = 40;
+
+ private static final int MIN_STRUCTURAL_STATE_HEIGHT = 20;
+
/**
* Default class logger.
*/
@@ -582,4 +595,40 @@ public class CellDesignerSpecies<T extends Species> extends CellDesignerElement<
public void updateModelElementAfterLayoutAdded(Species element) {
}
+ protected StructuralState createStructuralState(Species species, String structuralState, Double angle) {
+ if (structuralState == null) {
+ return null;
+ }
+
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(species, false);
+
+ Font font = new Font(Font.SANS_SERIF, 0, STRUCTURAL_STATE_FONT_SIZE);
+ Canvas c = new Canvas();
+ FontMetrics fm = c.getFontMetrics(font);
+
+ double width = MIN_STRUCTURAL_STATE_WIDTH;
+ double height = MIN_STRUCTURAL_STATE_HEIGHT;
+ if (!structuralState.trim().equals("")) {
+ width = Math.max(MIN_STRUCTURAL_STATE_WIDTH,
+ fm.stringWidth(structuralState) + TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC);
+ }
+ width = Math.min(width, species.getWidth());
+
+ StructuralState result = new StructuralState();
+ result.setFontSize(STRUCTURAL_STATE_FONT_SIZE);
+ result.setHeight(height);
+ result.setWidth(width);
+ result.setValue(structuralState);
+
+ if (angle == null) {
+ logger.warn("Angle is not defined using 0 as default");
+ angle = 0.0;
+ }
+ Point2D position = converter.getResidueCoordinates(species, angle);
+ position.setLocation(position.getX() - width / 2, position.getY() - height / 2);
+ result.setPosition(position);
+
+ return result;
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
index dbd505bdc0146d6447c04b8d75817e723be33c0b..c428669472af041edab0c569c121f327ea28a332 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
@@ -54,14 +54,18 @@ public class SpeciesState {
public SpeciesState(Species species) {
if (species instanceof Protein) {
Protein protein = (Protein) species;
- setStructuralState(protein.getStructuralState());
+ if (protein.getStructuralState() != null) {
+ setStructuralState(protein.getStructuralState().getValue());
+ }
for (ModificationResidue mr : protein.getModificationResidues()) {
addModificationResidue(new CellDesignerModificationResidue(mr));
}
} else if (species instanceof Complex) {
Complex complex = (Complex) species;
- setStructuralState(complex.getStructuralState());
+ if (complex.getStructuralState() != null) {
+ setStructuralState(complex.getStructuralState().getValue());
+ }
} else if (species instanceof Rna) {
Rna rna = (Rna) species;
for (ModificationResidue region : rna.getRegions()) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
index c8774ca65fac033130cafe9f8f74fe04de88145d..ea4ede726074ee477abb7bfd28ce1e56f3ea3697 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ProteinConverterTest.java
@@ -11,8 +11,7 @@ import org.junit.*;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.*;
public class ProteinConverterTest extends CellDesignerTestFunctions {
static Logger logger = LogManager.getLogger(ProteinConverterTest.class);
@@ -59,6 +58,23 @@ public class ProteinConverterTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testAngleConversionForReceptor() {
+ Protein protein = new ReceptorProtein("id");
+ protein.setWidth(10);
+ protein.setHeight(60);
+ protein.setX(200);
+ protein.setY(500);
+
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(protein, false);
+
+ for (double angle = 0.0; angle < Math.PI * 2; angle += 0.1) {
+ Point2D point = converter.getResidueCoordinates(protein, angle);
+ double angle2 = converter.getAngleForPoint(protein, point);
+ assertEquals(angle, angle2, Configuration.EPSILON);
+ }
+ }
+
@Test
public void testGetResidueCoords() throws Exception {
GenericProtein protein = new GenericProtein("id");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
index 336f829172c1f94d90da9a2e1763061d5779ea35..287682346d12324fb01fa4c4346606a39055cdca 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ComplexParserTest.java
@@ -44,8 +44,17 @@ public class ComplexParserTest extends CellDesignerTestFunctions {
@Test
public void testComplexState() throws Exception {
Model model = getModelForFile("testFiles/problematic/complex_with_state.xml");
- Complex complex = (Complex) model.getElementByElementId("csa1");
- assertEquals("test state", complex.getStructuralState());
+ Complex complex = model.getElementByElementId("csa1");
+ assertNotNull(complex.getStructuralState());
+ assertEquals("test state", complex.getStructuralState().getValue());
+
+ assertEquals(0, getWarnings().size());
+ }
+
+ @Test
+ public void testMovedState() throws Exception {
+ Model model = getModelForFile("testFiles/protein_with_moved_state.xml");
+ testXmlSerialization(model);
}
@Test(expected = InvalidXmlSchemaException.class)
diff --git a/converter-CellDesigner/testFiles/protein_with_moved_state.xml b/converter-CellDesigner/testFiles/protein_with_moved_state.xml
new file mode 100644
index 0000000000000000000000000000000000000000..4bb1c80897c345b03769cd147f3768e1610f1525
--- /dev/null
+++ b/converter-CellDesigner/testFiles/protein_with_moved_state.xml
@@ -0,0 +1,92 @@
+<?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="192.0" y="176.0" w="80.0" h="50.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:structuralState angle="5.338676308955931"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="50.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffffcc" 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="RECEPTOR"/>
+</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:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="open"/>
+</celldesigner:listOfStructuralStates>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index c3cc9949f4e74f5f32037df7a5c1afbafb24bf4e..eb61780079473b5aee3f2b50461db7d2dc0943f7 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -10,8 +10,8 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbgn.*;
import org.sbgn.bindings.*;
-import org.sbgn.bindings.Map;
import org.sbgn.bindings.Arc.*;
+import org.sbgn.bindings.Map;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -24,8 +24,7 @@ import lcsb.mapviewer.model.map.modifier.*;
import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.*;
-import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.*;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -170,8 +169,8 @@ public class SbgnmlXmlExporter {
stateVariableGlyph.setId(newGlyph.getId().concat("-").concat(stateVariableGlyph.getId()));
newGlyph.getGlyph().add(stateVariableGlyph);
}
- if (protein.getStructuralState() != null && !protein.getStructuralState().isEmpty()) {
- newGlyph.getGlyph().add(createStateVariableForStructuralState(protein, protein.getStructuralState()));
+ if (protein.getStructuralState() != null && !protein.getStructuralState().getValue().isEmpty()) {
+ newGlyph.getGlyph().add(createStateVariableForStructuralState(protein.getStructuralState()));
}
}
@@ -186,8 +185,8 @@ public class SbgnmlXmlExporter {
Glyph childGlyph = elementToGlyph(child);
newGlyph.getGlyph().add(childGlyph);
}
- if (complex.getStructuralState() != null && !complex.getStructuralState().isEmpty()) {
- newGlyph.getGlyph().add(createStateVariableForStructuralState(complex, complex.getStructuralState()));
+ if (complex.getStructuralState() != null && !complex.getStructuralState().getValue().isEmpty()) {
+ newGlyph.getGlyph().add(createStateVariableForStructuralState(complex.getStructuralState()));
}
}
}
@@ -196,24 +195,24 @@ public class SbgnmlXmlExporter {
return newGlyph;
}
- private Glyph createStateVariableForStructuralState(Element element, String structuralState) {
+ private Glyph createStateVariableForStructuralState(StructuralState structuralState) {
Glyph glyph = new Glyph();
- glyph.setId(element.getElementId() + "-state");
+ glyph.setId(structuralState.getSpecies().getElementId() + "-state");
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
Glyph.State state = new Glyph.State();
- state.setValue(structuralState);
+ state.setValue(structuralState.getValue());
glyph.setState(state);
Bbox bbox = new Bbox();
-
- float width = (float) (element.getWidth() - 20);
- float height = 28.0f;
- bbox.setH(width);
- bbox.setW(height);
-
- bbox.setX((float) (element.getX() + 10));
- bbox.setY((float) (element.getY() - height / 2));
+
+ float width = structuralState.getWidth().floatValue();
+ float height = structuralState.getHeight().floatValue();
+ bbox.setH(height);
+ bbox.setW(width);
+
+ bbox.setX((float) structuralState.getPosition().getX());
+ bbox.setY((float) structuralState.getPosition().getY());
glyph.setBbox(bbox);
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 9423bb9f7c6c77d64b303c5dccd1ff232d4fa6f6..fcc383be6082580f2306d4e6be98410b1064480d 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.awt.*;
+import java.awt.Color;
import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
@@ -34,6 +34,7 @@ import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.reaction.type.*;
import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.*;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This class is a parser for SBGN-ML files.
@@ -590,13 +591,14 @@ public class SbgnmlXmlParser {
logger.warn(ex.getMessage());
}
} else {
- String structuralState = child.getState().getValue();
if (newSpecies instanceof Protein) {
Protein protein = (Protein) newSpecies;
- protein.setStructuralState(structuralState);
+ protein.setStructuralState(createStructuralState(child));
} else if (newSpecies instanceof Complex) {
Complex complex = (Complex) newSpecies;
- complex.setStructuralState(structuralState);
+ complex.setStructuralState(createStructuralState(child));
+ } else {
+ logger.warn(new ElementUtils().getElementTag(newSpecies) + "State is not supported");
}
}
}
@@ -608,6 +610,23 @@ public class SbgnmlXmlParser {
}
+ private StructuralState createStructuralState(Glyph glyph) {
+ StructuralState structuralState = new StructuralState();
+
+ double height = new Double(glyph.getBbox().getH());
+ double width = new Double(glyph.getBbox().getW());
+ double x = new Double(glyph.getBbox().getX());
+ double y = new Double(glyph.getBbox().getY());
+
+ structuralState.setFontSize(10);
+ structuralState.setValue(glyph.getState().getValue());
+ structuralState.setHeight(height);
+ structuralState.setWidth(width);
+ structuralState.setPosition(new Point2D.Double(x, y));
+
+ return structuralState;
+ }
+
/**
* {@link ModificationResidue} in element might have slightly off coordinates
* (due to different symbol shapes). For that we need to align them to match our
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
index 54da7290fb6832b0ba4fa5a8452d4207d682a457..f040b806171515f7216a1c6d90a205ce27994221 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/CellDesignerToSbgnTest.java
@@ -18,6 +18,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.field.StructuralStateComparator;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class CellDesignerToSbgnTest extends SbgnmlTestFunctions {
@@ -108,7 +109,9 @@ public class CellDesignerToSbgnTest extends SbgnmlTestFunctions {
protein1 = model.getElementByElementId("sa2");
protein2 = model2.getElementByElementId("sa2");
- assertEquals(protein1.getStructuralState(), protein2.getStructuralState());
+ StructuralStateComparator comparator = new StructuralStateComparator();
+
+ assertEquals(0, comparator.compare(protein1.getStructuralState(), protein2.getStructuralState()));
}
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
index 7f6000f2a56ada60c4643a425c3fe4f4d8d9d2d1..c2a66df954416f2e6130fed94b951ff32c5aa72e 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/DbSerializationTest.java
@@ -3,35 +3,61 @@ package lcsb.mapviewer.converter.model.sbgnml;
import static org.junit.Assert.assertEquals;
import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.*;
import org.junit.runner.RunWith;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.AnnotationConfigApplicationContext;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.persist.dao.map.ModelDao;
-@Transactional
-@ContextConfiguration(classes = SpringSBGNMLConverterTestConfig.class)
-@RunWith(SpringJUnit4ClassRunner.class)
+@RunWith(Parameterized.class)
public class DbSerializationTest extends SbgnmlTestFunctions {
- @Autowired
- ModelDao modelDao;
- @Autowired
- DbUtils dbUtils;
+
+ static ApplicationContext applicationContext;
Logger logger = LogManager.getLogger(DbSerializationTest.class.getName());
- private void makeDbSerializationTest(String filePath) throws Exception {
+ private String fileName;
+
+ public DbSerializationTest(String filePath) {
+ this.fileName = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ applicationContext = new AnnotationConfigApplicationContext(
+ SpringSBGNMLConverterTestConfig.class);
+
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/VANTEDdiagram.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/activated_stat1alpha_induction_of_the_irf1_gene.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/adh.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/clone-marker.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/glycolysis.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlCellDesignerInompatible/insulin-like_growth_factor_signaling.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling.sbgn"});
+ data.add(new Object[] {"testFiles/sbgnmlParserTestFiles/sbgnmlFiles/phenotypeTest.sbgn"});
+ return data;
+ }
+
+ @Test
+ @Transactional
+ public void dbSerializationTest() throws Exception {
+ ModelDao modelDao = applicationContext.getBean(ModelDao.class);
+
SbgnmlXmlParser parser = new SbgnmlXmlParser();
- String fileName = "testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(filePath);
Model model = parser.createModel(fileName, new File(fileName));
modelDao.add(model);
@@ -47,6 +73,7 @@ public class DbSerializationTest extends SbgnmlTestFunctions {
@Before
public void setUp() throws Exception {
+ DbUtils dbUtils = applicationContext.getBean(DbUtils.class);
// we use custom threads because in layoutservice there is commit method
// called, and because of that hibernate session injected by spring
// cannot
@@ -58,48 +85,9 @@ public class DbSerializationTest extends SbgnmlTestFunctions {
@After
public void tearDown() throws Exception {
+ DbUtils dbUtils = applicationContext.getBean(DbUtils.class);
// close session
dbUtils.closeSessionForCurrentThread();
}
- @Test
- public void VANTEDdiagramTest() throws Exception {
- makeDbSerializationTest("VANTEDdiagram.sbgn");
- }
-
- @Test
- public void activatedStat1AlphaTest() throws Exception {
- makeDbSerializationTest("activated_stat1alpha_induction_of_the_irf1_gene.sbgn");
- }
-
- @Test
- public void adhTest() throws Exception {
- makeDbSerializationTest("adh.sbgn");
- }
-
- @Test
- public void cloneMarkerTest() throws Exception {
- makeDbSerializationTest("clone-marker.sbgn");
- }
-
- @Test
- public void glycolysisTest() throws Exception {
- makeDbSerializationTest("glycolysis.sbgn");
- }
-
- @Test
- public void insulinLikeGrowthFactorSignalingTest() throws Exception {
- makeDbSerializationTest("insulin-like_growth_factor_signaling.sbgn");
- }
-
- @Test
- public void neuronalMuscleSignallingTest() throws Exception {
- makeDbSerializationTest("neuronal_muscle_signalling.sbgn");
- }
-
- @Test
- public void phenotypeTest() throws Exception {
- makeDbSerializationTest("phenotypeTest.sbgn");
- }
-
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 6618aa6b875d2537e726727d023248770e913141..e840c5e16d1ed486b4946077d43046a4ed49acf7 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -2,8 +2,7 @@ package lcsb.mapviewer.converter.model.sbgnml;
import java.io.File;
import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Paths;
+import java.nio.file.*;
import java.util.ArrayList;
import java.util.Collection;
@@ -23,10 +22,10 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
Logger logger = LogManager.getLogger(SbgnmlXmlExporterTest.class.getName());
- private String testName;
+ private Path filePath;
- public SbgnmlXmlExporterTest(String testName) {
- this.testName = testName;
+ public SbgnmlXmlExporterTest(Path filePath) {
+ this.filePath = filePath;
}
@Parameters(name = "{index} : {0}")
@@ -34,25 +33,29 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
Collection<Object[]> data = new ArrayList<Object[]>();
Files.walk(Paths.get("testFiles/sbgnmlParserTestFiles/sbgnmlFiles")).forEach(fPath -> {
if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")) {
- String tName = fPath.getFileName().toString().substring(0, fPath.getFileName().toString().indexOf(".sbgn"));
- data.add(new Object[] { tName });
+ data.add(new Object[] { fPath});
+ }
+ });
+ Files.walk(Paths.get("testFiles/sbgnmlCellDesignerInompatible")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".sbgn")) {
+ data.add(new Object[] { fPath});
}
});
return data;
}
- private void parseAndExport(String testName) throws Exception {
+ private void parseAndExport(Path filePath) throws Exception {
Converter converter = new SbgnmlXmlConverter();
Model model = converter.createModel(new ConverterParams()
- .filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/".concat(testName).concat(".sbgn")));
+ .filename(filePath.toAbsolutePath().toString()));
converter.model2File(model, File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath());
}
@Test
public void test() throws Exception {
- parseAndExport(testName);
+ parseAndExport(filePath);
}
}
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/insulin-like_growth_factor_signaling.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/insulin-like_growth_factor_signaling.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/insulin-like_growth_factor_signaling.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/insulin-like_growth_factor_signaling.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/mapk_cascade.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/mapk_cascade.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/mapk_cascade.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/mapk_cascade.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling_color.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling_color.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/neuronal_muscle_signalling_color.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/neuronal_muscle_signalling_color.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/states.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/states.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/states.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/states.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/submap.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/submap.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/submap.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/submap.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/theWeirdOne.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/theWeirdOne.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/theWeirdOne.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/theWeirdOne.sbgn
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/unitOfInformation.sbgn b/converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/unitOfInformation.sbgn
similarity index 100%
rename from converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/unitOfInformation.sbgn
rename to converter-SBGNML/testFiles/sbgnmlCellDesignerInompatible/unitOfInformation.sbgn
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
index 5f523dfa78f3e23f30d2f07408f80f10dbaec854..7a91e5485a2907c63f3928490a00193a94e018f4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
@@ -52,70 +52,69 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
}
@Override
- protected void drawImpl(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
- if (alias.getState().equalsIgnoreCase("complexnoborder")) {
+ protected void drawImpl(final Complex complex, final Graphics2D graphics, final ConverterParams params) {
+ if (complex.getState().equalsIgnoreCase("complexnoborder")) {
return;
}
int homodir;
if (params.isSbgnFormat()) {
- // If the SBGN display mode is set, multimer is shown as two stacked
- // glyphs
- if (alias.getHomodimer() > 1) {
+ // If the SBGN display mode is set, multimer is shown as two stacked glyphs
+ if (complex.getHomodimer() > 1) {
homodir = 2;
} else {
homodir = 1;
}
} else {
- homodir = alias.getHomodimer();
+ homodir = complex.getHomodimer();
}
- alias.setWidth(alias.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ complex.setWidth(complex.getWidth() - SpeciesConverter.HOMODIMER_OFFSET * (complex.getHomodimer() - 1));
+ complex.setHeight(complex.getHeight() - SpeciesConverter.HOMODIMER_OFFSET * (complex.getHomodimer() - 1));
- alias.setX(alias.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
- alias.setY(alias.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ complex.setX(complex.getX() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
+ complex.setY(complex.getY() + SpeciesConverter.HOMODIMER_OFFSET * (homodir));
for (int i = 0; i < homodir; i++) {
- alias.setX(alias.getX() - SpeciesConverter.HOMODIMER_OFFSET);
- alias.setY(alias.getY() - SpeciesConverter.HOMODIMER_OFFSET);
+ complex.setX(complex.getX() - SpeciesConverter.HOMODIMER_OFFSET);
+ complex.setY(complex.getY() - SpeciesConverter.HOMODIMER_OFFSET);
- GeneralPath path = getAliasPath(alias);
+ GeneralPath path = getAliasPath(complex);
Color c = graphics.getColor();
Stroke stroke = graphics.getStroke();
- graphics.setColor(alias.getColor());
+ graphics.setColor(complex.getColor());
graphics.fill(path);
graphics.setColor(c);
- graphics.setStroke(getBorderLine(alias));
+ graphics.setStroke(getBorderLine(complex));
graphics.draw(path);
- if (alias.getState().equals("brief")) {
- alias.increaseBorder(-INTERNAL_BORDER_DIST);
- path = getAliasPath(alias);
- alias.increaseBorder(INTERNAL_BORDER_DIST);
+ if (complex.getState().equals("brief")) {
+ complex.increaseBorder(-INTERNAL_BORDER_DIST);
+ path = getAliasPath(complex);
+ complex.increaseBorder(INTERNAL_BORDER_DIST);
graphics.setStroke(LineType.DOTTED.getStroke());
graphics.draw(path);
}
- if (alias.getActivity() && !params.isSbgnFormat()) {
- alias.increaseBorder(INTERNAL_BORDER_DIST);
- path = getAliasPath(alias);
- alias.increaseBorder(-INTERNAL_BORDER_DIST);
+ if (complex.getActivity() && !params.isSbgnFormat()) {
+ complex.increaseBorder(INTERNAL_BORDER_DIST);
+ path = getAliasPath(complex);
+ complex.increaseBorder(-INTERNAL_BORDER_DIST);
graphics.setStroke(LineType.DOTTED.getStroke());
graphics.draw(path);
}
graphics.setStroke(stroke);
}
- alias.setWidth(alias.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
- alias.setHeight(alias.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (alias.getHomodimer() - 1));
+ complex.setWidth(complex.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (complex.getHomodimer() - 1));
+ complex.setHeight(complex.getHeight() + SpeciesConverter.HOMODIMER_OFFSET * (complex.getHomodimer() - 1));
// SBGN view - multimers are displayed with a unit of information containing
// cardinality
if (params.isSbgnFormat()) {
String unitOfInformationText = null;
- if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
- unitOfInformationText = alias.getStatePrefix() + ":" + alias.getStateLabel();
+ if (complex.getStatePrefix() != null && complex.getStateLabel() != null) {
+ unitOfInformationText = complex.getStatePrefix() + ":" + complex.getStateLabel();
}
if (homodir == 2 && (unitOfInformationText == null || !unitOfInformationText.contains("N:"))) {
if (unitOfInformationText != null) {
@@ -123,17 +122,15 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
} else {
unitOfInformationText = "";
}
- unitOfInformationText += "N:" + alias.getHomodimer();
+ unitOfInformationText += "N:" + complex.getHomodimer();
}
- drawUnitOfInformation(unitOfInformationText, alias, graphics);
+ drawUnitOfInformation(unitOfInformationText, complex, graphics);
}
- String text = alias.getStructuralState();
+ drawStructuralState(complex.getStructuralState(), graphics);
- drawStructuralState(text, alias, graphics);
-
- drawText(alias, graphics, params);
+ drawText(complex, graphics, params);
}
@Override
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
index 5f223086fb12bcfbd2b8b391fd916e7c3551081e..4ebc97efca6c927136d6d10bb452dd57ce5318a2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
@@ -194,8 +194,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
unitOfInformationText = null;
}
- String text = protein.getStructuralState();
- drawStructuralState(text, protein, graphics);
+ drawStructuralState(protein.getStructuralState(), graphics);
drawUnitOfInformation(unitOfInformationText, protein, graphics);
drawText(protein, graphics, params);
protein.setWidth(protein.getWidth() + SpeciesConverter.HOMODIMER_OFFSET * (protein.getHomodimer() - 1));
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index eec1afd1cb80bf19db460c2d381facd4f1eb4ac5..65cf866433d187701eedd45620a90e11e3a42d66 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -43,10 +43,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
* What is the distance between homodimer aliases when homodimer>1.
*/
public static final int HOMODIMER_OFFSET = 6;
- /**
- * Default font size for the modifier description.
- */
- protected static final int DEFAULT_SPECIES_MODIFIER_FONT_SIZE = 10;
+
/**
* Default diameter of the modification residues.
*/
@@ -59,30 +56,25 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
* Default species font size.
*/
protected static final int DEFAULT_SPECIES_FONT_SIZE = 12;
- /**
- * Height of the ellipse that contain structural state description.
- */
- private static final int STRUCTURAL_STATE_HEIGHT = 20;
+
/**
* Height of the rectangle that contains unit of information.
*/
private static final int UNIT_OF_INFORMATION_HEIGHT = 20;
- /**
- * Size of the margin in the structural state description.
- */
- private static final int TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC = 40;
+
/**
* Size of the margin in the unit of information description.
*/
private static final int TEXT_MARGIN_FOR_UNIT_OF_INFORMATION_DESC = 20;
- /**
- * Minimum width of the structural state ellipse.
- */
- private static final int MIN_STRUCTURAL_STATE_WIDTH = 60;
+
/**
* Minimum width of the unit of information rectangle.
*/
private static final int MIN_UNIT_OF_INFORMATION_WIDTH = 40;
+ /**
+ * Default font size for the modifier description.
+ */
+ protected static final int DEFAULT_SPECIES_MODIFIER_FONT_SIZE = 10;
/**
* Default class logger.
*/
@@ -93,10 +85,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
*/
private LineTransformation lineTransformation = new LineTransformation();
private ArrowTransformation arrowTransformation = new ArrowTransformation();
- /**
- * Default font used to draw structural state of the species.
- */
- private Font structuralFont = null;
+
/**
* Default font used to draw unit of information of the species.
*/
@@ -114,7 +103,6 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
* when drawing {@link Species}
*/
protected SpeciesConverter(ColorExtractor colorExtractor) {
- structuralFont = new Font(Font.SANS_SERIF, 0, DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
this.colorExtractor = colorExtractor;
};
@@ -300,21 +288,6 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
this.lineTransformation = lineTransformation;
}
- /**
- * @return the structuralFont
- */
- protected Font getStructuralFont() {
- return structuralFont;
- }
-
- /**
- * @param structuralFont
- * the structuralFont to set
- */
- protected void setStructuralFont(Font structuralFont) {
- this.structuralFont = structuralFont;
- }
-
/**
* @return the unitOfInformationFont
*/
@@ -334,43 +307,40 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
* Draws structural state description of the alias (ellipse in the top part of
* the alias).
*
- * @param text
+ * @param state
* state description text
* @param species
* state description should be drawn on this {@link Species}
* @param graphics
* where the drawing should be performed
*/
- protected void drawStructuralState(String text, T species, final Graphics2D graphics) {
- if (text == null) {
+ protected void drawStructuralState(StructuralState state, final Graphics2D graphics) {
+ if (state == null) {
return;
}
- Point2D p = new Point2D.Double(species.getCenterX(), species.getY());
-
- double width = MIN_STRUCTURAL_STATE_WIDTH;
- if (!text.trim().equals("")) {
- width = Math.max(MIN_STRUCTURAL_STATE_WIDTH,
- graphics.getFontMetrics().stringWidth(text) + TEXT_MARGIN_FOR_STRUCTURAL_STATE_DESC);
- }
- width = Math.min(width, species.getWidth());
- double height = STRUCTURAL_STATE_HEIGHT;
+ double width = state.getWidth();
+ double height = state.getHeight();
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - width / 2, p.getY() - height / 2, width, height);
+ Ellipse2D ellipse = new Ellipse2D.Double(state.getPosition().getX(), state.getPosition().getY(), width, height);
Color c = graphics.getColor();
graphics.setColor(Color.WHITE);
graphics.fill(ellipse);
graphics.setColor(c);
graphics.draw(ellipse);
- if (!text.trim().equals("")) {
- Font font = graphics.getFont();
- graphics.setFont(getStructuralFont());
+ if (!state.getValue().equals("")) {
+ Font tmpFont = graphics.getFont();
+ Font font = new Font(Font.SANS_SERIF, 0, state.getFontSize().intValue());
+ graphics.setFont(font);
- width = graphics.getFontMetrics().stringWidth(text);
+ width = graphics.getFontMetrics().stringWidth(state.getValue());
height = graphics.getFontMetrics().getAscent() - graphics.getFontMetrics().getDescent();
- graphics.drawString(text, (int) (p.getX() - width / 2), (int) (p.getY() + height / 2));
- graphics.setFont(font);
+ double x = state.getPosition().getX() + (state.getWidth() - width) / 2;
+ double y = state.getPosition().getY() + (state.getHeight() + height) / 2;
+
+ graphics.drawString(state.getValue(), (int) x, (int) y);
+ graphics.setFont(tmpFont);
}
}
@@ -529,6 +499,10 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
}
+ private Font getStructuralFont() {
+ return new Font(Font.SANS_SERIF, 0, DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
+ }
+
/**
* This method draws {@link ModificationSite} of the {@link Species}. If
* drawEmptyModification is set to false then modification is not drawn if
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 a7cf1fdfd142f2eb56c6266bbb900b91d4b2b71d..3688c5e1e8d2ae66297f04c9326e1736a75259a4 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
@@ -32,6 +32,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private SbmlCompartmentExporter compartmentExporter;
private int modificationResidueCounter = 0;
+ private int structuralStateCounter = 0;
private Map<String, String> modificationResidueIds = new HashMap<>();
public SbmlSpeciesExporter(Model sbmlModel,
@@ -172,14 +173,15 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private void assignStructuralStateToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
- String structuralState = null;
+ StructuralState structuralState = null;
if (element instanceof Protein) {
structuralState = ((Protein) element).getStructuralState();
} else if (element instanceof Complex) {
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
- assignValueToFeature(element, multiExtension, speciesType, structuralState, BioEntityFeature.STRUCTURAL_STATE);
+ assignValueToFeature(element, multiExtension, speciesType, structuralState.getValue(),
+ BioEntityFeature.STRUCTURAL_STATE);
}
}
@@ -374,13 +376,16 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
String multiDistinguisher = null;
if (isExtensionEnabled(SbmlExtension.MULTI)) {
- String structuralState = null;
+ StructuralState structuralState = null;
if (element instanceof Protein) {
+
structuralState = ((Protein) element).getStructuralState();
} else if (element instanceof Complex) {
structuralState = ((Complex) element).getStructuralState();
}
- multiDistinguisher = structuralState;
+ if (structuralState != null) {
+ multiDistinguisher = structuralState.getValue();
+ }
if (element instanceof SpeciesWithModificationResidue) {
List<String> modifications = new ArrayList<>();
@@ -465,6 +470,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
createModificationGlyph(mr, speciesGlyph);
}
}
+ if (element.getStructuralState() != null) {
+ createStructuralStateGlyph(element, speciesGlyph);
+ }
}
TextGlyph textGlyph = getLayout().createTextGlyph("text_" + element.getElementId(), element.getName());
textGlyph
@@ -484,6 +492,44 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
+ private void createStructuralStateGlyph(Species element, AbstractReferenceGlyph speciesGlyph) {
+ org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
+
+ MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
+
+ SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), getMultiSpeciesType(element),
+ BioEntityFeature.STRUCTURAL_STATE);
+
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = getPosibleFeatureIdByName(
+ element.getStructuralState().getValue(), structuralStateFeature);
+
+ SpeciesFeature feature = null;
+ for (SpeciesFeature existingFeature : speciesExtension.getListOfSpeciesFeatures()) {
+ if (existingFeature.getSpeciesFeatureType().equals(structuralStateFeature.getId())) {
+ feature = existingFeature;
+ }
+ }
+
+ SpeciesFeatureValue modificationFeatureValue = null;
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ if (possibleSpeciesFeatureValue.getId().equals(featureValue.getValue())) {
+ modificationFeatureValue = featureValue;
+ }
+ }
+
+ modificationFeatureValue.setId(getStructuralStateUniqueId(element.getStructuralState()));
+
+ GeneralGlyph modificationGlyph = getLayout().createGeneralGlyph("structural_state_" + (idCounter++),
+ modificationFeatureValue.getId());
+ ReferenceGlyph referenceGlyph = new ReferenceGlyph("structural_state_reference_" + (idCounter++));
+ referenceGlyph.setGlyph(speciesGlyph.getId());
+ referenceGlyph.setBoundingBox(createBoundingBoxForStructuralState(element.getStructuralState()));
+
+ modificationGlyph.addReferenceGlyph(referenceGlyph);
+ modificationGlyph.setBoundingBox(createBoundingBoxForStructuralState(element.getStructuralState()));
+
+ }
+
@SuppressWarnings("unchecked")
private MultiSpeciesType createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
MultiSpeciesType speciesType = new MultiSpeciesType();
@@ -560,6 +606,20 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
modificationGlyph.setBoundingBox(createBoundingBoxForModification(mr));
}
+ private BoundingBox createBoundingBoxForStructuralState(StructuralState structuralState) {
+ double width = structuralState.getWidth();
+ double height = structuralState.getHeight();
+ double x = structuralState.getPosition().getX();
+ double y = structuralState.getPosition().getY();
+ BoundingBox boundingBox = new BoundingBox();
+ boundingBox.setPosition(new Point(x, y, structuralState.getSpecies().getZ() + 1));
+ Dimensions dimensions = new Dimensions();
+ dimensions.setWidth(width);
+ dimensions.setHeight(height);
+ boundingBox.setDimensions(dimensions);
+ return boundingBox;
+ }
+
private BoundingBox createBoundingBoxForModification(ModificationResidue mr) {
double width, height;
if (mr instanceof AbstractRegionModification) {
@@ -592,4 +652,15 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return result;
}
+ private String getStructuralStateUniqueId(StructuralState mr) {
+ String modificationId = "structural_state_" + getSbmlIdKey(mr.getSpecies());
+ String result = modificationResidueIds.get(modificationId);
+ if (result == null) {
+ result = "structural_state_" + (structuralStateCounter++);
+ modificationResidueIds.put(modificationId, result);
+ }
+ return result;
+
+ }
+
}
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 d6c62603e56fed5901a482ff763dccf1af371669..7a98e43eeac412cd360778610a9f8e0596ad0960 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
@@ -2,8 +2,7 @@ package lcsb.mapviewer.converter.model.sbml.species;
import java.awt.geom.Point2D;
import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -31,6 +30,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
private static String ARTIFITIAL_SOURCE_ID = "sbml_artifitial_source";
Logger logger = LogManager.getLogger(SbmlSpeciesParser.class);
+ Map<String, String> structuralStateIdMap = new HashMap<>();
+
public SbmlSpeciesParser(Model model, lcsb.mapviewer.model.map.model.Model minervaModel) {
super(model, minervaModel);
}
@@ -65,13 +66,20 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
String featureTypeString = feature.getSpeciesFeatureType();
List<String> featureValues = getFeatureValues(speciesType, feature);
if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.STRUCTURAL_STATE)) {
+ String structuralStateId = null;
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ if (featureValue.getId() != null) {
+ structuralStateId = featureValue.getId();
+ }
+ }
if (minervaElement instanceof Protein) {
- ((Protein) minervaElement).setStructuralState(String.join("; ", featureValues));
+ minervaElement.setStructuralState(createStructuralState(featureValues));
} else if (minervaElement instanceof Complex) {
- ((Complex) minervaElement).setStructuralState(String.join("; ", featureValues));
+ minervaElement.setStructuralState(createStructuralState(featureValues));
} else {
logger.warn(warnPrefix + "Structural state not supported");
}
+ structuralStateIdMap.put(minervaElement.getElementId(), structuralStateId);
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.POSITION_TO_COMPARTMENT)) {
if (featureValues.size() != 1) {
logger.warn(warnPrefix + "Position to compartment must have exactly one value");
@@ -161,6 +169,12 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
}
+ private StructuralState createStructuralState(List<String> featureValues) {
+ StructuralState structuralState = new StructuralState();
+ structuralState.setValue(String.join("; ", featureValues));
+ return structuralState;
+ }
+
private List<String> getFeatureValues(MultiSpeciesType speciesType, SpeciesFeature feature) {
SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(feature.getSpeciesFeatureType());
@@ -320,7 +334,29 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
// find a reference to the alias in layout, so we know it's the proper value
ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
if (Objects.equal(referenceGlyph.getGlyph(), mr.getSpecies().getElementId())) {
-// if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
+ // if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ } else {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ }
+ }
+ }
+ return residueGlyph;
+ }
+
+ private GeneralGlyph getResidueGlyphForStructuralState(StructuralState mr) {
+ GeneralGlyph residueGlyph = null;
+ String structurlaStateId = structuralStateIdMap.get(mr.getSpecies().getElementId());
+ for (GraphicalObject graphicalObject : getLayout().getListOfAdditionalGraphicalObjects()) {
+ if (graphicalObject instanceof GeneralGlyph) {
+ if (Objects.equal(((GeneralGlyph) graphicalObject).getReference(), structurlaStateId)) {
+ if (((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().size() > 0) {
+ // find a reference to the alias in layout, so we know it's the proper value
+ ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
+ if (Objects.equal(referenceGlyph.getGlyph(), mr.getSpecies().getElementId())) {
+ // if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
residueGlyph = (GeneralGlyph) graphicalObject;
}
} else {
@@ -366,21 +402,54 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
for (Element element : result) {
String compartmentId = null;
+ String speciesId = element.getElementId();
if (getLayout().getSpeciesGlyph(element.getElementId()) != null) {
compartmentId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId())
.getSpeciesInstance()).getCompartment();
+ speciesId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId()).getSpeciesInstance())
+ .getId();
} else {
if (!element.getElementId().equals(ARTIFITIAL_SINK_ID)
&& !element.getElementId().equals(ARTIFITIAL_SOURCE_ID)) {
compartmentId = getSbmlModel().getSpecies(element.getElementId()).getCompartment();
}
}
+ structuralStateIdMap.put(element.getElementId(), structuralStateIdMap.get(speciesId));
assignCompartment(element, compartmentId);
assignModificationResiduesLayout(element);
+ assignStructuralStateLayout(element);
}
return result;
}
+ private void assignStructuralStateLayout(Element element) {
+ if (element instanceof Protein || element instanceof Complex) {
+ StructuralState state = ((Species) element).getStructuralState();
+ if (state != null) {
+ state.setFontSize(10);
+ state.setHeight(20);
+ state.setWidth(element.getWidth());
+ state.setPosition(new Point2D.Double(element.getX(), element.getY() - 10));
+ GeneralGlyph residueGlyph = getResidueGlyphForStructuralState(state);
+ if (residueGlyph != null) {
+ if (residueGlyph.getBoundingBox() == null || residueGlyph.getBoundingBox().getDimensions() == null) {
+ logger.warn(
+ new ElementUtils().getElementTag(element) + " Layout doesn't contain coordinates for structural state");
+ } else {
+ double width = residueGlyph.getBoundingBox().getDimensions().getWidth();
+ double height = residueGlyph.getBoundingBox().getDimensions().getHeight();
+ double x = residueGlyph.getBoundingBox().getPosition().getX();
+ double y = residueGlyph.getBoundingBox().getPosition().getY();
+ state.setPosition(new Point2D.Double(x, y));
+ state.setWidth(width);
+ state.setHeight(height);
+ }
+ }
+
+ }
+ }
+ }
+
@Override
protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
super.applyStyleToElement(elementWithLayout, style);
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 145e36e21ba025019f5d521ee7215783aa88f87d..6a2c07c77127c0aabfe643620122fcb181d75c57 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
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbml;
import static org.junit.Assert.*;
import java.awt.Color;
-import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
import java.lang.reflect.Modifier;
@@ -17,7 +16,6 @@ import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.ext.multi.*;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.LineComparator;
import lcsb.mapviewer.common.comparator.ListComparator;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
@@ -397,7 +395,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
public void testExportProteinState() throws Exception {
Model model = createEmptyModel();
GenericProtein element = createProtein();
- element.setStructuralState("xxx");
+ element.setStructuralState(createStructuralState(element));
model.addElement(element);
Model deserializedModel = getModelAfterSerializing(model);
@@ -430,9 +428,9 @@ public class SbmlExporterTest extends SbmlTestFunctions {
@Test
public void testMultiExtensionProteinStateInTypes() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = createProtein();
+ StructuralState structuralState = createStructuralState(element);
element.setStructuralState(structuralState);
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
@@ -442,7 +440,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
for (MultiSpeciesType speciesType : multiPlugin.getListOfSpeciesTypes()) {
for (SpeciesFeatureType featureType : speciesType.getListOfSpeciesFeatureTypes()) {
for (PossibleSpeciesFeatureValue featureValue : featureType.getListOfPossibleSpeciesFeatureValues()) {
- if (featureValue.getName().equals(structuralState)) {
+ if (featureValue.getName().equals(structuralState.getValue())) {
structuralStateValueFound = true;
}
}
@@ -454,13 +452,12 @@ public class SbmlExporterTest extends SbmlTestFunctions {
@Test
public void testMultiExtensionProteinStateSuplicateInTypes() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = createProtein();
- element.setStructuralState(structuralState);
+ element.setStructuralState(createStructuralState(element));
model.addElement(element);
element = createProtein();
- element.setStructuralState(structuralState);
+ element.setStructuralState(createStructuralState(element));
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
MultiModelPlugin multiPlugin = (MultiModelPlugin) sbmlModel.getExtension("multi");
@@ -498,9 +495,9 @@ public class SbmlExporterTest extends SbmlTestFunctions {
@Test
public void testMultiExtensionStructuralStateTypeDefinition() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = createProtein();
+ StructuralState structuralState = createStructuralState(element);
element.setStructuralState(structuralState);
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
@@ -512,6 +509,16 @@ public class SbmlExporterTest extends SbmlTestFunctions {
speciesExtension.getListOfSpeciesFeatures().size() > 0);
}
+ private StructuralState createStructuralState(Element element) {
+ StructuralState structuralState = new StructuralState();
+ structuralState.setValue("xxx");
+ structuralState.setPosition(new Point2D.Double(element.getX(), element.getY() - 10));
+ structuralState.setWidth(element.getWidth());
+ structuralState.setHeight(20.0);
+ structuralState.setFontSize(10.0);
+ return structuralState;
+ }
+
@Test
public void testExportResidue() throws Exception {
Model model = createEmptyModel();
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
index 190972f43443201ddee1a11afdb1c384a9409707..caa0240f2b894166f11938ac505f3fe3254f1830 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
@@ -18,6 +18,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.*;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
@@ -84,7 +85,9 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
public void testIdsOfSpeciesWithStructuralStates() throws InconsistentModelException {
Species protein1 = createProtein();
Protein protein2 = createProtein();
- protein2.setStructuralState("X");
+ StructuralState state = new StructuralState();
+ state.setValue("X");
+ protein2.setStructuralState(state);
Model model = new ModelFullIndexed(null);
model.addElement(protein1);
model.addElement(protein2);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
index 4c3e4c4e70c7dac30ed8cc5ea1c86891bc676ebd..45c439cffa28965d9e077f2fc6dd22fc0b449583 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Complex.java
@@ -10,6 +10,7 @@ import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
/**
* Class that represents complex in the model. Complex elements contain
@@ -40,11 +41,6 @@ public class Complex extends Species {
@OneToMany(fetch = FetchType.EAGER, mappedBy = "complex")
private List<Species> elements = new ArrayList<>();
- /**
- * State of the complex species.
- */
- private String structuralState = null;
-
/**
* Empty constructor required by hibernate.
*/
@@ -65,7 +61,6 @@ public class Complex extends Species {
for (Species element : original.getElements()) {
addSpecies(element.copy());
}
- this.structuralState = original.getStructuralState();
}
/**
@@ -151,23 +146,6 @@ public class Complex extends Species {
}
}
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
/**
* Returns all children and sub-children elements for this element. Only non
* {@link Complex} children will be returned.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
index 07af665d13a33bd851c47e4e0498efbbd2cbade4..5335d79fd1a3e37af0ba84768f1c81bdbb01dc18 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ComplexComparator.java
@@ -9,8 +9,8 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.IntegerComparator;
-import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.field.StructuralStateComparator;
/**
* This class implements comparator interface for {@link Complex}.
@@ -88,12 +88,12 @@ public class ComplexComparator extends Comparator<Complex> {
}
}
- StringComparator stringComparator = new StringComparator();
+ StructuralStateComparator structuralStateComparator = new StructuralStateComparator();
- if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
+ if (structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
logger
.debug("Species structuralState different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
- return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
+ return structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
}
return 0;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 81bec9f3e7c3c7fa5fcea33bb21014af421fbee9..18d932e02658eee1e67420ff2d6dfede0baa0387 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -26,11 +26,6 @@ public abstract class Protein extends Species implements SpeciesWithBindingRegio
*/
private static final long serialVersionUID = 1L;
- /**
- * State of the protein.
- */
- private String structuralState = null;
-
/**
* List of modifications for the Protein.
*/
@@ -53,7 +48,6 @@ public abstract class Protein extends Species implements SpeciesWithBindingRegio
*/
protected Protein(Protein original) {
super(original);
- this.structuralState = original.getStructuralState();
for (ModificationResidue mr : original.getModificationResidues()) {
addModificationResidue(mr.copy());
}
@@ -107,23 +101,6 @@ public abstract class Protein extends Species implements SpeciesWithBindingRegio
this.modificationResidues = modificationResidues;
}
- /**
- * @return the structuralState
- * @see #structuralState
- */
- public String getStructuralState() {
- return structuralState;
- }
-
- /**
- * @param structuralState
- * the structuralState to set
- * @see #structuralState
- */
- public void setStructuralState(String structuralState) {
- this.structuralState = structuralState;
- }
-
@Override
public String getStringType() {
return "Protein";
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
index b2930d68d811f270fe4b5488f82502e016f8dd3c..3d60941368c8116e3dd0cd5e54922887a3f8dd5f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
@@ -8,9 +8,9 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.comparator.StringSetComparator;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.StructuralStateComparator;
/**
* Comparator class used for comparing {@link Protein} objects.
@@ -59,12 +59,12 @@ public class ProteinComparator extends Comparator<Protein> {
@Override
protected int internalCompare(Protein arg0, Protein arg1) {
- StringComparator stringComparator = new StringComparator();
+ StructuralStateComparator structuralStateComparator = new StructuralStateComparator();
StringSetComparator stringSetComparator = new StringSetComparator();
- if (stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
+ if (structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState()) != 0) {
logger.debug("structural state different: " + arg0.getStructuralState() + ", " + arg1.getStructuralState());
- return stringComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
+ return structuralStateComparator.compare(arg0.getStructuralState(), arg1.getStructuralState());
}
Set<String> set1 = new HashSet<>();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index 19eb0d2e4b88567723e5fea893e6483cea81f641..8d39fb32d1cf5d5ca605739b4466e36dd97040ec 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -12,8 +12,7 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
-import lcsb.mapviewer.model.map.species.field.UniprotRecord;
+import lcsb.mapviewer.model.map.species.field.*;
/**
* Structure used for representing information about single element.
@@ -139,6 +138,15 @@ public abstract class Species extends Element {
@Cascade({ CascadeType.ALL })
private SbmlUnit substanceUnitComlexType;
+ /**
+ * State of the complex/protein species.
+ */
+ // it should be in protein/complex, but due to hibernate reversed mappedBy
+ // property it
+ // must be in species.
+ @OneToOne(orphanRemoval = true, cascade = javax.persistence.CascadeType.ALL)
+ private StructuralState structuralState = null;
+
/**
* Constructor that set element identifier.
*
@@ -191,6 +199,9 @@ public abstract class Species extends Element {
substanceUnitRawType = original.substanceUnitRawType;
uniprots = original.getUniprots();
+ if (original.structuralState != null) {
+ setStructuralState(original.structuralState.copy());
+ }
// don't copy reaction nodes
}
@@ -511,4 +522,15 @@ public abstract class Species extends Element {
this.substanceUnitRawType = null;
}
+ public StructuralState getStructuralState() {
+ return structuralState;
+ }
+
+ public void setStructuralState(StructuralState structuralState) {
+ this.structuralState = structuralState;
+ if (structuralState != null) {
+ structuralState.setSpecies(this);
+ }
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralState.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralState.java
new file mode 100644
index 0000000000000000000000000000000000000000..bc8637150d99ba6c281a751d06579af299d2c57f
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralState.java
@@ -0,0 +1,146 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.text.DecimalFormat;
+
+import javax.persistence.*;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This class represent structural state of a {@link Species}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+@Entity
+public class StructuralState implements Serializable {
+
+ private static final long serialVersionUID = 1L;
+
+ @SuppressWarnings("unused")
+ private static Logger logger = LogManager.getLogger();
+
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ private int id;
+
+ @Column(nullable = false)
+ private String value;
+
+ @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+ @Column(nullable = false)
+ private Point2D position = null;
+
+ @Column(nullable = false)
+ private Double width;
+
+ @Column(nullable = false)
+ private Double height;
+
+ @Column(nullable = false)
+ private Double fontSize;
+
+ @OneToOne(fetch = FetchType.LAZY, cascade = javax.persistence.CascadeType.ALL, mappedBy = "structuralState", optional = false)
+ private Species species;
+
+ public StructuralState() {
+ }
+
+ /**
+ * Constructor that initialize object with the data taken from the parameter.
+ *
+ * @param mr
+ * original object from which data is taken
+ */
+ public StructuralState(StructuralState mr) {
+ this.value = mr.getValue();
+ this.position = mr.position;
+ this.width = mr.getWidth();
+ this.height = mr.getHeight();
+ this.fontSize = mr.getFontSize();
+ }
+
+ public Species getSpecies() {
+ return species;
+ }
+
+ public void setSpecies(Species species) {
+ this.species = species;
+ }
+
+ public Point2D getPosition() {
+ return position;
+ }
+
+ public void setPosition(Point2D position) {
+ this.position = position;
+ }
+
+ public StructuralState copy() {
+ return new StructuralState(this);
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public void setValue(String value) {
+ this.value = value;
+ }
+
+ @Override
+ public String toString() {
+ DecimalFormat format = new DecimalFormat("#.##");
+ String positionString = "Point2D[null]";
+ if (getPosition() != null) {
+ positionString = "Point2D[" + format.format(getPosition().getX()) + "," + format.format(getPosition().getY())
+ + "]";
+ }
+ String result = getValue() + "," + positionString;
+ return result;
+ }
+
+ public Double getWidth() {
+ return width;
+ }
+
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ public Double getHeight() {
+ return height;
+ }
+
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+ public void setHeight(Integer height) {
+ this.height = height.doubleValue();
+ }
+
+ public Double getFontSize() {
+ return fontSize;
+ }
+
+ public void setFontSize(Double fontSize) {
+ this.fontSize = fontSize;
+ }
+
+ public void setFontSize(int fontSize) {
+ this.fontSize = (double) fontSize;
+ }
+
+ public Point2D getCenter() {
+ return new Point2D.Double(position.getX() + width / 2, position.getY() + height / 2);
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralStateComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralStateComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..86e3334500ae02d0342485a7cf7df8af435771cb
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/StructuralStateComparator.java
@@ -0,0 +1,52 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.*;
+import lcsb.mapviewer.model.map.MiriamData;
+
+/**
+ * Comparator of {@link MiriamData} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class StructuralStateComparator extends Comparator<StructuralState> {
+
+ private static Logger logger = LogManager.getLogger();
+
+ /**
+ * Default constructor.
+ */
+ public StructuralStateComparator() {
+ super(StructuralState.class);
+ }
+
+ @Override
+ protected int internalCompare(StructuralState arg0, StructuralState arg1) {
+ StringComparator stringComparator = new StringComparator();
+ if (stringComparator.compare(arg0.getValue(), arg1.getValue()) != 0) {
+ return stringComparator.compare(arg0.getValue(), arg1.getValue());
+ }
+ PointComparator pointComparator = new PointComparator();
+ if (pointComparator.compare(arg0.getPosition(), arg1.getPosition()) != 0) {
+ logger.debug("position different: " + arg0.getPosition() + ", " + arg1.getPosition());
+ return pointComparator.compare(arg0.getPosition(), arg1.getPosition());
+ }
+
+ DoubleComparator doubleComparator = new DoubleComparator();
+ if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
+ logger.debug("width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ }
+ if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
index 60ba2db455ff203618e5701b0fb3f288a8230bea..196210dedfe8090877afdae03295eb9d84240433 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
@@ -4,7 +4,7 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.when;
-import java.awt.*;
+import java.awt.Color;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -14,6 +14,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
public class ComplexComparatorTest extends ModelTestFunctions {
@@ -234,7 +235,7 @@ public class ComplexComparatorTest extends ModelTestFunctions {
complex1 = createComplex();
complex2 = createComplex();
- complex1.setStructuralState("str");
+ complex1.setStructuralState(new StructuralState());
assertTrue(comparator.compare(complex1, complex2) != 0);
assertTrue(comparator.compare(complex2, complex1) != 0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
index a0c3b2b7f33c0f0abb6c768e15fa319b812a18c3..60ab973e7c934441f314d70d278fe4ac67a54b76 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
@@ -12,8 +12,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.*;
public class ProteinComparatorTest extends ModelTestFunctions {
Logger logger = LogManager.getLogger(ProteinComparatorTest.class);
@@ -82,12 +81,6 @@ public class ProteinComparatorTest extends ModelTestFunctions {
assertTrue(comparator.compare(protein1, protein2) != 0);
assertTrue(comparator.compare(protein2, protein1) != 0);
- protein1 = createProtein();
- protein2 = createProtein();
- protein1.setStructuralState("a");
- assertTrue(comparator.compare(protein1, protein2) != 0);
- assertTrue(comparator.compare(protein2, protein1) != 0);
-
protein1 = createProtein();
protein2 = createProtein();
protein1.setHomodimer(1);
@@ -97,10 +90,21 @@ public class ProteinComparatorTest extends ModelTestFunctions {
assertTrue(comparator.compare(new GenericProtein(), new TruncatedProtein()) != 0);
}
+ @Test
+ public void testDifferentStructuralState() {
+ GenericProtein protein1 = createProtein();
+ GenericProtein protein2 = createProtein();
+ StructuralState str = new StructuralState();
+ str.setValue("STR");
+ protein1.setStructuralState(str);
+ assertTrue(comparator.compare(protein1, protein2) != 0);
+ assertTrue(comparator.compare(protein2, protein1) != 0);
+ }
+
public GenericProtein createProtein() {
GenericProtein result = new GenericProtein();
result.setHomodimer(12);
- result.setStructuralState("id1");
+ result.setStructuralState(new StructuralState());
result.setHypothetical(true);
Residue residue = new Residue();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
index 8fd69b5dc0fd41e7ad3ad682c3bd80fa22bd4094..cdef9115e03b119b77a00c0c72dd142b1198d366 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
@@ -12,8 +12,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.*;
public class ProteinTest extends ModelTestFunctions {
@@ -33,7 +32,7 @@ public class ProteinTest extends ModelTestFunctions {
@Test
public void testConstructor1() {
GenericProtein protein = new GenericProtein();
- protein.setStructuralState("srt");
+ protein.setStructuralState(new StructuralState());
List<ModificationResidue> residues = new ArrayList<>();
residues.add(new Residue());
@@ -45,10 +44,12 @@ public class ProteinTest extends ModelTestFunctions {
@Test
public void testSetStructuralState() {
GenericProtein protein = new GenericProtein();
- protein.setStructuralState("str");
- protein.setStructuralState("str1");
+ protein.setStructuralState(new StructuralState());
+ StructuralState str = new StructuralState();
+ str.setValue("str1");
+ protein.setStructuralState(str);
- assertEquals("str1", protein.getStructuralState());
+ assertEquals("str1", protein.getStructuralState().getValue());
}
@Test
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 8b56cec9646a576120bf18bf5212807300dab11e..f8a1a67c3bd28930db8c17856c65953a9bc34ef3 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -11,8 +11,7 @@ import org.apache.logging.log4j.Logger;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.*;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
@@ -338,7 +337,7 @@ public class ModelContructor {
if (species instanceof Protein) {
Protein protein = ((Protein) species);
if (protein.getStructuralState() == null) {
- protein.setStructuralState(state.getStructuralState());
+ protein.setStructuralState(createStructuralState(state, protein));
} else {
logger.warn(state.getWarningPrefix() + " tries to override another state: " + protein.getStructuralState());
}
@@ -350,6 +349,18 @@ public class ModelContructor {
}
}
+ private StructuralState createStructuralState(State state, Species species) {
+ Double x = state.getRelX() * species.getWidth() + species.getX();
+ Double y = state.getRelY() * species.getHeight() + species.getY();
+ StructuralState structuralState= new StructuralState();
+ structuralState.setPosition(new Point2D.Double(x, y));
+ structuralState.setFontSize(10);
+ structuralState.setHeight(state.getHeight());
+ structuralState.setWidth(state.getWidth());
+ structuralState.setValue(state.getStructuralState());
+ return structuralState;
+ }
+
/**
* {@link ModificationResidue} in element might have slightly off coordinates
* (due to different symbol shapes). For that we need to align them to match our
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index ea1b53f84105eaedb7ac7434cf36736d09c5b162..3d7e5bab20526882f1efbb274272ec131cc5fd85 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -351,11 +351,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
Protein protein = (Protein) model1.getElementsByName("Protein").get(0);
assertEquals(0, protein.getModificationResidues().size());
- assertEquals("GTP", protein.getStructuralState());
-
- Model model2 = serializeModelOverCellDesignerParser(model1);
-
- assertEquals(0, mc.compare(model1, model2));
+ assertNotNull(protein.getStructuralState());
}
}
diff --git a/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191022_2__structural_state_table.sql b/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191022_2__structural_state_table.sql
new file mode 100644
index 0000000000000000000000000000000000000000..65934bb21f0aaf2869528fef120c6682781b3d48
--- /dev/null
+++ b/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191022_2__structural_state_table.sql
@@ -0,0 +1,43 @@
+CREATE SEQUENCE structural_state_sequence
+ INCREMENT 1
+ MINVALUE 1
+ MAXVALUE 9223372036854775807
+ START 1
+ CACHE 1;
+
+CREATE TABLE structural_state_table
+(
+ id integer NOT NULL DEFAULT nextval('structural_state_sequence'::regclass),
+ value varchar NOT NULL,
+ position varchar NOT NULL,
+ width numeric(6,2) NOT NULL,
+ height numeric(6,2) NOT NULL,
+ font_size numeric(6,2) NOT NULL,
+ species_id integer NOT NULL,
+
+ CONSTRAINT structural_state_pk PRIMARY KEY (id),
+ CONSTRAINT structural_state_table_species_fk FOREIGN KEY (species_id)
+ REFERENCES element_table (id) MATCH SIMPLE
+ ON UPDATE NO ACTION ON DELETE NO ACTION
+)
+WITH (
+ OIDS=FALSE
+);
+
+alter table element_table add column structural_state_id integer;
+alter table element_table add constraint element_table_structural_state_fk FOREIGN KEY (structural_state_id)
+ REFERENCES structural_state_table (id) MATCH SIMPLE
+ ON UPDATE NO ACTION ON DELETE NO ACTION;
+
+insert into structural_state_table (position, width, height, value, font_size, species_id) select
+ concat(x+width/2-least(greatest(60, 60+4*(length(structural_state)-7)), width)/2,',', y-10), --position
+ least(greatest(60, 60+4*(length(structural_state)-7)), width), --width
+ 20, --height
+ structural_state, --state
+ 10, --font_size
+ id
+ from element_table where structural_state is not null;
+
+update element_table set structural_state_id = (select id from structural_state_table where species_id = element_table.id);
+
+alter table element_table drop column structural_state;
diff --git a/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191023__structural_state_table.sql b/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191023__structural_state_table.sql
new file mode 100644
index 0000000000000000000000000000000000000000..362a96dfab82c93cf4d37c2ee6c8218184b9d088
--- /dev/null
+++ b/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191023__structural_state_table.sql
@@ -0,0 +1 @@
+alter table structural_state_table alter column species_id drop not null;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
index 8baf0a46d567d91f0b8bd1e97a01750c3b978597..07056a49770ccc546a504d9c1f1dff720fba20dd 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementsRestImpl.java
@@ -225,7 +225,7 @@ public class ElementsRestImpl extends BaseRestImpl {
protected Map<String, Object> getOthersForElement(Element element) {
Map<String, Object> result = new TreeMap<>();
List<Map<String, Object>> modifications = new ArrayList<>();
- String structuralState = null;
+ StructuralState structuralState = null;
Map<String, Object> structures = new TreeMap<>();
if (element instanceof Protein) {
Protein protein = ((Protein) element);
@@ -234,21 +234,22 @@ public class ElementsRestImpl extends BaseRestImpl {
} else if (element instanceof Rna) {
Rna rna = ((Rna) element);
modifications = getModifications(rna.getRegions());
- structuralState = rna.getState();
} else if (element instanceof AntisenseRna) {
AntisenseRna antisenseRna = ((AntisenseRna) element);
modifications = getModifications(antisenseRna.getRegions());
- structuralState = antisenseRna.getState();
} else if (element instanceof Gene) {
Gene gene = ((Gene) element);
modifications = getModifications(gene.getModificationResidues());
- structuralState = gene.getState();
}
if (element instanceof Species) {
structures = getStructures(((Species) element).getUniprots());
}
result.put("modifications", modifications);
- result.put("structuralState", structuralState);
+ if (structuralState != null) {
+ result.put("structuralState", structuralState.getValue());
+ } else {
+ result.put("structuralState", null);
+ }
result.put("structures", structures);
return result;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index 13e2a706c13e6cb663a71e13403e77cc4e9d560c..c792b27de1d2e9f38a391ecd98b99dd0cef64101 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -82,7 +82,8 @@ public class ElementRestImplTest extends RestTestFunctions {
@SuppressWarnings("unchecked")
@Test
public void testGetModificationsForProtein() throws Exception {
- String state = "asd";
+ StructuralState state = new StructuralState();
+ state.setValue("asd");
GenericProtein protein = new GenericProtein("s1");
Residue mr = new Residue();
mr.setState(ModificationState.ACETYLATED);
@@ -91,7 +92,7 @@ public class ElementRestImplTest extends RestTestFunctions {
protein.setStructuralState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(protein);
assertNotNull(result.get("modifications"));
- assertEquals(state, result.get("structuralState"));
+ assertEquals(state.getValue(), result.get("structuralState"));
List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
assertEquals(1, modifications.size());
}
@@ -99,16 +100,14 @@ public class ElementRestImplTest extends RestTestFunctions {
@SuppressWarnings("unchecked")
@Test
public void testGetModificationsForRna() throws Exception {
- String state = "asd";
Rna rna = new Rna("s1");
ModificationSite mr = new ModificationSite();
mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
rna.addModificationSite(mr);
- rna.setState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(rna);
assertNotNull(result.get("modifications"));
- assertEquals(state, result.get("structuralState"));
+ assertEquals(null, result.get("structuralState"));
List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
assertEquals(1, modifications.size());
}
@@ -116,15 +115,13 @@ public class ElementRestImplTest extends RestTestFunctions {
@SuppressWarnings("unchecked")
@Test
public void testGetModificationsForAntisenseRna() throws Exception {
- String state = "asd";
AntisenseRna antisenseRna = new AntisenseRna("s1");
ModificationSite mr = new ModificationSite();
mr.setName("S250");
antisenseRna.addModificationSite(mr);
- antisenseRna.setState(state);
Map<String, Object> result = _elementsRestImpl.getOthersForElement(antisenseRna);
assertNotNull(result.get("modifications"));
- assertEquals(state, result.get("structuralState"));
+ assertEquals(null, result.get("structuralState"));
List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
assertEquals(1, modifications.size());
}