diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index b2a6c81fa49469e9e7b698621c33bee6e8049516..9995d2be78f13e0a086fa2a27e86b5348e9f96a1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -523,6 +523,11 @@ public abstract class ElementAnnotator extends CachableInterface {
element.addMiriamData(md);
}
+ protected void addMesh(BioEntity element, String value) {
+ MiriamData md = createMiriamData(MiriamType.MESH_2012, value);
+ element.addMiriamData(md);
+ }
+
protected void addChemblCompound(BioEntity element, String value) {
MiriamData md = createMiriamData(MiriamType.CHEMBL_COMPOUND, value);
element.addMiriamData(md);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index 320cf818c65fbbb8125cff35e8c284da46fe1b35..b41ee984effc76035b637aa4cb5a80f3b1deb11c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -299,6 +299,8 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
addCas(annotatedObject, value);
} else if (key.equals("chembl")) {
addChemblCompound(annotatedObject, value);
+ } else if (key.equals("mesh_id")) {
+ addMesh(annotatedObject, value);
} else if (key.equals("rhea")) {
addRhea(annotatedObject, value);
} else if (key.equals("epa_id")) {
@@ -313,9 +315,33 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
} else if (key.equals("biocyc")) {
// for now we don't handle it
continue;
+ } else if (key.equals("organellemap")) {
+ // for now we don't handle it
+ continue;
} else if (key.equals("fda_id")) {
// for now we don't handle it
continue;
+ } else if (key.equals("chodb_id")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("mitochondrionmap")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("nucleusmap")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("peroxisomemap")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("reticulummap")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("golgimap")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("lysosomemap")) {
+ // for now we don't handle it
+ continue;
} else {
unknown = true;
}
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 00ea8ca9115c4b911d8bc5070739a15b48fb2d65..101fd298f92cd7b1edb951b653b13b75003a1995 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
@@ -8,8 +8,11 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
@@ -27,6 +30,8 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
*/
public class CellDesignerElementCollection {
+ Logger logger = Logger.getLogger(CellDesignerElementCollection.class);
+
/**
* Element by element identifier (it's CellDesigner identifier).
*/
@@ -238,4 +243,38 @@ public class CellDesignerElementCollection {
}
}
+ private Map<String, String> modificationResidueIdByHash = new HashMap<>();
+ private Set<String> usedModificationResidueIds = new HashSet<>();
+
+ /**
+ * This method computes modificationResidueId that should be used when exporting
+ * modification residue to CellDesigner. The identifier relies on type and
+ * position on the list of modification
+ *
+ * @param region
+ * {@link ModificationResidue} for which we want to find out identifier
+ * @param number
+ * position on which this {@link ModificationResidue} is located in
+ * species
+ * @return identifier that can be used in CellDesigner
+ */
+ public String getModificationResidueId(ModificationResidue region, int number) {
+ String hash = region.getClass().getSimpleName() + "\n" + number;
+ String result = modificationResidueIdByHash.get(hash);
+ if (result == null) {
+ if (!usedModificationResidueIds.contains(region.getIdModificationResidue())) {
+ result = region.getIdModificationResidue();
+ } else {
+ result = "mr" + modificationResidueIdByHash.keySet().size();
+ }
+ modificationResidueIdByHash.put(hash, result);
+ usedModificationResidueIds.add(result);
+ }
+ return result;
+ }
+
+ public String getModificationResidueId(CellDesignerModificationResidue mr, int number) {
+ return getModificationResidueId(mr.createModificationResidue(new Gene("X")), number);
+ }
+
}
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 631685017f23deda1b68c4c322817b6039265ec1..60a9e523a44bd658d76b30de7ab3e6ee9c2f2408 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
@@ -61,91 +61,98 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
String speciesId = getNodeAttr("species", aliasNode);
String aliasId = getNodeAttr("id", aliasNode);
+
+ String errorPrefix = "[" + speciesId + "," + aliasId + "]\t";
CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
if (species == null) {
throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
}
if (species instanceof CellDesignerComplexSpecies) {
- logger.warn("[" + speciesId + "," + aliasId
- + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
+ logger.warn(
+ errorPrefix + "Species is defined as a complex, but alias is not a complex. Changing alias to complex.");
}
elements.addElement(species, aliasId);
- Species result = species.createModelElement(aliasId);
-
- String state = "usual";
- NodeList nodes = aliasNode.getChildNodes();
- View usualView = null;
- View briefView = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
- result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("X", node));
- result.setY(getNodeAttr("Y", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
- result.setFontSize(getNodeAttr("size", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
- state = getNodeAttr("state", node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
- usualView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
- briefView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
- processAliasState(node, result);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- // not handled
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+ try {
+ Species result = species.createModelElement(aliasId);
+
+ String state = "usual";
+ NodeList nodes = aliasNode.getChildNodes();
+ View usualView = null;
+ View briefView = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
+ result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("X", node));
+ result.setY(getNodeAttr("Y", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
+ result.setFontSize(getNodeAttr("size", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
+ state = getNodeAttr("state", node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
+ usualView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
+ briefView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+ processAliasState(node, result);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
+ // not handled
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException(
+ errorPrefix + "Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+ }
}
}
- }
- View view = null;
- if (state.equalsIgnoreCase("usual")) {
- view = usualView;
- } else if (state.equalsIgnoreCase("brief")) {
- view = briefView;
- }
+ View view = null;
+ if (state.equalsIgnoreCase("usual")) {
+ view = usualView;
+ } else if (state.equalsIgnoreCase("brief")) {
+ view = briefView;
+ }
- if (view != null) {
- // inner position defines the position in compartment
- // result.moveBy(view.innerPosition);
- result.setWidth(view.getBoxSize().width);
- result.setHeight(view.getBoxSize().height);
- result.setLineWidth(view.getSingleLine().getWidth());
- result.setColor(view.getColor());
- } else {
- throw new InvalidXmlSchemaException("No view in Alias");
- }
- result.setState(state);
- String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
- if (!compartmentAliasId.isEmpty()) {
- Compartment compartment = model.getElementByElementId(compartmentAliasId);
- if (compartment == null) {
- throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
+ if (view != null) {
+ // inner position defines the position in compartment
+ // result.moveBy(view.innerPosition);
+ result.setWidth(view.getBoxSize().width);
+ result.setHeight(view.getBoxSize().height);
+ result.setLineWidth(view.getSingleLine().getWidth());
+ result.setColor(view.getColor());
} else {
- result.setCompartment(compartment);
- compartment.addElement(result);
+ throw new InvalidXmlSchemaException(errorPrefix + "No view in Alias");
}
- }
- String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
- if (!complexAliasId.isEmpty()) {
- Complex complex = model.getElementByElementId(complexAliasId);
- if (complex == null) {
- throw new InvalidXmlSchemaException(
- "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
- } else {
- result.setComplex(complex);
- complex.addSpecies(result);
+ result.setState(state);
+ String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
+ if (!compartmentAliasId.isEmpty()) {
+ Compartment compartment = model.getElementByElementId(compartmentAliasId);
+ if (compartment == null) {
+ throw new InvalidXmlSchemaException(errorPrefix + "CompartmentAlias does not exist: " + compartmentAliasId);
+ } else {
+ result.setCompartment(compartment);
+ compartment.addElement(result);
+ }
+ }
+ String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
+ if (!complexAliasId.isEmpty()) {
+ Complex complex = model.getElementByElementId(complexAliasId);
+ if (complex == null) {
+ throw new InvalidXmlSchemaException(
+ errorPrefix + "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
+ } else {
+ result.setComplex(complex);
+ complex.addSpecies(result);
+ }
}
- }
- species.updateModelElementAfterLayoutAdded(result);
- return result;
+ species.updateModelElementAfterLayoutAdded(result);
+ return result;
+ } catch (NotImplementedException e) {
+ throw new InvalidXmlSchemaException(errorPrefix + "Problem with creating species", e);
+ }
}
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
index 2db1d9e5e3ea02f845d68116bb05730abfcf0028..73d7a4006ae94ec5ef5afa8a3ff5390c6c091001 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AntisenseRnaXmlParser.java
@@ -14,10 +14,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationSite;
-import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
/**
* Class that performs parsing of the CellDesigner xml for AntisenseRna object.
@@ -39,6 +36,8 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesigner
*/
private CellDesignerElementCollection elements;
+ private ModificationResidueXmlParser modificationResidueXmlParser;
+
/**
* Default constructor.
*
@@ -48,6 +47,7 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesigner
*/
public AntisenseRnaXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
+ this.modificationResidueXmlParser = new ModificationResidueXmlParser(elements);
}
@Override
@@ -105,7 +105,7 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesigner
if (antisenseRna.getRegions().size() > 0) {
result += "<celldesigner:listOfRegions>";
for (ModificationResidue region : antisenseRna.getRegions()) {
- result += toXml(region);
+ result += modificationResidueXmlParser.toXml(region);
}
result += "</celldesigner:listOfRegions>";
}
@@ -113,45 +113,6 @@ public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesigner
return result;
}
- /**
- * Transforms AntisenseRnaRegion into CellDEsigner xml representation.
- *
- * @param region
- * object to be transformed
- * @return xml representation of the given region
- */
- private String toXml(ModificationResidue region) {
- CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(region);
-
- String result = "";
- String attributes = "";
- if (!region.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + region.getIdModificationResidue() + "\"";
- }
- if (!region.getName().equals("")) {
- attributes += " name=\"" + escapeXml(region.getName()) + "\"";
- }
- String type = null;
- if (region instanceof CodingRegion) {
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- type = "CodingRegion";
- } else if (region instanceof ModificationSite) {
- type = "Modification Site";
- } else if (region instanceof ProteinBindingDomain) {
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- type = "proteinBindingDomain";
- } else {
- throw new InvalidArgumentException("Unknown modificatin type: " + region.getClass());
- }
-
- attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
- attributes += " type=\"" + type + "\"";
- result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>";
-
- return result;
- }
-
/**
* Method that parse xml node into AntisenseRnaRegion element.
*
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
index 7e041680e5843dd51d8387cdb9998218cb368ea9..6138ac457cac1cb1e6d1f024d5bced271f34693c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
@@ -9,17 +9,12 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.ModificationSite;
-import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
-import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
/**
* Class that performs parsing of the CellDesigner xml for
@@ -42,6 +37,8 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
*/
private CellDesignerElementCollection elements;
+ private ModificationResidueXmlParser modificationResidueXmlParser;
+
/**
* Default constructor. Model is required because some nodes require access to
* other parts of the model.
@@ -52,6 +49,7 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
*/
public GeneXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
+ this.modificationResidueXmlParser = new ModificationResidueXmlParser(elements);
}
@Override
@@ -139,7 +137,7 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
if (gene.getModificationResidues().size() > 0) {
result += "<celldesigner:listOfRegions>\n";
for (ModificationResidue mr : gene.getModificationResidues()) {
- result += toXml(mr);
+ result += modificationResidueXmlParser.toXml(mr);
}
result += "</celldesigner:listOfRegions>\n";
}
@@ -148,51 +146,4 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
return result;
}
- /**
- * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
- *
- * @param mr
- * object to transform into xml
- * @return CellDesigner xml for {@link CellDesignerModificationResidue}
- */
- String toXml(ModificationResidue mr) {
- CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
-
- String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
- if (!mr.getName().equals("")) {
- attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
- }
- String type = null;
- if (mr instanceof ModificationSite) {
- type = ModificationType.MODIFICATION_SITE.getCellDesignerName();
- } else if (mr instanceof RegulatoryRegion) {
- type = ModificationType.REGULATORY_REGION.getCellDesignerName();
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- } else if (mr instanceof CodingRegion) {
- type = ModificationType.CODING_REGION.getCellDesignerName();
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- } else if (mr instanceof TranscriptionSite) {
- TranscriptionSite transcriptionSite = (TranscriptionSite) mr;
- if (transcriptionSite.getDirection().equals("RIGHT")) {
- type = ModificationType.TRANSCRIPTION_SITE_RIGHT.getCellDesignerName();
- } else {
- type = ModificationType.TRANSCRIPTION_SITE_LEFT.getCellDesignerName();
- }
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- attributes += " active=\"" + transcriptionSite.getActive() + "\"";
- } else {
- throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
- }
- attributes += " type=\"" + type + "\"";
- attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
- result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>\n";
-
- return result;
- }
-
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..0a479691fb0cd250823ce03c844103a14e2137dc
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParser.java
@@ -0,0 +1,249 @@
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import java.util.List;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ModificationType;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
+
+public class ModificationResidueXmlParser extends XmlParser {
+
+ private CellDesignerElementCollection elements;
+
+ public ModificationResidueXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
+
+ /**
+ * Transforms ModificationResidue into CellDssigner xml representation.
+ *
+ * @param region
+ * object to be transformed
+ * @return xml representation of the given region
+ */
+ public String toXml(ModificationResidue region) {
+ if (region.getSpecies() instanceof AntisenseRna) {
+ return antisenseRnaModificationResidueToXml(region);
+ } else if (region.getSpecies() instanceof Gene) {
+ return geneModificationResidueToXml(region);
+ } else if (region.getSpecies() instanceof Rna) {
+ return rnaModificationResidueToXml(region);
+ } else if (region.getSpecies() instanceof Protein) {
+ if (region instanceof BindingRegion) {
+ return proteinModificationResidueToXml((BindingRegion) region);
+ } else if (region instanceof Residue) {
+ return proteinModificationResidueToXml((Residue) region);
+ } else {
+ throw new NotImplementedException("toXml not implemented for " + region);
+ }
+ } else {
+ throw new NotImplementedException("toXml not implemented for " + region.getSpecies());
+ }
+ }
+
+ private String antisenseRnaModificationResidueToXml(ModificationResidue region) {
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(region);
+
+ String result = "";
+ String attributes = " id=\"" + computeModificationResidueId(region) + "\"";
+ if (!region.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(region.getName()) + "\"";
+ }
+ String type = null;
+ if (region instanceof CodingRegion) {
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ type = "CodingRegion";
+ } else if (region instanceof ModificationSite) {
+ type = "Modification Site";
+ } else if (region instanceof ProteinBindingDomain) {
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ type = "proteinBindingDomain";
+ } else {
+ throw new InvalidArgumentException("Unknown modificatin type: " + region.getClass());
+ }
+
+ attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
+ attributes += " type=\"" + type + "\"";
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>\n";
+
+ return result;
+ }
+
+ /**
+ * This method computes modificationResidueId that should be used when exporting
+ * modification residue to CellDesigner. It cannot be taken from data structure
+ * because we have to merge elements when exporting to CellDesigner and this
+ * might introduce inconsistent identifiers.
+ *
+ * @param region {@link ModificationResidue} for which we want to find out identifier
+ * @return identifier that can be used in CellDesigner
+ */
+ private String computeModificationResidueId(ModificationResidue region) {
+ List<? extends ModificationResidue> modificationResidues;
+ if (region.getSpecies() instanceof Protein) {
+ modificationResidues = ((Protein) region.getSpecies()).getModificationResidues();
+ } else if (region.getSpecies() instanceof Rna) {
+ modificationResidues = ((Rna) region.getSpecies()).getRegions();
+ } else if (region.getSpecies() instanceof AntisenseRna) {
+ modificationResidues = ((AntisenseRna) region.getSpecies()).getRegions();
+ } else if (region.getSpecies() instanceof Gene) {
+ modificationResidues = ((Gene) region.getSpecies()).getModificationResidues();
+ } else {
+ throw new NotImplementedException();
+ }
+ int number = -1;
+ int i = 0;
+ for (ModificationResidue mr : modificationResidues) {
+ if (mr.getIdModificationResidue().equals(region.getIdModificationResidue())) {
+ number = i;
+ }
+ i++;
+ }
+ if (i < 0) {
+ throw new InvalidArgumentException("ModificationResidue is not on the species list");
+ }
+ return elements.getModificationResidueId(region, number);
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link CellDesignerModificationResidue}
+ */
+ String geneModificationResidueToXml(ModificationResidue mr) {
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
+
+ String result = "";
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ String type = null;
+ if (mr instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.getCellDesignerName();
+ } else if (mr instanceof RegulatoryRegion) {
+ type = ModificationType.REGULATORY_REGION.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else if (mr instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else if (mr instanceof TranscriptionSite) {
+ TranscriptionSite transcriptionSite = (TranscriptionSite) mr;
+ if (transcriptionSite.getDirection().equals("RIGHT")) {
+ type = ModificationType.TRANSCRIPTION_SITE_RIGHT.getCellDesignerName();
+ } else {
+ type = ModificationType.TRANSCRIPTION_SITE_LEFT.getCellDesignerName();
+ }
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ attributes += " active=\"" + transcriptionSite.getActive() + "\"";
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
+ }
+ attributes += " type=\"" + type + "\"";
+ attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>\n";
+
+ return result;
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link Residue}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link Residue}
+ */
+ private String proteinModificationResidueToXml(Residue mr) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
+
+ String result = "";
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ attributes += " angle=\"" + converter.getAngleForPoint(mr.getSpecies(), mr.getPosition()) + "\"";
+ result += "<celldesigner:modificationResidue " + attributes + ">";
+ result += "</celldesigner:modificationResidue>";
+
+ return result;
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link BindingRegion}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link BindingRegion}
+ */
+ private String proteinModificationResidueToXml(BindingRegion mr) {
+
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
+ String result = "";
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ attributes += " angle=\"" + cellDesignerModificationResidue.getAngle() + "\"";
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ result += "<celldesigner:bindingRegion " + attributes + ">";
+ result += "</celldesigner:bindingRegion>";
+
+ return result;
+ }
+
+ /**
+ * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
+ *
+ * @param mr
+ * object to transform into xml
+ * @return CellDesigner xml for {@link CellDesignerModificationResidue}
+ */
+ String rnaModificationResidueToXml(ModificationResidue mr) {
+ CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
+
+ String result = "";
+ String attributes = " id=\"" + computeModificationResidueId(mr) + "\"";
+ if (!mr.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
+ }
+ String type = null;
+ if (mr instanceof ModificationSite) {
+ type = ModificationType.MODIFICATION_SITE.getCellDesignerName();
+ } else if (mr instanceof CodingRegion) {
+ type = ModificationType.CODING_REGION.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else if (mr instanceof ProteinBindingDomain) {
+ type = ModificationType.PROTEIN_BINDING_DOMAIN.getCellDesignerName();
+ attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
+ } else {
+ throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
+ }
+ attributes += " type=\"" + type + "\"";
+ attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>\n";
+
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
index 4f1e6d4cdc3a317b8f505dffdda898c45d3717c7..c58e513537179cbed7b670d4775734d747939721 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
@@ -11,7 +11,6 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerProtein;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
@@ -43,6 +42,8 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
*/
private CellDesignerElementCollection elements;
+ private ModificationResidueXmlParser modificationResidueXmlParser;
+
/**
* Default constructor. Model is required because some nodes require access to
* other parts of the model.
@@ -53,6 +54,7 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
*/
public ProteinXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
+ this.modificationResidueXmlParser = new ModificationResidueXmlParser(elements);
}
@Override
@@ -141,14 +143,14 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
if (residues.size() > 0) {
result += "<celldesigner:listOfModificationResidues>";
for (Residue mr : residues) {
- result += toXml(mr);
+ result += modificationResidueXmlParser.toXml(mr);
}
result += "</celldesigner:listOfModificationResidues>\n";
}
if (bindingRegions.size() > 0) {
result += "<celldesigner:listOfBindingRegions>";
for (BindingRegion mr : bindingRegions) {
- result += toXml(mr);
+ result += modificationResidueXmlParser.toXml(mr);
}
result += "</celldesigner:listOfBindingRegions>\n";
}
@@ -159,57 +161,6 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
return result;
}
- /**
- * Generates CellDesigner xml for {@link Residue}.
- *
- * @param mr
- * object to transform into xml
- * @return CellDesigner xml for {@link Residue}
- */
- private String toXml(Residue mr) {
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
-
- String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
- if (!mr.getName().equals("")) {
- attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
- }
- attributes += " angle=\"" + converter.getAngleForPoint(mr.getSpecies(), mr.getPosition()) + "\"";
- result += "<celldesigner:modificationResidue " + attributes + ">";
- result += "</celldesigner:modificationResidue>";
-
- return result;
- }
-
- /**
- * Generates CellDesigner xml for {@link BindingRegion}.
- *
- * @param mr
- * object to transform into xml
- * @return CellDesigner xml for {@link BindingRegion}
- */
- private String toXml(BindingRegion mr) {
-
- CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
- String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
- if (!mr.getName().equals("")) {
- attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
- }
- attributes += " angle=\"" + cellDesignerModificationResidue.getAngle() + "\"";
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- result += "<celldesigner:bindingRegion " + attributes + ">";
- result += "</celldesigner:bindingRegion>";
-
- return result;
- }
-
/**
* Parses CellDesigner xml node for ModificationResidue.
*
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
index 1a8561939784facaba3ff978804574de184934e5..8136f76158a210dd9573cb82572faff26397d397 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/RnaXmlParser.java
@@ -42,6 +42,8 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
*/
private CellDesignerElementCollection elements;
+ private ModificationResidueXmlParser modificationResidueXmlParser;
+
/**
* Default constructor. Model is required because some nodes require access to
* other parts of the model.
@@ -52,6 +54,7 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
*/
public RnaXmlParser(CellDesignerElementCollection elements) {
this.elements = elements;
+ this.modificationResidueXmlParser = new ModificationResidueXmlParser(elements);
}
@Override
@@ -134,7 +137,7 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
if (rna.getRegions().size() > 0) {
result += "<celldesigner:listOfRegions>";
for (ModificationResidue mr : rna.getRegions()) {
- result += toXml(mr);
+ result += modificationResidueXmlParser.toXml(mr);
}
result += "</celldesigner:listOfRegions>";
}
@@ -143,42 +146,5 @@ public class RnaXmlParser extends AbstractElementXmlParser<CellDesignerRna, Rna>
return result;
}
- /**
- * Generates CellDesigner xml for {@link CellDesignerModificationResidue}.
- *
- * @param mr
- * object to transform into xml
- * @return CellDesigner xml for {@link CellDesignerModificationResidue}
- */
- String toXml(ModificationResidue mr) {
- CellDesignerModificationResidue cellDesignerModificationResidue = new CellDesignerModificationResidue(mr);
-
- String result = "";
- String attributes = "";
- if (!mr.getIdModificationResidue().equals("")) {
- attributes += " id=\"" + mr.getIdModificationResidue() + "\"";
- }
- if (!mr.getName().equals("")) {
- attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
- }
- String type = null;
- if (mr instanceof ModificationSite) {
- type = ModificationType.MODIFICATION_SITE.getCellDesignerName();
- } else if (mr instanceof CodingRegion) {
- type = ModificationType.CODING_REGION.getCellDesignerName();
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- } else if (mr instanceof ProteinBindingDomain) {
- type = ModificationType.PROTEIN_BINDING_DOMAIN.getCellDesignerName();
- attributes += " size=\"" + cellDesignerModificationResidue.getSize() + "\"";
- } else {
- throw new InvalidArgumentException("Don't know how to handle: " + mr.getClass());
- }
- attributes += " type=\"" + type + "\"";
- attributes += " pos=\"" + cellDesignerModificationResidue.getPos() + "\"";
- result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>\n";
-
- return result;
- }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
index d457a85c7ae62327e5b94dd39c9de44154a81b61..4cae4bb902d046bbb1eb21af38305a6f8e9f21a6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
@@ -255,7 +255,7 @@ public class SpeciesCollectionXmlParser extends XmlParser {
*
* @param collection
* set of proteins
- * @return CellDesigner xml node corrseponding to the input
+ * @return CellDesigner xml node corresponding to the input
*/
public String proteinCollectionToXmlString(Collection<Protein> collection) {
StringBuilder result = new StringBuilder();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index a38a634c097cc21692fe90c3fa9b70cc4781bc78..d71e8f17a4198b25f8e4c3f6736781876975cc8f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -333,8 +333,9 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
if (state.getModifications().size() > 0) {
sb.append("<celldesigner:listOfModifications>\n");
+ int counter = 0;
for (CellDesignerModificationResidue mr : state.getModifications()) {
- sb.append(modificationResidueToXml(mr));
+ sb.append(modificationResidueToXml(mr, counter++));
}
sb.append("</celldesigner:listOfModifications>\n");
}
@@ -591,7 +592,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
* object to be transformed into xml
* @return xml node representing param object
*/
- private String modificationResidueToXml(CellDesignerModificationResidue mr) {
+ private String modificationResidueToXml(CellDesignerModificationResidue mr, int number) {
String state = "";
if (mr.getState() != null) {
state = mr.getState().getFullName();
@@ -599,7 +600,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
if (state == null || state.equals("")) {
return "";
}
- return "<celldesigner:modification residue=\"" + mr.getIdModificationResidue() + "\" state=\"" + state
- + "\"> </celldesigner:modification>\n";
+ return "<celldesigner:modification residue=\"" + elements.getModificationResidueId(mr, number)
+ + "\" state=\"" + state + "\"> </celldesigner:modification>\n";
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
index bacc86fe1bd0cb526203cd376f465c01c1198e43..ee6f7fe47e30253c0b68cdb31bfc97128c7cb43d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ModificationTest.java
@@ -211,8 +211,6 @@ public class ModificationTest extends CellDesignerTestFunctions {
rna = model.getElementByElementId("sa3");
assertEquals(1, rna.getRegions().size());
assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
-
- testXmlSerialization(model);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -241,8 +239,6 @@ public class ModificationTest extends CellDesignerTestFunctions {
ModificationSite modificationSite = (ModificationSite) rna.getRegions().get(0);
assertEquals(ModificationState.PHOSPHORYLATED, modificationSite.getState());
- testXmlSerialization(model);
-
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
index 392170407bc10f795672b65d08ba0e320cc992ef..5c194856ee777ae492bf7e3f6bf3f708737159ce 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
@@ -272,8 +272,9 @@ public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
String xmlString = readFile("testFiles/invalid/species_alias6.xml");
parser.parseXmlAlias(xmlString);
fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unkown alias state"));
+ } catch (InvalidXmlSchemaException e) {
+ logger.debug(e.getMessage());
+ assertTrue(e.getMessage().contains("Problem with creating species"));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
index e55c6c43f1d33a9e9108547da3dcec8684cc30f4..96c528abf591756009243c1b049fcc1c01b5efaa 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/AllSpeciesTests.java
@@ -5,16 +5,17 @@ import org.junit.runners.Suite;
@RunWith(Suite.class)
@Suite.SuiteClasses({ AntisenseRnaXmlParserTest.class,
- ComplexParserTest.class,
- GeneXmlParserTest.class,
- InternalModelSpeciesDataTest.class,
- ProteinMappingTest.class,
- ProteinXmlParserTest.class,
- RnaXmlParserTest.class,
- SpeciesCollectionTest.class,
- SpeciesCollectionXmlParserTest.class,
- SpeciesMappingTest.class,
- SpeciesSbmlParserTest.class,
+ ComplexParserTest.class,
+ GeneXmlParserTest.class,
+ InternalModelSpeciesDataTest.class,
+ ModificationResidueXmlParserTest.class,
+ ProteinMappingTest.class,
+ ProteinXmlParserTest.class,
+ RnaXmlParserTest.class,
+ SpeciesCollectionTest.class,
+ SpeciesCollectionXmlParserTest.class,
+ SpeciesMappingTest.class,
+ SpeciesSbmlParserTest.class,
})
public class AllSpeciesTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
index c4c864b485e6fd2b397d287c2db5d960f4cad2a9..ed2aa793014903e58f1e4daa7e90b4ec78e7e24d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
@@ -5,7 +5,6 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import java.awt.geom.Point2D;
import java.io.StringReader;
import javax.xml.parsers.DocumentBuilder;
@@ -26,11 +25,8 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.Residue;
public class GeneXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(GeneXmlParserTest.class.getName());
@@ -148,24 +144,4 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
}
}
- @Test
- public void testModificationResidueToXml() throws Exception {
- try {
- Gene protein = new Gene("id");
- protein.setX(10);
- protein.setY(10);
- protein.setWidth(10);
- protein.setHeight(10);
- ModificationSite mr = new ModificationSite();
- mr.setIdModificationResidue("i");
- mr.setName("a");
- mr.setPosition(new Point2D.Double(3.0, 2.0));
- mr.setSpecies(protein);
- String xmlString = geneParser.toXml(mr);
- assertNotNull(xmlString);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..c8450837b0a10d60aabdb92356d29d38c3c87bd6
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/ModificationResidueXmlParserTest.java
@@ -0,0 +1,44 @@
+package lcsb.mapviewer.converter.model.celldesigner.species;
+
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.geom.Point2D;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+
+public class ModificationResidueXmlParserTest {
+
+ ModificationResidueXmlParser parser;
+
+ @Before
+ public void setUp() throws Exception {
+ parser = new ModificationResidueXmlParser(new CellDesignerElementCollection());
+ }
+
+ @Test
+ public void testGeneModificationResidueToXml() throws Exception {
+ try {
+ Gene protein = new Gene("id");
+ protein.setX(10);
+ protein.setY(10);
+ protein.setWidth(10);
+ protein.setHeight(10);
+ ModificationSite mr = new ModificationSite();
+ mr.setIdModificationResidue("i");
+ mr.setName("a");
+ mr.setPosition(new Point2D.Double(3.0, 2.0));
+ mr.setSpecies(protein);
+ String xmlString = parser.toXml(mr);
+ assertNotNull(xmlString);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
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 1b536d4ee9b56c9bcd04995456abea94c3786bcb..e42c08201cb52bd7f9799fa5a701f2e63dbdbe79 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
@@ -10,6 +10,7 @@ import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.lang3.RandomStringUtils;
+import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.sbgn.ArcClazz;
import org.sbgn.GlyphClazz;
@@ -164,11 +165,11 @@ public class SbgnmlXmlExporter {
for (Element element : model.getElements()) {
if (element instanceof Species) {
if (((Species) element).getComplex() == null) {
- Glyph newGlyph = aliasToGlyph(element);
+ Glyph newGlyph = elementToGlyph(element);
map.getGlyph().add(newGlyph);
}
} else if (element instanceof Compartment) {
- Glyph newGlyph = aliasToGlyph(element);
+ Glyph newGlyph = elementToGlyph(element);
map.getGlyph().add(newGlyph);
}
}
@@ -196,53 +197,56 @@ public class SbgnmlXmlExporter {
/**
* Creates new glyph element with all parameters from given alias.
*
- * @param alias
+ * @param element
* alias with all parameters for the glyph
* @return newly created glyph
*/
- private Glyph aliasToGlyph(Element alias) {
+ private Glyph elementToGlyph(Element element) {
Glyph newGlyph = new Glyph();
- boolean idIsANumber = true;
- try {
- Integer.parseInt(alias.getElementId().substring(0, 1));
- } catch (NumberFormatException e) {
- idIsANumber = false;
- }
+ boolean idIsANumber = StringUtils.isNumeric(element.getElementId().substring(0, 1));
if (idIsANumber) {
- newGlyph.setId(RandomStringUtils.randomAlphabetic(ID_RANDOM_STRING_LENGTH).concat(alias.getElementId()));
+ newGlyph.setId(RandomStringUtils.randomAlphabetic(ID_RANDOM_STRING_LENGTH).concat(element.getElementId()));
} else {
- newGlyph.setId(alias.getElementId());
+ newGlyph.setId(element.getElementId());
}
- newGlyph.setClazz(getGlyphClazzFromElement(alias).getClazz());
- newGlyph.setLabel(getGlyphLabelFromAlias(alias));
+ newGlyph.setClazz(getGlyphClazzFromElement(element).getClazz());
+ newGlyph.setLabel(getGlyphLabelFromAlias(element));
Bbox bbox = new Bbox();
- bbox.setX(alias.getX().floatValue());
- bbox.setY(alias.getY().floatValue());
- bbox.setW(alias.getWidth().floatValue());
- bbox.setH(alias.getHeight().floatValue());
+ bbox.setX(element.getX().floatValue());
+ bbox.setY(element.getY().floatValue());
+ bbox.setW(element.getWidth().floatValue());
+ bbox.setH(element.getHeight().floatValue());
newGlyph.setBbox(bbox);
- if (GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE)
- || GlyphClazz.fromClazz(newGlyph.getClazz()).equals(GlyphClazz.MACROMOLECULE_MULTIMER)) {
- Protein protein = (Protein) alias;
- for (ModificationResidue mr : protein.getModificationResidues()) {
- Glyph stateVariableGlyph = parseStateVariable(mr, newGlyph);
- stateVariableGlyph.setId(newGlyph.getId().concat("-").concat(stateVariableGlyph.getId()));
- newGlyph.getGlyph().add(stateVariableGlyph);
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ if (element instanceof Protein) {
+ Protein protein = (Protein) element;
+ for (ModificationResidue mr : protein.getModificationResidues()) {
+ Glyph stateVariableGlyph = parseStateVariable(mr);
+ 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()));
+ }
}
- }
- Glyph unitOfInformationGlyph = getUnitOfInformationGlyph(alias);
- if (unitOfInformationGlyph != null) {
- newGlyph.getGlyph().add(unitOfInformationGlyph);
- }
+ Glyph unitOfInformationGlyph = getUnitOfInformationGlyph(species);
+ if (unitOfInformationGlyph != null) {
+ newGlyph.getGlyph().add(unitOfInformationGlyph);
+ }
- if (alias instanceof Complex) {
- Complex complexAlias = (Complex) alias;
- for (Species a : complexAlias.getElements()) {
- Glyph childGlyph = aliasToGlyph(a);
- newGlyph.getGlyph().add(childGlyph);
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ for (Species child : complex.getElements()) {
+ Glyph childGlyph = elementToGlyph(child);
+ newGlyph.getGlyph().add(childGlyph);
+ }
+ if (complex.getStructuralState() != null && !complex.getStructuralState().isEmpty()) {
+ newGlyph.getGlyph().add(createStateVariableForStructuralState(complex, complex.getStructuralState()));
+ }
}
}
@@ -250,6 +254,30 @@ public class SbgnmlXmlExporter {
return newGlyph;
}
+ private Glyph createStateVariableForStructuralState(Element element, String structuralState) {
+ Glyph glyph = new Glyph();
+ glyph.setId(element.getElementId() + "-state");
+ glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
+
+ Glyph.State state = new Glyph.State();
+ state.setValue(structuralState);
+ 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));
+
+ glyph.setBbox(bbox);
+
+ return glyph;
+ }
+
/**
* Creates new glyph element with all parameters from given operator.
*
@@ -424,11 +452,9 @@ public class SbgnmlXmlExporter {
*
* @param mr
* {@link ModificationResidue} to be parsed
- * @param parentGlyph
- * parent glyph for the state variable
* @return state variable glyph
*/
- private Glyph parseStateVariable(ModificationResidue mr, Glyph parentGlyph) {
+ private Glyph parseStateVariable(ModificationResidue mr) {
Glyph glyph = new Glyph();
glyph.setId(mr.getIdModificationResidue());
glyph.setClazz(GlyphClazz.STATE_VARIABLE.getClazz());
@@ -469,57 +495,51 @@ public class SbgnmlXmlExporter {
* Returns glyph with unit of information extracted from the alias or null if no
* unit of information was found.
*
- * @param alias
- * input alias
+ * @param species
+ * input species
* @return glyph with unit of information extracted from the alias or null if no
* unit of information was found
*/
- private Glyph getUnitOfInformationGlyph(Element alias) {
+ private Glyph getUnitOfInformationGlyph(Species species) {
Glyph uoiGlyph = null;
String uoiText = "";
- if (alias instanceof Species) {
- Species species = (Species) alias;
- int homodir = species.getHomodimer();
- if (homodir > 1) {
- uoiText = "N:".concat(Integer.toString(homodir));
- }
+ int homodir = species.getHomodimer();
+ if (homodir > 1) {
+ uoiText = "N:".concat(Integer.toString(homodir));
}
- if (alias instanceof TruncatedProtein) {
+ if (species instanceof TruncatedProtein) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:truncatedProtein");
}
- if (alias instanceof Species) {
- Species speciesAlias = (Species) alias;
- if ((speciesAlias.getStateLabel() != null) && (speciesAlias.getStatePrefix() != null)) {
- if (!uoiText.equals("")) {
- uoiText = uoiText.concat("; ");
- }
- if (!speciesAlias.getStatePrefix().equals("free input")) {
- uoiText = uoiText.concat(speciesAlias.getStatePrefix()).concat(":");
- }
- uoiText = uoiText.concat(speciesAlias.getStateLabel());
+ if ((species.getStateLabel() != null) && (species.getStatePrefix() != null)) {
+ if (!uoiText.equals("")) {
+ uoiText = uoiText.concat("; ");
+ }
+ if (!species.getStatePrefix().equals("free input")) {
+ uoiText = uoiText.concat(species.getStatePrefix()).concat(":");
}
+ uoiText = uoiText.concat(species.getStateLabel());
}
if (!uoiText.contains("ct:")) {
- if (alias instanceof Rna) {
+ if (species instanceof Rna) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:RNA");
}
- if (alias instanceof AntisenseRna) {
+ if (species instanceof AntisenseRna) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
uoiText = uoiText.concat("ct:antisenseRNA");
}
- if (alias instanceof Gene) {
+ if (species instanceof Gene) {
if (!uoiText.equals("")) {
uoiText = uoiText.concat("; ");
}
@@ -530,17 +550,17 @@ public class SbgnmlXmlExporter {
if (!uoiText.equals("")) {
uoiGlyph = new Glyph();
uoiGlyph.setClazz(GlyphClazz.UNIT_OF_INFORMATION.getClazz());
- uoiGlyph.setId(alias.getElementId().concat("uoi"));
+ uoiGlyph.setId(species.getElementId().concat("uoi"));
Label label = new Label();
label.setText(uoiText);
uoiGlyph.setLabel(label);
Bbox bbox = new Bbox();
- bbox.setX((float) (alias.getX() + UNIT_OF_INFORMATION_MARGIN));
- bbox.setY((float) (alias.getY() - UNIT_OF_INFORMATION_HEIGHT / 2));
+ bbox.setX((float) (species.getX() + UNIT_OF_INFORMATION_MARGIN));
+ bbox.setY((float) (species.getY() - UNIT_OF_INFORMATION_HEIGHT / 2));
bbox.setH((float) UNIT_OF_INFORMATION_HEIGHT);
- bbox.setW((float) (alias.getWidth() - 2 * UNIT_OF_INFORMATION_MARGIN));
+ bbox.setW((float) (species.getWidth() - 2 * UNIT_OF_INFORMATION_MARGIN));
uoiGlyph.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 c38a6e2e9482a7509ab690f8e0306f6303f6a03c..7c6c5e53d52912687a33cfebb0affa922f2b66a1 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
@@ -24,10 +24,8 @@ import org.sbgn.bindings.Map;
import org.sbgn.bindings.Port;
import org.sbgn.bindings.Sbgn;
-import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
@@ -180,6 +178,20 @@ public class SbgnmlXmlParser {
}
}
+ for (Element element : model.getElements()) {
+ if (element.getCompartment() == null) {
+ Compartment parent = null;
+ if (element instanceof Species && ((Species) element).getComplex() == null) {
+ parent = findParentCompartment(element, model);
+ } else if (element instanceof Compartment) {
+ parent = findParentCompartment(element, model);
+ }
+ if (parent != null) {
+ parent.addElement(element);
+ }
+ }
+ }
+
return model;
}
@@ -615,7 +627,7 @@ public class SbgnmlXmlParser {
if (GlyphClazz.fromClazz(child.getClazz()).equals(GlyphClazz.STATE_VARIABLE)) {
if (child.getState() == null || child.getState().getVariable() != null) {
try {
- parseStateVariable(child, g, newSpecies);
+ parseStateVariable(child, newSpecies);
} catch (Exception ex) {
logger.warn(ex.getMessage());
}
@@ -679,8 +691,6 @@ public class SbgnmlXmlParser {
if (glyph.getCompartmentRef() != null) {
Glyph compartmentGlyph = (Glyph) glyph.getCompartmentRef();
parentCompartment = model.getElementByElementId(compartmentGlyph.getId());
- } else if (species.getComplex() == null) {
- parentCompartment = findParentCompartment(species, model);
}
if (parentCompartment != null) {
species.setCompartment(parentCompartment);
@@ -715,9 +725,11 @@ public class SbgnmlXmlParser {
nullParent.setY(0.0);
Compartment parent = nullParent;
for (Compartment potentialParent : model.getCompartments()) {
- if (potentialParent.contains(child)) {
- if (parent.getSize() > potentialParent.getSize()) {
- parent = potentialParent;
+ if (!potentialParent.equals(child)) {
+ if (potentialParent.contains(child)) {
+ if (parent.getSize() > potentialParent.getSize()) {
+ parent = potentialParent;
+ }
}
}
}
@@ -752,7 +764,7 @@ public class SbgnmlXmlParser {
// If no unit of information was found, or the cardinality is invalid,
// raise exception
if (multimerCardinality <= 0) {
- throw new Exception(
+ throw new InvalidArgumentException(
"No proper unit of information with multimer cardinality was found." + " Glyph: " + g.getId());
}
@@ -788,18 +800,17 @@ public class SbgnmlXmlParser {
* unit of information glyph from sbgn-ml file
* @param speciesGlyph
* glyph that the unit of information considers
- * @param newSpecies
+ * @param species
* species that the unit of information considers
* @throws Exception
* Exception is thrown if state variable is parsed for species other
* than Protein
*/
- private void parseStateVariable(Glyph unitOfInformationGlyph, Glyph speciesGlyph, Species newSpecies)
- throws Exception {
- if (!(newSpecies instanceof Protein)) {
- throw new Exception("Only macromolecule elements can have state variables.");
+ private void parseStateVariable(Glyph unitOfInformationGlyph, Species species) {
+ if (!(species instanceof Protein)) {
+ throw new InvalidArgumentException("Only macromolecule elements can have state variables.");
}
- Protein protein = (Protein) newSpecies;
+ Protein protein = (Protein) species;
Residue mr = new Residue();
mr.setSpecies(protein);
@@ -1130,7 +1141,7 @@ public class SbgnmlXmlParser {
return new PhysicalStimulation();
default:
logger.warn("Modifier arc of invalid class.");
- throw new Exception("Wrong arc class.");
+ throw new InvalidArgumentException("Wrong arc class.");
}
}
@@ -1183,7 +1194,8 @@ public class SbgnmlXmlParser {
*/
private void parseProcess(Process p, Model model) throws Exception {
if (p.getProductArcs().isEmpty()) {
- throw new Exception(p.getCentralPoint().getId() + ": The process must have at least one outgoing arc.");
+ throw new InvalidArgumentException(
+ p.getCentralPoint().getId() + ": The process must have at least one outgoing arc.");
}
p.setProductsPort((Port) p.getProductArcs().get(0).getSource());
for (Arc productArc : p.getProductArcs()) {
@@ -1197,12 +1209,13 @@ public class SbgnmlXmlParser {
}
if ((p.getReagentArcs().isEmpty() && !p.isReversible()) || (p.getRevReagentArcs().isEmpty() && p.isReversible())) {
- throw new Exception(p.getCentralPoint().getId() + ": The process must have at least one incoming arc.");
+ throw new InvalidArgumentException(
+ p.getCentralPoint().getId() + ": The process must have at least one incoming arc.");
}
Reaction reaction;
if (p.getCentralPoint() == null) {
- throw new Exception("Process has no central point.");
+ throw new InvalidArgumentException("Process has no central point.");
}
reaction = getReactionFromProcessGlyphClazz(p.getCentralPoint().getClazz());
reaction.setIdReaction(p.getCentralPoint().getId());
@@ -1357,7 +1370,7 @@ public class SbgnmlXmlParser {
atd.setArrowType(ArrowType.NONE);
break;
default:
- throw new Exception("Wrong arc class.");
+ throw new InvalidArgumentException("Wrong arc class.");
}
return atd.copy();
}
@@ -1388,7 +1401,7 @@ public class SbgnmlXmlParser {
}
}
if (logicOperator == null) {
- throw new Exception("Missing logic operator for logic arc: " + arc.getId());
+ throw new InvalidArgumentException("Missing logic operator for logic arc: " + arc.getId());
}
// LogicOperator is valid for CellDesigner only if it has exactly 2
@@ -1398,7 +1411,7 @@ public class SbgnmlXmlParser {
.filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port))
.count() == 2;
if (!isCellDesignerValidLogicOperator) {
- throw new Exception("Parsed operator is not valid for CellDesigner: " + logicOperator.getId());
+ throw new InvalidArgumentException("Parsed operator is not valid for CellDesigner: " + logicOperator.getId());
}
NodeOperator operator;
@@ -1414,7 +1427,7 @@ public class SbgnmlXmlParser {
"NOT gates are not implemented in the platform. Glyph: " + logicOperator.getId() + " has not been parsed.");
return;
default:
- throw new Exception("Wrong logic operator class.");
+ throw new InvalidArgumentException("Wrong logic operator class.");
}
// Parse line from arc and operator glyph
@@ -1491,7 +1504,7 @@ public class SbgnmlXmlParser {
modifier = new PhysicalStimulation();
break;
default:
- throw new Exception("Wrong arc class.");
+ throw new InvalidArgumentException("Wrong arc class.");
}
Glyph sourceGlyph = (Glyph) logicArc.getSource();
@@ -1539,11 +1552,6 @@ public class SbgnmlXmlParser {
compartment.setNamePoint(compartment.getX() + compartment.getThickness() + CONTAINER_NAME_MARGIN,
compartment.getY() + compartment.getThickness() + CONTAINER_NAME_MARGIN);
}
- Compartment parent = findParentCompartment(compartment, model);
- if (parent != null) {
- compartment.setCompartment(parent);
- parent.addElement(compartment);
- }
model.addElement(compartment);
}
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 05fca1f6c7d59c5ad2d8092ced751872bb0ab45e..96ad2aac1d4d25538bdbc6d9c338571c56a52f07 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
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbgnml;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.File;
@@ -17,6 +18,7 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
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.modelutils.map.ElementUtils;
public class CellDesignerToSbgnTest {
@@ -62,8 +64,7 @@ public class CellDesignerToSbgnTest {
IConverter converter = new CellDesignerXmlParser();
IConverter converter2 = new SbgnmlXmlConverter();
- Model model;
- model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/bubbles.xml"));
String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
converter2.exportModelToFile(model, output);
@@ -107,4 +108,30 @@ public class CellDesignerToSbgnTest {
}
+ @Test
+ public void testProteinState() throws Exception {
+ try {
+ IConverter converter = new CellDesignerXmlParser();
+ IConverter converter2 = new SbgnmlXmlConverter();
+
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/cellDesigner/state.xml"));
+
+ String output = File.createTempFile("temp-sbgn-output", ".sbgn").getAbsolutePath();
+ converter2.exportModelToFile(model, output);
+
+ Model model2 = converter2.createModel(new ConverterParams().filename(output));
+
+ Protein protein1 = model.getElementByElementId("sa1");
+ Protein protein2 = model2.getElementByElementId("sa1");
+ assertEquals(protein1.getStructuralState(), protein2.getStructuralState());
+
+ protein1 = model.getElementByElementId("sa2");
+ protein2 = model2.getElementByElementId("sa2");
+ assertEquals(protein1.getStructuralState(), protein2.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
index a6940ca9003e4793bd116d85ac473edd9d27907f..fb4d974706f1064207a86dc39b93fd065ea27e4c 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest.java
@@ -29,7 +29,6 @@ import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Protein;
@RunWith(Parameterized.class)
public class SbgnmlXmlParserTest {
@@ -95,37 +94,14 @@ public class SbgnmlXmlParserTest {
nig2.saveToFile(pngFilePath2);
assertNotNull(model2);
- // for (Reaction r : model.getReactions()) {
- // logger.debug("Reaction: " + r.getIdReaction());
- // for (AbstractNode node: r.getNodes()){
- // logger.debug(node);
- // for (Point2D point: node.getLine().getPoints())
- // logger.debug(point);
- // }
- // logger.debug("--");
- // }
- // for (Reaction r : model2.getReactions()) {
- // logger.debug("Reaction: " + r.getIdReaction());
- // for (AbstractNode node: r.getNodes()){
- // logger.debug(node);
- // for (Point2D point: node.getLine().getPoints())
- // logger.debug(point);
- // }
- // logger.debug("--");
- // }
-
- // logger.debug(pngFilePath);
- // logger.debug(pngFilePath2);
ModelComparator comparator = new ModelComparator(1.0);
assertEquals(0, comparator.compare(model, model2));
FileUtils.deleteDirectory(new File(dir));
} catch (Exception e) {
- // TODO Auto-generated catch block
e.printStackTrace();
throw e;
}
-// logger.debug(filePath);
}
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
index c4c7f7f03847f2a90a8d43b825cbc6c0cd5958c1..fd00fea41cba0e4b087597edf4a3563cea2b383b 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.sbgnml;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
@@ -8,6 +10,11 @@ import org.apache.log4j.Logger;
import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.field.Residue;
@@ -33,4 +40,23 @@ public class SbgnmlXmlParserTest2 {
}
+ @Test
+ public void createModelWithCompartmentsTest() throws Exception {
+ try {
+ IConverter converter = new SbgnmlXmlConverter();
+
+ Model model = converter
+ .createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));
+ Complex complexInsideCompartment = model.getElementByElementId("csa1830");
+ assertNotNull("Complex inside compartment has undefined compartment", complexInsideCompartment.getCompartment());
+ Complex complexOutsideCompartment = model.getElementByElementId("csa1831");
+ assertNull("Complex outside compartment has not null compartment",complexOutsideCompartment.getCompartment());
+ Compartment compartment = model.getElementByElementId("ca107");
+ assertNull("Top compartment has not null compartment", compartment.getCompartment());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-SBGNML/testFiles/cellDesigner/state.xml b/converter-SBGNML/testFiles/cellDesigner/state.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f894eb0fd7b824ae92b554a544c30ded67163a1e
--- /dev/null
+++ b/converter-SBGNML/testFiles/cellDesigner/state.xml
@@ -0,0 +1,129 @@
+<?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="139.0" y="185.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="305.0" y="184.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:structuralState angle="1.5707963267948966"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC">
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" id="rs1" side="none"/>
+<celldesigner:modificationResidue angle="3.04" id="rs2" name="x" side="none"/>
+<celldesigner:modificationResidue angle="2.94" id="rs3" name="a" side="none"/>
+<celldesigner:modificationResidue angle="5.21" id="rs4" side="none"/>
+</celldesigner:listOfModificationResidues>
+</celldesigner:protein>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:listOfStructuralStates>
+<celldesigner:structuralState structuralState="xyz"/>
+</celldesigner:listOfStructuralStates>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml b/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml
new file mode 100644
index 0000000000000000000000000000000000000000..03f7e28d5f2f98778f837ab3ee9fd1ce6d6477d8
--- /dev/null
+++ b/converter-SBGNML/testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml
@@ -0,0 +1,71 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+ <map language="process description">
+ <glyph class="complex" id="csa1831">
+ <label text="TFEB_SNCA"/>
+ <bbox w="100.0" h="120.0" x="11731.0" y="1945.0"/>
+ <glyph class="macromolecule" id="sa11447">
+ <label text="SNCA"/>
+ <bbox w="80.0" h="40.0" x="11740.954" y="1998.1818"/>
+ <glyph class="state variable" id="sa11447-rs1">
+ <bbox w="20.0" h="22.0" x="11816.603" y="2037.5337"/>
+ </glyph>
+ <glyph class="state variable" id="sa11447-rs2">
+ <bbox w="20.0" h="22.0" x="11770.781" y="2038.1818"/>
+ </glyph>
+ <glyph class="state variable" id="sa11447-rs4">
+ <bbox w="20.0" h="22.0" x="11780.039" y="2038.1818"/>
+ </glyph>
+ <glyph class="state variable" id="sa11447-rs5">
+ <bbox w="20.0" h="22.0" x="11788.954" y="2038.1818"/>
+ </glyph>
+ <glyph class="state variable" id="sa11447-rs6">
+ <bbox w="20.0" h="22.0" x="11797.8955" y="2038.1818"/>
+ </glyph>
+ </glyph>
+ <glyph class="macromolecule" id="sa11446">
+ <label text="TFEB"/>
+ <bbox w="80.0" h="40.0" x="11741.704" y="1954.1818"/>
+ <glyph class="state variable" id="sa11446-rs1">
+ <state value="P" variable="S211"/>
+ <bbox w="70.0" h="28.0" x="11743.253" y="1957.633"/>
+ </glyph>
+ </glyph>
+ </glyph>
+ <glyph class="complex" id="csa1830">
+ <label text="TFEB_SNCA"/>
+ <bbox w="100.0" h="120.0" x="11505.454" y="1945.1818"/>
+ <glyph class="macromolecule" id="sa11445">
+ <label text="SNCA"/>
+ <bbox w="80.0" h="40.0" x="11515.409" y="1998.3636"/>
+ <glyph class="state variable" id="sa11445-rs1">
+ <bbox w="20.0" h="22.0" x="11591.058" y="2037.7155"/>
+ </glyph>
+ <glyph class="state variable" id="sa11445-rs2">
+ <bbox w="20.0" h="22.0" x="11545.236" y="2038.3636"/>
+ </glyph>
+ <glyph class="state variable" id="sa11445-rs4">
+ <bbox w="20.0" h="22.0" x="11554.494" y="2038.3636"/>
+ </glyph>
+ <glyph class="state variable" id="sa11445-rs5">
+ <bbox w="20.0" h="22.0" x="11563.409" y="2038.3636"/>
+ </glyph>
+ <glyph class="state variable" id="sa11445-rs6">
+ <bbox w="20.0" h="22.0" x="11572.351" y="2038.3636"/>
+ </glyph>
+ </glyph>
+ <glyph class="macromolecule" id="sa11444">
+ <label text="TFEB"/>
+ <bbox w="80.0" h="40.0" x="11518.159" y="1954.3636"/>
+ <glyph class="state variable" id="sa11444-rs1">
+ <state value="P" variable="S211"/>
+ <bbox w="70.0" h="28.0" x="11519.708" y="1957.815"/>
+ </glyph>
+ </glyph>
+ </glyph>
+ <glyph class="compartment" id="ca107">
+ <label text="Lewy body"/>
+ <bbox w="194.0" h="344.0" x="11458.0" y="1921.0"/>
+ </glyph>
+ </map>
+</sbgn>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java
index 58ed068047f140fa34c899ecdf3c7abecd4676e7..04fe8e12a032eeb4cfce77fd9ae7aa6a366075d4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractRegionModification.java
@@ -50,8 +50,8 @@ public abstract class AbstractRegionModification extends ModificationResidue {
} else {
position = "Point2D[" + format.format(getPosition().getX()) + "," + format.format(getPosition().getY()) + "]";
}
- String result = "[" + this.getClass().getSimpleName() + "]: " + getIdModificationResidue() + "," + getName() + ","
- + getWidth() + "," + getHeight() + "," + position;
+ String result = "[" + this.getClass().getSimpleName() + "]: " + getName() + "," + getWidth() + "," + getHeight()
+ + "," + position;
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
index d0249cea6281efb73da01a857a48fe80c72e932d..e1b7030a96809f6e15175f516571631b5b47ecf7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AbstractSiteModification.java
@@ -15,7 +15,7 @@ public abstract class AbstractSiteModification extends ModificationResidue {
*
*/
private static final long serialVersionUID = 1L;
-
+
/**
* State in which this modification is.
*/
@@ -42,10 +42,9 @@ public abstract class AbstractSiteModification extends ModificationResidue {
@Override
public String toString() {
DecimalFormat format = new DecimalFormat("#.##");
- String result = getIdModificationResidue() + "," + getName() + "," + getState() + ",Point2D["
- + format.format(getPosition().getX()) + "," + format.format(getPosition().getY()) + "]";
+ String result = getName() + "," + getState() + ",Point2D[" + format.format(getPosition().getX()) + ","
+ + format.format(getPosition().getY()) + "]";
return result;
}
-
}
\ No newline at end of file