From b833152e3c62f25508eea85ce9ab28c0eabffc69 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 13 Jul 2018 10:45:07 +0200
Subject: [PATCH] processing modification site for rna/antisense rna uses
proper modification type
---
.../alias/SpeciesAliasXmlParser.java | 508 +++++++++---------
.../structure/CellDesignerAntisenseRna.java | 4 -
.../structure/CellDesignerRna.java | 3 -
.../CellDesignerModificationResidue.java | 1 -
.../structure/fields/SpeciesState.java | 7 +
.../model/celldesigner/ModificationTest.java | 8 +
.../antisense_rna_with_region.xml | 43 +-
7 files changed, 309 insertions(+), 265 deletions(-)
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 a194db9c50..30ab817536 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
@@ -1,253 +1,255 @@
-package lcsb.mapviewer.converter.model.celldesigner.alias;
-
-import org.apache.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
-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;
-
-/**
- * Parser of CellDesigner xml used for parsing SpeciesAlias.
- *
- * @author Piotr Gawron
- *
- * @see Complex
- */
-public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed from
- * xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Model for which we parse elements.
- */
- private Model model;
-
- /**
- * Default constructor with model object for which we parse data.
- *
- * @param model
- * model for which we parse elements
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
- this.elements = elements;
- this.model = model;
- }
-
- @Override
- Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
-
- String speciesId = getNodeAttr("species", aliasNode);
- String aliasId = getNodeAttr("id", aliasNode);
- 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.");
- }
-
- 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());
- }
- }
- }
-
- 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);
- } 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(
- "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
- } else {
- result.setComplex(complex);
- complex.addSpecies(result);
- }
- }
- species.updateModelElementAfterLayoutAdded(result);
- return result;
- }
-
- /**
- * Process node with information about alias state and puts data into alias.
- *
- * @param node
- * node where information about alias state is stored
- * @param alias
- * alias object to be modified if necessary
- */
- private void processAliasState(Node node, Species alias) {
- String state = getNodeAttr("state", node);
- if ("open".equalsIgnoreCase(state)) {
- String prefix = getNodeAttr("prefix", node);
- String label = getNodeAttr("label", node);
- alias.setStatePrefix(prefix);
- alias.setStateLabel(label);
- } else if ("empty".equalsIgnoreCase(state)) {
- return;
- } else if (state == null || state.isEmpty()) {
- return;
- } else {
- throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
- }
-
- }
-
- @Override
- public String toXml(Species species) {
- Compartment ca = null;
- // artificial compartment aliases should be excluded
- if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
- ca = (Compartment) species.getCompartment();
- } else if (species.getComplex() == null) {
- ModelData model = species.getModelData();
- if (model != null) {
- for (Compartment cAlias : model.getModel().getCompartments()) {
- if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
- if (ca == null) {
- ca = cAlias;
- } else if (ca.getSize() > cAlias.getSize()) {
- ca = cAlias;
- }
- }
- }
- }
- }
-
- Complex complex = species.getComplex();
-
- String compartmentAliasId = null;
- if (ca != null) {
- compartmentAliasId = ca.getElementId();
- }
- StringBuilder sb = new StringBuilder("");
- sb.append("<celldesigner:speciesAlias ");
- sb.append("id=\"" + species.getElementId() + "\" ");
- sb.append("species=\"" + elements.getElementId(species) + "\" ");
- if (compartmentAliasId != null) {
- sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
- }
-
- if (complex != null) {
- sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
- }
- sb.append(">\n");
-
- if (species.getActivity() != null) {
- if (species.getActivity()) {
- sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
- } else {
- sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
- }
- }
-
- sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + species.getX() + "\" ");
- sb.append("y=\"" + species.getY() + "\" ");
- sb.append("w=\"" + species.getWidth() + "\" ");
- sb.append("h=\"" + species.getHeight() + "\" ");
- sb.append("/>\n");
-
- sb.append("<celldesigner:font size=\"" + species.getFontSize() + "\"/>\n");
-
- // TODO to be improved
- sb.append("<celldesigner:view state=\"usual\"/>\n");
- sb.append("<celldesigner:usualView>");
- sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:usualView>\n");
- sb.append("<celldesigner:briefView>");
- sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:briefView>\n");
- if (species.getStateLabel() != null || species.getStatePrefix() != null) {
- sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
- + species.getStateLabel() + "\"/>\n");
- }
- sb.append("</celldesigner:speciesAlias>\n");
- return sb.toString();
- }
-}
+package lcsb.mapviewer.converter.model.celldesigner.alias;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+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;
+
+/**
+ * Parser of CellDesigner xml used for parsing SpeciesAlias.
+ *
+ * @author Piotr Gawron
+ *
+ * @see Complex
+ */
+public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Model for which we parse elements.
+ */
+ private Model model;
+
+ /**
+ * Default constructor with model object for which we parse data.
+ *
+ * @param model
+ * model for which we parse elements
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.elements = elements;
+ this.model = model;
+ }
+
+ @Override
+ Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+
+ String speciesId = getNodeAttr("species", aliasNode);
+ String aliasId = getNodeAttr("id", aliasNode);
+ 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.");
+ }
+
+ 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());
+ }
+ }
+ }
+
+ 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);
+ } 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(
+ "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
+ } else {
+ result.setComplex(complex);
+ complex.addSpecies(result);
+ }
+ }
+
+
+ species.updateModelElementAfterLayoutAdded(result);
+ return result;
+ }
+
+ /**
+ * Process node with information about alias state and puts data into alias.
+ *
+ * @param node
+ * node where information about alias state is stored
+ * @param alias
+ * alias object to be modified if necessary
+ */
+ private void processAliasState(Node node, Species alias) {
+ String state = getNodeAttr("state", node);
+ if ("open".equalsIgnoreCase(state)) {
+ String prefix = getNodeAttr("prefix", node);
+ String label = getNodeAttr("label", node);
+ alias.setStatePrefix(prefix);
+ alias.setStateLabel(label);
+ } else if ("empty".equalsIgnoreCase(state)) {
+ return;
+ } else if (state == null || state.isEmpty()) {
+ return;
+ } else {
+ throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
+ }
+
+ }
+
+ @Override
+ public String toXml(Species species) {
+ Compartment ca = null;
+ // artificial compartment aliases should be excluded
+ if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
+ ca = (Compartment) species.getCompartment();
+ } else if (species.getComplex() == null) {
+ ModelData model = species.getModelData();
+ if (model != null) {
+ for (Compartment cAlias : model.getModel().getCompartments()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
+ if (ca == null) {
+ ca = cAlias;
+ } else if (ca.getSize() > cAlias.getSize()) {
+ ca = cAlias;
+ }
+ }
+ }
+ }
+ }
+
+ Complex complex = species.getComplex();
+
+ String compartmentAliasId = null;
+ if (ca != null) {
+ compartmentAliasId = ca.getElementId();
+ }
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<celldesigner:speciesAlias ");
+ sb.append("id=\"" + species.getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(species) + "\" ");
+ if (compartmentAliasId != null) {
+ sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
+ }
+
+ if (complex != null) {
+ sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
+ }
+ sb.append(">\n");
+
+ if (species.getActivity() != null) {
+ if (species.getActivity()) {
+ sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
+ } else {
+ sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
+ }
+ }
+
+ sb.append("<celldesigner:bounds ");
+ sb.append("x=\"" + species.getX() + "\" ");
+ sb.append("y=\"" + species.getY() + "\" ");
+ sb.append("w=\"" + species.getWidth() + "\" ");
+ sb.append("h=\"" + species.getHeight() + "\" ");
+ sb.append("/>\n");
+
+ sb.append("<celldesigner:font size=\"" + species.getFontSize() + "\"/>\n");
+
+ // TODO to be improved
+ sb.append("<celldesigner:view state=\"usual\"/>\n");
+ sb.append("<celldesigner:usualView>");
+ sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:usualView>\n");
+ sb.append("<celldesigner:briefView>");
+ sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:briefView>\n");
+ if (species.getStateLabel() != null || species.getStatePrefix() != null) {
+ sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
+ + species.getStateLabel() + "\"/>\n");
+ }
+ sb.append("</celldesigner:speciesAlias>\n");
+ return sb.toString();
+ }
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
index dd6373dc29..9ad77efd72 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerAntisenseRna.java
@@ -91,10 +91,6 @@ public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna>
super.update(sp);
if (sp instanceof CellDesignerAntisenseRna) {
CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
- for (CellDesignerModificationResidue mr : getRegions()) {
- mr.setState(null);
- }
-
for (CellDesignerModificationResidue region : rna.getRegions()) {
updateRegion(region);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index 745cc58d1b..64e121ad9a 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -71,9 +71,6 @@ public class CellDesignerRna extends CellDesignerSpecies<Rna> {
super.update(species);
if (species instanceof CellDesignerRna) {
CellDesignerRna rna = (CellDesignerRna) species;
- for (CellDesignerModificationResidue mr : getRegions()) {
- mr.setState(null);
- }
for (CellDesignerModificationResidue region : rna.getRegions()) {
updateRegion(region);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index 8dc7e0c0f9..9ce8b7956f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -460,7 +460,6 @@ public class CellDesignerModificationResidue implements Serializable {
result.setIdModificationResidue(idModificationResidue);
result.setName(name);
result.setActive(active);
- logger.debug(angle);
result.setPosition(converter.getCoordinatesByPosition(element, angle));
if (modificationType.equals(ModificationType.TRANSCRIPTION_SITE_LEFT)) {
result.setDirection("LEFT");
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 8ae901497d..2e9562224a 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
@@ -6,6 +6,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
@@ -87,6 +88,12 @@ public class SpeciesState {
CellDesignerModificationResidue mr = new CellDesignerModificationResidue(region);
addModificationResidue(mr);
}
+ } else if (species instanceof AntisenseRna) {
+ AntisenseRna rna = (AntisenseRna) species;
+ for (ModificationResidue region : rna.getRegions()) {
+ CellDesignerModificationResidue mr = new CellDesignerModificationResidue(region);
+ addModificationResidue(mr);
+ }
} else if (species instanceof Gene) {
Gene gene = (Gene) species;
for (ModificationResidue mr : gene.getModificationResidues()) {
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 46c1aa2e24..bacc86fe1b 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
@@ -27,6 +27,7 @@ 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.ModificationState;
import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
import lcsb.mapviewer.model.map.species.field.Residue;
@@ -233,6 +234,13 @@ public class ModificationTest extends CellDesignerTestFunctions {
rna = model.getElementByElementId("sa3");
assertEquals(1, rna.getRegions().size());
assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+
+ rna = model.getElementByElementId("sa4");
+ assertEquals(1, rna.getRegions().size());
+ assertTrue(rna.getRegions().get(0) instanceof ModificationSite);
+ ModificationSite modificationSite = (ModificationSite) rna.getRegions().get(0);
+ assertEquals(ModificationState.PHOSPHORYLATED, modificationSite.getState());
+
testXmlSerialization(model);
} catch (Exception e) {
diff --git a/converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml b/converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml
index 91a7ef532f..1fe9f35b36 100644
--- a/converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml
+++ b/converter-CellDesigner/testFiles/modifications/antisense_rna_with_region.xml
@@ -22,7 +22,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -41,12 +41,12 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa3" species="s4">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="192.0" y="247.5" w="90.0" h="25.0"/>
<celldesigner:font size="12"/>
@@ -60,7 +60,26 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="0.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa4" species="s3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="300.0" y="207.0" w="90.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="90.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffff6666" 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="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -151,6 +170,22 @@
<celldesigner:speciesIdentity>
<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
<celldesigner:antisensernaReference>arn3</celldesigner:antisensernaReference>
+<celldesigner:state>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="tr1" state="phosphorylated"/>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn3</celldesigner:antisensernaReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
--
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