ModificationSite and Residue classes extracted

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java

@@ -6,14 +6,17 @@ import org.w3c.dom.NodeList;
 
 import lcsb.mapviewer.common.Pair;
 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.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.CellDesignerGeneRegion;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
 import lcsb.mapviewer.model.map.species.Gene;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
 
 /**
  * Class that performs parsing of the CellDesigner xml for
@@ -89,12 +92,18 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
    * @throws InvalidXmlSchemaException
    *           thrown when input xml node doesn't follow defined schema
    */
-  CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
-    CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+  CellDesignerGeneRegion getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
+    CellDesignerGeneRegion residue = new CellDesignerGeneRegion();
     residue.setIdModificationResidue(getNodeAttr("id", residueNode));
     residue.setName(getNodeAttr("name", residueNode));
     residue.setSide(getNodeAttr("side", residueNode));
     residue.setAngle(getNodeAttr("pos", residueNode));
+    String type = getNodeAttr("type", residueNode);
+    if (type.equals("Modification Site")) {
+      residue.setModificationType("MODIFICATION_SITE");
+    } else if (!type.equals("")) {
+      throw new NotImplementedException("Unknown type: " + type);
+    }
     NodeList list = residueNode.getChildNodes();
     for (int i = 0; i < list.getLength(); i++) {
       Node node = list.item(i);
@@ -152,6 +161,9 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
     if (!mr.getName().equals("")) {
       attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
     }
+    if (mr instanceof ModificationSite) {
+      attributes += " type=\"Modification Site\"";
+    }
     attributes += " pos=\"" + converter.getAngleForPoint(mr.getSpecies(), mr.getPosition()) + "\"";
     result += "<celldesigner:region " + attributes + ">";
     result += "</celldesigner:region>\n";

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java

@@ -161,6 +161,7 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
     residue.setName(getNodeAttr("name", residueNode));
     residue.setSide(getNodeAttr("side", residueNode));
     residue.setAngle(getNodeAttr("angle", residueNode));
+    residue.setModificationType("RESIDUE");
     NodeList list = residueNode.getChildNodes();
     for (int i = 0; i < list.getLength(); i++) {
       Node node = list.item(i);

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java

@@ -21,6 +21,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerGeneRegion;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
@@ -211,7 +212,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
       attributesBuilder.append(" constant=\"" + species.getConstant().toString().toLowerCase() + "\"");
     }
     if (species.getBoundaryCondition() != null) {
-      attributesBuilder.append(" boundaryCondition=\"" + species.getBoundaryCondition().toString().toLowerCase() + "\"");
+      attributesBuilder
+          .append(" boundaryCondition=\"" + species.getBoundaryCondition().toString().toLowerCase() + "\"");
     }
 
     Compartment comp = null;
@@ -444,7 +446,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
         throw new NotImplementedException("StructuralState not supported in Gene");
       }
       for (CellDesignerModificationResidue mr : state.getModifications()) {
-        gene.addModificationResidue(mr);
+        gene.addModificationResidue(createGeneRegion(mr));
       }
     } else if (species instanceof CellDesignerProtein) {
       CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
@@ -490,6 +492,23 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
 
   }
 
+  private CellDesignerGeneRegion createGeneRegion(CellDesignerModificationResidue mr) {
+    CellDesignerGeneRegion region = new CellDesignerGeneRegion();
+    region.setIdModificationResidue(mr.getIdModificationResidue());
+    if (mr.getSize() != null) {
+      region.setSize(mr.getSize());
+    }
+    region.setState(mr.getState());
+    region.setName(mr.getName());
+    if (mr.getAngle() != null) {
+      region.setAngle(mr.getAngle());
+    }
+    if (mr.getModificationType() != null) {
+      region.setModificationType(mr.getModificationType());
+    }
+    return region;
+  }
+
   /**
    * Creates {@link SpeciesState} from xml node.
    * 
@@ -549,7 +568,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
   }
 
   /**
-   * Creates {@link CellDesignerModificationResidue} from the apropriate xml node.
+   * Creates {@link CellDesignerModificationResidue} from the appropriate xml
+   * node.
    * 
    * @param rootNode
    *          xml node
@@ -632,7 +652,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
    * 
    * @param mr
    *          object from which we create {@link CellDesignerRnaRegion}
-   * @return {@link CellDesignerRnaRegion} object created from param
+   * @return {@link CellDesignerRnaRegion} object created from parameter
    */
   public CellDesignerRnaRegion createRnaRegion(CellDesignerModificationResidue mr) {
     CellDesignerRnaRegion result = new CellDesignerRnaRegion();

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java

@@ -4,9 +4,8 @@ import java.util.ArrayList;
 import java.util.List;
 
 import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerGeneRegion;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
 import lcsb.mapviewer.model.map.species.Gene;
 import lcsb.mapviewer.model.map.species.Species;
 
@@ -26,7 +25,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
   /**
    * List of modifications for the Gene.
    */
-  private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
+  private List<CellDesignerGeneRegion> modificationResidues = new ArrayList<>();
 
   /**
    * Constructor that initializes gene with the data passed in the argument.
@@ -38,8 +37,8 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
     super(species);
     if (species instanceof CellDesignerGene) {
       CellDesignerGene gene = (CellDesignerGene) species;
-      for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
-        addModificationResidue(new CellDesignerModificationResidue(mr));
+      for (CellDesignerGeneRegion mr : gene.getModificationResidues()) {
+        addModificationResidue(new CellDesignerGeneRegion(mr));
       }
     }
   }
@@ -50,7 +49,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
     if (species instanceof CellDesignerGene) {
       CellDesignerGene gene = (CellDesignerGene) species;
 
-      for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+      for (CellDesignerGeneRegion mr : gene.getModificationResidues()) {
         addModificationResidue(mr);
       }
     }
@@ -76,10 +75,10 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
    * Adds modification to the gene.
    * 
    * @param modificationResidue
-   *          modifiaction to add
+   *          modification to add
    */
-  public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
-    for (CellDesignerModificationResidue mr : modificationResidues) {
+  public void addModificationResidue(CellDesignerGeneRegion modificationResidue) {
+    for (CellDesignerGeneRegion mr : modificationResidues) {
       if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
         mr.update(modificationResidue);
         return;
@@ -94,7 +93,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
    * @return the modificationResidues
    * @see #modificationResidues
    */
-  public List<CellDesignerModificationResidue> getModificationResidues() {
+  public List<CellDesignerGeneRegion> getModificationResidues() {
     return modificationResidues;
   }
 
@@ -103,7 +102,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
    *          the modificationResidues to set
    * @see #modificationResidues
    */
-  public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
+  public void setModificationResidues(List<CellDesignerGeneRegion> modificationResidues) {
     this.modificationResidues = modificationResidues;
   }
 
@@ -116,8 +115,8 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
 
   @Override
   public void updateModelElementAfterLayoutAdded(Species element) {
-    for (CellDesignerModificationResidue region : modificationResidues) {
-      ((Gene) element).addModificationResidue(region.createModificationResidueAlias(element));
+    for (CellDesignerGeneRegion region : modificationResidues) {
+      ((Gene) element).addModificationResidue(region.createGeneModification(element));
     }
   }
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java

@@ -152,7 +152,7 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
   @Override
   public void updateModelElementAfterLayoutAdded(Species element) {
     for (CellDesignerModificationResidue mr : modificationResidues) {
-      ((Protein) element).addModificationResidue(mr.createModificationResidueAlias(element));
+      ((Protein) element).addModificationResidue(mr.createProteinModification(element));
     }
   }
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerGeneRegion.java

+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.io.Serializable;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+/**
+ * This class represent modification residue in protein and gene. However, it is
+ * sometimes also used for storing information about AntisenseRna/Rna regions...
+ * (due to CellDesigner xml strange structure).
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class CellDesignerGeneRegion implements Serializable {
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Default class logger.
+   */
+  private static Logger logger = Logger.getLogger(CellDesignerGeneRegion.class.getName());
+
+  /**
+   * Identifier of the modification. Must be unique in single map model.
+   */
+  private String idModificationResidue = "";
+
+  /**
+   * Name of the modification.
+   */
+  private String name = "";
+
+  private String modificationType;
+
+  /**
+   * Some strange parameter in CellDesigner. No idea what is it for.
+   */
+  private String side = "";
+
+  /**
+   * State in which this modification is.
+   */
+  private ModificationState state = null;
+
+  /**
+   * Where this modification is located (on which side of the border).
+   */
+  private Double angle = null;
+
+  /**
+   * How big is this modification (used only for some types of the modification).
+   */
+  private Double size = null;
+
+  /**
+   * Species to which this modification belong to.
+   */
+  private CellDesignerSpecies<?> species;
+
+  /**
+   * Default constructor.
+   */
+  public CellDesignerGeneRegion() {
+  }
+
+  /**
+   * Constructor that initialize object with the data taken from the parameter.
+   * 
+   * @param mr
+   *          original object from which data is taken
+   */
+  public CellDesignerGeneRegion(CellDesignerGeneRegion mr) {
+    this.idModificationResidue = mr.idModificationResidue;
+    this.name = mr.name;
+    this.angle = mr.angle;
+    this.size = mr.size;
+    this.side = mr.side;
+    this.state = mr.state;
+    this.modificationType = mr.getModificationType();
+
+    logger.debug(this);
+  }
+
+  /**
+   * Constructor that creates object from model representation of modification.
+   * 
+   * @param mr
+   *          model representation of {@link ModificationResidue}
+   */
+  public CellDesignerGeneRegion(ModificationResidue mr) {
+    CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
+    this.setIdModificationResidue(mr.getIdModificationResidue());
+    this.name = mr.getName();
+    this.angle = converter.getAngleForPoint(mr.getSpecies(), mr.getPosition());
+    this.state = mr.getState();
+    if (mr instanceof ModificationSite) {
+      this.setModificationType("MODIFICATION_SITE");
+    } else {
+      throw new InvalidArgumentException("Unknown gene modification: " + mr.getClass());
+    }
+    logger.debug(this);
+  }
+
+  /**
+   * Default constructor.
+   * 
+   * @param id
+   *          identifier of the modification residue
+   */
+  public CellDesignerGeneRegion(String id) {
+    this.idModificationResidue = id;
+  }
+
+  /**
+   * Updates fields in the object with the data given in the parameter
+   * modification.
+   * 
+   * @param mr
+   *          modification residue from which data will be used to update
+   */
+  public void update(CellDesignerGeneRegion mr) {
+    if (mr.getName() != null && !mr.getName().equals("")) {
+      this.name = mr.name;
+    }
+    if (mr.getAngle() != null) {
+      this.angle = mr.angle;
+    }
+    if (mr.getSize() != null) {
+      this.size = mr.size;
+    }
+    if (mr.getSide() != null && !mr.getSide().equals("")) {
+      this.side = mr.side;
+    }
+    if (mr.getState() != null) {
+      this.state = mr.state;
+    }
+    if (mr.getModificationType() != null) {
+      this.setModificationType(mr.modificationType);
+    }
+  }
+
+  @Override
+  public String toString() {
+    String result = getIdModificationResidue() + "," + getName() + "," + getState() + "," + getAngle() + "," + getSize()
+        + "," + getSide() + "," + getModificationType();
+    return result;
+  }
+
+  /**
+   * Creates copy of the object.
+   * 
+   * @return copy of the object.
+   */
+  public CellDesignerGeneRegion copy() {
+    if (this.getClass() == CellDesignerGeneRegion.class) {
+      return new CellDesignerGeneRegion(this);
+    } else {
+      throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+    }
+  }
+
+  /**
+   * Sets {@link #angle} .
+   * 
+   * @param text
+   *          angle in text format
+   */
+  public void setAngle(String text) {
+    try {
+      if (text != null && !text.equals("")) {
+        angle = Double.parseDouble(text);
+      } else {
+        angle = null;
+      }
+    } catch (NumberFormatException e) {
+      throw new InvalidArgumentException("Invalid angle: " + text, e);
+    }
+
+  }
+
+  /**
+   * Sets {@link #size}.
+   * 
+   * @param text
+   *          size in text format.
+   */
+  public void setSize(String text) {
+    try {
+      if (text != null && !text.equals("")) {
+        size = Double.parseDouble(text);
+      } else {
+        size = null;
+      }
+    } catch (NumberFormatException e) {
+      throw new InvalidArgumentException("Invalid size: " + text, e);
+    }
+  }
+
+  /**
+   * @return the id
+   * @see #idModificationResidue
+   */
+  public String getIdModificationResidue() {
+    return idModificationResidue;
+  }
+
+  /**
+   * @param idModificationResidue
+   *          the id to set
+   * @see #idModificationResidue
+   */
+  public void setIdModificationResidue(String idModificationResidue) {
+    this.idModificationResidue = idModificationResidue;
+  }
+
+  /**
+   * @return the name
+   * @see #name
+   */
+  public String getName() {
+    return name;
+  }
+
+  /**
+   * @param name
+   *          the name to set
+   * @see #name
+   */
+  public void setName(String name) {
+    this.name = name;
+  }
+
+  /**
+   * @return the side
+   * @see #side
+   */
+  public String getSide() {
+    return side;
+  }
+
+  /**
+   * @param side
+   *          the side to set
+   * @see #side
+   */
+  public void setSide(String side) {
+    this.side = side;
+  }
+
+  /**
+   * @return the state
+   * @see #state
+   */
+  public ModificationState getState() {
+    return state;
+  }
+
+  /**
+   * @param state
+   *          the state to set
+   * @see #state
+   */
+  public void setState(ModificationState state) {
+    this.state = state;
+  }
+
+  /**
+   * @return the angle
+   * @see #angle
+   */
+  public Double getAngle() {
+    return angle;
+  }
+
+  /**
+   * @param angle
+   *          the angle to set
+   * @see #angle
+   */
+  public void setAngle(Double angle) {
+    this.angle = angle;
+  }
+
+  /**
+   * @return the size
+   * @see #size
+   */
+  public Double getSize() {
+    return size;
+  }
+
+  /**
+   * @param size
+   *          the size to set
+   * @see #size
+   */
+  public void setSize(Double size) {
+    this.size = size;
+  }
+
+  /**
+   * @return the species
+   * @see #species
+   */
+  public CellDesignerSpecies<?> getSpecies() {
+    return species;
+  }
+
+  /**
+   * @param species
+   *          the species to set
+   * @see #species
+   */
+  public void setSpecies(CellDesignerSpecies<?> species) {
+    this.species = species;
+  }
+
+  /**
+   * Creates model representation of {@link ModificationResidue}.
+   * 
+   * @return {@link ModificationResidue} representing this object in a model
+   */
+  public ModificationResidue createGeneModification(Element element) {
+    CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, false);