protein modification uses string mapping for state

model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java

-package lcsb.mapviewer.model.map.species.field;
-
-import java.awt.geom.Point2D;
-import java.io.Serializable;
-import java.text.DecimalFormat;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Type;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.Species;
-
-/**
- * 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
- * 
- */
-@Entity
-@Table(name = "modification_residue_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class ModificationResidue implements Serializable, ElementModification {
-
-  /**
-   * 
-   */
-  private static final long serialVersionUID = 1L;
-
-  /**
-   * Default class logger.
-   */
-  @SuppressWarnings("unused")
-  private static Logger logger = Logger.getLogger(ModificationResidue.class.getName());
-
-  /**
-   * Unique identifier in the database.
-   */
-  @Id
-  @GeneratedValue(strategy = GenerationType.IDENTITY)
-  @Column(name = "iddb", unique = true, nullable = false)
-  private int id;
-
-  /**
-   * Identifier of the modification. Must be unique in single map model.
-   */
-  private String idModificationResidue = "";
-
-  /**
-   * Name of the modification.
-   */
-  private String name = "";
-
-  /**
-   * State in which this modification is.
-   */
-  private ModificationState state = null;
-
-  @Column(name = "position")
-  @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
-  private Point2D position = null;
-
-  /**
-   * Species to which this modification belong to.
-   */
-  @ManyToOne(fetch = FetchType.LAZY)
-  @JoinColumn(name = "idSpeciesDb", nullable = false)
-  private Species species;
-
-  /**
-   * Default constructor.
-   */
-  public ModificationResidue() {
-  }
-
-  /**
-   * Constructor that initialize object with the data taken from the parameter.
-   * 
-   * @param mr
-   *          original object from which data is taken
-   */
-  public ModificationResidue(ModificationResidue mr) {
-    this.idModificationResidue = mr.idModificationResidue;
-    this.name = mr.name;
-    this.state = mr.state;
-    this.position = mr.position;
-  }
-
-  @Override
-  public String toString() {
-    DecimalFormat format = new DecimalFormat("#.##");
-    String result = getIdModificationResidue() + "," + getName() + "," + getState() + ",Point2D["
-        + format.format(getPosition().getX()) + "," + format.format(getPosition().getY()) + "]";
-    return result;
-  }
-
-  /**
-   * Creates copy of the object.
-   * 
-   * @return copy of the object.
-   */
-  public ModificationResidue copy() {
-    if (this.getClass() == ModificationResidue.class) {
-      return new ModificationResidue(this);
-    } else {
-      throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
-    }
-  }
-
-  /**
-   * @return the idModificationResidue
-   * @see #id
-   */
-  public int getId() {
-    return id;
-  }
-
-  /**
-   * @param id
-   *          the idModificationResidue to set
-   * @see #id
-   */
-  public void setId(int id) {
-    this.id = id;
-  }
-
-  /**
-   * @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 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 species
-   * @see #species
-   */
-  public Species getSpecies() {
-    return species;
-  }
-
-  /**
-   * @param species
-   *          the species to set
-   * @see #species
-   */
-  public void setSpecies(Species species) {
-    this.species = species;
-  }
-
-  public Point2D getPosition() {
-    return position;
-  }
-
-  public void setPosition(Point2D position) {
-    this.position = position;
-  }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.text.DecimalFormat;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * 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
+ * 
+ */
+@Entity
+@Table(name = "modification_residue_table")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+public class ModificationResidue implements Serializable, ElementModification {
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Default class logger.
+   */
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(ModificationResidue.class.getName());
+
+  /**
+   * Unique identifier in the database.
+   */
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  @Column(name = "iddb", unique = true, nullable = false)
+  private int id;
+
+  /**
+   * Identifier of the modification. Must be unique in single map model.
+   */
+  private String idModificationResidue = "";
+
+  /**
+   * Name of the modification.
+   */
+  private String name = "";
+
+  /**
+   * State in which this modification is.
+   */
+  @Enumerated(EnumType.STRING)
+  private ModificationState state = null;
+
+  @Column(name = "position")
+  @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+  private Point2D position = null;
+
+  /**
+   * Species to which this modification belong to.
+   */
+  @ManyToOne(fetch = FetchType.LAZY)
+  @JoinColumn(name = "idSpeciesDb", nullable = false)
+  private Species species;
+
+  /**
+   * Default constructor.
+   */
+  public ModificationResidue() {
+  }
+
+  /**
+   * Constructor that initialize object with the data taken from the parameter.
+   * 
+   * @param mr
+   *          original object from which data is taken
+   */
+  public ModificationResidue(ModificationResidue mr) {
+    this.idModificationResidue = mr.idModificationResidue;
+    this.name = mr.name;
+    this.state = mr.state;
+    this.position = mr.position;
+  }
+
+  @Override
+  public String toString() {
+    DecimalFormat format = new DecimalFormat("#.##");
+    String result = getIdModificationResidue() + "," + getName() + "," + getState() + ",Point2D["
+        + format.format(getPosition().getX()) + "," + format.format(getPosition().getY()) + "]";
+    return result;
+  }
+
+  /**
+   * Creates copy of the object.
+   * 
+   * @return copy of the object.
+   */
+  public ModificationResidue copy() {
+    if (this.getClass() == ModificationResidue.class) {
+      return new ModificationResidue(this);
+    } else {
+      throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+    }
+  }
+
+  /**
+   * @return the idModificationResidue
+   * @see #id
+   */
+  public int getId() {
+    return id;
+  }
+
+  /**
+   * @param id
+   *          the idModificationResidue to set
+   * @see #id
+   */
+  public void setId(int id) {
+    this.id = id;
+  }
+
+  /**
+   * @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 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 species
+   * @see #species
+   */
+  public Species getSpecies() {
+    return species;
+  }
+
+  /**
+   * @param species
+   *          the species to set
+   * @see #species
+   */
+  public void setSpecies(Species species) {
+    this.species = species;
+  }
+
+  public Point2D getPosition() {
+    return position;
+  }
+
+  public void setPosition(Point2D position) {
+    this.position = position;
+  }
+
+}

model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationState.java

-package lcsb.mapviewer.model.map.species.field;
-
-/**
- * Defines a type of modification (in protein or rna). Possible values are:
- * <ul>
- * <li>{@link ModificationState#ACETYLATED ACETYLATED},</li>
- * <li>{@link ModificationState#DONT_CARE DON'T CARE},</li>
- * <li>{@link ModificationState#EMPTY EMPTY},</li>
- * <li>{@link ModificationState#GLYCOSYLATED GLYCOSYLATED},</li>
- * <li>{@link ModificationState#HYDROXYLATED HYDROXYLATED},</li>
- * <li>{@link ModificationState#METHYLATED METHYLATED},</li>
- * <li>{@link ModificationState#MYRISTOYLATED MYRISTOYLATED},</li>
- * <li>{@link ModificationState#PALMYTOYLATED PALMYTOYLATED},</li>
- * <li>{@link ModificationState#PHOSPHORYLATED PHOSPHORYLATED},</li>
- * <li>{@link ModificationState#PRENYLATED PRENYLATED},</li>
- * <li>{@link ModificationState#PROTONATED PROTONATED},</li>
- * <li>{@link ModificationState#SULFATED SULFATED},</li>
- * <li>{@link ModificationState#UBIQUITINATED UBIQUITINATED},</li>
- * <li>{@link ModificationState#UNKNOWN UNKNOWN}.</li>
- * </ul>
- * 
- * @author Piotr Gawron
- * 
- */
-public enum ModificationState {
-	
-	/**
-	 * Phosporylated state.
-	 */
-	PHOSPHORYLATED("phosphorylated", "P"), //
-
-	/**
-	 * Acetylated state.
-	 */
-	ACETYLATED("acetylated", "Ac"), //
-
-	/**
-	 * Ubiquitinated state.
-	 */
-	UBIQUITINATED("ubiquitinated", "Ub"), //
-
-	/**
-	 * Methylated state.
-	 */
-	METHYLATED("methylated", "Me"), //
-
-	/**
-	 * Hydroxylated state.
-	 */
-	HYDROXYLATED("hydroxylated", "OH"), //
-
-	/**
-	 * Myristoylated state.
-	 */
-	MYRISTOYLATED("myristoylated", "My"), //
-
-	/**
-	 * Sulfated state.
-	 */
-	SULFATED("sulfated", "S"), //
-
-	/**
-	 * Prenylated state.
-	 */
-	PRENYLATED("prenylated", "Pr"), //
-
-	/**
-	 * Glycosylated state.
-	 */
-	GLYCOSYLATED("glycosylated", "G"), //
-
-	/**
-	 * Palmytoylated state.
-	 */
-	PALMYTOYLATED("palmytoylated", "Pa"), //
-
-	/**
-	 * Unknown state.
-	 */
-	UNKNOWN("unknown", "?"), //
-
-	/**
-	 * Empty state.
-	 */
-	EMPTY("empty", ""), //
-
-	/**
-	 * Protonated state.
-	 */
-	PROTONATED("protonated", "H"), //
-
-	/**
-	 * We don't care in which state it is.
-	 */
-	DONT_CARE("don't care", "*");
-
-	/**
-	 * Full name of the modification.
-	 */
-
-	private String fullName;
-	/**
-	 * Abbreviation used for the modification.
-	 */
-	private String abbreviation;
-
-	/**
-	 * Default constructor with the name and abbreviation.
-	 * 
-	 * @param name
-	 *          name used for this state
-	 * @param abbreviation
-	 *          abbreviation used in this state
-	 */
-	ModificationState(String name, String abbreviation) {
-		this.fullName = name;
-		this.abbreviation = abbreviation;
-	}
-
-	/**
-	 * @return the fullName
-	 * @see #fullName
-	 */
-	public String getFullName() {
-		return fullName;
-	}
-
-	/**
-	 * @return the abbreviation
-	 * @see #abbreviation
-	 */
-	public String getAbbreviation() {
-		return abbreviation;
-	}
-
-	/**
-	 * Returns {@link ModificationState} identified by the full name.
-	 * 
-	 * @param name
-	 *          full name of the state
-	 * @return {@link ModificationState} identified by the full name
-	 */
-	public static ModificationState getByName(String name) {
-		for (ModificationState state : values()) {
-			if (state.getFullName().equalsIgnoreCase(name)) {
-				return state;
-			}
-		}
-		return null;
-	}
-