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 1213df96ac1b3cb495499cfb166636eb1a3ee052..766abbbdefe37d5c1744182d3ee59f13bbcde3c1 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
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
+import java.awt.geom.Point2D;
+
import org.apache.log4j.Logger;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -23,151 +25,157 @@ import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
*/
public class AntisenseRnaXmlParser extends AbstractElementXmlParser<CellDesignerAntisenseRna, AntisenseRna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(AntisenseRnaXmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(AntisenseRnaXmlParser.class.getName());
+
+ /**
+ * List of {@link CellDesignerElement celldesigner elements} obtained during
+ * parsing process.
+ */
+ private CellDesignerElementCollection elements;
- /**
- * List of {@link CellDesignerElement celldesigner elements} obtained during
- * parsing process.
- */
- private CellDesignerElementCollection elements;
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * list of {@link CellDesignerElement celldesigner elements} obtained
+ * during parsing process
+ */
+ public AntisenseRnaXmlParser(CellDesignerElementCollection elements) {
+ this.elements = elements;
+ }
- /**
- * Default constructor.
- *
- * @param elements
- * list of {@link CellDesignerElement celldesigner elements} obtained
- * during parsing process
- */
- public AntisenseRnaXmlParser(CellDesignerElementCollection elements) {
- this.elements = elements;
- }
+ @Override
+ public Pair<String, CellDesignerAntisenseRna> parseXmlElement(Node antisenseRnaNode)
+ throws InvalidXmlSchemaException {
+ CellDesignerAntisenseRna antisenseRna = new CellDesignerAntisenseRna();
+ String identifier = getNodeAttr("id", antisenseRnaNode);
+ antisenseRna.setName(decodeName(getNodeAttr("name", antisenseRnaNode)));
+ NodeList list = antisenseRnaNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("celldesigner:notes")) {
+ antisenseRna.setNotes(getRap().getNotes(node));
+ } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
+ NodeList residueList = node.getChildNodes();
+ for (int j = 0; j < residueList.getLength(); j++) {
+ Node residueNode = residueList.item(j);
+ if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
+ antisenseRna.addRegion(getAntisenseRnaRegion(residueNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:antisenseRna " + node.getNodeName());
+ }
+ }
+ }
+ Pair<String, CellDesignerAntisenseRna> result = new Pair<String, CellDesignerAntisenseRna>(identifier,
+ antisenseRna);
+ return result;
+ }
- @Override
- public Pair<String, CellDesignerAntisenseRna> parseXmlElement(Node antisenseRnaNode) throws InvalidXmlSchemaException {
- CellDesignerAntisenseRna antisenseRna = new CellDesignerAntisenseRna();
- String identifier = getNodeAttr("id", antisenseRnaNode);
- antisenseRna.setName(decodeName(getNodeAttr("name", antisenseRnaNode)));
- NodeList list = antisenseRnaNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("celldesigner:notes")) {
- antisenseRna.setNotes(getRap().getNotes(node));
- } else if (node.getNodeName().equals("celldesigner:listOfRegions")) {
- NodeList residueList = node.getChildNodes();
- for (int j = 0; j < residueList.getLength(); j++) {
- Node residueNode = residueList.item(j);
- if (residueNode.getNodeType() == Node.ELEMENT_NODE) {
- if (residueNode.getNodeName().equalsIgnoreCase("celldesigner:region")) {
- antisenseRna.addRegion(getAntisenseRnaRegion(residueNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:listOfRegions " + residueNode.getNodeName());
- }
- }
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:antisenseRna " + node.getNodeName());
- }
- }
- }
- Pair<String, CellDesignerAntisenseRna> result = new Pair<String, CellDesignerAntisenseRna>(identifier, antisenseRna);
- return result;
- }
+ @Override
+ public String toXml(AntisenseRna antisenseRna) {
+ String attributes = "";
+ String result = "";
+ attributes += " id=\"ar_" + elements.getElementId(antisenseRna) + "\"";
+ if (!antisenseRna.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(encodeName(antisenseRna.getName())) + "\"";
+ }
+ result += "<celldesigner:AntisenseRNA" + attributes + ">";
+ result += "<celldesigner:notes>";
+ result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
- @Override
- public String toXml(AntisenseRna antisenseRna) {
- String attributes = "";
- String result = "";
- attributes += " id=\"ar_" + elements.getElementId(antisenseRna) + "\"";
- if (!antisenseRna.getName().equals("")) {
- attributes += " name=\"" + escapeXml(encodeName(antisenseRna.getName())) + "\"";
- }
- result += "<celldesigner:AntisenseRNA" + attributes + ">";
- result += "<celldesigner:notes>";
- result += "<html xmlns=\"http://www.w3.org/1999/xhtml\"><head><title/></head><body>";
+ RestAnnotationParser rap = new RestAnnotationParser();
+ result += rap.createAnnotationString(antisenseRna);
+ result += antisenseRna.getNotes();
+ result += "</body></html>";
+ result += "</celldesigner:notes>";
+ if (antisenseRna.getRegions().size() > 0) {
+ result += "<celldesigner:listOfRegions>";
+ for (AntisenseRnaRegion region : antisenseRna.getRegions()) {
+ result += toXml(region);
+ }
+ result += "</celldesigner:listOfRegions>";
+ }
+ result += "</celldesigner:AntisenseRNA>";
+ return result;
+ }
- RestAnnotationParser rap = new RestAnnotationParser();
- result += rap.createAnnotationString(antisenseRna);
- result += antisenseRna.getNotes();
- result += "</body></html>";
- result += "</celldesigner:notes>";
- if (antisenseRna.getRegions().size() > 0) {
- result += "<celldesigner:listOfRegions>";
- for (AntisenseRnaRegion region : antisenseRna.getRegions()) {
- result += toXml(region);
- }
- result += "</celldesigner:listOfRegions>";
- }
- result += "</celldesigner:AntisenseRNA>";
- return result;
- }
+ /**
+ * Transforms AntisenseRnaRegion into CellDEsigner xml representation.
+ *
+ * @param region
+ * object to be transformed
+ * @return xml representation of the given region
+ */
+ private String toXml(AntisenseRnaRegion region) {
+ String result = "";
+ String attributes = "";
+ if (!region.getIdAntisenseRnaRegion().equals("")) {
+ attributes += " id=\"" + region.getIdAntisenseRnaRegion() + "\"";
+ }
+ if (!region.getName().equals("")) {
+ attributes += " name=\"" + escapeXml(region.getName()) + "\"";
+ }
+ if (region.getSize() != 0) {
+ attributes += " size=\"" + region.getSize() + "\"";
+ }
+ if (region.getPosition() != null) {
+ double pos = (region.getPosition().getX() - region.getSpecies().getWidth())
+ / (region.getSpecies().getWidth() * 3 / 4);
- /**
- * Transforms AntisenseRnaRegion into CellDEsigner xml representation.
- *
- * @param region
- * object to be transformed
- * @return xml representation of the given region
- */
- private String toXml(AntisenseRnaRegion region) {
- String result = "";
- String attributes = "";
- if (!region.getIdAntisenseRnaRegion().equals("")) {
- attributes += " id=\"" + region.getIdAntisenseRnaRegion() + "\"";
- }
- if (!region.getName().equals("")) {
- attributes += " name=\"" + escapeXml(region.getName()) + "\"";
- }
- if (region.getSize() != 0) {
- attributes += " size=\"" + region.getSize() + "\"";
- }
- if (region.getPos() != 0) {
- attributes += " pos=\"" + region.getPos() + "\"";
- }
- if (region.getType() != null) {
- attributes += " type=\"" + region.getType().getName() + "\"";
- }
- result += "<celldesigner:region " + attributes + ">";
- result += "</celldesigner:region>";
+ attributes += " pos=\"" + pos + "\"";
+ }
+ if (region.getType() != null) {
+ attributes += " type=\"" + region.getType().getName() + "\"";
+ }
+ result += "<celldesigner:region " + attributes + ">";
+ result += "</celldesigner:region>";
- return result;
- }
+ return result;
+ }
- /**
- * Method that parse xml node into AntisenseRnaRegion element.
- *
- * @param regionNode
- * xml node to parse
- * @return AntisenseRnaRegion object from xml node
- * @throws InvalidXmlSchemaException
- * thrown when input xml node doesn't follow defined schema
- */
- private CellDesignerAntisenseRnaRegion getAntisenseRnaRegion(Node regionNode) throws InvalidXmlSchemaException {
- CellDesignerAntisenseRnaRegion residue = new CellDesignerAntisenseRnaRegion();
- residue.setIdAntisenseRnaRegion(getNodeAttr("id", regionNode));
- residue.setName(getNodeAttr("name", regionNode));
- residue.setSize(getNodeAttr("size", regionNode));
- residue.setPos(getNodeAttr("pos", regionNode));
- String typeString = getNodeAttr("type", regionNode);
- if (typeString != null) {
- AntisenseRnaRegionType type = AntisenseRnaRegionType.getTypeByString(typeString);
- if (type == null) {
- throw new InvalidXmlSchemaException("Unknown antisense rna region type: " + typeString);
- }
- residue.setType(type);
- }
- NodeList list = regionNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
- }
- }
- return residue;
- }
+ /**
+ * Method that parse xml node into AntisenseRnaRegion element.
+ *
+ * @param regionNode
+ * xml node to parse
+ * @return AntisenseRnaRegion object from xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when input xml node doesn't follow defined schema
+ */
+ private CellDesignerAntisenseRnaRegion getAntisenseRnaRegion(Node regionNode) throws InvalidXmlSchemaException {
+ CellDesignerAntisenseRnaRegion residue = new CellDesignerAntisenseRnaRegion();
+ residue.setIdAntisenseRnaRegion(getNodeAttr("id", regionNode));
+ residue.setName(getNodeAttr("name", regionNode));
+ residue.setSize(getNodeAttr("size", regionNode));
+ residue.setPos(getNodeAttr("pos", regionNode));
+ String typeString = getNodeAttr("type", regionNode);
+ if (typeString != null) {
+ AntisenseRnaRegionType type = AntisenseRnaRegionType.getTypeByString(typeString);
+ if (type == null) {
+ throw new InvalidXmlSchemaException("Unknown antisense rna region type: " + typeString);
+ }
+ residue.setType(type);
+ }
+ NodeList list = regionNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:region " + node.getNodeName());
+ }
+ }
+ return residue;
+ }
}
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 e3456b1c883be2e35b467ce847c334b709a798fa..c69ba1a709b52ea2cfcb1ff8c4fae717c5075713 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
@@ -1,150 +1,149 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-/**
- * Class representing CellDesigner {@link AntisenseRna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerAntisenseRna.class);
-
- /**
- * List of antisense rna regions (some rna sequences) in this object.
- */
- private List<CellDesignerAntisenseRnaRegion> regions = new ArrayList<CellDesignerAntisenseRnaRegion>();
-
- /**
- * Constructor that copies the data from species given in the argument.
- *
- * @param species
- * parent species from which we want to copy data
- */
- public CellDesignerAntisenseRna(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerAntisenseRna) {
- CellDesignerAntisenseRna asRna = (CellDesignerAntisenseRna) species;
- for (CellDesignerAntisenseRnaRegion region : asRna.getRegions()) {
- addRegion(new CellDesignerAntisenseRnaRegion(region));
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerAntisenseRna() {
- super();
- }
-
- @Override
- public CellDesignerAntisenseRna copy() {
- if (this.getClass() == CellDesignerAntisenseRna.class) {
- return new CellDesignerAntisenseRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * Addd antisense rna region (part of rna sequence that has some meaning) to
- * the object. If the region with given id exists then the data of this region
- * is copied to the one that is already in the
- * {@link CellDesignerAntisenseRna}.
- *
- *
- * @param region
- * region to add
- */
- public void addRegion(CellDesignerAntisenseRnaRegion region) {
- for (CellDesignerAntisenseRnaRegion region2 : regions) {
- if (region2.getIdAntisenseRnaRegion().equals(region.getIdAntisenseRnaRegion())) {
- region2.update(region);
- return;
- }
- }
-
- regions.add(region);
- region.setSpecies(this);
- }
-
- @Override
- public void update(CellDesignerSpecies<?> sp) {
- super.update(sp);
- if (sp instanceof CellDesignerAntisenseRna) {
- CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
- for (CellDesignerAntisenseRnaRegion mr : getRegions()) {
- mr.setState(null);
- }
-
- for (CellDesignerAntisenseRnaRegion region : rna.getRegions()) {
- updateRegion(region);
- }
- }
- }
-
- /**
- * Method update antisense rna region from the object in params (if the object
- * with the same id already exists). If there is no object with given id then
- * new object is added to antisense rna.
- *
- * @param param
- * - object with new data from where update should be performed
- */
- private void updateRegion(CellDesignerAntisenseRnaRegion param) {
- for (CellDesignerAntisenseRnaRegion region : regions) {
- if (region.getIdAntisenseRnaRegion().equals(param.getIdAntisenseRnaRegion())) {
- region.update(param);
- return;
- }
- }
- regions.add(param);
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<CellDesignerAntisenseRnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<CellDesignerAntisenseRnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public AntisenseRna createModelElement(String aliasId) {
- AntisenseRna result = new AntisenseRna(aliasId);
- super.setModelObjectFields(result);
- for (CellDesignerAntisenseRnaRegion region : regions) {
- result.addRegion(region.createAntisenseRegionAlias());
- }
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+
+/**
+ * Class representing CellDesigner {@link AntisenseRna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerAntisenseRna extends CellDesignerSpecies<AntisenseRna> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerAntisenseRna.class);
+
+ /**
+ * List of antisense rna regions (some rna sequences) in this object.
+ */
+ private List<CellDesignerAntisenseRnaRegion> regions = new ArrayList<CellDesignerAntisenseRnaRegion>();
+
+ /**
+ * Constructor that copies the data from species given in the argument.
+ *
+ * @param species
+ * parent species from which we want to copy data
+ */
+ public CellDesignerAntisenseRna(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna asRna = (CellDesignerAntisenseRna) species;
+ for (CellDesignerAntisenseRnaRegion region : asRna.getRegions()) {
+ addRegion(new CellDesignerAntisenseRnaRegion(region));
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerAntisenseRna() {
+ super();
+ }
+
+ @Override
+ public CellDesignerAntisenseRna copy() {
+ if (this.getClass() == CellDesignerAntisenseRna.class) {
+ return new CellDesignerAntisenseRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Addd antisense rna region (part of rna sequence that has some meaning) to the
+ * object. If the region with given id exists then the data of this region is
+ * copied to the one that is already in the {@link CellDesignerAntisenseRna}.
+ *
+ *
+ * @param region
+ * region to add
+ */
+ public void addRegion(CellDesignerAntisenseRnaRegion region) {
+ for (CellDesignerAntisenseRnaRegion region2 : regions) {
+ if (region2.getIdAntisenseRnaRegion().equals(region.getIdAntisenseRnaRegion())) {
+ region2.update(region);
+ return;
+ }
+ }
+
+ regions.add(region);
+ region.setSpecies(this);
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> sp) {
+ super.update(sp);
+ if (sp instanceof CellDesignerAntisenseRna) {
+ CellDesignerAntisenseRna rna = (CellDesignerAntisenseRna) sp;
+ for (CellDesignerAntisenseRnaRegion mr : getRegions()) {
+ mr.setState(null);
+ }
+
+ for (CellDesignerAntisenseRnaRegion region : rna.getRegions()) {
+ updateRegion(region);
+ }
+ }
+ }
+
+ /**
+ * Method update antisense rna region from the object in params (if the object
+ * with the same id already exists). If there is no object with given id then
+ * new object is added to antisense rna.
+ *
+ * @param param
+ * - object with new data from where update should be performed
+ */
+ private void updateRegion(CellDesignerAntisenseRnaRegion param) {
+ for (CellDesignerAntisenseRnaRegion region : regions) {
+ if (region.getIdAntisenseRnaRegion().equals(param.getIdAntisenseRnaRegion())) {
+ region.update(param);
+ return;
+ }
+ }
+ regions.add(param);
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<CellDesignerAntisenseRnaRegion> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<CellDesignerAntisenseRnaRegion> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public AntisenseRna createModelElement(String aliasId) {
+ AntisenseRna result = new AntisenseRna(aliasId);
+ super.setModelObjectFields(result);
+ for (CellDesignerAntisenseRnaRegion region : regions) {
+ result.addRegion(region.createAntisenseRegionAlias(result));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
index 36decddc98a49f81ef86a92f4431a0349825d4c2..ec607f2dfe74a03e05ba368aca803372a4b84339 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerAntisenseRnaRegion.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+import java.awt.geom.Point2D;
import java.io.Serializable;
import org.apache.log4j.Logger;
@@ -7,6 +8,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -22,313 +24,316 @@ import lcsb.mapviewer.model.map.species.field.ModificationState;
*/
public class CellDesignerAntisenseRnaRegion implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default size of the object (in graphical representation).
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerAntisenseRnaRegion.class.getName());
-
- /**
- * Unique identifier in the database.
- */
- private int id;
-
- /**
- * String identifier of the element. Unique in the model.
- */
- private String idAntisenseRnaRegion = "";
-
- /**
- * Name of the region.
- */
- private String name = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- private ModificationState state = null;
-
- /**
- * Type of the region in the rna. There are three possible values:
- * <ul>
- * <li>Coding region,</li>
- * <li>Protein binding domain,</li>
- * <li>Modification site.</li>
- * </ul>
- */
- private AntisenseRnaRegionType type;
-
- /**
- * Size of the region in the graphic representation.
- */
- private double size = DEFAULT_SIZE;
-
- /**
- * Position on the species in graphic representation.
- */
- private Double pos;
-
- /**
- * Defines a species where the region belongs to.
- */
- private CellDesignerAntisenseRna species;
-
- /**
- * Default constructor.
- */
- public CellDesignerAntisenseRnaRegion() {
-
- }
-
- /**
- * Constructor that initialize object with the data from the parameter.
- *
- * @param original
- * object from which we initialize data
- */
- public CellDesignerAntisenseRnaRegion(CellDesignerAntisenseRnaRegion original) {
- this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
- this.name = original.name;
- this.size = original.size;
- this.pos = original.pos;
- this.type = original.type;
- }
-
- /**
- * Creates a copy of current object.
- *
- * @return copy of the object
- */
- public CellDesignerAntisenseRnaRegion copy() {
- if (this.getClass() == CellDesignerAntisenseRnaRegion.class) {
- return new CellDesignerAntisenseRnaRegion(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
-
- }
-
- /**
- * Sets size from the string.
- *
- * @param text
- * size to parse and set
- * @see #size
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
- }
-
- /**
- * Sets position from the string.
- *
- * @param text
- * position to parse and set
- * @see #pos
- */
- public void setPos(String text) {
- try {
- pos = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
- }
-
- /**
- * Update data in this object from parameter (only if values in parameter
- * object are valid).
- *
- * @param mr
- * object from which we are updating data
- */
- public void update(CellDesignerAntisenseRnaRegion mr) {
- if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("") && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
- throw new InvalidArgumentException("Cannot update from mr with different id");
- }
- this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
- if (mr.getName() != null) {
- this.name = mr.getName();
- }
- if (mr.getPos() != null) {
- this.setPos(mr.getPos());
- }
-
- }
-
- @Override
- public String toString() {
- String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPos() + "," + getSize() + ",";
- return result;
- }
-
- /**
- * @return the idAntisenseRnaRegion
- * @see #idAntisenseRnaRegion
- */
- public String getIdAntisenseRnaRegion() {
- return idAntisenseRnaRegion;
- }
-
- /**
- * @param idAntisenseRnaRegion
- * the id to set
- * @see #idAntisenseRnaRegion
- */
- public void setIdAntisenseRnaRegion(String idAntisenseRnaRegion) {
- this.idAntisenseRnaRegion = idAntisenseRnaRegion;
- }
-
- /**
- * @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 type
- * @see #type
- */
- public AntisenseRnaRegionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(AntisenseRnaRegionType type) {
- this.type = type;
- }
-
- /**
- * @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 pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- * @see #pos
- */
- public void setPos(Double pos) {
- this.pos = pos;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public CellDesignerAntisenseRna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(CellDesignerAntisenseRna species) {
- this.species = species;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Creates model representation of {@link AntisenseRnaRegion}.
- *
- * @return {@link AntisenseRnaRegion} representing this object in a model
- */
- public AntisenseRnaRegion createAntisenseRegionAlias() {
- AntisenseRnaRegion result = new AntisenseRnaRegion();
- result.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
- result.setName(name);
- result.setSize(size);
- result.setPos(pos);
- result.setType(type);
- return result;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default size of the object (in graphical representation).
+ */
+ private static final double DEFAULT_SIZE = 0.1;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerAntisenseRnaRegion.class.getName());
+
+ /**
+ * Unique identifier in the database.
+ */
+ private int id;
+
+ /**
+ * String identifier of the element. Unique in the model.
+ */
+ private String idAntisenseRnaRegion = "";
+
+ /**
+ * Name of the region.
+ */
+ private String name = "";
+
+ /**
+ * Defines a state of the region (for instance ubiquitinated etc).
+ *
+ * @see ModificationState
+ */
+ private ModificationState state = null;
+
+ /**
+ * Type of the region in the rna. There are three possible values:
+ * <ul>
+ * <li>Coding region,</li>
+ * <li>Protein binding domain,</li>
+ * <li>Modification site.</li>
+ * </ul>
+ */
+ private AntisenseRnaRegionType type;
+
+ /**
+ * Size of the region in the graphic representation.
+ */
+ private double size = DEFAULT_SIZE;
+
+ /**
+ * Position on the species in graphic representation.
+ */
+ private Double pos;
+
+ /**
+ * Defines a species where the region belongs to.
+ */
+ private CellDesignerAntisenseRna species;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerAntisenseRnaRegion() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public CellDesignerAntisenseRnaRegion(CellDesignerAntisenseRnaRegion original) {
+ this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
+ this.name = original.name;
+ this.size = original.size;
+ this.pos = original.pos;
+ this.type = original.type;
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public CellDesignerAntisenseRnaRegion copy() {
+ if (this.getClass() == CellDesignerAntisenseRnaRegion.class) {
+ return new CellDesignerAntisenseRnaRegion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+
+ /**
+ * Sets size from the string.
+ *
+ * @param text
+ * size to parse and set
+ * @see #size
+ */
+ public void setSize(String text) {
+ try {
+ size = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+ }
+
+ /**
+ * Sets position from the string.
+ *
+ * @param text
+ * position to parse and set
+ * @see #pos
+ */
+ public void setPos(String text) {
+ try {
+ pos = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid pos: " + text, e);
+ }
+ }
+
+ /**
+ * Update data in this object from parameter (only if values in parameter object
+ * are valid).
+ *
+ * @param mr
+ * object from which we are updating data
+ */
+ public void update(CellDesignerAntisenseRnaRegion mr) {
+ if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("")
+ && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
+ throw new InvalidArgumentException("Cannot update from mr with different id");
+ }
+ this.size = mr.getSize();
+ if (mr.getState() != null) {
+ this.state = mr.getState();
+ }
+ if (mr.getName() != null) {
+ this.name = mr.getName();
+ }
+ if (mr.getPos() != null) {
+ this.setPos(mr.getPos());
+ }
+
+ }
+
+ @Override
+ public String toString() {
+ String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPos() + "," + getSize()
+ + ",";
+ return result;
+ }
+
+ /**
+ * @return the idAntisenseRnaRegion
+ * @see #idAntisenseRnaRegion
+ */
+ public String getIdAntisenseRnaRegion() {
+ return idAntisenseRnaRegion;
+ }
+
+ /**
+ * @param idAntisenseRnaRegion
+ * the id to set
+ * @see #idAntisenseRnaRegion
+ */
+ public void setIdAntisenseRnaRegion(String idAntisenseRnaRegion) {
+ this.idAntisenseRnaRegion = idAntisenseRnaRegion;
+ }
+
+ /**
+ * @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 type
+ * @see #type
+ */
+ public AntisenseRnaRegionType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(AntisenseRnaRegionType type) {
+ this.type = type;
+ }
+
+ /**
+ * @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 pos
+ * @see #pos
+ */
+ public Double getPos() {
+ return pos;
+ }
+
+ /**
+ * @param pos
+ * the pos to set
+ * @see #pos
+ */
+ public void setPos(Double pos) {
+ this.pos = pos;
+ }
+
+ /**
+ * @return the species
+ * @see #species
+ */
+ public CellDesignerAntisenseRna getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(CellDesignerAntisenseRna species) {
+ this.species = species;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * Creates model representation of {@link AntisenseRnaRegion}.
+ *
+ * @return {@link AntisenseRnaRegion} representing this object in a model
+ */
+ public AntisenseRnaRegion createAntisenseRegionAlias(Element element) {
+ AntisenseRnaRegion result = new AntisenseRnaRegion();
+ result.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
+ result.setName(name);
+ result.setSize(size);
+
+ result.setPosition(new Point2D.Double(element.getX() + element.getWidth() * 3.0 / 4.0 * pos, element.getY()));
+ result.setType(type);
+ return result;
+ }
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index f8b7777cdc7a41ecf1397b49f59c5ff9c86d61e8..f2ee56366f204beddcebf3bd30f791573ac36442 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -1,151 +1,144 @@
-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.Stroke;
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.GeneralPath;
-import java.awt.geom.Path2D;
-import java.awt.geom.PathIterator;
-import java.awt.geom.Point2D;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-
-/**
- * This class defines methods used for drawing {@link AntisenseRna} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-
-public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public AntisenseRnaConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getAntisenseRnaPath(antisenseRna);
- Color c = graphics.getColor();
- graphics.setColor(antisenseRna.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(antisenseRna));
- graphics.draw(path);
- graphics.setStroke(stroke);
-
- for (AntisenseRnaRegion mr : antisenseRna.getRegions()) {
- drawRegion(antisenseRna, mr, graphics, false, false);
- }
-
- drawText(antisenseRna, graphics, params);
- }
-
- /**
- * Returns {@link AntisenseRna} border as a {@link GeneralPath} object.
- *
- * @param antisenseRna
- * {@link AntisenseRna} for which we want to get border
- * @return border of the {@link AntisenseRna}
- */
- private GeneralPath getAntisenseRnaPath(final AntisenseRna antisenseRna) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
- path.moveTo(antisenseRna.getX(), antisenseRna.getY());
- path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() * 3 / 4, antisenseRna.getY());
- path.lineTo(antisenseRna.getX() + antisenseRna.getWidth(), antisenseRna.getY() + antisenseRna.getHeight());
- path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() / 4, antisenseRna.getY() + antisenseRna.getHeight());
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final AntisenseRna alias) {
- return getAntisenseRnaPath(alias).getPathIterator(new AffineTransform());
- }
-
- /**
- * This method draws antisense rna region for given alias.
- *
- * @param antisenseRna
- * {@link AntisenseRna} on which region should be drawn
- * @param region
- * {@link AntisenseRnaRegion} to be drawn
- * @param graphics
- * {@link Graphics2D} where we draw region
- * @param drawEmptyRegion
- * flag determining if we shoudl draw empty regions
- * @param drawDescription
- * flag determining if we want to draw description as well
- */
- private void drawRegion(final AntisenseRna antisenseRna, final AntisenseRnaRegion region, final Graphics2D graphics, final boolean drawEmptyRegion,
- final boolean drawDescription) {
- if ((!drawEmptyRegion) && (region.getState() == null)) {
- return;
- }
- double diameter = DEFAULT_MODIFICATION_DIAMETER;
-
- double x = antisenseRna.getX();
- double y = antisenseRna.getY();
-
- double width = antisenseRna.getWidth();
-
- // CHECKSTYLE:OFF
- // we draw modifier on the upper border of antisense rna (which is only in
- // 3/4 of the width of alias)
- Point2D p = new Point2D.Double(x + width * 3.0 / 4.0 * region.getPos(), y - diameter);
- // CHECKSTYLE:ON
-
- Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
- Color c = graphics.getColor();
- graphics.setColor(Color.WHITE);
- graphics.fill(ellipse);
- graphics.setColor(c);
- graphics.draw(ellipse);
- graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
-
- String text = region.getName();
- if (!text.equals("") && drawDescription) {
- double textWidth = graphics.getFontMetrics().stringWidth(text);
- Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
- graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
- }
- ModificationState state = region.getState();
- if (state != null) {
- String str = state.getAbbreviation();
- Font tmpFont = graphics.getFont();
- graphics.setFont(getStructuralFont());
- double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
- double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
- graphics.drawString(str, (int) textX, (int) textY);
- graphics.setFont(tmpFont);
- }
-
- }
-}
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.Stroke;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Path2D;
+import java.awt.geom.PathIterator;
+import java.awt.geom.Point2D;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+/**
+ * This class defines methods used for drawing {@link AntisenseRna} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+
+public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AntisenseRnaConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public AntisenseRnaConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getAntisenseRnaPath(antisenseRna);
+ Color c = graphics.getColor();
+ graphics.setColor(antisenseRna.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(antisenseRna));
+ graphics.draw(path);
+ graphics.setStroke(stroke);
+
+ for (AntisenseRnaRegion mr : antisenseRna.getRegions()) {
+ drawRegion(antisenseRna, mr, graphics, false, false);
+ }
+
+ drawText(antisenseRna, graphics, params);
+ }
+
+ /**
+ * Returns {@link AntisenseRna} border as a {@link GeneralPath} object.
+ *
+ * @param antisenseRna
+ * {@link AntisenseRna} for which we want to get border
+ * @return border of the {@link AntisenseRna}
+ */
+ private GeneralPath getAntisenseRnaPath(final AntisenseRna antisenseRna) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
+ path.moveTo(antisenseRna.getX(), antisenseRna.getY());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() * 3 / 4, antisenseRna.getY());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth(), antisenseRna.getY() + antisenseRna.getHeight());
+ path.lineTo(antisenseRna.getX() + antisenseRna.getWidth() / 4, antisenseRna.getY() + antisenseRna.getHeight());
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final AntisenseRna alias) {
+ return getAntisenseRnaPath(alias).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * This method draws antisense rna region for given alias.
+ *
+ * @param antisenseRna
+ * {@link AntisenseRna} on which region should be drawn
+ * @param region
+ * {@link AntisenseRnaRegion} to be drawn
+ * @param graphics
+ * {@link Graphics2D} where we draw region
+ * @param drawEmptyRegion
+ * flag determining if we should draw empty regions
+ * @param drawDescription
+ * flag determining if we want to draw description as well
+ */
+ private void drawRegion(final AntisenseRna antisenseRna, final AntisenseRnaRegion region, final Graphics2D graphics,
+ final boolean drawEmptyRegion, final boolean drawDescription) {
+ if ((!drawEmptyRegion) && (region.getState() == null)) {
+ return;
+ }
+ double diameter = DEFAULT_MODIFICATION_DIAMETER;
+
+ double y = antisenseRna.getY();
+
+ Point2D p = new Point2D.Double(region.getPosition().getX(), region.getPosition().getY() - diameter);
+
+ Ellipse2D ellipse = new Ellipse2D.Double(p.getX() - diameter / 2, p.getY() - diameter / 2, diameter, diameter);
+ Color c = graphics.getColor();
+ graphics.setColor(Color.WHITE);
+ graphics.fill(ellipse);
+ graphics.setColor(c);
+ graphics.draw(ellipse);
+ graphics.drawLine((int) p.getX(), (int) (p.getY() + diameter / 2), (int) p.getX(), (int) y);
+
+ String text = region.getName();
+ if (!text.equals("") && drawDescription) {
+ double textWidth = graphics.getFontMetrics().stringWidth(text);
+ Point2D p2 = new Point2D.Double(p.getX() - textWidth / 2, p.getY() - DEFAULT_SPECIES_MODIFIER_FONT_SIZE);
+ graphics.drawString(text, (int) p2.getX(), (int) p2.getY());
+ }
+ ModificationState state = region.getState();
+ if (state != null) {
+ String str = state.getAbbreviation();
+ Font tmpFont = graphics.getFont();
+ graphics.setFont(getStructuralFont());
+ double textX = p.getX() - graphics.getFontMetrics().stringWidth(str) / 2;
+ double textY = p.getY() + graphics.getFontMetrics().getAscent() / 2;
+ graphics.drawString(str, (int) textX, (int) textY);
+ graphics.setFont(tmpFont);
+ }
+
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
index 2208709e2dcc5975e740f76c339de0e5dedbf255..a7e3916c2ac693e2cc945458a86d253aa7058fef 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRna.java
@@ -1,113 +1,113 @@
-package lcsb.mapviewer.model.map.species;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.LazyCollection;
-import org.hibernate.annotations.LazyCollectionOption;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-
-/**
- * Entity representing antisense rna element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
-public class AntisenseRna extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of {@link AntisenseRnaRegion regions} related to this
- * {@link AntisenseRna}.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species")
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<AntisenseRnaRegion> regions = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- AntisenseRna() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public AntisenseRna(AntisenseRna original) {
- super(original);
- for (AntisenseRnaRegion region : original.getRegions()) {
- addRegion(new AntisenseRnaRegion(region));
- }
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public AntisenseRna(String elementId) {
- setElementId(elementId);
- }
-
- /**
- * Adds {@link AntisenseRnaRegion} to the object.
- *
- * @param antisenseRnaRegion
- * alement to be added
- */
- public void addRegion(AntisenseRnaRegion antisenseRnaRegion) {
- regions.add(antisenseRnaRegion);
- antisenseRnaRegion.setSpecies(this);
- }
-
- @Override
- public AntisenseRna copy() {
- if (this.getClass() == AntisenseRna.class) {
- return new AntisenseRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<AntisenseRnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<AntisenseRnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public String getStringType() {
- return "Antisense RNA";
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+import javax.persistence.OneToMany;
+
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
+
+/**
+ * Entity representing antisense rna element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("ANTISENSE_RNA_ALIAS")
+public class AntisenseRna extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of {@link AntisenseRnaRegion regions} related to this
+ * {@link AntisenseRna}.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species")
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<AntisenseRnaRegion> regions = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ AntisenseRna() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public AntisenseRna(AntisenseRna original) {
+ super(original);
+ for (AntisenseRnaRegion region : original.getRegions()) {
+ addRegion(new AntisenseRnaRegion(region));
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * unique (within model) element identifier
+ */
+ public AntisenseRna(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link AntisenseRnaRegion} to the object.
+ *
+ * @param antisenseRnaRegion
+ * region to be added
+ */
+ public void addRegion(AntisenseRnaRegion antisenseRnaRegion) {
+ regions.add(antisenseRnaRegion);
+ antisenseRnaRegion.setSpecies(this);
+ }
+
+ @Override
+ public AntisenseRna copy() {
+ if (this.getClass() == AntisenseRna.class) {
+ return new AntisenseRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<AntisenseRnaRegion> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<AntisenseRnaRegion> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Antisense RNA";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
index ed51da8943b7682fb0ee357f8d9c5b7ee01377fc..fe74b066d00d68fd350c1238db92180091c96528 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegion.java
@@ -1,341 +1,322 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import java.io.Serializable;
-
-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.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-
-/**
- * This structure contains information about antisense rna region (rna fragment
- * of interest) for a specific {@link AntisenseRna}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "antisense_rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class AntisenseRnaRegion implements Serializable, ElementModification {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default size of the object (in graphical representation).
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AntisenseRnaRegion.class);
-
- /**
- * Unique identifier in the database.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "iddb", unique = true, nullable = false)
- private int id;
-
- /**
- * String identifier of the element. Unique in the model.
- */
- @Column(name = "idantisensernaregion")
- private String idAntisenseRnaRegion = "";
-
- /**
- * Name of the region.
- */
- @Column(name = "name")
- private String name = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- @Column(name = "state")
- private ModificationState state = null;
-
- /**
- * Type of the region in the rna. There are three possible values:
- * <ul>
- * <li>Coding region,</li>
- * <li>Protein binding domain,</li>
- * <li>Modification site.</li>
- * </ul>
- */
- @Column(name = "type")
- private AntisenseRnaRegionType type;
-
- /**
- * Size of the region in the graphic representation.
- */
- @Column(name = "size")
- private double size = DEFAULT_SIZE;
-
- /**
- * Position on the species in graphic representation.
- */
- @Column(name = "pos")
- private Double pos;
-
- /**
- * Defines a species where the region belongs to.
- */
- @Cascade({ CascadeType.ALL })
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private AntisenseRna species;
-
- /**
- * Default constructor.
- */
- public AntisenseRnaRegion() {
-
- }
-
- /**
- * Constructor that initialize object with the data from the parameter.
- *
- * @param original
- * object from which we initialize data
- */
- public AntisenseRnaRegion(AntisenseRnaRegion original) {
- this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
- this.name = original.name;
- this.size = original.size;
- this.pos = original.pos;
- this.type = original.type;
- }
-
- /**
- * Creates a copy of current object.
- *
- * @return copy of the object
- */
- public AntisenseRnaRegion copy() {
- if (this.getClass() == AntisenseRnaRegion.class) {
- return new AntisenseRnaRegion(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
-
- }
-
- /**
- * Sets size from the string.
- *
- * @param text
- * size to parse and set
- * @see #size
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
- }
-
- /**
- * Sets position from the string.
- *
- * @param text
- * position to parse and set
- * @see #pos
- */
- public void setPos(String text) {
- try {
- pos = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
- }
-
- /**
- * Update data in this object from parameter (only if values in parameter
- * object are valid).
- *
- * @param mr
- * object from which we are updating data
- */
- public void update(AntisenseRnaRegion mr) {
- if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("") && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
- throw new InvalidArgumentException("Cannot update from mr with different id");
- }
- this.size = mr.getSize();
- if (mr.getState() != null) {
- this.state = mr.getState();
- }
- if (mr.getName() != null) {
- this.name = mr.getName();
- }
- if (mr.getPos() != null) {
- this.setPos(mr.getPos());
- }
-
- }
-
- @Override
- public String toString() {
- String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPos() + "," + getSize() + ",";
- return result;
- }
-
- /**
- * @return the idAntisenseRnaRegion
- * @see #idAntisenseRnaRegion
- */
- public String getIdAntisenseRnaRegion() {
- return idAntisenseRnaRegion;
- }
-
- /**
- * @param idAntisenseRnaRegion
- * the id to set
- * @see #idAntisenseRnaRegion
- */
- public void setIdAntisenseRnaRegion(String idAntisenseRnaRegion) {
- this.idAntisenseRnaRegion = idAntisenseRnaRegion;
- }
-
- /**
- * @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 type
- * @see #type
- */
- public AntisenseRnaRegionType getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(AntisenseRnaRegionType type) {
- this.type = type;
- }
-
- /**
- * @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 pos
- * @see #pos
- */
- public Double getPos() {
- return pos;
- }
-
- /**
- * @param pos
- * the pos to set
- * @see #pos
- */
- public void setPos(Double pos) {
- this.pos = pos;
- }
-
- /**
- * @return the species
- * @see #species
- */
- public AntisenseRna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(AntisenseRna species) {
- this.species = species;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+
+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.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Type;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+
+/**
+ * This structure contains information about antisense rna region (rna fragment
+ * of interest) for a specific {@link AntisenseRna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "antisense_rna_region_table")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+public class AntisenseRnaRegion implements Serializable, ElementModification {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default size of the object (in graphical representation).
+ */
+ private static final double DEFAULT_SIZE = 0.1;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(AntisenseRnaRegion.class);
+
+ /**
+ * Unique identifier in the database.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "iddb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * String identifier of the element. Unique in the model.
+ */
+ @Column(name = "idantisensernaregion")
+ private String idAntisenseRnaRegion = "";
+
+ /**
+ * Name of the region.
+ */
+ @Column(name = "name")
+ private String name = "";
+
+ /**
+ * Defines a state of the region (for instance ubiquitinated etc).
+ *
+ * @see ModificationState
+ */
+ @Column(name = "state")
+ private ModificationState state = null;
+
+ /**
+ * Type of the region in the rna. There are three possible values:
+ * <ul>
+ * <li>Coding region,</li>
+ * <li>Protein binding domain,</li>
+ * <li>Modification site.</li>
+ * </ul>
+ */
+ @Column(name = "type")
+ private AntisenseRnaRegionType type;
+
+ /**
+ * Size of the region in the graphic representation.
+ */
+ @Column(name = "size")
+ private double size = DEFAULT_SIZE;
+
+ /**
+ * Position on the species in graphic representation.
+ */
+ @Column(name = "position")
+ @Type(type = "lcsb.mapviewer.persist.mapper.Point2DMapper")
+ private Point2D position;
+
+ /**
+ * Defines a species where the region belongs to.
+ */
+ @Cascade({ CascadeType.ALL })
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = "idSpeciesDb")
+ private AntisenseRna species;
+
+ /**
+ * Default constructor.
+ */
+ public AntisenseRnaRegion() {
+
+ }
+
+ /**
+ * Constructor that initialize object with the data from the parameter.
+ *
+ * @param original
+ * object from which we initialize data
+ */
+ public AntisenseRnaRegion(AntisenseRnaRegion original) {
+ this.idAntisenseRnaRegion = original.idAntisenseRnaRegion;
+ this.name = original.name;
+ this.size = original.size;
+ this.type = original.type;
+ this.setPosition(original.getPosition());
+ }
+
+ /**
+ * Creates a copy of current object.
+ *
+ * @return copy of the object
+ */
+ public AntisenseRnaRegion copy() {
+ if (this.getClass() == AntisenseRnaRegion.class) {
+ return new AntisenseRnaRegion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+
+ }
+
+ /**
+ * Sets size from the string.
+ *
+ * @param text
+ * size to parse and set
+ * @see #size
+ */
+ public void setSize(String text) {
+ try {
+ size = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+ }
+
+ /**
+ * Update data in this object from parameter (only if values in parameter object
+ * are valid).
+ *
+ * @param mr
+ * object from which we are updating data
+ */
+ public void update(AntisenseRnaRegion mr) {
+ if (this.idAntisenseRnaRegion != null && !this.idAntisenseRnaRegion.equals("")
+ && !this.idAntisenseRnaRegion.equals(mr.getIdAntisenseRnaRegion())) {
+ throw new InvalidArgumentException("Cannot update from mr with different id");
+ }
+ this.size = mr.getSize();
+ if (mr.getState() != null) {
+ this.state = mr.getState();
+ }
+ if (mr.getName() != null) {
+ this.name = mr.getName();
+ }
+ if (mr.getPosition() != null) {
+ this.setPosition(mr.getPosition());
+ }
+
+ }
+
+ @Override
+ public String toString() {
+ String result = getIdAntisenseRnaRegion() + "," + getName() + "," + getType() + "," + getPosition() + ","
+ + getSize() + ",";
+ return result;
+ }
+
+ /**
+ * @return the idAntisenseRnaRegion
+ * @see #idAntisenseRnaRegion
+ */
+ public String getIdAntisenseRnaRegion() {
+ return idAntisenseRnaRegion;
+ }
+
+ /**
+ * @param idAntisenseRnaRegion
+ * the id to set
+ * @see #idAntisenseRnaRegion
+ */
+ public void setIdAntisenseRnaRegion(String idAntisenseRnaRegion) {
+ this.idAntisenseRnaRegion = idAntisenseRnaRegion;
+ }
+
+ /**
+ * @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 type
+ * @see #type
+ */
+ public AntisenseRnaRegionType getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(AntisenseRnaRegionType type) {
+ this.type = type;
+ }
+
+ /**
+ * @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 AntisenseRna getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(AntisenseRna species) {
+ this.species = species;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ public Point2D getPosition() {
+ return position;
+ }
+
+ public void setPosition(Point2D position) {
+ this.position = position;
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
index 690e5c3e23d2e03934ca30e16ceeedd2feede7bd..3f8a0ab1488b511949afc0cc9b7cddc8212d8fd9 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparatorTest.java
@@ -4,6 +4,8 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.awt.geom.Point2D;
+
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -81,7 +83,7 @@ public class AntisenseRnaComparatorTest {
result.addRegion(region1);
region1.setIdAntisenseRnaRegion("a");
region1.setName("name");
- region1.setPos("1");
+ region1.setPosition(new Point2D.Double(0, 1));
region1.setSize("2");
region1.setType(AntisenseRnaRegionType.CODING_REGION);
return result;
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
index a84a65a85391024557a6268a2551a156cd78bcf4..9f91ffb5ad4bff39f4fd1a5827c0237b8b0bf963 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AntisenseRnaRegionTest.java
@@ -1,170 +1,164 @@
-package lcsb.mapviewer.model.map.species.field;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import org.apache.commons.lang3.SerializationUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
-import lcsb.mapviewer.model.map.species.Drug;
-
-public class AntisenseRnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new AntisenseRnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion(antisenseRna);
- assertNotNull(antisenseRna2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- antisenseRna.setState(ModificationState.EMPTY);
- antisenseRna.setName("as");
- antisenseRna.setPos(3.0);
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
- antisenseRna2.update(antisenseRna);
- assertEquals(antisenseRna.getState(), antisenseRna2.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidUpdate() {
- try {
- AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
- AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
- antisenseRna.setIdAntisenseRnaRegion("@1");
- antisenseRna2.setIdAntisenseRnaRegion("@");
- antisenseRna2.update(antisenseRna);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- AntisenseRnaRegion region = new AntisenseRnaRegion(new AntisenseRnaRegion());
- int id = 91;
- AntisenseRna species = new AntisenseRna("id");
- double pos = 4.6;
- double size = 5.3;
- AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
- String name = "nam";
- String idAntisenseRnaRegion = "iddd";
-
- region.setId(id);
- region.setSpecies(species);
- region.setPos(pos);
- region.setSize(size);
- region.setType(type);
- region.setName(name);
- region.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
- region.setState(ModificationState.ACETYLATED);
-
- assertEquals(id, region.getId());
- assertEquals(species, region.getSpecies());
- assertEquals(pos, region.getPos(), Configuration.EPSILON);
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(type, region.getType());
- assertEquals(name, region.getName());
- assertEquals(idAntisenseRnaRegion, region.getIdAntisenseRnaRegion());
-
- assertEquals(ModificationState.ACETYLATED, region.getState());
-
- try {
- region.setSize("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- try {
- region.setPos("text");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
-
- region.setSize("1.0");
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- assertEquals(1.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToString() {
- try {
- assertNotNull(new AntisenseRnaRegion().toString());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- AntisenseRnaRegion degraded = new AntisenseRnaRegion().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Mockito.mock(AntisenseRnaRegion.class, Mockito.CALLS_REAL_METHODS).copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species.field;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.awt.geom.Point2D;
+
+import org.apache.commons.lang3.SerializationUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Drug;
+
+public class AntisenseRnaRegionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new AntisenseRnaRegion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
+ AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion(antisenseRna);
+ assertNotNull(antisenseRna2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
+ antisenseRna.setState(ModificationState.EMPTY);
+ antisenseRna.setName("as");
+ antisenseRna.setPosition(new Point2D.Double(10, 0));
+ AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
+ antisenseRna2.update(antisenseRna);
+ assertEquals(antisenseRna.getState(), antisenseRna2.getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidUpdate() {
+ try {
+ AntisenseRnaRegion antisenseRna = new AntisenseRnaRegion();
+ AntisenseRnaRegion antisenseRna2 = new AntisenseRnaRegion();
+ antisenseRna.setIdAntisenseRnaRegion("@1");
+ antisenseRna2.setIdAntisenseRnaRegion("@");
+ antisenseRna2.update(antisenseRna);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ AntisenseRnaRegion region = new AntisenseRnaRegion(new AntisenseRnaRegion());
+ int id = 91;
+ AntisenseRna species = new AntisenseRna("id");
+ Point2D position = new Point2D.Double(10, 20);
+ double size = 5.3;
+ AntisenseRnaRegionType type = AntisenseRnaRegionType.CODING_REGION;
+ String name = "nam";
+ String idAntisenseRnaRegion = "iddd";
+
+ region.setId(id);
+ region.setSpecies(species);
+ region.setPosition(position);
+ region.setSize(size);
+ region.setType(type);
+ region.setName(name);
+ region.setIdAntisenseRnaRegion(idAntisenseRnaRegion);
+ region.setState(ModificationState.ACETYLATED);
+
+ assertEquals(id, region.getId());
+ assertEquals(species, region.getSpecies());
+ assertEquals(position.distance(region.getPosition()), 0, Configuration.EPSILON);
+ assertEquals(size, region.getSize(), Configuration.EPSILON);
+ assertEquals(type, region.getType());
+ assertEquals(name, region.getName());
+ assertEquals(idAntisenseRnaRegion, region.getIdAntisenseRnaRegion());
+
+ assertEquals(ModificationState.ACETYLATED, region.getState());
+
+ try {
+ region.setSize("text");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+
+ region.setSize("1.0");
+ assertEquals(1.0, region.getSize(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToString() {
+ try {
+ assertNotNull(new AntisenseRnaRegion().toString());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ AntisenseRnaRegion degraded = new AntisenseRnaRegion().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Mockito.mock(AntisenseRnaRegion.class, Mockito.CALLS_REAL_METHODS).copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180705.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180705.sql
new file mode 100644
index 0000000000000000000000000000000000000000..d7bfbb3822d9b7af353d10b4e91556e39c903273
--- /dev/null
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180705.sql
@@ -0,0 +1,7 @@
+-- coordinates for antisense rna changed into absolute x,y
+
+alter table antisense_rna_region_table add column position varchar(255);
+update antisense_rna_region_table set position=concat(element_table.x+(element_table.width*3/4*antisense_rna_region_table.pos),',',element_table.y) from element_table where element_table.iddb = antisense_rna_region_table.idspeciesdb and not pos is null;
+update antisense_rna_region_table set position=concat(element_table.x,',',element_table.y) from element_table where element_table.iddb = antisense_rna_region_table.idspeciesdb and pos is null;
+alter table antisense_rna_region_table drop column pos;
+