diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
index a1d476c3f02c9681fed20b53cf0bbd62b8d869ef..aafc654fbfc5bd0541873786b84f35e272779e06 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerRna.java
@@ -1,147 +1,152 @@
-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.CellDesignerRnaRegion;
-import lcsb.mapviewer.model.map.species.Rna;
-
-/**
- * Class representing CellDesigner {@link Rna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerRna extends CellDesignerSpecies<Rna> {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerRna.class.getName());
-
- /**
- * List of rna regions (some rna sequences) in this object.
- */
- private List<CellDesignerRnaRegion> regions = new ArrayList<>();
-
- /**
- * Constructor that initializes rna with the data passed in the argument.
- *
- * @param species
- * original species used for data initialization
- */
- public CellDesignerRna(CellDesignerSpecies<?> species) {
- super(species);
- if (species instanceof CellDesignerRna) {
- CellDesignerRna rna = (CellDesignerRna) species;
- for (CellDesignerRnaRegion region : rna.getRegions()) {
- addRegion(new CellDesignerRnaRegion(region));
- }
- }
- }
-
- /**
- * Default constructor.
- */
- public CellDesignerRna() {
- super();
- }
-
- @Override
- public CellDesignerRna copy() {
- if (this.getClass() == CellDesignerRna.class) {
- return new CellDesignerRna(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- @Override
- public void update(CellDesignerSpecies<?> species) {
- super.update(species);
- if (species instanceof CellDesignerRna) {
- CellDesignerRna rna = (CellDesignerRna) species;
- for (CellDesignerRnaRegion mr : getRegions()) {
- mr.setState(null);
- }
-
- for (CellDesignerRnaRegion region : rna.getRegions()) {
- updateRegion(region);
- }
- }
- }
-
- /**
- * Updates region in the rna. If region doesn't exist then it is added.
- *
- * @param param
- * region that with the data to update
- */
- private void updateRegion(CellDesignerRnaRegion param) {
- for (CellDesignerRnaRegion region : regions) {
- if (region.getIdRnaRegion().equals(param.getIdRnaRegion())) {
- region.update(param);
- return;
- }
- }
- addRegion(new CellDesignerRnaRegion(param));
- }
-
- /**
- * Adds region. If the region with given id exists then the data of this
- * region is copied to the one that is already in the {@link CellDesignerRna}.
- *
- * @param rnaRegion
- * region to add
- */
- public void addRegion(CellDesignerRnaRegion rnaRegion) {
- for (CellDesignerRnaRegion region2 : regions) {
- if (region2.getIdRnaRegion().equals(rnaRegion.getIdRnaRegion())) {
- region2.update(rnaRegion);
- return;
- }
- }
-
- regions.add(rnaRegion);
- rnaRegion.setSpecies(this);
-
- }
-
- /**
- * @return the regions
- * @see #regions
- */
- public List<CellDesignerRnaRegion> getRegions() {
- return regions;
- }
-
- /**
- * @param regions
- * the regions to set
- * @see #regions
- */
- public void setRegions(List<CellDesignerRnaRegion> regions) {
- this.regions = regions;
- }
-
- @Override
- public Rna createModelElement(String aliasId) {
- Rna result = new Rna(aliasId);
- super.setModelObjectFields(result);
- for (CellDesignerRnaRegion region : regions) {
- result.addRegion(region.createRnaRegionAlias());
- }
-
- 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.CellDesignerRnaRegion;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * Class representing CellDesigner {@link Rna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerRna extends CellDesignerSpecies<Rna> {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerRna.class.getName());
+
+ /**
+ * List of rna regions (some rna sequences) in this object.
+ */
+ private List<CellDesignerRnaRegion> regions = new ArrayList<>();
+
+ /**
+ * Constructor that initializes rna with the data passed in the argument.
+ *
+ * @param species
+ * original species used for data initialization
+ */
+ public CellDesignerRna(CellDesignerSpecies<?> species) {
+ super(species);
+ if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+ for (CellDesignerRnaRegion region : rna.getRegions()) {
+ addRegion(new CellDesignerRnaRegion(region));
+ }
+ }
+ }
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerRna() {
+ super();
+ }
+
+ @Override
+ public CellDesignerRna copy() {
+ if (this.getClass() == CellDesignerRna.class) {
+ return new CellDesignerRna(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ @Override
+ public void update(CellDesignerSpecies<?> species) {
+ super.update(species);
+ if (species instanceof CellDesignerRna) {
+ CellDesignerRna rna = (CellDesignerRna) species;
+ for (CellDesignerRnaRegion mr : getRegions()) {
+ mr.setState(null);
+ }
+
+ for (CellDesignerRnaRegion region : rna.getRegions()) {
+ updateRegion(region);
+ }
+ }
+ }
+
+ /**
+ * Updates region in the rna. If region doesn't exist then it is added.
+ *
+ * @param param
+ * region that with the data to update
+ */
+ private void updateRegion(CellDesignerRnaRegion param) {
+ for (CellDesignerRnaRegion region : regions) {
+ if (region.getIdRnaRegion().equals(param.getIdRnaRegion())) {
+ region.update(param);
+ return;
+ }
+ }
+ addRegion(new CellDesignerRnaRegion(param));
+ }
+
+ /**
+ * Adds region. If the region with given id exists then the data of this region
+ * is copied to the one that is already in the {@link CellDesignerRna}.
+ *
+ * @param rnaRegion
+ * region to add
+ */
+ public void addRegion(CellDesignerRnaRegion rnaRegion) {
+ for (CellDesignerRnaRegion region2 : regions) {
+ if (region2.getIdRnaRegion().equals(rnaRegion.getIdRnaRegion())) {
+ region2.update(rnaRegion);
+ return;
+ }
+ }
+
+ regions.add(rnaRegion);
+ rnaRegion.setSpecies(this);
+
+ }
+
+ /**
+ * @return the regions
+ * @see #regions
+ */
+ public List<CellDesignerRnaRegion> getRegions() {
+ return regions;
+ }
+
+ /**
+ * @param regions
+ * the regions to set
+ * @see #regions
+ */
+ public void setRegions(List<CellDesignerRnaRegion> regions) {
+ this.regions = regions;
+ }
+
+ @Override
+ public Rna createModelElement(String aliasId) {
+ Rna result = new Rna(aliasId);
+ super.setModelObjectFields(result);
+ return result;
+ }
+
+ @Override
+ public void updateModelElementAfterLayoutAdded(Species element) {
+ for (CellDesignerRnaRegion region : regions) {
+ Rna rna = (Rna) element;
+ rna.addRegion(region.createRnaRegionAlias(rna));
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
index bbb44414758cd125082930ee1f9f62f290b94edd..3741aaa8fa4a099b1301a5f1a1170e51ccec34f7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerRnaRegion.java
@@ -1,301 +1,302 @@
-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.converter.model.celldesigner.structure.CellDesignerRna;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-/**
- * This structure contains information about rna region (rna fragment of
- * interest) for a specific
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna
- * Rna}.
- *
- * @author Piotr Gawron
- *
- */
-public class CellDesignerRnaRegion implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default {@link #size} of the region.
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CellDesignerRnaRegion.class.getName());
-
- /**
- * Identifier of the region. Unique in the
- * {@link lcsb.mapviewer.model.map.model.Model}.
- */
- private String idRnaRegion = "";
-
- /**
- * 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 String type = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- private ModificationState state = null;
-
- /**
- * Name of the region.
- */
- private String name = "";
-
- /**
- * 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 CellDesignerRna species;
-
- /**
- * Default constructor.
- */
- public CellDesignerRnaRegion() {
-
- }
-
- /**
- * Creates object with the data taken from paramter region.
- *
- * @param mr
- * original {@link CellDesignerRnaRegion}
- */
- public CellDesignerRnaRegion(CellDesignerRnaRegion mr) {
- this.idRnaRegion = mr.idRnaRegion;
- this.size = mr.size;
- setPos(mr.getPos());
- this.type = mr.type;
- this.state = mr.state;
- this.name = mr.name;
- }
-
- /**
- * Sets {@link #size}.
- *
- * @param text
- * new size value in string format
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
-
- }
-
- /**
- * Sets {@link #pos}.
- *
- * @param text
- * new {@link #pos} value in string format
- */
- public void setPos(String text) {
- try {
- setPos(Double.parseDouble(text));
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
-
- }
-
- /**
- * Updates fields in the object with the data given in the parameter rna
- * region.
- *
- * @param mr
- * {@link CellDesignerRnaRegion} from which data will be used to
- * update
- */
- public void update(CellDesignerRnaRegion mr) {
- if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
- 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 = "" + getIdRnaRegion() + "," + getType() + "," + getPos() + "," + getSize() + "," + getState() + ",";
- return result;
-
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getIdRnaRegion() {
- return idRnaRegion;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setIdRnaRegion(String id) {
- this.idRnaRegion = id;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * @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 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 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 CellDesignerRna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(CellDesignerRna species) {
- this.species = species;
- }
-
- /**
- * Creates model representation of {@link RnaRegion}.
- *
- * @return {@link RnaRegion} representing this object in a model
- */
- public RnaRegion createRnaRegionAlias() {
- RnaRegion result = new RnaRegion();
- result.setIdRnaRegion(this.idRnaRegion);
- result.setSize(this.size);
- result.setPos(this.getPos());
- result.setType(this.getType());
- result.setState(this.state);
- result.setName(this.name);
- return result;
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
+
+/**
+ * This structure contains information about rna region (rna fragment of
+ * interest) for a specific
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna
+ * Rna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerRnaRegion implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default {@link #size} of the region.
+ */
+ private static final double DEFAULT_SIZE = 0.1;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CellDesignerRnaRegion.class.getName());
+
+ /**
+ * Identifier of the region. Unique in the
+ * {@link lcsb.mapviewer.model.map.model.Model}.
+ */
+ private String idRnaRegion = "";
+
+ /**
+ * 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 String type = "";
+
+ /**
+ * Defines a state of the region (for instance ubiquitinated etc).
+ *
+ * @see ModificationState
+ */
+ private ModificationState state = null;
+
+ /**
+ * Name of the region.
+ */
+ private String name = "";
+
+ /**
+ * 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 CellDesignerRna species;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerRnaRegion() {
+
+ }
+
+ /**
+ * Creates object with the data taken from paramter region.
+ *
+ * @param mr
+ * original {@link CellDesignerRnaRegion}
+ */
+ public CellDesignerRnaRegion(CellDesignerRnaRegion mr) {
+ this.idRnaRegion = mr.idRnaRegion;
+ this.size = mr.size;
+ setPos(mr.getPos());
+ this.type = mr.type;
+ this.state = mr.state;
+ this.name = mr.name;
+ }
+
+ /**
+ * Sets {@link #size}.
+ *
+ * @param text
+ * new size value in string format
+ */
+ public void setSize(String text) {
+ try {
+ size = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+
+ }
+
+ /**
+ * Sets {@link #pos}.
+ *
+ * @param text
+ * new {@link #pos} value in string format
+ */
+ public void setPos(String text) {
+ try {
+ setPos(Double.parseDouble(text));
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid pos: " + text, e);
+ }
+
+ }
+
+ /**
+ * Updates fields in the object with the data given in the parameter rna region.
+ *
+ * @param mr
+ * {@link CellDesignerRnaRegion} from which data will be used to update
+ */
+ public void update(CellDesignerRnaRegion mr) {
+ if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
+ 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 = "" + getIdRnaRegion() + "," + getType() + "," + getPos() + "," + getSize() + "," + getState() + ",";
+ return result;
+
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getIdRnaRegion() {
+ return idRnaRegion;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setIdRnaRegion(String id) {
+ this.idRnaRegion = id;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ /**
+ * @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 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 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 CellDesignerRna getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(CellDesignerRna species) {
+ this.species = species;
+ }
+
+ /**
+ * Creates model representation of {@link RnaRegion}.
+ *
+ * @return {@link RnaRegion} representing this object in a model
+ */
+ public RnaRegion createRnaRegionAlias(Rna element) {
+ RnaRegion result = new RnaRegion();
+ result.setIdRnaRegion(this.idRnaRegion);
+ result.setSize(this.size);
+ result.setPosition(new Point2D.Double(
+ element.getX() + element.getWidth() / 4.0 + element.getWidth() * 3.0 / 4.0 * pos, element.getY()));
+ result.setType(this.getType());
+ result.setState(this.state);
+ result.setName(this.name);
+ return result;
+ }
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index bf0b0533f521cf4572b7b00fdcca619f978c9263..ab2e0cf26c2c17101a1950a2b272535e0eb901a0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
@@ -1,162 +1,154 @@
-/**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into colors
- * when drawing {@link Species}
- */
-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.Rna;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-/**
- * This class defines methods used for drawing {@link Rna} on the
- * {@link Graphics2D} object.
- *
- * @author Piotr Gawron
- *
- */
-public class RnaConverter extends SpeciesConverter<Rna> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * Object that helps to convert {@link ColorSchema} values into
- * colors when drawing {@link Species}
- */
- public RnaConverter(ColorExtractor colorExtractor) {
- super(colorExtractor);
- }
-
- @Override
- public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
- GeneralPath path = getRnaPath(rna);
- Color c = graphics.getColor();
- graphics.setColor(rna.getColor());
- graphics.fill(path);
- graphics.setColor(c);
- Stroke stroke = graphics.getStroke();
- graphics.setStroke(getBorderLine(rna));
- graphics.draw(path);
- graphics.setStroke(stroke);
-
- for (RnaRegion mr : rna.getRegions()) {
- drawModification(rna, mr, graphics, false, false);
- }
-
- drawText(rna, graphics, params);
- }
-
- /**
- * Returns shape of the {@link Rna} as a {@link GeneralPath} object.
- *
- * @param rna
- * {@link Rna} for which we are looking for a border
- * @return {@link GeneralPath} object defining border of the given {@link Rna}
- */
- private GeneralPath getRnaPath(final Rna rna) {
- // CHECKSTYLE:OFF
- GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
- path.moveTo(rna.getX() + rna.getWidth() / 4, rna.getY());
- path.lineTo(rna.getX() + rna.getWidth(), rna.getY());
- path.lineTo(rna.getX() + rna.getWidth() * 3 / 4, rna.getY() + rna.getHeight());
- path.lineTo(rna.getX(), rna.getY() + rna.getHeight());
- // CHECKSTYLE:ON
- path.closePath();
- return path;
- }
-
- @Override
- public PathIterator getBoundPathIterator(final Rna rna) {
- return getRnaPath(rna).getPathIterator(new AffineTransform());
- }
-
- /**
- * This method draws modification of the alias. If drawEmptyModification is
- * set to false then modification is not drawn if empty. If drawDescription is
- * set then also description (position) of the modification is drawn on the
- * canvas.
- *
- * @param rna
- * object that is 'parent' of the residue
- * @param region
- * {@link RnaRegion modification} to be drawn
- * @param graphics
- * - where the modification should be drawn
- * @param drawEmptyModification
- * flag that indicates if we should draw empty modification
- * @param drawDescription
- * flag that indicates if we should draw description of the
- * modification
- */
- private void drawModification(final Rna rna, final RnaRegion region, final Graphics2D graphics, final boolean drawEmptyModification,
- final boolean drawDescription) {
- if ((!drawEmptyModification) && (region.getState() == null)) {
- return;
- }
- double diameter = DEFAULT_MODIFICATION_DIAMETER;
-
- double x = rna.getX();
- double y = rna.getY();
-
- double width = rna.getWidth();
-
- // CHECKSTYLE:OFF
- // we draw modifier on the upper border of rna (which is only in
- // 3/4 of the width of alias, but starts in 1/4 of the width)
- Point2D p = new Point2D.Double(x + width / 4.0 + width * 3.0 / 4.0 * region.getPos(), y - DEFAULT_MODIFICATION_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);
- }
-
- }
-
-}
+/**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+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.Rna;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
+
+/**
+ * This class defines methods used for drawing {@link Rna} on the
+ * {@link Graphics2D} object.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class RnaConverter extends SpeciesConverter<Rna> {
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RnaConverter.class.getName());
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * Object that helps to convert {@link ColorSchema} values into colors
+ * when drawing {@link Species}
+ */
+ public RnaConverter(ColorExtractor colorExtractor) {
+ super(colorExtractor);
+ }
+
+ @Override
+ public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
+ GeneralPath path = getRnaPath(rna);
+ Color c = graphics.getColor();
+ graphics.setColor(rna.getColor());
+ graphics.fill(path);
+ graphics.setColor(c);
+ Stroke stroke = graphics.getStroke();
+ graphics.setStroke(getBorderLine(rna));
+ graphics.draw(path);
+ graphics.setStroke(stroke);
+
+ for (RnaRegion mr : rna.getRegions()) {
+ drawModification(rna, mr, graphics, false, false);
+ }
+
+ drawText(rna, graphics, params);
+ }
+
+ /**
+ * Returns shape of the {@link Rna} as a {@link GeneralPath} object.
+ *
+ * @param rna
+ * {@link Rna} for which we are looking for a border
+ * @return {@link GeneralPath} object defining border of the given {@link Rna}
+ */
+ private GeneralPath getRnaPath(final Rna rna) {
+ // CHECKSTYLE:OFF
+ GeneralPath path = new GeneralPath(Path2D.WIND_EVEN_ODD, 4);
+ path.moveTo(rna.getX() + rna.getWidth() / 4, rna.getY());
+ path.lineTo(rna.getX() + rna.getWidth(), rna.getY());
+ path.lineTo(rna.getX() + rna.getWidth() * 3 / 4, rna.getY() + rna.getHeight());
+ path.lineTo(rna.getX(), rna.getY() + rna.getHeight());
+ // CHECKSTYLE:ON
+ path.closePath();
+ return path;
+ }
+
+ @Override
+ public PathIterator getBoundPathIterator(final Rna rna) {
+ return getRnaPath(rna).getPathIterator(new AffineTransform());
+ }
+
+ /**
+ * This method draws modification of the alias. If drawEmptyModification is set
+ * to false then modification is not drawn if empty. If drawDescription is set
+ * then also description (position) of the modification is drawn on the canvas.
+ *
+ * @param rna
+ * object that is 'parent' of the residue
+ * @param region
+ * {@link RnaRegion modification} to be drawn
+ * @param graphics
+ * - where the modification should be drawn
+ * @param drawEmptyModification
+ * flag that indicates if we should draw empty modification
+ * @param drawDescription
+ * flag that indicates if we should draw description of the
+ * modification
+ */
+ private void drawModification(final Rna rna, final RnaRegion region, final Graphics2D graphics,
+ final boolean drawEmptyModification, final boolean drawDescription) {
+ if ((!drawEmptyModification) && (region.getState() == null)) {
+ return;
+ }
+ double diameter = DEFAULT_MODIFICATION_DIAMETER;
+
+ double y = rna.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/field/RnaRegion.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
index 9c5e32a201e2f8d6e4f84d40db4b6af0beab72e1..4dd65ffe78d7066baa1b3bdf0543fb2127c77463 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/RnaRegion.java
@@ -1,327 +1,305 @@
-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 lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Rna;
-
-/**
- * This structure contains information about rna region (rna fragment of
- * interest) for a specific {@link Rna}.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "rna_region_table")
-@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
-public class RnaRegion implements Serializable, ElementModification {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default {@link #size} of the region.
- */
- private static final double DEFAULT_SIZE = 0.1;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RnaRegion.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 region. Unique in the
- * {@link lcsb.mapviewer.model.map.model.Model}.
- */
- @Column(name = "idrnaregion")
- private String idRnaRegion = "";
- /**
- * 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 String type = "";
-
- /**
- * Defines a state of the region (for instance ubiquitinated etc).
- *
- * @see ModificationState
- */
- @Column(name = "state")
- private ModificationState state = null;
-
- /**
- * Name of the region.
- */
- @Column(name = "name")
- private String name = "";
-
- /**
- * 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.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- @JoinColumn(name = "idSpeciesDb")
- private Rna species;
-
- /**
- * Default constructor.
- */
- public RnaRegion() {
-
- }
-
- /**
- * Creates object with the data taken from paramter region.
- *
- * @param mr
- * original {@link RnaRegion}
- */
- public RnaRegion(RnaRegion mr) {
- this.id = mr.id;
- this.idRnaRegion = mr.idRnaRegion;
- this.size = mr.size;
- setPos(mr.getPos());
- this.type = mr.type;
- this.state = mr.state;
- this.name = mr.name;
- }
-
- /**
- * Sets {@link #size}.
- *
- * @param text
- * new size value in string format
- */
- public void setSize(String text) {
- try {
- size = Double.parseDouble(text);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid angle: " + text, e);
- }
-
- }
-
- /**
- * Sets {@link #pos}.
- *
- * @param text
- * new {@link #pos} value in string format
- */
- public void setPos(String text) {
- try {
- setPos(Double.parseDouble(text));
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid pos: " + text, e);
- }
-
- }
-
- /**
- * Updates fields in the object with the data given in the parameter rna
- * region.
- *
- * @param mr
- * {@link RnaRegion} from which data will be used to update
- */
- public void update(RnaRegion mr) {
- if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
- 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 = "" + getIdRnaRegion() + "," + getType() + "," + getPos() + "," + getSize() + "," + getState() + ",";
- return result;
-
- }
-
- /**
- * @return the idRnaRegion
- * @see #idRnaRegion
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the idRnaRegion to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getIdRnaRegion() {
- return idRnaRegion;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setIdRnaRegion(String id) {
- this.idRnaRegion = id;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * @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 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 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 Rna getSpecies() {
- return species;
- }
-
- /**
- * @param species
- * the species to set
- * @see #species
- */
- public void setSpecies(Rna species) {
- this.species = species;
- }
-
-}
+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.Type;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.Rna;
+
+/**
+ * This structure contains information about rna region (rna fragment of
+ * interest) for a specific {@link Rna}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "rna_region_table")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+public class RnaRegion implements Serializable, ElementModification {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default {@link #size} of the region.
+ */
+ private static final double DEFAULT_SIZE = 0.1;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(RnaRegion.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 region. Unique in the
+ * {@link lcsb.mapviewer.model.map.model.Model}.
+ */
+ @Column(name = "idrnaregion")
+ private String idRnaRegion = "";
+ /**
+ * 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 String type = "";
+
+ /**
+ * Defines a state of the region (for instance ubiquitinated etc).
+ *
+ * @see ModificationState
+ */
+ @Column(name = "state")
+ private ModificationState state = null;
+
+ /**
+ * Name of the region.
+ */
+ @Column(name = "name")
+ private String name = "";
+
+ /**
+ * 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.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ @JoinColumn(name = "idSpeciesDb")
+ private Rna species;
+
+ /**
+ * Default constructor.
+ */
+ public RnaRegion() {
+
+ }
+
+ /**
+ * Creates object with the data taken from paramter region.
+ *
+ * @param mr
+ * original {@link RnaRegion}
+ */
+ public RnaRegion(RnaRegion mr) {
+ this.id = mr.id;
+ this.idRnaRegion = mr.idRnaRegion;
+ this.size = mr.size;
+ setPosition(mr.getPosition());
+ this.type = mr.type;
+ this.state = mr.state;
+ this.name = mr.name;
+ }
+
+ /**
+ * Sets {@link #size}.
+ *
+ * @param text
+ * new size value in string format
+ */
+ public void setSize(String text) {
+ try {
+ size = Double.parseDouble(text);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+
+ }
+
+ /**
+ * Updates fields in the object with the data given in the parameter rna region.
+ *
+ * @param mr
+ * {@link RnaRegion} from which data will be used to update
+ */
+ public void update(RnaRegion mr) {
+ if (this.idRnaRegion != null && !this.idRnaRegion.equals("") && !this.idRnaRegion.equals(mr.getIdRnaRegion())) {
+ 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 = "" + getIdRnaRegion() + "," + getType() + "," + getPosition() + "," + getSize() + "," + getState() + ",";
+ return result;
+
+ }
+
+ /**
+ * @return the idRnaRegion
+ * @see #idRnaRegion
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the idRnaRegion to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public String getIdRnaRegion() {
+ return idRnaRegion;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setIdRnaRegion(String id) {
+ this.idRnaRegion = id;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ /**
+ * @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 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 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 Rna getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(Rna species) {
+ this.species = species;
+ }
+
+ 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/RnaComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
index 3ead55dee76b0c53b570b725795334aed2bfa48c..6f57d01966e8951fc74d3fca102c0f19a3d5a934 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/RnaComparatorTest.java
@@ -1,108 +1,110 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationState;
-import lcsb.mapviewer.model.map.species.field.RnaRegion;
-
-public class RnaComparatorTest {
-
- RnaComparator comparator = new RnaComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testEquals() {
- try {
- Rna aRna1 = createRna();
- Rna aRna2 = createRna();
-
- assertEquals(0, comparator.compare(aRna1, aRna1));
-
- assertEquals(0, comparator.compare(aRna1, aRna2));
- assertEquals(0, comparator.compare(aRna2, aRna1));
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- @Test
- public void testDifferent() {
- try {
- Rna aRna1 = createRna();
- Rna aRna2 = createRna();
- aRna1.getRegions().get(0).setState(ModificationState.ACETYLATED);
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createRna();
- aRna2 = createRna();
- aRna1.getRegions().clear();
- assertTrue(comparator.compare(aRna1, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, aRna1) != 0);
-
- aRna1 = createRna();
- aRna2 = createRna();
- assertTrue(comparator.compare(null, aRna2) != 0);
- assertTrue(comparator.compare(aRna2, null) != 0);
- assertTrue(comparator.compare(null, null) == 0);
-
- Rna rna = createRna();
- rna.setName("n");
- assertTrue(comparator.compare(rna, aRna2) != 0);
-
- assertTrue(comparator.compare(rna, Mockito.mock(Rna.class)) != 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
- public Rna createRna() {
- Rna result = new Rna();
- result.setHypothetical(true);
-
- RnaRegion region1 = new RnaRegion();
- result.addRegion(region1);
- region1.setIdRnaRegion("a");
- region1.setState(ModificationState.DONT_CARE);
- region1.setPos("1");
- region1.setSize("2");
- region1.setType("type");
- return result;
- }
-
- @Test
- public void testInvalid() {
- try {
- Rna object = Mockito.mock(Rna.class);
-
- comparator.compare(object, object);
-
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- } catch (Exception e) {
- e.printStackTrace();
- fail("Unknowne exception occurred");
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+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;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.RnaRegion;
+
+public class RnaComparatorTest {
+
+ RnaComparator comparator = new RnaComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testEquals() {
+ try {
+ Rna aRna1 = createRna();
+ Rna aRna2 = createRna();
+
+ assertEquals(0, comparator.compare(aRna1, aRna1));
+
+ assertEquals(0, comparator.compare(aRna1, aRna2));
+ assertEquals(0, comparator.compare(aRna2, aRna1));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ @Test
+ public void testDifferent() {
+ try {
+ Rna aRna1 = createRna();
+ Rna aRna2 = createRna();
+ aRna1.getRegions().get(0).setState(ModificationState.ACETYLATED);
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createRna();
+ aRna2 = createRna();
+ aRna1.getRegions().clear();
+ assertTrue(comparator.compare(aRna1, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, aRna1) != 0);
+
+ aRna1 = createRna();
+ aRna2 = createRna();
+ assertTrue(comparator.compare(null, aRna2) != 0);
+ assertTrue(comparator.compare(aRna2, null) != 0);
+ assertTrue(comparator.compare(null, null) == 0);
+
+ Rna rna = createRna();
+ rna.setName("n");
+ assertTrue(comparator.compare(rna, aRna2) != 0);
+
+ assertTrue(comparator.compare(rna, Mockito.mock(Rna.class)) != 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+ public Rna createRna() {
+ Rna result = new Rna();
+ result.setHypothetical(true);
+
+ RnaRegion region1 = new RnaRegion();
+ result.addRegion(region1);
+ region1.setIdRnaRegion("a");
+ region1.setState(ModificationState.DONT_CARE);
+ region1.setPosition(new Point2D.Double(0, 10));
+ region1.setSize("2");
+ region1.setType("type");
+ return result;
+ }
+
+ @Test
+ public void testInvalid() {
+ try {
+ Rna object = Mockito.mock(Rna.class);
+
+ comparator.compare(object, object);
+
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("Unknowne exception occurred");
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java
index 11e0edc346820fc24d8807caa425f8ed8d7e138e..bd87bdb2e71c36f0e4e92aa4db114cc3d3a4653e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/RnaRegionTest.java
@@ -1,133 +1,119 @@
-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 lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.species.Rna;
-
-public class RnaRegionTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new RnaRegion());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor() {
- try {
- RnaRegion region = new RnaRegion(new RnaRegion());
- assertNotNull(region);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetSize() {
- try {
- RnaRegion region = new RnaRegion();
- try {
- region.setSize("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setSize("0.0");
- assertEquals(0.0, region.getSize(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetPos() {
- try {
- RnaRegion region = new RnaRegion();
- try {
- region.setPos("as");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- region.setPos("1.0");
- assertEquals(1.0, region.getPos(), Configuration.EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- RnaRegion region = new RnaRegion();
- RnaRegion region2 = new RnaRegion();
- region2.setState(ModificationState.ACETYLATED);
- region2.setName("asd");
- region2.setPos(2.2);
- region.update(region2);
- assertEquals(region2.getName(), region.getName());
- assertEquals(region2.getPos(), region.getPos());
- assertEquals(region2.getState(), region.getState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate2() {
- try {
- RnaRegion region = new RnaRegion();
- region.setIdRnaRegion("1");
- RnaRegion region2 = new RnaRegion();
- region2.setIdRnaRegion("2");
- region.update(region2);
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- RnaRegion region = new RnaRegion();
- double size = 2.5;
- int id = 58;
- Rna species = new Rna("id");
- region.setSize(size);
- region.setSpecies(species);
- region.setId(id);
- assertEquals(id, region.getId());
- assertEquals(size, region.getSize(), Configuration.EPSILON);
- assertEquals(species, region.getSpecies());
- } 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.assertTrue;
+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 lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.species.Rna;
+
+public class RnaRegionTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new RnaRegion());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor() {
+ try {
+ RnaRegion region = new RnaRegion(new RnaRegion());
+ assertNotNull(region);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetSize() {
+ try {
+ RnaRegion region = new RnaRegion();
+ try {
+ region.setSize("as");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ region.setSize("0.0");
+ assertEquals(0.0, region.getSize(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ RnaRegion region = new RnaRegion();
+ RnaRegion region2 = new RnaRegion();
+ region2.setState(ModificationState.ACETYLATED);
+ region2.setName("asd");
+ region2.setPosition(new Point2D.Double(0, 10));
+ region.update(region2);
+ assertEquals(region2.getName(), region.getName());
+ assertTrue(region2.getPosition().distance(region.getPosition()) <= Configuration.EPSILON);
+ assertEquals(region2.getState(), region.getState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate2() {
+ try {
+ RnaRegion region = new RnaRegion();
+ region.setIdRnaRegion("1");
+ RnaRegion region2 = new RnaRegion();
+ region2.setIdRnaRegion("2");
+ region.update(region2);
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ RnaRegion region = new RnaRegion();
+ double size = 2.5;
+ int id = 58;
+ Rna species = new Rna("id");
+ region.setSize(size);
+ region.setSpecies(species);
+ region.setId(id);
+ assertEquals(id, region.getId());
+ assertEquals(size, region.getSize(), Configuration.EPSILON);
+ assertEquals(species, region.getSpecies());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql
index a82728a19d662c7e435277f85036891252aed455..c391524b79276d2df05443cda3f190fafd25ae18 100644
--- a/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180710.sql
@@ -17,3 +17,11 @@ update modification_residue_table set state_string='PROTONATED' where state=12;
update modification_residue_table set state_string='DONT_CARE' where state=13;
alter table modification_residue_table drop column state;
alter table modification_residue_table rename column state_string to state;
+
+-- coordinates for rna region changed into absolute x,y
+
+alter table rna_region_table add column position varchar(255);
+update rna_region_table set position=concat(element_table.x+element_table.width/4 +(element_table.width*3/4*rna_region_table.pos),',',element_table.y) from element_table where element_table.iddb = rna_region_table.idspeciesdb and not pos is null;
+update rna_region_table set position=concat(element_table.x,',',element_table.y) from element_table where element_table.iddb = rna_region_table.idspeciesdb and pos is null;
+alter table rna_region_table drop column pos;
+