From 14a66f69b4162a27df505eafde1c1f79be141b5b Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 11 Jul 2018 14:08:01 +0200
Subject: [PATCH] ModificationSite and Residue classes extracted
---
.../celldesigner/species/GeneXmlParser.java | 16 +-
.../species/ProteinXmlParser.java | 1 +
.../species/SpeciesSbmlParser.java | 28 +-
.../structure/CellDesignerGene.java | 25 +-
.../structure/CellDesignerProtein.java | 2 +-
.../fields/CellDesignerGeneRegion.java | 372 ++++++++++++++
.../CellDesignerModificationResidue.java | 35 +-
.../structure/fields/SpeciesState.java | 2 +-
.../CellDesignerXmlParserTest.java | 5 +-
.../species/GeneXmlParserTest.java | 3 +-
.../celldesigner/structure/GeneTest.java | 257 +++++-----
.../structure/SpeciesStateTest.java | 4 +-
.../model/sbgnml/SbgnmlXmlParser.java | 3 +-
.../model/sbgnml/SbgnmlXmlParserTest2.java | 4 +-
.../mapviewer/model/map/species/Gene.java | 226 ++++-----
.../mapviewer/model/map/species/Protein.java | 2 +-
.../species/field/ElementModification.java | 2 +
.../species/field/ModificationResidue.java | 28 +-
.../map/species/field/ModificationSite.java | 39 ++
.../model/map/species/field/Residue.java | 39 ++
.../model/map/species/field/RnaRegion.java | 5 +
.../model/map/species/GeneComparatorTest.java | 3 +-
.../mapviewer/model/map/species/GeneTest.java | 181 +++----
.../map/species/ProteinComparatorTest.java | 4 +-
.../model/map/species/ProteinTest.java | 211 ++++----
.../map/species/field/AllFieldTests.java | 2 +-
.../field/ModificationResidueTest.java | 61 ---
.../model/map/species/field/ResidueTest.java | 50 ++
.../wikipathway/XML/ModelContructor.java | 32 +-
.../src/db/12.1.0~alpha.0/fix_db_20180711.sql | 5 +
.../persist/dao/map/CommentDaoTest.java | 371 +++++++-------
.../persist/dao/map/LayoutDaoTest.java | 460 +++++++++---------
.../persist/dao/map/ModelDaoTest.java | 7 +-
.../dao/map/layout/alias/AliasDaoTest2.java | 4 +-
.../elements/ElementRestImplTest.java | 5 +-
35 files changed, 1512 insertions(+), 982 deletions(-)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerGeneRegion.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
delete mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java
create mode 100644 model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
index 5ff9dc7333..9810664c58 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParser.java
@@ -6,14 +6,17 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerGeneRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
/**
* Class that performs parsing of the CellDesigner xml for
@@ -89,12 +92,18 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
* @throws InvalidXmlSchemaException
* thrown when input xml node doesn't follow defined schema
*/
- CellDesignerModificationResidue getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
- CellDesignerModificationResidue residue = new CellDesignerModificationResidue();
+ CellDesignerGeneRegion getModificationResidue(Node residueNode) throws InvalidXmlSchemaException {
+ CellDesignerGeneRegion residue = new CellDesignerGeneRegion();
residue.setIdModificationResidue(getNodeAttr("id", residueNode));
residue.setName(getNodeAttr("name", residueNode));
residue.setSide(getNodeAttr("side", residueNode));
residue.setAngle(getNodeAttr("pos", residueNode));
+ String type = getNodeAttr("type", residueNode);
+ if (type.equals("Modification Site")) {
+ residue.setModificationType("MODIFICATION_SITE");
+ } else if (!type.equals("")) {
+ throw new NotImplementedException("Unknown type: " + type);
+ }
NodeList list = residueNode.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
@@ -152,6 +161,9 @@ public class GeneXmlParser extends AbstractElementXmlParser<CellDesignerGene, Ge
if (!mr.getName().equals("")) {
attributes += " name=\"" + escapeXml(mr.getName()) + "\"";
}
+ if (mr instanceof ModificationSite) {
+ attributes += " type=\"Modification Site\"";
+ }
attributes += " pos=\"" + converter.getAngleForPoint(mr.getSpecies(), mr.getPosition()) + "\"";
result += "<celldesigner:region " + attributes + ">";
result += "</celldesigner:region>\n";
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
index 5e841c9319..6a54e8e212 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/ProteinXmlParser.java
@@ -161,6 +161,7 @@ public class ProteinXmlParser extends AbstractElementXmlParser<CellDesignerProte
residue.setName(getNodeAttr("name", residueNode));
residue.setSide(getNodeAttr("side", residueNode));
residue.setAngle(getNodeAttr("angle", residueNode));
+ residue.setModificationType("RESIDUE");
NodeList list = residueNode.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index c573707a20..02fb359838 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -21,6 +21,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSimpleMolecule;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerGeneRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerRnaRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
@@ -211,7 +212,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
attributesBuilder.append(" constant=\"" + species.getConstant().toString().toLowerCase() + "\"");
}
if (species.getBoundaryCondition() != null) {
- attributesBuilder.append(" boundaryCondition=\"" + species.getBoundaryCondition().toString().toLowerCase() + "\"");
+ attributesBuilder
+ .append(" boundaryCondition=\"" + species.getBoundaryCondition().toString().toLowerCase() + "\"");
}
Compartment comp = null;
@@ -444,7 +446,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
throw new NotImplementedException("StructuralState not supported in Gene");
}
for (CellDesignerModificationResidue mr : state.getModifications()) {
- gene.addModificationResidue(mr);
+ gene.addModificationResidue(createGeneRegion(mr));
}
} else if (species instanceof CellDesignerProtein) {
CellDesignerProtein<?> protein = (CellDesignerProtein<?>) species;
@@ -490,6 +492,23 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
+ private CellDesignerGeneRegion createGeneRegion(CellDesignerModificationResidue mr) {
+ CellDesignerGeneRegion region = new CellDesignerGeneRegion();
+ region.setIdModificationResidue(mr.getIdModificationResidue());
+ if (mr.getSize() != null) {
+ region.setSize(mr.getSize());
+ }
+ region.setState(mr.getState());
+ region.setName(mr.getName());
+ if (mr.getAngle() != null) {
+ region.setAngle(mr.getAngle());
+ }
+ if (mr.getModificationType() != null) {
+ region.setModificationType(mr.getModificationType());
+ }
+ return region;
+ }
+
/**
* Creates {@link SpeciesState} from xml node.
*
@@ -549,7 +568,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
/**
- * Creates {@link CellDesignerModificationResidue} from the apropriate xml node.
+ * Creates {@link CellDesignerModificationResidue} from the appropriate xml
+ * node.
*
* @param rootNode
* xml node
@@ -632,7 +652,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
*
* @param mr
* object from which we create {@link CellDesignerRnaRegion}
- * @return {@link CellDesignerRnaRegion} object created from param
+ * @return {@link CellDesignerRnaRegion} object created from parameter
*/
public CellDesignerRnaRegion createRnaRegion(CellDesignerModificationResidue mr) {
CellDesignerRnaRegion result = new CellDesignerRnaRegion();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
index e7001e7286..c184bc570e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerGene.java
@@ -4,9 +4,8 @@ import java.util.ArrayList;
import java.util.List;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerAntisenseRnaRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerGeneRegion;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Species;
@@ -26,7 +25,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
/**
* List of modifications for the Gene.
*/
- private List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
+ private List<CellDesignerGeneRegion> modificationResidues = new ArrayList<>();
/**
* Constructor that initializes gene with the data passed in the argument.
@@ -38,8 +37,8 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
super(species);
if (species instanceof CellDesignerGene) {
CellDesignerGene gene = (CellDesignerGene) species;
- for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
- addModificationResidue(new CellDesignerModificationResidue(mr));
+ for (CellDesignerGeneRegion mr : gene.getModificationResidues()) {
+ addModificationResidue(new CellDesignerGeneRegion(mr));
}
}
}
@@ -50,7 +49,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
if (species instanceof CellDesignerGene) {
CellDesignerGene gene = (CellDesignerGene) species;
- for (CellDesignerModificationResidue mr : gene.getModificationResidues()) {
+ for (CellDesignerGeneRegion mr : gene.getModificationResidues()) {
addModificationResidue(mr);
}
}
@@ -76,10 +75,10 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
* Adds modification to the gene.
*
* @param modificationResidue
- * modifiaction to add
+ * modification to add
*/
- public void addModificationResidue(CellDesignerModificationResidue modificationResidue) {
- for (CellDesignerModificationResidue mr : modificationResidues) {
+ public void addModificationResidue(CellDesignerGeneRegion modificationResidue) {
+ for (CellDesignerGeneRegion mr : modificationResidues) {
if (mr.getIdModificationResidue().equals(modificationResidue.getIdModificationResidue())) {
mr.update(modificationResidue);
return;
@@ -94,7 +93,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
* @return the modificationResidues
* @see #modificationResidues
*/
- public List<CellDesignerModificationResidue> getModificationResidues() {
+ public List<CellDesignerGeneRegion> getModificationResidues() {
return modificationResidues;
}
@@ -103,7 +102,7 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
* the modificationResidues to set
* @see #modificationResidues
*/
- public void setModificationResidues(List<CellDesignerModificationResidue> modificationResidues) {
+ public void setModificationResidues(List<CellDesignerGeneRegion> modificationResidues) {
this.modificationResidues = modificationResidues;
}
@@ -116,8 +115,8 @@ public class CellDesignerGene extends CellDesignerSpecies<Gene> {
@Override
public void updateModelElementAfterLayoutAdded(Species element) {
- for (CellDesignerModificationResidue region : modificationResidues) {
- ((Gene) element).addModificationResidue(region.createModificationResidueAlias(element));
+ for (CellDesignerGeneRegion region : modificationResidues) {
+ ((Gene) element).addModificationResidue(region.createGeneModification(element));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
index 6e80e6bb94..12892adc56 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerProtein.java
@@ -152,7 +152,7 @@ public class CellDesignerProtein<T extends Protein> extends CellDesignerSpecies<
@Override
public void updateModelElementAfterLayoutAdded(Species element) {
for (CellDesignerModificationResidue mr : modificationResidues) {
- ((Protein) element).addModificationResidue(mr.createModificationResidueAlias(element));
+ ((Protein) element).addModificationResidue(mr.createProteinModification(element));
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerGeneRegion.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerGeneRegion.java
new file mode 100644
index 0000000000..732b54d238
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerGeneRegion.java
@@ -0,0 +1,372 @@
+package lcsb.mapviewer.converter.model.celldesigner.structure.fields;
+
+import java.io.Serializable;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
+import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
+
+/**
+ * This class represent modification residue in protein and gene. However, it is
+ * sometimes also used for storing information about AntisenseRna/Rna regions...
+ * (due to CellDesigner xml strange structure).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class CellDesignerGeneRegion implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CellDesignerGeneRegion.class.getName());
+
+ /**
+ * Identifier of the modification. Must be unique in single map model.
+ */
+ private String idModificationResidue = "";
+
+ /**
+ * Name of the modification.
+ */
+ private String name = "";
+
+ private String modificationType;
+
+ /**
+ * Some strange parameter in CellDesigner. No idea what is it for.
+ */
+ private String side = "";
+
+ /**
+ * State in which this modification is.
+ */
+ private ModificationState state = null;
+
+ /**
+ * Where this modification is located (on which side of the border).
+ */
+ private Double angle = null;
+
+ /**
+ * How big is this modification (used only for some types of the modification).
+ */
+ private Double size = null;
+
+ /**
+ * Species to which this modification belong to.
+ */
+ private CellDesignerSpecies<?> species;
+
+ /**
+ * Default constructor.
+ */
+ public CellDesignerGeneRegion() {
+ }
+
+ /**
+ * Constructor that initialize object with the data taken from the parameter.
+ *
+ * @param mr
+ * original object from which data is taken
+ */
+ public CellDesignerGeneRegion(CellDesignerGeneRegion mr) {
+ this.idModificationResidue = mr.idModificationResidue;
+ this.name = mr.name;
+ this.angle = mr.angle;
+ this.size = mr.size;
+ this.side = mr.side;
+ this.state = mr.state;
+ this.modificationType = mr.getModificationType();
+
+ logger.debug(this);
+ }
+
+ /**
+ * Constructor that creates object from model representation of modification.
+ *
+ * @param mr
+ * model representation of {@link ModificationResidue}
+ */
+ public CellDesignerGeneRegion(ModificationResidue mr) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(mr.getSpecies(), false);
+ this.setIdModificationResidue(mr.getIdModificationResidue());
+ this.name = mr.getName();
+ this.angle = converter.getAngleForPoint(mr.getSpecies(), mr.getPosition());
+ this.state = mr.getState();
+ if (mr instanceof ModificationSite) {
+ this.setModificationType("MODIFICATION_SITE");
+ } else {
+ throw new InvalidArgumentException("Unknown gene modification: " + mr.getClass());
+ }
+ logger.debug(this);
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param id
+ * identifier of the modification residue
+ */
+ public CellDesignerGeneRegion(String id) {
+ this.idModificationResidue = id;
+ }
+
+ /**
+ * Updates fields in the object with the data given in the parameter
+ * modification.
+ *
+ * @param mr
+ * modification residue from which data will be used to update
+ */
+ public void update(CellDesignerGeneRegion mr) {
+ if (mr.getName() != null && !mr.getName().equals("")) {
+ this.name = mr.name;
+ }
+ if (mr.getAngle() != null) {
+ this.angle = mr.angle;
+ }
+ if (mr.getSize() != null) {
+ this.size = mr.size;
+ }
+ if (mr.getSide() != null && !mr.getSide().equals("")) {
+ this.side = mr.side;
+ }
+ if (mr.getState() != null) {
+ this.state = mr.state;
+ }
+ if (mr.getModificationType() != null) {
+ this.setModificationType(mr.modificationType);
+ }
+ }
+
+ @Override
+ public String toString() {
+ String result = getIdModificationResidue() + "," + getName() + "," + getState() + "," + getAngle() + "," + getSize()
+ + "," + getSide() + "," + getModificationType();
+ return result;
+ }
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public CellDesignerGeneRegion copy() {
+ if (this.getClass() == CellDesignerGeneRegion.class) {
+ return new CellDesignerGeneRegion(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * Sets {@link #angle} .
+ *
+ * @param text
+ * angle in text format
+ */
+ public void setAngle(String text) {
+ try {
+ if (text != null && !text.equals("")) {
+ angle = Double.parseDouble(text);
+ } else {
+ angle = null;
+ }
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid angle: " + text, e);
+ }
+
+ }
+
+ /**
+ * Sets {@link #size}.
+ *
+ * @param text
+ * size in text format.
+ */
+ public void setSize(String text) {
+ try {
+ if (text != null && !text.equals("")) {
+ size = Double.parseDouble(text);
+ } else {
+ size = null;
+ }
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid size: " + text, e);
+ }
+ }
+
+ /**
+ * @return the id
+ * @see #idModificationResidue
+ */
+ public String getIdModificationResidue() {
+ return idModificationResidue;
+ }
+
+ /**
+ * @param idModificationResidue
+ * the id to set
+ * @see #idModificationResidue
+ */
+ public void setIdModificationResidue(String idModificationResidue) {
+ this.idModificationResidue = idModificationResidue;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the side
+ * @see #side
+ */
+ public String getSide() {
+ return side;
+ }
+
+ /**
+ * @param side
+ * the side to set
+ * @see #side
+ */
+ public void setSide(String side) {
+ this.side = side;
+ }
+
+ /**
+ * @return the state
+ * @see #state
+ */
+ public ModificationState getState() {
+ return state;
+ }
+
+ /**
+ * @param state
+ * the state to set
+ * @see #state
+ */
+ public void setState(ModificationState state) {
+ this.state = state;
+ }
+
+ /**
+ * @return the angle
+ * @see #angle
+ */
+ public Double getAngle() {
+ return angle;
+ }
+
+ /**
+ * @param angle
+ * the angle to set
+ * @see #angle
+ */
+ public void setAngle(Double angle) {
+ this.angle = angle;
+ }
+
+ /**
+ * @return the size
+ * @see #size
+ */
+ public Double getSize() {
+ return size;
+ }
+
+ /**
+ * @param size
+ * the size to set
+ * @see #size
+ */
+ public void setSize(Double size) {
+ this.size = size;
+ }
+
+ /**
+ * @return the species
+ * @see #species
+ */
+ public CellDesignerSpecies<?> getSpecies() {
+ return species;
+ }
+
+ /**
+ * @param species
+ * the species to set
+ * @see #species
+ */
+ public void setSpecies(CellDesignerSpecies<?> species) {
+ this.species = species;
+ }
+
+ /**
+ * Creates model representation of {@link ModificationResidue}.
+ *
+ * @return {@link ModificationResidue} representing this object in a model
+ */
+ public ModificationResidue createGeneModification(Element element) {
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, false);
+ ModificationResidue result;
+
+ if (modificationType == null) {
+ logger.debug(this);
+ throw new InvalidArgumentException("Unknown gene modification type");
+ } else if (modificationType.equals("MODIFICATION_SITE")) {
+ result = new ModificationSite();
+ } else {
+ logger.debug(this);
+ throw new InvalidArgumentException("Unknown gene modification type: " + modificationType);
+ }
+
+ result.setIdModificationResidue(this.getIdModificationResidue());
+ result.setName(this.getName());
+ if (angle == null) {
+ logger.warn("Angle is not defined using 0 as default");
+ angle = 0.0;
+ }
+ result.setPosition(converter.getResidueCoordinates(element, angle));
+ result.setState(this.getState());
+ return result;
+ }
+
+ public String getModificationType() {
+ return modificationType;
+ }
+
+ public void setModificationType(String modificationType) {
+ if (modificationType == null) {
+ throw new NullPointerException();
+ }
+ this.modificationType = modificationType;
+ }
+
+}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
index 00ed521672..341836fc7c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/CellDesignerModificationResidue.java
@@ -10,7 +10,9 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasCon
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
/**
* This class represent modification residue in protein and gene. However, it is
@@ -30,7 +32,6 @@ public class CellDesignerModificationResidue implements Serializable {
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(CellDesignerModificationResidue.class.getName());
/**
@@ -43,6 +44,8 @@ public class CellDesignerModificationResidue implements Serializable {
*/
private String name = "";
+ private String modificationType;
+
/**
* Some strange parameter in CellDesigner. No idea what is it for.
*/
@@ -87,6 +90,7 @@ public class CellDesignerModificationResidue implements Serializable {
this.size = mr.size;
this.side = mr.side;
this.state = mr.state;
+ this.modificationType = mr.modificationType;
}
/**
@@ -101,6 +105,13 @@ public class CellDesignerModificationResidue implements Serializable {
this.name = mr.getName();
this.angle = converter.getAngleForPoint(mr.getSpecies(), mr.getPosition());
this.state = mr.getState();
+ if (mr instanceof Residue) {
+ this.modificationType = "RESIDUE";
+ } else if (mr instanceof ModificationSite) {
+ this.modificationType = "MODIFICATION_SITE";
+ } else {
+ throw new InvalidArgumentException("Unknown modification type: " + mr.getClass());
+ }
}
/**
@@ -136,6 +147,9 @@ public class CellDesignerModificationResidue implements Serializable {
if (mr.getState() != null) {
this.state = mr.state;
}
+ if (mr.getModificationType() != null) {
+ this.setModificationType(mr.modificationType);
+ }
}
@Override
@@ -319,10 +333,17 @@ public class CellDesignerModificationResidue implements Serializable {
*
* @return {@link ModificationResidue} representing this object in a model
*/
- public ModificationResidue createModificationResidueAlias(Element element) {
+ public ModificationResidue createProteinModification(Element element) {
CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, false);
- ModificationResidue result = new ModificationResidue();
+ ModificationResidue result = null;
+ if (modificationType == null) {
+ throw new InvalidArgumentException("No type information for modification: " + idModificationResidue);
+ } else if (modificationType.equals("RESIDUE")) {
+ result = new Residue();
+ } else {
+ throw new InvalidArgumentException("Unknown protein modification type: " + modificationType);
+ }
result.setIdModificationResidue(this.getIdModificationResidue());
result.setName(this.getName());
@@ -335,4 +356,12 @@ public class CellDesignerModificationResidue implements Serializable {
return result;
}
+ public String getModificationType() {
+ return modificationType;
+ }
+
+ public void setModificationType(String modificationType) {
+ this.modificationType = modificationType;
+ }
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
index f830143a14..c94eff8a5f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/SpeciesState.java
@@ -41,7 +41,7 @@ public class SpeciesState {
/**
* List of species modification.
*/
- private List<CellDesignerModificationResidue> modifications = new ArrayList<CellDesignerModificationResidue>();
+ private List<CellDesignerModificationResidue> modifications = new ArrayList<>();
/**
* Adds modification to the state.
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 6f97c0fbcd..362268ede5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -26,6 +26,7 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -120,8 +121,8 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
parser.createModel(new ConverterParams().filename("testFiles/invalid/sample10.xml"));
fail("Exceptin expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("Unknown element of model/listOfReactions"));
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("No type information for modification"));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
index 1402647401..da9e20d35c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/species/GeneXmlParserTest.java
@@ -30,6 +30,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
public class GeneXmlParserTest extends CellDesignerTestFunctions {
Logger logger = Logger.getLogger(GeneXmlParserTest.class.getName());
@@ -155,7 +156,7 @@ public class GeneXmlParserTest extends CellDesignerTestFunctions {
protein.setY(10);
protein.setWidth(10);
protein.setHeight(10);
- ModificationResidue mr = new ModificationResidue();
+ Residue mr = new Residue();
mr.setIdModificationResidue("i");
mr.setName("a");
mr.setPosition(new Point2D.Double(3.0, 2.0));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
index d3ab45debf..d58377255b 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/GeneTest.java
@@ -1,128 +1,129 @@
-package lcsb.mapviewer.converter.model.celldesigner.structure;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-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.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
-import lcsb.mapviewer.model.map.species.Gene;
-
-public class GeneTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new CellDesignerGene());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- CellDesignerGene original = new CellDesignerGene();
- original.addModificationResidue(new CellDesignerModificationResidue());
- CellDesignerGene gene = new CellDesignerGene(original);
- assertNotNull(gene);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- List<CellDesignerModificationResidue> modificationResidues = new ArrayList<>();
- CellDesignerGene gene = new CellDesignerGene(new CellDesignerSpecies<Gene>());
- gene.setModificationResidues(modificationResidues);
- assertEquals(modificationResidues, gene.getModificationResidues());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- CellDesignerGene degraded = new CellDesignerGene().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- CellDesignerGene gene = Mockito.spy(CellDesignerGene.class);
- gene.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdate() {
- try {
- CellDesignerGene gene = new CellDesignerGene();
- CellDesignerGene gene2 = new CellDesignerGene();
- List<CellDesignerModificationResidue> residues = new ArrayList<>();
- residues.add(new CellDesignerModificationResidue());
-
- gene2.setModificationResidues(residues);
-
- gene.update(gene2);
- assertEquals(1, gene.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddModificationResidue() {
- try {
- CellDesignerGene gene = new CellDesignerGene();
- CellDesignerModificationResidue mr = new CellDesignerModificationResidue("id1");
- CellDesignerModificationResidue mr2 = new CellDesignerModificationResidue("id1");
- CellDesignerModificationResidue mr3 = new CellDesignerModificationResidue("id2");
-
- gene.addModificationResidue(mr);
- assertEquals(1, gene.getModificationResidues().size());
- gene.addModificationResidue(mr2);
- assertEquals(1, gene.getModificationResidues().size());
- gene.addModificationResidue(mr3);
- assertEquals(2, gene.getModificationResidues().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.converter.model.celldesigner.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+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.exception.NotImplementedException;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerGeneRegion;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.map.species.Gene;
+
+public class GeneTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new CellDesignerGene());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ CellDesignerGene original = new CellDesignerGene();
+ original.addModificationResidue(new CellDesignerGeneRegion());
+ CellDesignerGene gene = new CellDesignerGene(original);
+ assertNotNull(gene);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ List<CellDesignerGeneRegion> modificationResidues = new ArrayList<>();
+ CellDesignerGene gene = new CellDesignerGene(new CellDesignerSpecies<>());
+ gene.setModificationResidues(modificationResidues);
+ assertEquals(modificationResidues, gene.getModificationResidues());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ CellDesignerGene degraded = new CellDesignerGene().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ CellDesignerGene gene = Mockito.spy(CellDesignerGene.class);
+ gene.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdate() {
+ try {
+ CellDesignerGene gene = new CellDesignerGene();
+ CellDesignerGene gene2 = new CellDesignerGene();
+ List<CellDesignerGeneRegion> residues = new ArrayList<>();
+ residues.add(new CellDesignerGeneRegion());
+
+ gene2.setModificationResidues(residues);
+
+ gene.update(gene2);
+ assertEquals(1, gene.getModificationResidues().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddModificationResidue() {
+ try {
+ CellDesignerGene gene = new CellDesignerGene();
+ CellDesignerGeneRegion mr = new CellDesignerGeneRegion("id1");
+ CellDesignerGeneRegion mr2 = new CellDesignerGeneRegion("id1");
+ CellDesignerGeneRegion mr3 = new CellDesignerGeneRegion("id2");
+
+ gene.addModificationResidue(mr);
+ assertEquals(1, gene.getModificationResidues().size());
+ gene.addModificationResidue(mr2);
+ assertEquals(1, gene.getModificationResidues().size());
+ gene.addModificationResidue(mr3);
+ assertEquals(2, gene.getModificationResidues().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
index 99451f67ca..804c4f87c4 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/structure/SpeciesStateTest.java
@@ -16,7 +16,7 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesigner
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
public class SpeciesStateTest {
@@ -62,7 +62,7 @@ public class SpeciesStateTest {
Gene gene = new Gene("2");
gene.setWidth(60);
gene.setHeight(10);
- ModificationResidue mr = new ModificationResidue();
+ ModificationSite mr = new ModificationSite();
mr.setPosition(new Point2D.Double(10, 40));
gene.addModificationResidue(mr);
SpeciesState state = new SpeciesState(gene);
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index 2aa1499af2..9bace29745 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -76,6 +76,7 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
/**
* This class is a parser for SBGN-ML files.
@@ -799,7 +800,7 @@ public class SbgnmlXmlParser {
throw new Exception("Only macromolecule elements can have state variables.");
}
Protein protein = (Protein) newSpecies;
- ModificationResidue mr = new ModificationResidue();
+ ModificationResidue mr = new Residue();
mr.setSpecies(protein);
mr.setIdModificationResidue(unitOfInformationGlyph.getId());
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
index 8f40e4864b..c4c7f7f038 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java
@@ -9,7 +9,7 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
public class SbgnmlXmlParserTest2 {
@@ -23,7 +23,7 @@ public class SbgnmlXmlParserTest2 {
protein.setHeight(30);
protein.setX(200);
protein.setX(300);
- ModificationResidue mr = new ModificationResidue();
+ Residue mr = new Residue();
Point2D position = new Point2D.Double(100, 20);
mr.setPosition(position);
protein.addModificationResidue(mr);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
index db6c9cb840..ae7a0cfc64 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Gene.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.ModificationResidue;
-
-/**
- * Entity representing gene element on the map.
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@DiscriminatorValue("GENE_ALIAS")
-public class Gene extends Species {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of modifications for the Gene.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "species", orphanRemoval = true)
- @LazyCollection(LazyCollectionOption.FALSE)
- private List<ModificationResidue> modificationResidues = new ArrayList<>();
-
- /**
- * Empty constructor required by hibernate.
- */
- Gene() {
- }
-
- /**
- * Constructor that creates a copy of the element given in the parameter.
- *
- * @param original
- * original object that will be used for creating copy
- */
- public Gene(Gene original) {
- super(original);
- for (ModificationResidue mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
- }
- }
-
- /**
- * Default constructor.
- *
- * @param elementId
- * uniqe (within model) element identifier
- */
- public Gene(String elementId) {
- setElementId(elementId);
- }
-
- /**
- * Adds {@link ModificationResidue}.
- *
- * @param modificationResidue
- * {@link ModificationResidue} to be added
- */
- public void addModificationResidue(ModificationResidue modificationResidue) {
- modificationResidues.add(modificationResidue);
- modificationResidue.setSpecies(this);
-
- }
-
- @Override
- public Gene copy() {
- if (this.getClass() == Gene.class) {
- return new Gene(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the modificationResidues
- * @see #modificationResidues
- */
- public List<ModificationResidue> getModificationResidues() {
- return modificationResidues;
- }
-
- /**
- * @param modificationResidues
- * the modificationResidues to set
- * @see #modificationResidues
- */
- public void setModificationResidues(List<ModificationResidue> modificationResidues) {
- this.modificationResidues = modificationResidues;
- }
-
- @Override
- public String getStringType() {
- return "Gene";
- }
-
-}
+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.ModificationResidue;
+
+/**
+ * Entity representing gene element on the map.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("GENE_ALIAS")
+public class Gene extends Species {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of modifications for the Gene.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "species", orphanRemoval = true)
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<ModificationResidue> modificationResidues = new ArrayList<>();
+
+ /**
+ * Empty constructor required by hibernate.
+ */
+ Gene() {
+ }
+
+ /**
+ * Constructor that creates a copy of the element given in the parameter.
+ *
+ * @param original
+ * original object that will be used for creating copy
+ */
+ public Gene(Gene original) {
+ super(original);
+ for (ModificationResidue mr : original.getModificationResidues()) {
+ addModificationResidue(mr.copy());
+ }
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * uniqe (within model) element identifier
+ */
+ public Gene(String elementId) {
+ setElementId(elementId);
+ }
+
+ /**
+ * Adds {@link ModificationResidue}.
+ *
+ * @param modificationResidue
+ * {@link ModificationResidue} to be added
+ */
+ public void addModificationResidue(ModificationResidue modificationResidue) {
+ modificationResidues.add(modificationResidue);
+ modificationResidue.setSpecies(this);
+
+ }
+
+ @Override
+ public Gene copy() {
+ if (this.getClass() == Gene.class) {
+ return new Gene(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the modificationResidues
+ * @see #modificationResidues
+ */
+ public List<ModificationResidue> getModificationResidues() {
+ return modificationResidues;
+ }
+
+ /**
+ * @param modificationResidues
+ * the modificationResidues to set
+ * @see #modificationResidues
+ */
+ public void setModificationResidues(List<ModificationResidue> modificationResidues) {
+ this.modificationResidues = modificationResidues;
+ }
+
+ @Override
+ public String getStringType() {
+ return "Gene";
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
index 9e891ddd9d..8f4cf0ecf0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Protein.java
@@ -58,7 +58,7 @@ public abstract class Protein extends Species {
super(original);
this.structuralState = original.getStructuralState();
for (ModificationResidue mr : original.getModificationResidues()) {
- addModificationResidue(new ModificationResidue(mr));
+ addModificationResidue(mr.copy());
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java
index 97db98c8d9..e9bd63b9f5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ElementModification.java
@@ -4,4 +4,6 @@ public interface ElementModification {
ModificationState getState();
String getName();
+
+ ElementModification copy();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
index 34d6a87ef9..c088c3f6f1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationResidue.java
@@ -4,7 +4,11 @@ import java.awt.geom.Point2D;
import java.io.Serializable;
import java.text.DecimalFormat;
+import javax.persistence.CascadeType;
import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.DiscriminatorType;
+import javax.persistence.DiscriminatorValue;
import javax.persistence.Entity;
import javax.persistence.EnumType;
import javax.persistence.Enumerated;
@@ -12,6 +16,8 @@ import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
+import javax.persistence.Inheritance;
+import javax.persistence.InheritanceType;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
@@ -30,8 +36,12 @@ import lcsb.mapviewer.model.map.species.Species;
* @author Piotr Gawron
*
*/
+
@Entity
@Table(name = "modification_residue_table")
+@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
+@DiscriminatorColumn(name = "modification_type", discriminatorType = DiscriminatorType.STRING)
+@DiscriminatorValue("GENERIC_MODIFICATION_RESIDUE")
@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
public class ModificationResidue implements Serializable, ElementModification {
@@ -77,7 +87,7 @@ public class ModificationResidue implements Serializable, ElementModification {
/**
* Species to which this modification belong to.
*/
- @ManyToOne(fetch = FetchType.LAZY)
+ @ManyToOne(fetch = FetchType.LAZY, cascade = CascadeType.ALL)
@JoinColumn(name = "idSpeciesDb", nullable = false)
private Species species;
@@ -108,18 +118,6 @@ public class ModificationResidue implements Serializable, ElementModification {
return result;
}
- /**
- * Creates copy of the object.
- *
- * @return copy of the object.
- */
- public ModificationResidue copy() {
- if (this.getClass() == ModificationResidue.class) {
- return new ModificationResidue(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
/**
* @return the idModificationResidue
@@ -213,5 +211,9 @@ public class ModificationResidue implements Serializable, ElementModification {
public void setPosition(Point2D position) {
this.position = position;
}
+
+ public ModificationResidue copy() {
+ throw new NotImplementedException();
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
new file mode 100644
index 0000000000..390c963779
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/ModificationSite.java
@@ -0,0 +1,39 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+@Entity
+@DiscriminatorValue("MODIFICATION_SITE")
+public class ModificationSite extends ModificationResidue {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public ModificationSite() {
+ super();
+ }
+
+ public ModificationSite(ModificationSite residue) {
+ super(residue);
+ }
+
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public ModificationSite copy() {
+ if (this.getClass() == ModificationSite.class) {
+ return new ModificationSite(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
new file mode 100644
index 0000000000..b03b751004
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/field/Residue.java
@@ -0,0 +1,39 @@
+package lcsb.mapviewer.model.map.species.field;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+
+@Entity
+@DiscriminatorValue("RESIDUE")
+public class Residue extends ModificationResidue {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ public Residue() {
+ super();
+ }
+
+ public Residue(Residue residue) {
+ super(residue);
+ }
+
+
+ /**
+ * Creates copy of the object.
+ *
+ * @return copy of the object.
+ */
+ public Residue copy() {
+ if (this.getClass() == Residue.class) {
+ return new Residue(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
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 2d0cd9b20b..0b245815db 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
@@ -278,4 +278,9 @@ public class RnaRegion implements Serializable, ElementModification {
this.width = width;
}
+ @Override
+ public RnaRegion copy() {
+ return new RnaRegion(this);
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
index 3a28ecf6ae..34dc67ef01 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneComparatorTest.java
@@ -13,6 +13,7 @@ import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
public class GeneComparatorTest {
@@ -81,7 +82,7 @@ public class GeneComparatorTest {
Gene result = new Gene();
result.setHypothetical(true);
- ModificationResidue residue = new ModificationResidue();
+ ModificationSite residue = new ModificationSite();
result.addModificationResidue(residue);
residue.setIdModificationResidue("a");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
index ec7c48dcd1..5dd200337e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/GeneTest.java
@@ -1,90 +1,91 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-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.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-public class GeneTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new Gene());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- Gene original = new Gene();
- original.addModificationResidue(new ModificationResidue());
- Gene gene = new Gene(original);
- assertNotNull(gene);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- List<ModificationResidue> modificationResidues = new ArrayList<>();
- Gene gene = new Gene("id");
- assertNotNull(gene.getStringType());
- gene.setModificationResidues(modificationResidues);
- assertEquals(modificationResidues, gene.getModificationResidues());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- Gene degraded = new Gene().copy();
- assertNotNull(degraded);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- Gene gene = Mockito.spy(Gene.class);
- gene.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+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.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+
+public class GeneTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new Gene());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ Gene original = new Gene();
+ original.addModificationResidue(new ModificationSite());
+ Gene gene = new Gene(original);
+ assertNotNull(gene);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ List<ModificationResidue> modificationResidues = new ArrayList<>();
+ Gene gene = new Gene("id");
+ assertNotNull(gene.getStringType());
+ gene.setModificationResidues(modificationResidues);
+ assertEquals(modificationResidues, gene.getModificationResidues());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ Gene degraded = new Gene().copy();
+ assertNotNull(degraded);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ Gene gene = Mockito.spy(Gene.class);
+ gene.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
index a118f593ed..4f3a722d8d 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinComparatorTest.java
@@ -12,8 +12,8 @@ import org.junit.Test;
import org.mockito.Mockito;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
public class ProteinComparatorTest {
@@ -123,7 +123,7 @@ public class ProteinComparatorTest {
result.setStructuralState("id1");
result.setHypothetical(true);
- ModificationResidue residue = new ModificationResidue();
+ Residue residue = new Residue();
result.addModificationResidue(residue);
residue.setIdModificationResidue("a");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
index 0a3a22c3db..6485005ac7 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ProteinTest.java
@@ -1,105 +1,106 @@
-package lcsb.mapviewer.model.map.species;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
-
-import java.util.ArrayList;
-import java.util.List;
-
-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.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
-public class ProteinTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testSerialization() {
- try {
- SerializationUtils.serialize(new GenericProtein());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testConstructor1() {
- try {
- GenericProtein protein = new GenericProtein();
- protein.setStructuralState("srt");
- List<ModificationResidue> residues = new ArrayList<>();
- residues.add(new ModificationResidue());
-
- protein.setModificationResidues(residues);
- Protein protein2 = new GenericProtein(protein);
- assertNotNull(protein2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSetStructuralState() {
- try {
- GenericProtein protein = new GenericProtein();
- protein.setStructuralState("str");
- protein.setStructuralState("str1");
-
- assertEquals("str1", protein.getStructuralState());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- GenericProtein protein = new GenericProtein("id");
- assertNotNull(protein.getStringType());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopy() {
- try {
- GenericProtein protein = new GenericProtein().copy();
- assertNotNull(protein);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidCopy() {
- try {
- GenericProtein mock = Mockito.spy(GenericProtein.class);
- mock.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.model.map.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.fail;
+
+import java.util.ArrayList;
+import java.util.List;
+
+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.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
+
+public class ProteinTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSerialization() {
+ try {
+ SerializationUtils.serialize(new GenericProtein());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testConstructor1() {
+ try {
+ GenericProtein protein = new GenericProtein();
+ protein.setStructuralState("srt");
+ List<ModificationResidue> residues = new ArrayList<>();
+ residues.add(new Residue());
+
+ protein.setModificationResidues(residues);
+ Protein protein2 = new GenericProtein(protein);
+ assertNotNull(protein2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSetStructuralState() {
+ try {
+ GenericProtein protein = new GenericProtein();
+ protein.setStructuralState("str");
+ protein.setStructuralState("str1");
+
+ assertEquals("str1", protein.getStructuralState());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ GenericProtein protein = new GenericProtein("id");
+ assertNotNull(protein.getStringType());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopy() {
+ try {
+ GenericProtein protein = new GenericProtein().copy();
+ assertNotNull(protein);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidCopy() {
+ try {
+ GenericProtein mock = Mockito.spy(GenericProtein.class);
+ mock.copy();
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
index 512ff1dab9..de4bd79233 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/AllFieldTests.java
@@ -8,7 +8,7 @@ import org.junit.runners.Suite.SuiteClasses;
@SuiteClasses({ AntisenseRnaRegionTest.class, //
AntisenseRnaRegionTypeTest.class, //
ModificationStateTest.class, //
- ModificationResidueTest.class, //
+ ResidueTest.class, //
PositionToCompartmentTest.class, //
RnaRegionTest.class,//
StructureTest.class,//
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java
deleted file mode 100644
index 6b839c1379..0000000000
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ModificationResidueTest.java
+++ /dev/null
@@ -1,61 +0,0 @@
-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.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-
-public class ModificationResidueTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- ModificationResidue mr = new ModificationResidue();
- Species species = new GenericProtein("id");
- int id = 94;
-
- mr.setSpecies(species);
- mr.setId(id);
-
- assertEquals(species, mr.getSpecies());
- assertEquals(id, mr.getId());
- }
-
- @Test
- public void testCopy() {
- ModificationResidue mr = new ModificationResidue().copy();
- assertNotNull(mr);
- }
-
- @Test
- public void testInvalidCopy() {
- ModificationResidue mr = Mockito.spy(ModificationResidue.class);
- try {
- mr.copy();
- fail("Exception expected");
- } catch (NotImplementedException e) {
-
- }
- }
-
-}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
new file mode 100644
index 0000000000..ff9289bb27
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/field/ResidueTest.java
@@ -0,0 +1,50 @@
+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.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class ResidueTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetters() {
+ Residue mr = new Residue();
+ Species species = new GenericProtein("id");
+ int id = 94;
+
+ mr.setSpecies(species);
+ mr.setId(id);
+
+ assertEquals(species, mr.getSpecies());
+ assertEquals(id, mr.getId());
+ }
+
+ @Test
+ public void testCopy() {
+ Residue mr = new Residue().copy();
+ assertNotNull(mr);
+ }
+
+}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index df349b05bb..90aed61065 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -60,6 +60,8 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.wikipathway.model.DataNode;
import lcsb.mapviewer.wikipathway.model.Edge;
@@ -309,8 +311,8 @@ public class ModelContructor {
}
alias.setX(rec.getX());
alias.setY(rec.getY());
- alias.setWidth((int)rec.getWidth());
- alias.setHeight((int)rec.getHeight());
+ alias.setWidth((int) rec.getWidth());
+ alias.setHeight((int) rec.getHeight());
alias.setColor(DEFAULT_COMPLEX_ALIAS_COLOR);
data.id2alias.put(group.getGraphId(), alias);
@@ -383,23 +385,27 @@ public class ModelContructor {
// TODO this might not work
Element species = data.id2alias.get(state.getGraphRef());
if (state.getType() != null) {
- ModificationResidue mr = new ModificationResidue();
- mr.setIdModificationResidue(state.getGraphId());
- mr.setState(state.getType());
-
- Double x = state.getRelX() * species.getWidth() / 2 + species.getCenterX();
- Double y = state.getRelY() * species.getHeight() / 2 + species.getCenterY();
- mr.setPosition(new Point2D.Double(x, y));
+ ModificationResidue mr = null;
if (species instanceof Protein) {
+ mr = new Residue();
((Protein) species).addModificationResidue(mr);
} else if (species instanceof Gene) {
+ mr = new ModificationSite();
((Gene) species).addModificationResidue(mr);
} else {
logger.warn(
state.getWarningPrefix() + "state for " + species.getClass().getSimpleName() + " is not supported.");
}
- adjustModificationCoordinates(species);
+ if (mr != null) {
+ mr.setIdModificationResidue(state.getGraphId());
+ mr.setState(state.getType());
+
+ Double x = state.getRelX() * species.getWidth() / 2 + species.getCenterX();
+ Double y = state.getRelY() * species.getHeight() / 2 + species.getCenterY();
+ mr.setPosition(new Point2D.Double(x, y));
+ adjustModificationCoordinates(species);
+ }
} else if (state.getStructuralState() != null) {
if (species instanceof Protein) {
Protein protein = ((Protein) species);
@@ -442,7 +448,7 @@ public class ModelContructor {
mr.setPosition(converter.getResidueCoordinates(species, angle));
}
}
-
+
}
}
@@ -532,8 +538,8 @@ public class ModelContructor {
Rectangle2D rec = gpmlElement.getRectangle();
alias.setX(rec.getX());
alias.setY(rec.getY());
- alias.setWidth((int)rec.getWidth());
- alias.setHeight((int)rec.getHeight());
+ alias.setWidth((int) rec.getWidth());
+ alias.setHeight((int) rec.getHeight());
alias.setColor(gpmlElement.getFillColor());
return alias;
}
diff --git a/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql b/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql
index dad28041e7..095168533e 100644
--- a/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql
+++ b/persist/src/db/12.1.0~alpha.0/fix_db_20180711.sql
@@ -2,3 +2,8 @@
alter table rna_region_table add column width numeric(6,2);
update rna_region_table set width=element_table.width*rna_region_table.size from element_table where element_table.iddb = rna_region_table.idspeciesdb and not size is null;
alter table rna_region_table drop column size;
+
+--modifications includes different type of modification (that will be resolved to different classes)
+alter table modification_residue_table add column modification_type varchar(255);
+update modification_residue_table set modification_type='MODIFICATION_SITE' from element_table where modification_residue_table.idspeciesdb=element_table.iddb and element_type_db='GENE_ALIAS';
+update modification_residue_table set modification_type='RESIDUE' from element_table where modification_residue_table.idspeciesdb=element_table.iddb and modification_type is null;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
index b18a7cba2a..e00f0b9d3a 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/CommentDaoTest.java
@@ -1,185 +1,186 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-
-import java.awt.Color;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.Comment;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class CommentDaoTest extends PersistTestFunctions {
- int identifierCounter = 1;
-
- private Project project;
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- }
-
- @After
- public void tearDown() throws Exception {
- projectDao.delete(project);
- }
-
- @Test
- public void testGetComments() {
- try {
- Model model = createModel();
- project.addModel(model);
- modelDao.add(model);
- projectDao.update(project);
-
- Comment comment = new Comment();
- comment.setDeleted(true);
- comment.setModel(model);
- commentDao.add(comment);
-
- Comment comment2 = new Comment();
- comment2.setPinned(true);
- comment2.setModel(model);
- commentDao.add(comment2);
-
- assertEquals(0, commentDao.getCommentByModel(model, true, true).size());
- assertEquals(1, commentDao.getCommentByModel(model, false, true).size());
- assertEquals(1, commentDao.getCommentByModel(model, null, true).size());
- assertEquals(1, commentDao.getCommentByModel(model, true, false).size());
- assertEquals(0, commentDao.getCommentByModel(model, false, false).size());
- assertEquals(1, commentDao.getCommentByModel(model, null, false).size());
- assertEquals(1, commentDao.getCommentByModel(model, true, null).size());
- assertEquals(1, commentDao.getCommentByModel(model, false, null).size());
- assertEquals(2, commentDao.getCommentByModel(model, null, null).size());
-
- assertEquals(0, commentDao.getCommentByModel(model.getModelData(), true, true).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, true).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, true).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, false).size());
- assertEquals(0, commentDao.getCommentByModel(model.getModelData(), false, false).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, false).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, null).size());
- assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, null).size());
- assertEquals(2, commentDao.getCommentByModel(model.getModelData(), null, null).size());
-
- commentDao.delete(comment);
- commentDao.delete(comment2);
- modelDao.delete(model);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(alias);
-
- ModificationResidue mr = new ModificationResidue();
- mr.setName("mr");
- alias.addModificationResidue(mr);
-
- alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein(aliasId);
- alias.setName("SNCA");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Color;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.Comment;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class CommentDaoTest extends PersistTestFunctions {
+ int identifierCounter = 1;
+
+ private Project project;
+ String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ projectDao.delete(project);
+ }
+
+ @Test
+ public void testGetComments() {
+ try {
+ Model model = createModel();
+ project.addModel(model);
+ modelDao.add(model);
+ projectDao.update(project);
+
+ Comment comment = new Comment();
+ comment.setDeleted(true);
+ comment.setModel(model);
+ commentDao.add(comment);
+
+ Comment comment2 = new Comment();
+ comment2.setPinned(true);
+ comment2.setModel(model);
+ commentDao.add(comment2);
+
+ assertEquals(0, commentDao.getCommentByModel(model, true, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model, false, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model, null, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model, true, false).size());
+ assertEquals(0, commentDao.getCommentByModel(model, false, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model, null, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model, true, null).size());
+ assertEquals(1, commentDao.getCommentByModel(model, false, null).size());
+ assertEquals(2, commentDao.getCommentByModel(model, null, null).size());
+
+ assertEquals(0, commentDao.getCommentByModel(model.getModelData(), true, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, true).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, false).size());
+ assertEquals(0, commentDao.getCommentByModel(model.getModelData(), false, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), null, false).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), true, null).size());
+ assertEquals(1, commentDao.getCommentByModel(model.getModelData(), false, null).size());
+ assertEquals(2, commentDao.getCommentByModel(model.getModelData(), null, null).size());
+
+ commentDao.delete(comment);
+ commentDao.delete(comment2);
+ modelDao.delete(model);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(alias);
+
+ ModificationResidue mr = new Residue();
+ mr.setName("mr");
+ alias.addModificationResidue(mr);
+
+ alias.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private GenericProtein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein(aliasId);
+ alias.setName("SNCA");
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
index 8b67d43aa9..83572545fd 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
@@ -1,230 +1,230 @@
-package lcsb.mapviewer.persist.dao.map;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.awt.Color;
-import java.nio.charset.StandardCharsets;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.cache.UploadedFileEntry;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-public class LayoutDaoTest extends PersistTestFunctions {
-
- @Autowired
- private LayoutDao layoutDao;
-
- final static Logger logger = Logger.getLogger(LayoutDaoTest.class);
-
- int identifierCounter = 0;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsWithData() throws Exception {
- try {
- Model model = createModel();
-
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle("temporary name");
-
- byte[] data = "test".getBytes();
- UploadedFileEntry fileEntry = new UploadedFileEntry();
- fileEntry.setFileContent(data);
-
- layout.setInputData(fileEntry);
- model.addLayout(layout);
- layoutDao.add(layout);
-
- layoutDao.evict(layout);
-
- layout = layoutDao.getById(layout.getId());
-
- assertEquals("test", new String(layout.getInputData().getFileContent(), StandardCharsets.UTF_8));
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding layouts to model.
- *
- * @throws Exception
- */
- @Test
- public void testLayoutsWithoutData() throws Exception {
- try {
- Model model = createModel();
- String tempName = "temporary name";
-
- createUser();
-
- Project project = new Project();
- project.addModel(model);
- projectDao.add(project);
-
- modelDao.evict(model);
- projectDao.evict(project);
-
- assertEquals(0, layoutDao.getCountByUser(user));
- assertEquals(0, layoutDao.getLayoutsByModel(model).size());
- assertNull(layoutDao.getLayoutByName(model, tempName));
-
- Layout layout = new Layout();
- layout.setDirectory("tmp");
- layout.setTitle(tempName);
- layout.setCreator(user);
- model.addLayout(layout);
- layoutDao.add(layout);
-
- layoutDao.evict(layout);
-
- layout = layoutDao.getById(layout.getId());
-
- assertEquals(1, layoutDao.getLayoutsByModel(model).size());
- assertNotNull(layoutDao.getLayoutByName(model, tempName));
- assertEquals(1, layoutDao.getCountByUser(user));
-
- assertNull(layout.getInputData());
-
- project = projectDao.getById(project.getId());
- projectDao.delete(project);
-
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- Species alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
- model.addElement(alias);
- alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
- model.addElement(alias);
- alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
- model.addElement(alias);
- alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
- model.addElement(alias);
-
- alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
- model.addElement(cAlias);
- model.setWidth(2000);
- model.setHeight(2000);
-
- Layer layer = new Layer();
- model.addLayer(layer);
-
- LayerRect lr = new LayerRect();
- lr.setColor(Color.YELLOW);
- layer.addLayerRect(lr);
-
- Reaction reaction = new TransportReaction();
- reaction.addProduct(new Product(alias));
- reaction.addReactant(new Reactant(alias2));
- reaction.setIdReaction("re" + identifierCounter++);
- model.addReaction(reaction);
-
- Protein protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
- model.addElement(protein);
-
- ModificationResidue mr = new ModificationResidue();
- mr.setName("mr");
- protein.addModificationResidue(mr);
-
- protein.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Protein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- GenericProtein alias = new GenericProtein("s" + identifierCounter++);
- alias.setElementId(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
-}
+package lcsb.mapviewer.persist.dao.map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.awt.Color;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.persist.PersistTestFunctions;
+
+public class LayoutDaoTest extends PersistTestFunctions {
+
+ @Autowired
+ private LayoutDao layoutDao;
+
+ final static Logger logger = Logger.getLogger(LayoutDaoTest.class);
+
+ int identifierCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsWithData() throws Exception {
+ try {
+ Model model = createModel();
+
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle("temporary name");
+
+ byte[] data = "test".getBytes();
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setFileContent(data);
+
+ layout.setInputData(fileEntry);
+ model.addLayout(layout);
+ layoutDao.add(layout);
+
+ layoutDao.evict(layout);
+
+ layout = layoutDao.getById(layout.getId());
+
+ assertEquals("test", new String(layout.getInputData().getFileContent(), StandardCharsets.UTF_8));
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding layouts to model.
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testLayoutsWithoutData() throws Exception {
+ try {
+ Model model = createModel();
+ String tempName = "temporary name";
+
+ createUser();
+
+ Project project = new Project();
+ project.addModel(model);
+ projectDao.add(project);
+
+ modelDao.evict(model);
+ projectDao.evict(project);
+
+ assertEquals(0, layoutDao.getCountByUser(user));
+ assertEquals(0, layoutDao.getLayoutsByModel(model).size());
+ assertNull(layoutDao.getLayoutByName(model, tempName));
+
+ Layout layout = new Layout();
+ layout.setDirectory("tmp");
+ layout.setTitle(tempName);
+ layout.setCreator(user);
+ model.addLayout(layout);
+ layoutDao.add(layout);
+
+ layoutDao.evict(layout);
+
+ layout = layoutDao.getById(layout.getId());
+
+ assertEquals(1, layoutDao.getLayoutsByModel(model).size());
+ assertNotNull(layoutDao.getLayoutByName(model, tempName));
+ assertEquals(1, layoutDao.getCountByUser(user));
+
+ assertNull(layout.getInputData());
+
+ project = projectDao.getById(project.getId());
+ projectDao.delete(project);
+
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ Species alias = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2");
+ model.addElement(alias);
+ alias = createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117");
+ model.addElement(alias);
+ alias = createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119");
+ model.addElement(alias);
+ alias = createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121");
+ model.addElement(alias);
+
+ alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ Compartment cAlias = createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1");
+ model.addElement(cAlias);
+ model.setWidth(2000);
+ model.setHeight(2000);
+
+ Layer layer = new Layer();
+ model.addLayer(layer);
+
+ LayerRect lr = new LayerRect();
+ lr.setColor(Color.YELLOW);
+ layer.addLayerRect(lr);
+
+ Reaction reaction = new TransportReaction();
+ reaction.addProduct(new Product(alias));
+ reaction.addReactant(new Reactant(alias2));
+ reaction.setIdReaction("re" + identifierCounter++);
+ model.addReaction(reaction);
+
+ Protein protein = createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
+ model.addElement(protein);
+
+ Residue mr = new Residue();
+ mr.setName("mr");
+ protein.addModificationResidue(mr);
+
+ protein.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "c"));
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Protein createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ GenericProtein alias = new GenericProtein("s" + identifierCounter++);
+ alias.setElementId(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index 15b56dadff..02bf55c42b 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -41,7 +41,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ModelDaoTest extends PersistTestFunctions {
@@ -86,6 +86,9 @@ public class ModelDaoTest extends PersistTestFunctions {
assertEquals(model.getLayers().size(), model2.getLayers().size());
assertEquals(model.getReactions().size(), model2.getReactions().size());
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, new ModelFullIndexed(model2)));
+
modelDao.delete(model2);
model2 = modelDao.getById(model.getId());
assertNull(model2);
@@ -424,7 +427,7 @@ public class ModelDaoTest extends PersistTestFunctions {
alias = createSpecies(264.8333333333335, 517.75, 86.0, 46.0, "pr1");
model.addElement(alias);
- ModificationResidue mr = new ModificationResidue();
+ Residue mr = new Residue();
mr.setName("mr");
mr.setPosition(new Point2D.Double(10, 20));
alias.addModificationResidue(mr);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
index 290777b975..0f264ff692 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AliasDaoTest2.java
@@ -25,8 +25,8 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.persist.PersistTestFunctions;
@@ -106,7 +106,7 @@ public class AliasDaoTest2 extends PersistTestFunctions {
try {
Protein protein = new GenericProtein(testIdAlias);
- ModificationResidue mr = new ModificationResidue();
+ Residue mr = new Residue();
mr.setPosition(new Point2D.Double(10, 20));
mr.setName("name");
mr.setState(ModificationState.GLYCOSYLATED);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index a5e898655c..042a0eb395 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -28,9 +28,8 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegion;
-import lcsb.mapviewer.model.map.species.field.AntisenseRnaRegionType;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationState;
+import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.services.interfaces.IModelService;
@@ -116,7 +115,7 @@ public class ElementRestImplTest extends RestTestFunctions {
try {
String state = "asd";
GenericProtein protein = new GenericProtein("s1");
- ModificationResidue mr = new ModificationResidue();
+ Residue mr = new Residue();
mr.setState(ModificationState.ACETYLATED);
mr.setName("S250");
protein.addModificationResidue(mr);
--
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