diff --git a/met4j-chemUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_chemUtils/FormulaParser.java b/met4j-chemUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_chemUtils/FormulaParser.java
index 0cdf9b5a630debdbbedc9e27cb2e071e942f04b7..d3147808dcfb91a05cee2be930647d85d6149981 100644
--- a/met4j-chemUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_chemUtils/FormulaParser.java
+++ b/met4j-chemUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_chemUtils/FormulaParser.java
@@ -15,12 +15,10 @@ public class FormulaParser {
String formula;
Pattern inorgaRegex;
Pattern groupMatch;
- Pattern genericFormula = Pattern.compile("^([\\*\\(\\)A-Z][a-z]*\\d*)+$");;
List<String> atoms = Arrays.asList("H","B","C","N","O","F","Na","Mg","Al","Si","P","S","Cl","K","Ca","Cr","Mn","Fe","Co","Cu","Zn","Se","Mo","Cd","Sn","I");
-
public FormulaParser(String formula){
- if(StringUtils.isVoid(formula) || !genericFormula.matcher(formula).find()) throw new IllegalArgumentException("Unable to parse formula");
+ if(StringUtils.isVoid(formula) || ! StringUtils.checkMetaboliteFormula(formula)) throw new IllegalArgumentException("Unable to parse formula");
this.formula=formula;
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
index 273c5a19c47524c761e1ff4ad9ed1ba7df38bea2..e180759448f53dfb9272909f2f0cf8c0ac10caad 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEntity.java
@@ -47,7 +47,7 @@ import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
*/
public abstract class BioEntity {
- private final String id;
+ final String id;
private String name;
private ArrayList<String> synonyms = new ArrayList<>();
private String comment;
@@ -103,26 +103,6 @@ public abstract class BioEntity {
this.setAttributes(new HashMap<>(e.getAttributes()));
}
-
- /**
- * {@inheritDoc}
- */
- @Override
- public boolean equals(Object o) {
- if (this == o) return true;
- if (o == null || getClass() != o.getClass()) return false;
- BioEntity bioEntity = (BioEntity) o;
- return id.equals(bioEntity.id);
- }
-
- /**
- * {@inheritDoc}
- */
- @Override
- public int hashCode() {
- return Objects.hashCode(id);
- }
-
/**
* Set the name of the entity
*
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipant.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipant.java
index 775d1be3498ae65c463ee76864ea4c419197d7db..b8e3836c41846c57440dcd6433d6702df37060ce 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipant.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipant.java
@@ -54,8 +54,8 @@ public class BioEnzymeParticipant extends BioParticipant {
* @param physicalEntity the physical entity that is contained in the enzyme
* @param stoichiometry the number of unities of the physical entity
*/
- public BioEnzymeParticipant(BioPhysicalEntity physicalEntity, Double stoichiometry) {
- super(physicalEntity, stoichiometry);
+ protected BioEnzymeParticipant(BioPhysicalEntity physicalEntity, Double stoichiometry) {
+ super(physicalEntity.getId() + "__" + stoichiometry, physicalEntity, stoichiometry);
}
/**
@@ -65,7 +65,7 @@ public class BioEnzymeParticipant extends BioParticipant {
* The stoichiometry is put to 1.
*/
public BioEnzymeParticipant(BioPhysicalEntity physicalEntity) {
- super(physicalEntity, 1.0);
+ this(physicalEntity, 1.0);
}
/**
@@ -92,7 +92,7 @@ public class BioEnzymeParticipant extends BioParticipant {
}
- String buffer = quantityStr + " " + this.getId();
+ String buffer = quantityStr + " " + this.getPhysicalEntity().getId();
return buffer;
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java
index 21761807927e69729370124184fd09eca0a58e72..03683bf579d1686ac2c41651c2f86a03a8ea594f 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetwork.java
@@ -41,10 +41,7 @@ package fr.inrae.toulouse.metexplore.met4j_core.biodata;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Objects;
-import java.util.Set;
+import java.util.*;
import java.util.stream.Collectors;
/**
@@ -72,6 +69,10 @@ public class BioNetwork extends BioEntity {
private final BioCollection<BioEnzyme> enzymes = new BioCollection<>();
+ private final BioCollection<BioReactant> reactants = new BioCollection<>();
+
+ private final BioCollection<BioEnzymeParticipant> enzymeParticipants = new BioCollection<>();
+
/**
* <p>Constructor for BioNetwork.</p>
*
@@ -533,7 +534,7 @@ public class BioNetwork extends BioEntity {
* @param reaction a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
* @param reactants a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant}
*/
- public void affectLeft(BioReaction reaction, BioCollection<BioReactant> reactants) {
+ protected void affectLeft(BioReaction reaction, BioCollection<BioReactant> reactants) {
this.affectLeft(reaction, reactants.toArray(new BioReactant[0]));
}
@@ -613,7 +614,7 @@ public class BioNetwork extends BioEntity {
* @param reaction a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction}
* @param reactants a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant} of {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant}
*/
- public void affectRight(BioReaction reaction, BioCollection<BioReactant> reactants) {
+ protected void affectRight(BioReaction reaction, BioCollection<BioReactant> reactants) {
this.affectRight(reaction, reactants.toArray(new BioReactant[0]));
}
@@ -629,8 +630,27 @@ public class BioNetwork extends BioEntity {
removeSideReaction(e, localisation, reaction, BioReaction.Side.RIGHT);
}
+ /**
+ * get a reactant with the same metabolite, stoichiometry and compartment
+ *
+ * @param metabolite
+ * @param stoichiometry
+ * @param compartment
+ * @return
+ */
+ protected BioReactant getReactant(BioMetabolite metabolite, Double stoichiometry, BioCompartment compartment) {
+ Optional<BioReactant> any = this.reactants.stream()
+ .filter(r -> r.getMetabolite().equals(metabolite) &&
+ r.getQuantity().equals(stoichiometry)
+ && r.getLocation().equals(compartment)).findAny();
+ if (any.isPresent()) {
+ return any.get();
+ }
+ return null;
+ }
+
private void affectSideReaction(BioReaction reaction, Double stoichiometry, BioCompartment localisation, BioReaction.Side side, BioMetabolite e) {
- BioReactant reactant = new BioReactant(e, stoichiometry, localisation);
+
// The network must contain the compartment
if (!this.compartments.contains(localisation)) {
@@ -651,6 +671,13 @@ public class BioNetwork extends BioEntity {
throw new IllegalArgumentException("Reaction " + reaction.getId() + " not in the network");
}
+ BioReactant reactant = this.getReactant(e, stoichiometry, localisation);
+
+ if (reactant == null) {
+ reactant = new BioReactant(e, stoichiometry, localisation);
+ this.reactants.add(reactant);
+ }
+
if (side.equals(BioReaction.Side.LEFT)) {
reaction.getLeftReactants().add(reactant);
} else {
@@ -658,11 +685,29 @@ public class BioNetwork extends BioEntity {
}
}
+ private void addReactant(BioReactant reactant) {
+ this.reactants.add(reactant);
+ }
+
+ /**
+ * Add reactants in the list of reactants
+ * @param reactants
+ */
+ protected void addReactants(BioReactant ...reactants) {
+ for(BioReactant r : reactants) {
+ this.addReactant(r);
+ }
+ }
+
private void affectSideReaction(BioReactant reactant, BioReaction reaction, BioReaction.Side side) {
BioCompartment localisation = reactant.getLocation();
+ if (! this.reactants.contains(reactant)) {
+ throw new IllegalArgumentException("Reactant " + reactant.getId() + " not in the network");
+ }
+
// The network must contain the compartment
if (!this.compartments.contains(localisation)) {
throw new IllegalArgumentException("Compartment " + localisation.getId() + " not in the network");
@@ -685,9 +730,13 @@ public class BioNetwork extends BioEntity {
}
if (side.equals(BioReaction.Side.LEFT)) {
- reaction.getLeftReactants().add(reactant);
+ if (!reaction.getLeftReactants().containsId(reactant.getId())) {
+ reaction.getLeftReactants().add(reactant);
+ }
} else {
- reaction.getRightReactants().add(reactant);
+ if (!reaction.getRightReactants().containsId(reactant.getId())) {
+ reaction.getRightReactants().add(reactant);
+ }
}
}
@@ -786,6 +835,23 @@ public class BioNetwork extends BioEntity {
}
+ /**
+ * Get enzyme participant with the same quantity and the same entity
+ *
+ * @param quantity
+ * @param unit
+ * @return
+ */
+ protected BioEnzymeParticipant getEnzymeParticipant(BioPhysicalEntity unit, Double quantity) {
+ Optional<BioEnzymeParticipant> any = this.enzymeParticipants.stream()
+ .filter(e -> e.getPhysicalEntity().equals(unit) && e.getQuantity().equals(quantity))
+ .findAny();
+
+ if (any.isPresent()) {
+ return any.get();
+ } else return null;
+ }
+
/**
* Add a subunit to an enzymes
*
@@ -796,8 +862,6 @@ public class BioNetwork extends BioEntity {
*/
private void affectSubUnit(BioEnzyme enzyme, Double quantity, BioPhysicalEntity unit) {
- BioEnzymeParticipant p = new BioEnzymeParticipant(unit, quantity);
-
if (!this.contains(enzyme)) {
throw new IllegalArgumentException("Enzyme " + enzyme.getId() + " not present in the network");
}
@@ -806,6 +870,12 @@ public class BioNetwork extends BioEntity {
throw new IllegalArgumentException("Physical entity " + unit.getId() + " not present in the network");
}
+ BioEnzymeParticipant p = this.getEnzymeParticipant(unit, quantity);
+ if (p == null) {
+ p = new BioEnzymeParticipant(unit, quantity);
+ this.enzymeParticipants.add(p);
+ }
+
enzyme.addParticipant(p);
}
@@ -819,6 +889,9 @@ public class BioNetwork extends BioEntity {
*/
private void affectSubUnit(BioEnzyme enzyme, BioEnzymeParticipant unit) {
+ if(! this.enzymeParticipants.contains(unit)) {
+ throw new IllegalArgumentException("Enzyme participant " + unit.getId() + " not present in the network");
+ }
if (!this.contains(enzyme)) {
throw new IllegalArgumentException("Enzyme " + enzyme.getId() + " not present in the network");
@@ -828,7 +901,9 @@ public class BioNetwork extends BioEntity {
throw new IllegalArgumentException("Physical entity " + unit.getPhysicalEntity().getId() + " not present in the network");
}
- enzyme.addParticipant(unit);
+ if(! enzyme.getParticipants().containsId(unit.getId())) {
+ enzyme.addParticipant(unit);
+ }
}
@@ -882,7 +957,7 @@ public class BioNetwork extends BioEntity {
* @param enzyme a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEnzyme}
* @param units a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection} of {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEnzymeParticipant}
*/
- public void affectSubUnit(BioEnzyme enzyme, BioCollection<BioEnzymeParticipant> units) {
+ protected void affectSubUnit(BioEnzyme enzyme, BioCollection<BioEnzymeParticipant> units) {
for (BioEnzymeParticipant unit : units) {
affectSubUnit(enzyme, unit);
@@ -1178,7 +1253,7 @@ public class BioNetwork extends BioEntity {
}
/**
- * @param m a {@link BioMetabolite}
+ * @param m a {@link BioMetabolite}
* @param isSubstrate a {@link Boolean} indicating if the metabolite is a substrate or a product
* @return a {@link BioCollection} of {@link BioReaction}
*/
@@ -1776,4 +1851,56 @@ public class BioNetwork extends BioEntity {
public int hashCode() {
return Objects.hash(super.hashCode(), pathways, metabolites, proteins, genes, reactions, compartments, enzymes);
}
+
+
+ /**
+ * @param e
+ * @return
+ */
+ public Boolean containsEntityWithSameId(BioEntity e) {
+ if (e == null) {
+ throw new NullPointerException();
+ }
+
+ String id = e.getId();
+
+ Boolean flag;
+
+ if (e instanceof BioPathway) {
+ flag = this.pathways.containsId(id);
+ } else if (e instanceof BioMetabolite) {
+ flag = this.metabolites.containsId(id);
+ } else if (e instanceof BioProtein) {
+ flag = this.proteins.containsId(id);
+ } else if (e instanceof BioGene) {
+ flag = this.genes.containsId(id);
+ } else if (e instanceof BioReaction) {
+ flag = this.reactions.containsId(id);
+ } else if (e instanceof BioCompartment) {
+ flag = this.compartments.containsId(id);
+ } else if (e instanceof BioEnzyme) {
+ flag = this.enzymes.containsId(id);
+ } else {
+
+ throw new IllegalArgumentException(
+ "BioEntity \"" + e.getClass().getSimpleName() + "\" not supported by BioNetwork");
+ }
+ return flag;
+
+ }
+
+ /**
+ * Adds enzymes participants in the network
+ * @param enzymeParticipants
+ */
+ protected void addEnzymeParticipants(BioEnzymeParticipant ...enzymeParticipants) {
+ for(BioEnzymeParticipant ep : enzymeParticipants) {
+ this.addEnzymeParticipant(ep);
+ }
+
+ }
+
+ private void addEnzymeParticipant(BioEnzymeParticipant ep) {
+ this.enzymeParticipants.add(ep);
+ }
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
index db972165a0f1214b4b86dd75ce8d39647d8cd617..d51b10db5b89bc5dd4effa824e3e5c77ba2d818c 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
@@ -38,6 +38,7 @@ package fr.inrae.toulouse.metexplore.met4j_core.biodata;
import fr.inrae.toulouse.metexplore.met4j_core.utils.ErrorUtils;
+import javax.annotation.Nonnull;
import java.util.Objects;
/**
@@ -48,9 +49,9 @@ import java.util.Objects;
*/
public abstract class BioParticipant extends BioEntity {
- private BioPhysicalEntity physicalEntity;
+ private final BioPhysicalEntity physicalEntity;
- private Double quantity;
+ private final Double quantity;
/**
* Constructor
@@ -58,13 +59,20 @@ public abstract class BioParticipant extends BioEntity {
* @param physicalEntity a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity}
* @param quantity number of units of physicalEntity
*/
- public BioParticipant(BioPhysicalEntity physicalEntity, Double quantity) {
- super(physicalEntity.getId());
+
+ public BioParticipant(String id, @Nonnull BioPhysicalEntity physicalEntity, Double quantity) {
+ super(id);
this.physicalEntity=physicalEntity;
- this.setQuantity(quantity);
+ if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
+ {
+ ErrorUtils.error("Illegal argument for "+quantity+" "+this.getPhysicalEntity().getId()+": the quantity must be finite and positive");
+ throw new IllegalArgumentException();
+ }
+
+ this.quantity = quantity;
}
-
-
+
+
/**
* <p>Getter for the field <code>physicalEntity</code>.</p>
*
@@ -75,18 +83,6 @@ public abstract class BioParticipant extends BioEntity {
}
- /**
- * <p>Setter for the field <code>physicalEntity</code>.</p>
- *
- * @param physicalEntity the physicalEntity to set
- */
- public void setPhysicalEntity(BioPhysicalEntity physicalEntity) {
- this.physicalEntity = physicalEntity;
- }
-
-
-
-
/**
* <p>Getter for the field <code>quantity</code>.</p>
*
@@ -97,28 +93,11 @@ public abstract class BioParticipant extends BioEntity {
}
- /**
- * <p>Setter for the field <code>quantity</code>.</p>
- *
- * @param quantity the quantity to set
- */
- public void setQuantity(Double quantity) {
-
- if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
- {
- ErrorUtils.error("Illegal argument for "+quantity+" "+this.getPhysicalEntity().getId()+": the quantity must be finite and positive");
- throw new IllegalArgumentException();
- }
-
- this.quantity = quantity;
- }
-
/** {@inheritDoc} */
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
- if (!super.equals(o)) return false;
BioParticipant that = (BioParticipant) o;
return Objects.equals(physicalEntity, that.physicalEntity) &&
Objects.equals(quantity, that.quantity);
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
index 876ae1564765257da6bc46f76f1b42be2f6b9436..fcb3b7ab9ff7f0b79fdc82bad59379662f820e41 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
@@ -35,6 +35,7 @@
*/
package fr.inrae.toulouse.metexplore.met4j_core.biodata;
+import javax.annotation.Nonnull;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
@@ -49,7 +50,7 @@ import java.util.Objects;
*/
public class BioReactant extends BioParticipant {
- private BioCompartment location = null;
+ private final BioCompartment location;
/**
* Constructor
@@ -58,9 +59,9 @@ public class BioReactant extends BioParticipant {
* @param stoichiometry stoichiometric coefficient
* @param location a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
*/
- public BioReactant(BioMetabolite metabolite, Double stoichiometry, BioCompartment location) {
- super(metabolite, stoichiometry);
- this.setLocation(location);
+ protected BioReactant(@Nonnull BioMetabolite metabolite, Double stoichiometry, @Nonnull BioCompartment location) {
+ super(metabolite.getId()+"__"+stoichiometry+"__"+location.getId(), metabolite, stoichiometry);
+ this.location = location;
}
/**
@@ -72,15 +73,6 @@ public class BioReactant extends BioParticipant {
return location;
}
- /**
- * Set location
- *
- * @param location a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
- */
- protected void setLocation(BioCompartment location) {
- this.location = location;
- }
-
/**
* Get the associated metabolite
*
@@ -114,7 +106,7 @@ public class BioReactant extends BioParticipant {
StringBuilder buffer = new StringBuilder(quantityStr);
buffer.append(" ");
- buffer.append(this.getId());
+ buffer.append(this.getPhysicalEntity().getId());
if (this.getLocation() != null) {
buffer.append("[");
buffer.append(this.getLocation().getId());
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java
index 9bd3b4991970582f5f7572378dfd61ccbe2f2e0c..6d78f8f54deeda7b83f88819970570d0e0cbb7e2 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollection.java
@@ -198,7 +198,15 @@ public class BioCollection<E extends BioEntity> implements Collection<E> {
/** {@inheritDoc} */
@Override
public boolean add(E e) {
- entities.put(e.getId(), e);
+ if(entities.containsValue(e)) {
+ return false;
+ }
+ else {
+ if (entities.keySet().contains(e.getId())) {
+ throw new IllegalArgumentException("An entity with the same id (" + e.getId() + ") is already present in the BioCollection");
+ }
+ entities.put(e.getId(), e);
+ }
return true;
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
index 39d85f44e2eea83ca6b75b7b9a4e0b9f89fb21fa..123c92b33ffa5316100ca28e5c282b3ce2540489 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtils.java
@@ -136,12 +136,14 @@ public class BioNetworkUtils {
}
for (BioMetabolite metabolite : metabolitesToCopy) {
- BioMetabolite newMetabolite = new BioMetabolite(metabolite);
- networkOut.add(newMetabolite);
+ BioMetabolite newMetabolite;
+ if (!networkOut.containsEntityWithSameId(metabolite)) {
+ newMetabolite = new BioMetabolite(metabolite);
+ networkOut.add(newMetabolite);
+ }
}
- // Copy compartments (empty for the moment)
- // Copy metabolites
+ // Copy compartments
BioCollection<BioCompartment> compartmentsToCopy = networkIn.getCompartmentsView();
if (keepPrevious) {
compartmentsToCopy.removeAll(networkOut.getCompartmentsView());
@@ -151,7 +153,7 @@ public class BioNetworkUtils {
BioCompartment newCpt;
- if (compartmentsToCopy.contains(cpt)) {
+ if (compartmentsToCopy.contains(cpt) && (!networkOut.containsEntityWithSameId(cpt))) {
newCpt = new BioCompartment(cpt);
networkOut.add(newCpt);
} else {
@@ -176,8 +178,10 @@ public class BioNetworkUtils {
}
for (BioGene gene : genesToCopy) {
- BioGene newGene = new BioGene(gene);
- networkOut.add(newGene);
+ if (!networkOut.containsEntityWithSameId(gene)) {
+ BioGene newGene = new BioGene(gene);
+ networkOut.add(newGene);
+ }
}
}
@@ -191,7 +195,7 @@ public class BioNetworkUtils {
BioProtein newProtein;
- if (proteinsToCopy.contains(protein)) {
+ if (proteinsToCopy.contains(protein) && (!networkOut.containsEntityWithSameId(protein))) {
newProtein = new BioProtein(protein);
networkOut.add(newProtein);
} else {
@@ -218,7 +222,7 @@ public class BioNetworkUtils {
BioEnzyme newEnzyme;
- if (enzymesToCopy.contains(enzyme)) {
+ if (enzymesToCopy.contains(enzyme) && !networkOut.containsEntityWithSameId(enzyme)) {
newEnzyme = new BioEnzyme(enzyme);
networkOut.add(newEnzyme);
} else {
@@ -230,25 +234,19 @@ public class BioNetworkUtils {
for (BioEnzymeParticipant participant : participants) {
Double quantity = participant.getQuantity();
- BioEnzymeParticipant newParticipant = null;
if (participant.getPhysicalEntity().getClass().equals(BioMetabolite.class)) {
BioMetabolite metabolite = (BioMetabolite) participant.getPhysicalEntity();
BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(metabolite.getId());
- newParticipant = new BioEnzymeParticipant(newMetabolite, quantity);
+ networkOut.affectSubUnit(newEnzyme, quantity, newMetabolite);
} else if (participant.getPhysicalEntity().getClass().equals(BioProtein.class)) {
BioProtein protein = (BioProtein) participant.getPhysicalEntity();
BioProtein newProtein = networkOut.getProteinsView().get(protein.getId());
- newParticipant = new BioEnzymeParticipant(newProtein, quantity);
+ networkOut.affectSubUnit(newEnzyme, quantity, newProtein);
} else {
System.err.println("BioPhysical entity not recognized as enzyme participant : "
+ participant.getPhysicalEntity().getId()
+ "(" + participant.getPhysicalEntity().getClass() + ")");
}
-
- if (newParticipant != null) {
- networkOut.affectSubUnit(newEnzyme, newParticipant);
- }
-
}
}
}
@@ -264,7 +262,7 @@ public class BioNetworkUtils {
BioReaction newReaction;
- if (reactionsToCopy.contains(r)) {
+ if (reactionsToCopy.contains(r) && !networkOut.containsEntityWithSameId(r)) {
newReaction = new BioReaction(r);
newReaction.setSpontaneous(r.isSpontaneous());
@@ -281,9 +279,7 @@ public class BioNetworkUtils {
BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(reactant.getMetabolite().getId());
BioCompartment newCpt = networkOut.getCompartmentsView().get(reactant.getLocation().getId());
Double sto = reactant.getQuantity();
- BioReactant newReactant = new BioReactant(newMetabolite, sto, newCpt);
-
- networkOut.affectLeft(newReaction, newReactant);
+ networkOut.affectLeft(newReaction, sto, newCpt, newMetabolite);
}
// Copy rights
@@ -291,9 +287,7 @@ public class BioNetworkUtils {
BioMetabolite newMetabolite = networkOut.getMetabolitesView().get(reactant.getMetabolite().getId());
BioCompartment newCpt = networkOut.getCompartmentsView().get(reactant.getLocation().getId());
Double sto = reactant.getQuantity();
- BioReactant newReactant = new BioReactant(newMetabolite, sto, newCpt);
-
- networkOut.affectRight(newReaction, newReactant);
+ networkOut.affectRight(newReaction, sto, newCpt, newMetabolite);
}
// Copy enzymes
@@ -313,7 +307,7 @@ public class BioNetworkUtils {
for (BioPathway pathway : networkIn.getPathwaysView()) {
- if (pathwaysToCopy.contains(pathway)) {
+ if (pathwaysToCopy.contains(pathway) && !networkOut.containsEntityWithSameId(pathway)) {
BioPathway newPathway = new BioPathway(pathway);
networkOut.add(newPathway);
}
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/utils/StringUtils.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/utils/StringUtils.java
index b96e5f5e75fa70bff25d8bf081f8d6e88074ce16..916fb7fcc1f0c093748b2cd05738aa2d895ff1fb 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/utils/StringUtils.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/utils/StringUtils.java
@@ -36,6 +36,9 @@
package fr.inrae.toulouse.metexplore.met4j_core.utils;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
/**
* <p>StringUtils class.</p>
*
@@ -44,6 +47,9 @@ package fr.inrae.toulouse.metexplore.met4j_core.utils;
*/
public class StringUtils {
+ private static Pattern patternEC = Pattern.compile("(EC\\s*)*\\d{1}(\\.(\\d{0,3}|-)){0,3}");
+ private static Pattern patternFormula = Pattern.compile("^([\\*\\(\\)A-Z][a-z]*\\d*)+$");;
+
/**
* <p>isVoid.</p>
*
@@ -90,4 +96,24 @@ public class StringUtils {
return true;
}
+ /**
+ * Check EC number
+ * @param ec
+ * @return
+ */
+ public static boolean checkEcNumber(String ec) {
+ Matcher m = patternEC.matcher(ec);
+ return m.matches();
+ }
+
+ /**
+ * Checks if a metabolite formula is well formatted
+ * @param formula
+ * @return
+ */
+ public static boolean checkMetaboliteFormula(String formula) {
+ Matcher m = patternFormula.matcher(formula);
+ return m.matches();
+ }
+
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipantTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipantTest.java
index 8ad561b5e5b5b81fa4bcd7dcc2e21146a5624286..0afd0b42f07a087b6fc0f8e445fbe0badd82334e 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipantTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioEnzymeParticipantTest.java
@@ -44,33 +44,16 @@ import org.junit.Test;
public class BioEnzymeParticipantTest {
-
+
@Test
public void testToString() {
-
+
BioEnzymeParticipant p = new BioEnzymeParticipant(new BioProtein("p1"), 2.0);
-
+
assertEquals("toString does not work", "2 p1", p.toString());
-
-
- }
- @Test
- public void testEquality() {
-
-
- BioEnzymeParticipant p = new BioEnzymeParticipant(new BioProtein("p1"), 2.0);
- BioEnzymeParticipant p2 = new BioEnzymeParticipant(new BioProtein("p2"), 2.0);
- BioEnzymeParticipant pBis = new BioEnzymeParticipant(new BioProtein("p1"), 2.0);
-
- assertNotEquals("p and p2 must not be equal", p, p2);
-
- assertEquals("p and pBis must be equal", p, pBis);
-
-
}
-
-
}
+
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java
index d5741d5ad6b29f6559d0b5ea40f1168b38165185..03379ecfc852fea8f0f0e8f90b972919bb42f64b 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioNetworkTest.java
@@ -467,14 +467,13 @@ public class BioNetworkTest {
network.affectLeft(reaction, 1.0, cpt, s1);
- BioReactant reactant = new BioReactant(s2, 1.0, cpt);
- network.affectLeft(reaction, reactant);
+ network.affectLeft(reaction, 1.0, cpt, s2);
assertEquals("Substrate not well added", 2, reaction.getLeftReactants().size());
}
- @Test (expected = IllegalArgumentException.class)
+ @Test(expected = IllegalArgumentException.class)
public void testAffectSubstrateMetaboliteNotPresent() {
BioReaction reaction = new BioReaction("r1");
@@ -493,7 +492,7 @@ public class BioNetworkTest {
* the metabolite has been removed from the network
* Must throw an exception
*/
- @Test (expected = IllegalArgumentException.class)
+ @Test(expected = IllegalArgumentException.class)
public void testAffectSubstrateMetaboliteNotPresent2() {
BioReaction reaction = new BioReaction("r1");
@@ -522,7 +521,7 @@ public class BioNetworkTest {
/**
*
*/
- @Test (expected = IllegalArgumentException.class)
+ @Test(expected = IllegalArgumentException.class)
public void testAffectSubstrateMetaboliteNotInCompartment() {
BioReaction reaction = new BioReaction("r1");
@@ -540,25 +539,15 @@ public class BioNetworkTest {
@Test
public void testAffectSubstrateCollection() {
- BioReaction reaction = new BioReaction("r1");
- network.add(reaction);
- BioMetabolite s1 = new BioMetabolite("s1");
- network.add(s1);
- BioMetabolite s2 = new BioMetabolite("s2");
- network.add(s2);
- BioCompartment cpt = new BioCompartment("cpt");
- network.add(cpt);
-
- BioReactant reactant1 = new BioReactant(s1, 1.0, cpt);
- BioReactant reactant2 = new BioReactant(s2, 1.0, cpt);
- BioCollection<BioReactant> reactants = new BioCollection<>();
- reactants.add(reactant1, reactant2);
+ BioReaction reaction1 = this.addTestReactionToNetwork();
+ BioCollection<BioReactant> reactants = reaction1.getLeftReactants();
- network.affectToCompartment(cpt, s1, s2);
+ BioReaction reaction2 = new BioReaction("r2");
+ this.network.add(reaction2);
- network.affectLeft(reaction, reactants);
+ network.affectLeft(reaction2, reactants);
- assertEquals("Substrate collection not well added", 2, reaction.getLeftReactants().size());
+ assertEquals("Substrate collection not well added", 2, reaction2.getLeftReactants().size());
}
@@ -587,25 +576,18 @@ public class BioNetworkTest {
@Test
public void testAffectProductsCollection() {
- BioReaction reaction = new BioReaction("r1");
- network.add(reaction);
- BioMetabolite s1 = new BioMetabolite("s1");
- network.add(s1);
- BioMetabolite s2 = new BioMetabolite("s2");
- network.add(s2);
- BioCompartment cpt = new BioCompartment("cpt");
- network.add(cpt);
+ BioReaction reaction1 = addTestReactionToNetwork();
+
+ BioReaction reaction2 = new BioReaction("r2");
+ network.add(reaction2);
- BioReactant reactant1 = new BioReactant(s1, 1.0, cpt);
- BioReactant reactant2 = new BioReactant(s2, 1.0, cpt);
- BioCollection<BioReactant> reactants = new BioCollection<>();
- reactants.add(reactant1, reactant2);
+ BioCollection<BioReactant> reactants = reaction1.getRightReactants();
network.affectToCompartment(cpt, s1, s2);
- network.affectRight(reaction, reactants);
+ network.affectRight(reaction2, reactants);
- assertEquals("Product collection not well added", 2, reaction.getRightReactants().size());
+ assertEquals("Product collection not well added", 2, reaction2.getRightReactants().size());
}
@@ -745,8 +727,7 @@ public class BioNetworkTest {
network.affectToCompartment(cpt, s1, s2);
network.affectRight(reaction, 1.0, cpt, s1);
- BioReactant reactant = new BioReactant(s2, 1.0, cpt);
- network.affectRight(reaction, reactant);
+ network.affectRight(reaction, 1.0, cpt, s2);
assertEquals("Product not well added", 2, reaction.getRightReactants().size());
}
@@ -1666,5 +1647,17 @@ public class BioNetworkTest {
}
+ @Test
+ public void testGetEnzymeParticipant() {
+ BioProtein p1 = new BioProtein("p1");
+ BioEnzyme e1 = new BioEnzyme("e1");
+ BioEnzymeParticipant participant = new BioEnzymeParticipant(p1, 2.0);
+
+ network.add(p1, e1);
+ network.affectSubUnit(e1, 2.0, p1);
+
+ assertNotNull(network.getEnzymeParticipant(p1, 2.0));
+ assertEquals(participant, network.getEnzymeParticipant(p1, 2.0));
+ }
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipantTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipantTest.java
index 8c7d7d9e46b0bdcc09e22458d0d6cba15d2ee341..42f9f7d57984f61bb66506d282bc73f58a331094 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipantTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipantTest.java
@@ -48,9 +48,7 @@ public class BioParticipantTest {
@Test(expected = IllegalArgumentException.class)
public void testSetNaNQuantity() {
- BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), 2.0);
- Double nan = Double.NaN;
- p.setQuantity(nan);
+ BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), Double.NaN);
}
@@ -60,9 +58,7 @@ public class BioParticipantTest {
@Test(expected = IllegalArgumentException.class)
public void testSetInfiniteQuantity() {
- BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), 2.0);
- Double inf = Double.POSITIVE_INFINITY;
- p.setQuantity(inf);
+ BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), Double.POSITIVE_INFINITY);
}
/**
@@ -71,12 +67,9 @@ public class BioParticipantTest {
@Test(expected = IllegalArgumentException.class)
public void testSetNegativeOrNullQuantity() {
- BioParticipant p = new BioParticipantFake(new BioMetabolite("test"), 2.0);
- Double n = 0.0;
- p.setQuantity(n);
-
- n = -10.0;
- p.setQuantity(n);
+ new BioParticipantFake(new BioMetabolite("test"), 0.0);
+
+ new BioParticipantFake(new BioMetabolite("test"), -10.0);
}
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactantTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactantTest.java
index a69953bb0cad9e7a70db8ca9e817f83e4ec97c13..f7c8fa061464dffb0a890ae87a6f908f4299143e 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactantTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactantTest.java
@@ -55,33 +55,19 @@ public class BioReactantTest {
reactant = new BioReactant(new BioMetabolite("cpdId"), 1.26666, new BioCompartment("cptId"));
assertEquals("reactant badly formatted (integer coefficient)", "1.27 cpdId[cptId]", reactant.toString());
- // Test when the biocompartment is null
- reactant = new BioReactant(new BioMetabolite("cpdId"), 1.0, null);
- assertEquals("reactant badly formatted (integer coefficient)", "1 cpdId", reactant.toString());
-
}
-
@Test
- public void testEquality() {
-
- BioMetabolite c1 = new BioMetabolite("c1");
- BioCompartment cpt1 = new BioCompartment("cpt1");
- BioMetabolite c2 = new BioMetabolite("c2");
- BioCompartment cpt2 = new BioCompartment("cpt2");
-
- BioReactant r1 = new BioReactant(c1, 1.0, cpt1);
- BioReactant r2 = new BioReactant(c1, 2.0, cpt1);
- BioReactant r3 = new BioReactant(c1, 1.0, cpt2);
- BioReactant r4 = new BioReactant(c2, 1.0, cpt1);
- BioReactant r5 = new BioReactant(c1, 1.0, cpt1);
-
- assertFalse("r1 and r2 must not be equal", r1.equals(r2));
- assertFalse("r1 and r3 must not be equal", r1.equals(r3));
- assertFalse("r1 and r4 must not be equal", r1.equals(r4));
- assertTrue("r1 and r5 must be equal", r1.equals(r5));
-
- }
+ public void testEquals() {
+
+ BioMetabolite m1 = new BioMetabolite("m1");
+ BioCompartment c1 = new BioCompartment("c1");
+
+ BioReactant reactant1 = new BioReactant(m1, 2.0, c1);
+ BioReactant reactant2 = new BioReactant(m1, 2.0, c1);
+ assertTrue(reactant1.equals(reactant2));
+
+ }
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactionTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactionTest.java
index 5aaf1bcbf1fcdd873bfb164d40c300f172a0c2d2..6388b5c9bf099492b68895758f97e865992b97d2 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactionTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactionTest.java
@@ -56,7 +56,7 @@ public class BioReactionTest {
public static BioMetabolite l1, l2, r1, r2;
public static BioReactant l1Reactant, l2Reactant, r1Reactant, r2Reactant;
- public static BioReaction reaction;
+ public static BioReaction reaction, reaction2;
public static BioGene g1, g2, g3;
@@ -79,15 +79,21 @@ public class BioReactionTest {
r2Reactant = new BioReactant(r2, 1.0, cpt2);
reaction = new BioReaction("testreaction");
+ reaction2 = new BioReaction("testreaction2");
- network.add(reaction, cpt1, cpt2, l1, l2, r1, r2);
+ network.add(reaction, reaction2, cpt1, cpt2, l1, l2, r1, r2);
network.affectToCompartment(cpt1, l1, l2);
network.affectToCompartment(cpt2, r1, r2);
+ network.addReactants(l1Reactant, l2Reactant, r1Reactant, r2Reactant);
+
network.affectLeft(reaction, l1Reactant, l2Reactant);
network.affectRight(reaction, r1Reactant, r2Reactant);
+ network.affectLeft(reaction2, l1Reactant);
+ network.affectRight(reaction2, l2Reactant);
+
BioEnzyme e1 = new BioEnzyme("e1");
BioProtein p1 = new BioProtein("p1");
BioProtein p2 = new BioProtein("p2");
@@ -104,6 +110,9 @@ public class BioReactionTest {
BioEnzymeParticipant ep1 = new BioEnzymeParticipant(p1);
BioEnzymeParticipant ep2 = new BioEnzymeParticipant(p2);
BioEnzymeParticipant ep3 = new BioEnzymeParticipant(p3);
+
+ network.addEnzymeParticipants(ep1, ep2, ep3);
+
network.affectSubUnit(e1, ep1);
network.affectSubUnit(e2, ep2, ep3);
@@ -136,11 +145,8 @@ public class BioReactionTest {
// Positive test
assertTrue("Must be a transport reaction", reaction.isTransportReaction());
- // Negative Test
- r1Reactant.setLocation(cpt1);
- r2Reactant.setLocation(cpt1);
- assertFalse("Must not be a transport reaction", reaction.isTransportReaction());
+ assertFalse("Must not be a transport reaction", reaction2.isTransportReaction());
}
/**
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioParticipantFake.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioParticipantFake.java
index 5f2b24b9d85887ef86f2fe870b681b1c8d8c2faf..98050a87766ac5dd262d34ac3dd643d863e0fd93 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioParticipantFake.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/classesForTests/BioParticipantFake.java
@@ -47,7 +47,7 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPhysicalEntity;
public class BioParticipantFake extends BioParticipant {
public BioParticipantFake(BioPhysicalEntity physicalEntity, Double quantity) {
- super(physicalEntity, quantity);
+ super(physicalEntity.getId()+"__"+quantity, physicalEntity, quantity);
}
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollectionTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollectionTest.java
index 2b97dc7875a80240627813dc9e90ef9f4445e804..e21ae7f1ca62526903c323254984a17b6b9fd9d1 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollectionTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/collection/BioCollectionTest.java
@@ -237,22 +237,4 @@ public class BioCollectionTest {
}
- @Test
- public void testEqualsObject() {
-
- BioCollection<BioMetabolite> c2 = new BioCollection<BioMetabolite>();
-
- BioMetabolite m1Bis = new BioMetabolite("m1", "metabolite1");
- BioMetabolite m2Bis = new BioMetabolite("m2", "metabolite2");
-
- c2.add(m1Bis);
-
- assertFalse(collec.equals(c2));
-
- c2.add(m2Bis);
-
- assertTrue(collec.equals(c2));
-
- }
-
}
diff --git a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java
index ea00bea8be88ad050d958aa60517dc4a339b69f6..1a627b9ad1d6ab9f7dfe630c6a0355dd8e5e107a 100644
--- a/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java
+++ b/met4j-core/src/test/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/utils/BioNetworkUtilsTest.java
@@ -264,7 +264,7 @@ public class BioNetworkUtilsTest {
assertEquals(2, newNetwork.getPathwaysView().size());
assertEquals(2, enzyme1.getParticipantsView().size());
// The gene must be updated
- assertEquals(gene1, protein1.getGene());
+ assertEquals(gene1.getId(), protein1.getGene().getId());
assertEquals(2, r1.getLeftReactantsView().size());
assertEquals(2, r1.getEnzymesView().size());
assertEquals(3, newNetwork.getReactionsFromPathways(pathway1).size());
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/compartment/CompartmentAttributes.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/compartment/CompartmentAttributes.java
index 9536199ba399d800c655d4796497c973106c8e83..105df1ceccd69b22ab09c32d30a95f4a6ad6fcec 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/compartment/CompartmentAttributes.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/compartment/CompartmentAttributes.java
@@ -67,8 +67,8 @@ public class CompartmentAttributes extends GenericAttributes {
*/
public static void setOutsideCompartment(BioCompartment c, BioCompartment outside) {
- if (c.equals(outside)) {
- throw new IllegalArgumentException("The compartment and the outside compartment must be different");
+ if (c.getId().equals(outside.getId())) {
+ throw new IllegalArgumentException("The compartment and the outside compartment have a different id");
}
c.setAttribute(OUTSIDE_COMPARTMENT, outside);
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/network/NetworkAttributes.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/network/NetworkAttributes.java
index 659e65edc5df5c261bb6d96a4c7b69e60ee0499c..4d4fcd10cdeee9d538e75336ff1b9d53bd921d7b 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/network/NetworkAttributes.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/network/NetworkAttributes.java
@@ -116,7 +116,13 @@ public class NetworkAttributes extends GenericAttributes {
addUnitDefinitions(network, new BioUnitDefinitionCollection());
}
- getUnitDefinitions(network).add(unit);
+ BioUnitDefinitionCollection unitDefinitions = getUnitDefinitions(network);
+
+ if(! unitDefinitions.containsId(unit.getId())) {
+ unitDefinitions.add(unit);
+ }
+
+
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/fbc/FluxReaction.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/fbc/FluxReaction.java
index eeaab3eec226ddf636097fefb461cf955d26708c..f6ea5ae19125345298e9cc7599945d1d2ff6af49 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/fbc/FluxReaction.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/fbc/FluxReaction.java
@@ -138,13 +138,14 @@ public class FluxReaction extends BioEntity {
if (protlist.size() == 1) {
BioProtein prot = protlist.iterator().next();
-
- BioEnzyme enz = new BioEnzyme(prot.getId(), prot.getName());
- enz.setName(prot.getName());
-
- if(! bn.contains(enz)) {
+
+ BioEnzyme enz = bn.getEnzymesView().get(prot.getId());
+ if(enz == null)
+ {
+ enz = new BioEnzyme(prot.getId(), prot.getName());
bn.add(enz);
}
+
bn.affectSubUnit(enz, 1.0, prot);
bn.affectEnzyme(rxn, enz);
@@ -152,10 +153,11 @@ public class FluxReaction extends BioEntity {
} else {
String id = createIdFromProteins(protlist);
-
- BioEnzyme enz = new BioEnzyme(id, id);
-
- if(! bn.contains(enz)) {
+
+ BioEnzyme enz = bn.getEnzymesView().get(id);
+
+ if(enz == null) {
+ enz = new BioEnzyme(id, id);
bn.add(enz);
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetwork.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetwork.java
index a8f1de190f46fffc199b83917576a9afb85bad38..570329394bccb932993911ec5ed3518cef196c21 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetwork.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetwork.java
@@ -59,7 +59,6 @@ import org.sbml.jsbml.UnitDefinition;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.compartment.BioCompartmentType;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.compartment.CompartmentAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.network.NetworkAttributes;
-import fr.inrae.toulouse.metexplore.met4j_io.annotations.reactant.ReactantAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.Flux;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.SbmlAnnotation;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
@@ -78,637 +77,614 @@ import org.sbml.jsbml.Unit.Kind;
* Abstract class that defines the different 'ListOf' parsing method.
*
* @author bmerlet
- * @since 3.0
* @version $Id: $Id
+ * @since 3.0
*/
public class JsbmlToBioNetwork {
- /**
- * The {@link BioNetwork} created by this class
- */
- private BioNetwork network;
+ /**
+ * The {@link BioNetwork} created by this class
+ */
+ private BioNetwork network;
+
+ private Model model;
+
+ /**
+ * The ordered list of {@link PackageParser} activated for this parser
+ */
+ public ArrayList<PackageParser> packages = new ArrayList<PackageParser>();
+
+ /**
+ * <p>Constructor for JsbmlToBioNetwork.</p>
+ *
+ * @param model a {@link org.sbml.jsbml.Model} object.
+ */
+ public JsbmlToBioNetwork(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * Main method of the parser. It should call the different list parser defined
+ * in the inheriting classes
+ *
+ * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
+ */
+ protected void parseModel() throws Met4jSbmlReaderException {
+
+ this.parseNetworkData();
+ this.parseListOfUnitDefinitions();
+ this.parseListOfCompartments();
+
+ this.parseListOfSpecies();
+
+ this.parseListOfReactions();
+
+ this.parsePackageAdditionalData();
+ }
+
+ /**
+ * Parse the jsbml Model object and retrieves basic information from it
+ */
+ private void parseNetworkData() {
+
+ BioNetwork bionet = new BioNetwork(model.getId());
+
+ bionet.setName(model.getName());
+
+ this.setNetwork(bionet);
+ }
- private Model model;
+ /**
+ * Default way of parsing sbml UnitDefinition. Needs to be overridden to modify
+ * behavior
+ */
+ private void parseListOfUnitDefinitions() {
- /**
- * The ordered list of {@link PackageParser} activated for this parser
- */
- public ArrayList<PackageParser> packages = new ArrayList<PackageParser>();
+ for (UnitDefinition jSBMLUD : model.getListOfUnitDefinitions()) {
- /**
- * <p>Constructor for JsbmlToBioNetwork.</p>
- *
- * @param model a {@link org.sbml.jsbml.Model} object.
- */
- public JsbmlToBioNetwork(Model model) {
- this.model = model;
- }
+ BioUnitDefinition bionetUD = new BioUnitDefinition(jSBMLUD.getId(), jSBMLUD.getName());
- /**
- * Main method of the parser. It should call the different list parser defined
- * in the inheriting classes
- *
- * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
- */
- protected void parseModel() throws Met4jSbmlReaderException {
+ if (jSBMLUD.getName().isEmpty()) {
+ bionetUD.setName(jSBMLUD.getId());
+ }
+ ListOf<Unit> listofunits = jSBMLUD.getListOfUnits();
- this.parseNetworkData();
- this.parseListOfUnitDefinitions();
- this.parseListOfCompartments();
+ if (listofunits.size() != 0) {
- this.parseListOfSpecies();
+ for (int n = 0; n < listofunits.size(); n++) {
- this.parseListOfReactions();
+ Unit jSBMLUnit = listofunits.get(n);
- this.parsePackageAdditionalData();
- }
+ Kind kind = jSBMLUnit.getKind();
+ Double Exp = jSBMLUnit.getExponent();
+ Integer Scale = jSBMLUnit.getScale();
+ Double Multiplier = jSBMLUnit.getMultiplier();
- /**
- * Parse the jsbml Model object and retrieves basic information from it
- *
- */
- private void parseNetworkData() {
+ UnitSbml bionetUnit = new UnitSbml(kind.getName(), Exp, Scale, Multiplier);
+ bionetUD.addUnit(bionetUnit);
+ }
+ }
- BioNetwork bionet = new BioNetwork(model.getId());
+ NetworkAttributes.addUnitDefinition(this.getNetwork(), bionetUD);
+ }
- bionet.setName(model.getName());
+ }
- this.setNetwork(bionet);
- }
+ /**
+ * Default way of parsing sbml compartements. Needs to be overridden to modify
+ * behavior
+ */
+ private void parseListOfCompartments() {
- /**
- * Default way of parsing sbml UnitDefinition. Needs to be overridden to modify
- * behavior
- *
- */
- private void parseListOfUnitDefinitions() {
+ if (model.getListOfCompartments().size() == 0) {
+ System.err.println("[WARNING] No compartment in the model !");
+ }
- for (UnitDefinition jSBMLUD : model.getListOfUnitDefinitions()) {
+ for (Compartment jSBMLCompart : model.getListOfCompartments()) {
- BioUnitDefinition bionetUD = new BioUnitDefinition(jSBMLUD.getId(), jSBMLUD.getName());
+ String compartId = jSBMLCompart.getId();
+ String compartName = jSBMLCompart.getName().trim();
- if (jSBMLUD.getName().isEmpty()) {
- bionetUD.setName(jSBMLUD.getId());
- }
- ListOf<Unit> listofunits = jSBMLUD.getListOfUnits();
+ if (StringUtils.isEmpty(compartName)) {
+ compartName = compartId;
+ }
- if (listofunits.size() != 0) {
+ BioCompartment bionetCompart = this.getNetwork().getCompartmentsView().get(compartId);
+ if (bionetCompart == null) {
+ bionetCompart = new BioCompartment(compartId, compartName);
+ this.getNetwork().add(bionetCompart);
+ }
- for (int n = 0; n < listofunits.size(); n++) {
+ /**
+ * SBML 2.0
+ */
+ if (jSBMLCompart.isSetCompartmentType()) {
+ BioCompartmentType type = new BioCompartmentType(
+ model.getCompartmentType(jSBMLCompart.getCompartmentType()).getId(),
+ model.getCompartmentType(jSBMLCompart.getCompartmentType()).getName());
+ CompartmentAttributes.setType(bionetCompart, type);
- Unit jSBMLUnit = listofunits.get(n);
+ }
- Kind kind = jSBMLUnit.getKind();
- Double Exp = jSBMLUnit.getExponent();
- Integer Scale = jSBMLUnit.getScale();
- Double Multiplier = jSBMLUnit.getMultiplier();
+ /*
+ * If the compartment has an outside attribute, we need to look if the outside
+ * compartment exists in the bioNetwork
+ */
+ if (jSBMLCompart.isSetOutside()) {
- UnitSbml bionetUnit = new UnitSbml(kind.getName(), Exp, Scale, Multiplier);
- bionetUD.addUnit(bionetUnit);
- }
- }
+ Compartment outsideJSBMLComp = model.getCompartment(jSBMLCompart.getOutside());
- NetworkAttributes.addUnitDefinition(this.getNetwork(), bionetUD);
- }
+ BioCompartment outsideCompart = this.getNetwork().getCompartmentsView()
+ .get(outsideJSBMLComp.getId());
- }
+ // if it's null, we create it and add it to the bionetwork
+ if (outsideCompart == null) {
+ outsideCompart = new BioCompartment(outsideJSBMLComp.getId(), outsideJSBMLComp.getName());
+ this.getNetwork().add(outsideCompart);
+ }
- /**
- * Default way of parsing sbml compartements. Needs to be overridden to modify
- * behavior
- *
- */
- private void parseListOfCompartments() {
+ // We can add it as outside compartment of the current
+ // compartment
+ CompartmentAttributes.setOutsideCompartment(bionetCompart, outsideCompart);
+ }
- if(model.getListOfCompartments().size()==0)
- {
- System.err.println("[WARNING] No compartment in the model !");
- }
+ if (jSBMLCompart.isSetUnits()) {
- for (Compartment jSBMLCompart : model.getListOfCompartments()) {
+ UnitDefinition JsbmlUnitDef = model.getUnitDefinition(jSBMLCompart.getUnits());
+ BioUnitDefinition bionetUnitDef = NetworkAttributes.getUnitDefinition(this.getNetwork(),
+ JsbmlUnitDef.getId());
+ CompartmentAttributes.setUnitDefinition(bionetCompart, bionetUnitDef);
+ }
- String compartId = jSBMLCompart.getId();
- String compartName = jSBMLCompart.getName().trim();
+ if (jSBMLCompart.getSBOTerm() != -1) {
+ CompartmentAttributes.setSboTerm(bionetCompart, jSBMLCompart.getSBOTermID());
+ }
- if (StringUtils.isEmpty(compartName)) {
- compartName = compartId;
- }
+ CompartmentAttributes.setConstant(bionetCompart, jSBMLCompart.getConstant());
- BioCompartment bionetCompart = this.getNetwork().getCompartmentsView().get(compartId);
- if (bionetCompart == null) {
- bionetCompart = new BioCompartment(compartId, compartName);
- this.getNetwork().add(bionetCompart);
- }
+ if (jSBMLCompart.isSetSize()) {
+ CompartmentAttributes.setSize(bionetCompart, jSBMLCompart.getSize());
+ }
- /**
- * SBML 2.0
- */
- if (jSBMLCompart.isSetCompartmentType()) {
- BioCompartmentType type = new BioCompartmentType(
- model.getCompartmentType(jSBMLCompart.getCompartmentType()).getId(),
- model.getCompartmentType(jSBMLCompart.getCompartmentType()).getName());
- CompartmentAttributes.setType(bionetCompart, type);
+ if (jSBMLCompart.isSetSpatialDimensions()) {
+ CompartmentAttributes.setSpatialDimensions(bionetCompart, (int) jSBMLCompart.getSpatialDimensions());
+ } else {
+ CompartmentAttributes.setSpatialDimensions(bionetCompart, 3);
+ }
- }
+ }
- /*
- * If the compartment has an outside attribute, we need to look if the outside
- * compartment exists in the bioNetwork
- */
- if (jSBMLCompart.isSetOutside()) {
+ }
- Compartment outsideJSBMLComp = model.getCompartment(jSBMLCompart.getOutside());
+ /**
+ * @return true if the parse contains the FBC package
+ */
+ private boolean containsFbcPackage() {
- BioCompartment outsideCompart = this.getNetwork().getCompartmentsView()
- .get(outsideJSBMLComp.getId());
+ for (PackageParser p : this.packages) {
+ if (p instanceof FBCParser) {
+ return true;
+ }
+ }
- // if it's null, we create it and add it to the bionetwork
- if (outsideCompart == null) {
- outsideCompart = new BioCompartment(outsideJSBMLComp.getId(), outsideJSBMLComp.getName());
- this.getNetwork().add(outsideCompart);
- }
+ return false;
- // We can add it as outside compartment of the current
- // compartment
- CompartmentAttributes.setOutsideCompartment(bionetCompart, outsideCompart);
- }
+ }
- if (jSBMLCompart.isSetUnits()) {
+ /**
+ * Method to parse the list of reaction of the jsbml model
+ *
+ * @throws Met4jSbmlReaderException
+ */
+ private void parseListOfReactions() throws Met4jSbmlReaderException {
- UnitDefinition JsbmlUnitDef = model.getUnitDefinition(jSBMLCompart.getUnits());
- BioUnitDefinition bionetUnitDef = NetworkAttributes.getUnitDefinition(this.getNetwork(),
- JsbmlUnitDef.getId());
- CompartmentAttributes.setUnitDefinition(bionetCompart, bionetUnitDef);
- }
+ Boolean hasModifiers = false;
- if (jSBMLCompart.getSBOTerm() != -1) {
- CompartmentAttributes.setSboTerm(bionetCompart, jSBMLCompart.getSBOTermID());
- }
+ for (Reaction jSBMLReaction : model.getListOfReactions()) {
+ String reactionId = jSBMLReaction.getId();
- CompartmentAttributes.setConstant(bionetCompart, jSBMLCompart.getConstant());
+ String reactionName = jSBMLReaction.getName();
+ if (reactionName.isEmpty()) {
+ reactionName = reactionId;
+ }
+ BioReaction bionetReaction = new BioReaction(reactionId, reactionName);
- if (jSBMLCompart.isSetSize()) {
- CompartmentAttributes.setSize(bionetCompart, jSBMLCompart.getSize());
- }
+ this.getNetwork().add(bionetReaction);
- if (jSBMLCompart.isSetSpatialDimensions()) {
- CompartmentAttributes.setSpatialDimensions(bionetCompart, (int) jSBMLCompart.getSpatialDimensions());
- } else {
- CompartmentAttributes.setSpatialDimensions(bionetCompart, 3);
- }
+ if (jSBMLReaction.isSetSBOTerm()) {
+ ReactionAttributes.setSboTerm(bionetReaction, jSBMLReaction.getSBOTermID());
+ }
- }
-
- }
+ if (jSBMLReaction.isSetFast()
+ && ((model.getLevel() < 3) || (model.getLevel() == 3 && model.getVersion() == 1))) {
+ ReactionAttributes.setFast(bionetReaction, jSBMLReaction.getFast());
+ }
- /**
- *
- * @return true if the parse contains the FBC package
- */
- private boolean containsFbcPackage() {
+ // if reversible attribute is present and is set to false
+ if (jSBMLReaction.isSetReversible()) {
+ bionetReaction.setReversible(jSBMLReaction.getReversible());
+ } else {
+ bionetReaction.setReversible(true);
+ }
- for (PackageParser p : this.packages) {
- if (p instanceof FBCParser) {
- return true;
- }
- }
+ this.parseReactionListOf(bionetReaction, jSBMLReaction.getListOfReactants(), "left");
+ this.parseReactionListOf(bionetReaction, jSBMLReaction.getListOfProducts(), "right");
- return false;
-
- }
+ BioUnitDefinitionCollection udList = NetworkAttributes.getUnitDefinitions(this.getNetwork());
- /**
- * Method to parse the list of reaction of the jsbml model
- *
- * @throws Met4jSbmlReaderException
- */
- private void parseListOfReactions() throws Met4jSbmlReaderException {
+ KineticLaw kine = jSBMLReaction.getKineticLaw();
+ if (kine != null) {
- Boolean hasModifiers = false;
+ ReactionAttributes.setKineticFormula(bionetReaction, kine.getMathMLString());
- for (Reaction jSBMLReaction : model.getListOfReactions()) {
- String reactionId = jSBMLReaction.getId();
+ if (model.getLevel() < 3) {
+ for (int n = 0; n < kine.getNumParameters(); n++) {
- String reactionName = jSBMLReaction.getName();
- if (reactionName.isEmpty()) {
- reactionName = reactionId;
- }
- BioReaction bionetReaction = new BioReaction(reactionId, reactionName);
+ UnitDefinition jsbmlUnit = model.getUnitDefinition(kine.getParameter(n).getUnits());
- this.getNetwork().add(bionetReaction);
+ // This means that <parameter id="REDUCED_COST" value="0.000000"/> won't be taken into account
+ if (jsbmlUnit != null) {
- if (jSBMLReaction.isSetSBOTerm()) {
- ReactionAttributes.setSboTerm(bionetReaction, jSBMLReaction.getSBOTermID());
- }
+ BioUnitDefinition UD = udList.get(jsbmlUnit.getId());
- if (jSBMLReaction.isSetFast()
- && ((model.getLevel() < 3) || (model.getLevel() == 3 && model.getVersion() == 1))) {
- ReactionAttributes.setFast(bionetReaction, jSBMLReaction.getFast());
- }
+ /**
+ * This is to make sure that the unit definition associated with the fluxes is
+ * not null, e.g dimensionless
+ */
+ if (UD == null) {
+ UD = new BioUnitDefinition(jsbmlUnit.getId(), jsbmlUnit.getName());
+ udList.add(UD);
+ }
- // if reversible attribute is present and is set to false
- if (jSBMLReaction.isSetReversible()) {
- bionetReaction.setReversible(jSBMLReaction.getReversible());
- } else {
- bionetReaction.setReversible(true);
- }
+ if (kine.getParameter(n).getId().equalsIgnoreCase("UPPER_BOUND")
+ || kine.getParameter(n).getName().equalsIgnoreCase("UPPER_BOUND")) {
- this.parseReactionListOf(bionetReaction, jSBMLReaction.getListOfReactants(), "left");
- this.parseReactionListOf(bionetReaction, jSBMLReaction.getListOfProducts(), "right");
+ Flux newflux = new Flux(kine.getParameter(n).getId(), kine.getParameter(n).getValue(),
+ UD);
- BioUnitDefinitionCollection udList = NetworkAttributes.getUnitDefinitions(this.getNetwork());
+ try {
+ ReactionAttributes.setUpperBound(bionetReaction, newflux);
+ } catch (IllegalArgumentException e) {
+ System.err.println("[Warning] Upper bound of reaction " + bionetReaction.getId() + " badly formatted : put to 0");
+ e.printStackTrace();
+ newflux.value = 0.0;
+ ReactionAttributes.setUpperBound(bionetReaction, newflux);
+ }
- KineticLaw kine = jSBMLReaction.getKineticLaw();
- if (kine != null) {
+ } else if (kine.getParameter(n).getId().equalsIgnoreCase("LOWER_BOUND")
+ || kine.getParameter(n).getName().equalsIgnoreCase("LOWER_BOUND")) {
- ReactionAttributes.setKineticFormula(bionetReaction, kine.getMathMLString());
+ Flux newflux = new Flux(kine.getParameter(n).getId(), kine.getParameter(n).getValue(),
+ UD);
- if (model.getLevel() < 3) {
- for (int n = 0; n < kine.getNumParameters(); n++) {
- UnitDefinition jsbmlUnit = model.getUnitDefinition(kine.getParameter(n).getUnits());
+ try {
+ ReactionAttributes.setLowerBound(bionetReaction, newflux);
+ } catch (IllegalArgumentException e) {
+ System.err.println("[Warning] Lower bound of reaction " + bionetReaction.getId() + " badly formatted : put to 0");
+ e.printStackTrace();
+ newflux.value = 0.0;
+ ReactionAttributes.setLowerBound(bionetReaction, newflux);
+ }
- // This means that <parameter id="REDUCED_COST" value="0.000000"/> won't be taken into account
- if (jsbmlUnit != null) {
+ } else {
+ Flux newflux = new Flux(kine.getParameter(n).getId(), kine.getParameter(n).getValue(),
+ UD);
- BioUnitDefinition UD = udList.get(jsbmlUnit.getId());
+ ReactionAttributes.addFlux(bionetReaction, newflux);
+
+ }
+ }
- /**
- * This is to make sure that the unit definition associated with the fluxes is
- * not null, e.g dimensionless
- */
- if (UD == null) {
- UD = new BioUnitDefinition(jsbmlUnit.getId(), jsbmlUnit.getName());
- udList.add(UD);
- }
+ }
+ } else if (!this.containsFbcPackage()) { // SBML V3.0 and not
+ // fbc package
- if (kine.getParameter(n).getId().equalsIgnoreCase("UPPER_BOUND")
- || kine.getParameter(n).getName().equalsIgnoreCase("UPPER_BOUND")) {
+ for (LocalParameter param : kine.getListOfLocalParameters()) {
+
+ UnitDefinition jsbmlUnit = model.getUnitDefinition(param.getUnits());
+ if (jsbmlUnit == null) {
+ throw new Met4jSbmlReaderException("Problem with the reaction " + bionetReaction.getId()
+ + " : the flux unit " + param.getUnits() + " does not exist in the model");
+ } else {
- Flux newflux = new Flux(kine.getParameter(n).getId(), kine.getParameter(n).getValue(),
- UD);
+ BioUnitDefinition UD = udList.get(jsbmlUnit.getId());
+
+ /**
+ * This is to make sure that the unit definition associated with the fluxes is
+ * not null
+ */
+ if (UD == null) {
+ UD = new BioUnitDefinition(jsbmlUnit.getId(), jsbmlUnit.getName());
+ udList.add(UD);
+ }
+
+ if (param.getId().equalsIgnoreCase("UPPER_BOUND")
+ || param.getName().equalsIgnoreCase("UPPER_BOUND")) {
+
+ String name = "UPPER_BOUND";
+ Flux newflux = new Flux(name, param.getValue(), UD);
+ ReactionAttributes.setUpperBound(bionetReaction, newflux);
- try {
- ReactionAttributes.setUpperBound(bionetReaction, newflux);
- } catch (IllegalArgumentException e) {
- System.err.println("[Warning] Upper bound of reaction "+bionetReaction.getId()+ " badly formatted : put to 0");
- e.printStackTrace();
- newflux.value = 0.0;
- ReactionAttributes.setUpperBound(bionetReaction, newflux);
- }
+ } else if (param.getId().equalsIgnoreCase("LOWER_BOUND")
+ || param.getName().equalsIgnoreCase("LOWER_BOUND")) {
- } else if (kine.getParameter(n).getId().equalsIgnoreCase("LOWER_BOUND")
- || kine.getParameter(n).getName().equalsIgnoreCase("LOWER_BOUND")) {
-
- Flux newflux = new Flux(kine.getParameter(n).getId(), kine.getParameter(n).getValue(),
- UD);
-
-
- try {
- ReactionAttributes.setLowerBound(bionetReaction, newflux);
- } catch (IllegalArgumentException e) {
- System.err.println("[Warning] Lower bound of reaction "+bionetReaction.getId()+ " badly formatted : put to 0");
- e.printStackTrace();
- newflux.value = 0.0;
- ReactionAttributes.setLowerBound(bionetReaction, newflux);
- }
-
- } else {
- Flux newflux = new Flux(kine.getParameter(n).getId(), kine.getParameter(n).getValue(),
- UD);
-
- ReactionAttributes.addFlux(bionetReaction, newflux);
-
- }
- }
+ String name = "LOWER_BOUND";
+ Flux newflux = new Flux(name, param.getValue(), UD);
+ ReactionAttributes.setLowerBound(bionetReaction, newflux);
- }
- } else if (!this.containsFbcPackage()) { // SBML V3.0 and not
- // fbc package
+ } else {
+ Flux newflux = new Flux(param.getId(), param.getValue(), UD);
+
+ ReactionAttributes.addFlux(bionetReaction, newflux);
+
+ }
+ }
+ }
+
+ }
+ }
+
+ if (jSBMLReaction.getModifierCount() > 0) {
+ hasModifiers = true;
+ }
+
+ }
+
+ if (hasModifiers) {
+ System.err.println("[warning] Some reactions have list of modifiers. Be careful, Met4j-io does not import list of modifiers");
+ }
+ }
- for (LocalParameter param : kine.getListOfLocalParameters()) {
-
- UnitDefinition jsbmlUnit = model.getUnitDefinition(param.getUnits());
- if (jsbmlUnit == null) {
- throw new Met4jSbmlReaderException("Problem with the reaction " + bionetReaction.getId()
- + " : the flux unit " + param.getUnits() + " does not exist in the model");
- } else {
-
- BioUnitDefinition UD = udList.get(jsbmlUnit.getId());
-
- /**
- * This is to make sure that the unit definition associated with the fluxes is
- * not null
- */
- if (UD == null) {
- UD = new BioUnitDefinition(jsbmlUnit.getId(), jsbmlUnit.getName());
- udList.add(UD);
- }
-
- if (param.getId().equalsIgnoreCase("UPPER_BOUND")
- || param.getName().equalsIgnoreCase("UPPER_BOUND")) {
-
- String name = "UPPER_BOUND";
- Flux newflux = new Flux(name, param.getValue(), UD);
- ReactionAttributes.setUpperBound(bionetReaction, newflux);
-
- } else if (param.getId().equalsIgnoreCase("LOWER_BOUND")
- || param.getName().equalsIgnoreCase("LOWER_BOUND")) {
-
- String name = "LOWER_BOUND";
- Flux newflux = new Flux(name, param.getValue(), UD);
- ReactionAttributes.setLowerBound(bionetReaction, newflux);
-
- } else {
- Flux newflux = new Flux(param.getId(), param.getValue(), UD);
-
- ReactionAttributes.addFlux(bionetReaction, newflux);
-
- }
- }
- }
-
- }
- }
-
- if(jSBMLReaction.getModifierCount() > 0)
- {
- hasModifiers = true;
- }
-
- }
-
- if(hasModifiers)
- {
- System.err.println("[warning] Some reactions have list of modifiers. Be careful, Met4j-io does not import list of modifiers");
- }
- }
-
- /**
- * Abstract class to parse the list of SpeciesReferences of a given Reaction
- *
- * @param bionetReaction the {@link BioReaction}
- * @param listOf the jsbml list of SpeciesReferences
- * @param side The side of the SpeciesReferences
- * <ul>
- * <li>left = reactants
- * <li>right = products
- * </ul>
- */
- private void parseReactionListOf(BioReaction bionetReaction, ListOf<SpeciesReference> listOf, String side) {
- for (SpeciesReference specieRef : listOf) {
- BioReactant reactant = this.parseParticipantSpecies(specieRef);
-
- if(reactant != null) {
- if (specieRef.isSetConstant()) {
- ReactantAttributes.setConstant(reactant, specieRef.getConstant());
- }
-
- if (side.equals("left")) {
- this.getNetwork().affectLeft(bionetReaction, reactant);
- } else {
- this.getNetwork().affectRight(bionetReaction, reactant);
- }
- }
-
- }
- }
-
- private void parseListOfSpecies() {
-
- Boolean hasInvalidSboTerms = false;
-
- for (Species specie : this.getModel().getListOfSpecies()) {
- String specieId = specie.getId();
-
- String specieName = specie.getName();
- if (specieName.isEmpty()) {
- specieName = specieId;
- }
-
- // Check if the sbo term is valid for a metabolite
- Boolean validSboTerm = true;
- String sboTerm = specie.getSBOTermID();
-
- if(sboTerm != null)
- {
- if(sboTerm.compareToIgnoreCase("SBO:0000252")==0)
- {
- validSboTerm = false;
- hasInvalidSboTerms = true;
- // It's considered as a gene
- // We replace the first "_" by "" if exists
-
- String oldId = specieId;
-
- specieId = specieId.replaceFirst("^_", "");
- specieId = specieId.replaceFirst("_.$", "");
- specieName = specieName.replaceFirst("^_", "");
- specieName = specieName.replaceFirst("_.$", "");
- BioGene gene = new BioGene(specieId, specieName);
-
- gene.setAttribute("oldId", oldId);
-
- this.getNetwork().add(gene);
- }
- else if(sboTerm.compareToIgnoreCase("SBO:0000014")==0 || sboTerm.compareToIgnoreCase("SBO:0000297")==0)
- {
- validSboTerm = false;
- hasInvalidSboTerms = true;
-
- String oldId = specieId;
- // It's considered as an enzyme
- specieId = specieId.replaceFirst("^_", "");
- specieId = specieId.replaceFirst("_.$", "");
- specieName = specieName.replaceFirst("^_", "");
- specieName = specieName.replaceFirst("_.$", "");
- BioEnzyme enz = new BioEnzyme(specieId, specieName);
-
- enz.setAttribute("oldId", oldId);
-
- this.getNetwork().add(enz);
- }
- }
-
- if(validSboTerm) {
-
- BioMetabolite bionetSpecies = new BioMetabolite(specieId, specieName);
-
- MetaboliteAttributes.setBoundaryCondition(bionetSpecies, specie.getBoundaryCondition());
- MetaboliteAttributes.setConstant(bionetSpecies, specie.getConstant());
-
- MetaboliteAttributes.setSubstanceUnits(bionetSpecies, specie.getSubstanceUnits());
- if (specie.getSBOTerm() != -1) {
- MetaboliteAttributes.setSboTerm(bionetSpecies, specie.getSBOTermID());
- }
-
- if (specie.isSetInitialAmount()) {
- MetaboliteAttributes.setInitialAmount(bionetSpecies, specie.getInitialAmount());
- } else if (specie.isSetInitialConcentration()) {
- MetaboliteAttributes.setInitialConcentration(bionetSpecies, specie.getInitialConcentration());
- }
-
- if (specie.isSetCharge()) {
- bionetSpecies.setCharge(specie.getCharge());
- }
-
- MetaboliteAttributes.setSubstanceUnits(bionetSpecies, specie.getSubstanceUnits());
-
- if (model.getLevel() == 2 && model.getVersion() >= 2 && model.getVersion() <= 4) {
- if (specie.isSetSpeciesType()) {
-
- SpeciesType stype = specie.getSpeciesTypeInstance();
- if (stype.isSetSBOTerm()) {
-
- MetaboliteAttributes.setSboTerm(bionetSpecies, stype.getSBOTermID());
-
- }
- try {
- if (stype.isSetAnnotation()) {
- MetaboliteAttributes.setAnnotation(bionetSpecies,
- new SbmlAnnotation(stype.getId(), stype.getAnnotationString()));
- }
- if (stype.isSetNotes()) {
- MetaboliteAttributes.setNotes(bionetSpecies, new Notes(stype.getNotesString()));
- }
- } catch (XMLStreamException e) {
- e.printStackTrace();
- }
- }
- }
-
- this.getNetwork().add(bionetSpecies);
-
- this.getNetwork().affectToCompartment(
- this.getNetwork().getCompartmentsView().get(specie.getCompartment()), bionetSpecies);
- }
- }
-
- if(hasInvalidSboTerms)
- {
- System.err.println("[warning] Sbo term for some species are not metabolite sbo terms, they haven't been imported or have been imported as genes, " +
- "depending on their sbo term (SBO:0000252) or as enzymes (SBO:0000014 or SBO:0000297).");
- }
- }
-
- /**
- * parse the jsbml species participating in a reaction and create the
- * corresponding metabolite
- */
- private BioReactant parseParticipantSpecies(SpeciesReference specieRef) {
- Species specie = this.getModel().getSpecies(specieRef.getSpecies());
- if(specie == null)
- {
- throw new IllegalArgumentException("The specie "+specieRef.getSpecies()+ " does not exist");
- }
-
- String specieId = specie.getId();
-
- Double stoDbl = specieRef.getStoichiometry();
-
- if(Double.isNaN(stoDbl) || Double.isInfinite(stoDbl)) {
- System.err.println("Warning : invalid coefficient : " + stoDbl + " for " + specieId+": set to 1.0");
- stoDbl = 1.0;
- }
-
- if(stoDbl < 0)
- {
- System.err.println("Warning : negative coefficient : " + stoDbl + " for " + specieId+" : set to positive");
- stoDbl = -stoDbl;
- }
-
- if(stoDbl == 0)
- {
- System.err.println("Warning : coefficient equals to 0 for " + specieId+" : This reactant won't be added to the reaction");
- stoDbl = -stoDbl;
- }
-
- BioReactant reactant = null;
-
- if(stoDbl != 0) {
- BioMetabolite bionetSpecies = this.getNetwork().getMetabolitesView().get(specieId);
-
- reactant = new BioReactant(bionetSpecies, stoDbl,
- this.getNetwork().getCompartmentsView().get(specie.getCompartment()));
- }
-
- return reactant;
- }
-
- /**
- * <p>Getter for the field <code>network</code>.</p>
- *
- * @return the bionet
- */
- public BioNetwork getNetwork() {
- return network;
- }
-
- /**
- * <p>Setter for the field <code>network</code>.</p>
- *
- * @param bionet the bionet to set
- */
- public void setNetwork(BioNetwork bionet) {
- this.network = bionet;
- }
-
- /**
- * <p>getSetOfPackage.</p>
- *
- * @return the setOfPackage
- */
- public ArrayList<PackageParser> getSetOfPackage() {
- return packages;
- }
-
- /**
- * Add a package to this parser
- *
- * @param pkg the package to add
- * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.JSBMLPackageReaderException if any.
- */
- public void addPackage(PackageParser pkg) throws JSBMLPackageReaderException {
-
- if ((this.getModel().getLevel() <= 2 && pkg instanceof ReaderSBML2Compatible)
- || (this.getModel().getLevel() > 2 && pkg instanceof ReaderSBML3Compatible)) {
- this.getSetOfPackage().add(pkg);
- } else {
- throw new JSBMLPackageReaderException("Invalid SBML level and package Reader combination");
- }
-
- }
-
- /**
- * Set the {@link #packages} to a new list
- *
- * @param packages the ordered list of packages to set
- * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.JSBMLPackageReaderException if any.
- */
- public void setPackages(ArrayList<PackageParser> packages) throws JSBMLPackageReaderException {
- for (PackageParser pkg : packages) {
- this.addPackage(pkg);
- }
- }
-
- /**
- * Launch the parsing of the jsbml model by the different packages
- *
- * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
- */
- public void parsePackageAdditionalData() throws Met4jSbmlReaderException {
- for (PackageParser parser : this.getSetOfPackage()) {
- parser.parseModel(model, this.getNetwork());
- }
- }
-
- /**
- * <p>Getter for the field <code>model</code>.</p>
- *
- * @return a {@link org.sbml.jsbml.Model} object.
- */
- public Model getModel() {
- return model;
- }
+ /**
+ * Abstract class to parse the list of SpeciesReferences of a given Reaction
+ *
+ * @param bionetReaction the {@link BioReaction}
+ * @param listOf the jsbml list of SpeciesReferences
+ * @param side The side of the SpeciesReferences
+ * <ul>
+ * <li>left = reactants
+ * <li>right = products
+ * </ul>
+ */
+ private void parseReactionListOf(BioReaction bionetReaction, ListOf<SpeciesReference> listOf, String side) {
+ for (SpeciesReference specieRef : listOf) {
+ this.parseParticipantSpecies(bionetReaction, specieRef, side);
+ }
+ }
+
+ private void parseListOfSpecies() {
+
+ Boolean hasInvalidSboTerms = false;
+
+ for (Species specie : this.getModel().getListOfSpecies()) {
+ String specieId = specie.getId();
+
+ String specieName = specie.getName();
+ if (specieName.isEmpty()) {
+ specieName = specieId;
+ }
+
+ // Check if the sbo term is valid for a metabolite
+ Boolean validSboTerm = true;
+ String sboTerm = specie.getSBOTermID();
+
+ if (sboTerm != null) {
+ if (sboTerm.compareToIgnoreCase("SBO:0000252") == 0) {
+ validSboTerm = false;
+ hasInvalidSboTerms = true;
+ // It's considered as a gene
+ // We replace the first "_" by "" if exists
+
+ String oldId = specieId;
+
+ specieId = specieId.replaceFirst("^_", "");
+ specieId = specieId.replaceFirst("_.$", "");
+ specieName = specieName.replaceFirst("^_", "");
+ specieName = specieName.replaceFirst("_.$", "");
+ BioGene gene = new BioGene(specieId, specieName);
+
+ gene.setAttribute("oldId", oldId);
+
+ this.getNetwork().add(gene);
+ } else if (sboTerm.compareToIgnoreCase("SBO:0000014") == 0 || sboTerm.compareToIgnoreCase("SBO:0000297") == 0) {
+ validSboTerm = false;
+ hasInvalidSboTerms = true;
+
+ String oldId = specieId;
+ // It's considered as an enzyme
+ specieId = specieId.replaceFirst("^_", "");
+ specieId = specieId.replaceFirst("_.$", "");
+ specieName = specieName.replaceFirst("^_", "");
+ specieName = specieName.replaceFirst("_.$", "");
+ BioEnzyme enz = new BioEnzyme(specieId, specieName);
+
+ enz.setAttribute("oldId", oldId);
+
+ this.getNetwork().add(enz);
+ }
+ }
+
+ if (validSboTerm) {
+
+ BioMetabolite bionetSpecies = new BioMetabolite(specieId, specieName);
+
+ MetaboliteAttributes.setBoundaryCondition(bionetSpecies, specie.getBoundaryCondition());
+ MetaboliteAttributes.setConstant(bionetSpecies, specie.getConstant());
+
+ MetaboliteAttributes.setSubstanceUnits(bionetSpecies, specie.getSubstanceUnits());
+ if (specie.getSBOTerm() != -1) {
+ MetaboliteAttributes.setSboTerm(bionetSpecies, specie.getSBOTermID());
+ }
+
+ if (specie.isSetInitialAmount()) {
+ MetaboliteAttributes.setInitialAmount(bionetSpecies, specie.getInitialAmount());
+ } else if (specie.isSetInitialConcentration()) {
+ MetaboliteAttributes.setInitialConcentration(bionetSpecies, specie.getInitialConcentration());
+ }
+
+ if (specie.isSetCharge()) {
+ bionetSpecies.setCharge(specie.getCharge());
+ }
+
+ MetaboliteAttributes.setSubstanceUnits(bionetSpecies, specie.getSubstanceUnits());
+
+ if (model.getLevel() == 2 && model.getVersion() >= 2 && model.getVersion() <= 4) {
+ if (specie.isSetSpeciesType()) {
+
+ SpeciesType stype = specie.getSpeciesTypeInstance();
+ if (stype.isSetSBOTerm()) {
+
+ MetaboliteAttributes.setSboTerm(bionetSpecies, stype.getSBOTermID());
+
+ }
+ try {
+ if (stype.isSetAnnotation()) {
+ MetaboliteAttributes.setAnnotation(bionetSpecies,
+ new SbmlAnnotation(stype.getId(), stype.getAnnotationString()));
+ }
+ if (stype.isSetNotes()) {
+ MetaboliteAttributes.setNotes(bionetSpecies, new Notes(stype.getNotesString()));
+ }
+ } catch (XMLStreamException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ this.getNetwork().add(bionetSpecies);
+
+ this.getNetwork().affectToCompartment(
+ this.getNetwork().getCompartmentsView().get(specie.getCompartment()), bionetSpecies);
+ }
+ }
+
+ if (hasInvalidSboTerms) {
+ System.err.println("[warning] Sbo term for some species are not metabolite sbo terms, they haven't been imported or have been imported as genes, " +
+ "depending on their sbo term (SBO:0000252) or as enzymes (SBO:0000014 or SBO:0000297).");
+ }
+ }
+
+ /**
+ * parse the jsbml species participating in a reaction and create the
+ * corresponding metabolite
+ */
+ private void parseParticipantSpecies(BioReaction reaction, SpeciesReference specieRef, String side) {
+ Species specie = this.getModel().getSpecies(specieRef.getSpecies());
+ if (specie == null) {
+ throw new IllegalArgumentException("The specie " + specieRef.getSpecies() + " does not exist");
+ }
+
+ String specieId = specie.getId();
+
+ Double stoDbl = specieRef.getStoichiometry();
+
+ if (Double.isNaN(stoDbl) || Double.isInfinite(stoDbl)) {
+ System.err.println("Warning : invalid coefficient : " + stoDbl + " for " + specieId + ": set to 1.0");
+ stoDbl = 1.0;
+ }
+
+ if (stoDbl < 0) {
+ System.err.println("Warning : negative coefficient : " + stoDbl + " for " + specieId + " : set to positive");
+ stoDbl = -stoDbl;
+ }
+
+ if (stoDbl == 0) {
+ System.err.println("Warning : coefficient equals to 0 for " + specieId + " : This reactant won't be added to the reaction");
+ stoDbl = -stoDbl;
+ }
+
+
+ if (stoDbl != 0) {
+ BioMetabolite bionetSpecies = this.getNetwork().getMetabolitesView().get(specieId);
+
+ if (side.equals("left")) {
+ this.network.affectLeft(reaction, stoDbl,
+ this.getNetwork().getCompartmentsView().get(specie.getCompartment()),
+ bionetSpecies);
+ }
+ else {
+ this.network.affectRight(reaction, stoDbl,
+ this.getNetwork().getCompartmentsView().get(specie.getCompartment()),
+ bionetSpecies);
+ }
+ }
+ }
+
+ /**
+ * <p>Getter for the field <code>network</code>.</p>
+ *
+ * @return the bionet
+ */
+ public BioNetwork getNetwork() {
+ return network;
+ }
+
+ /**
+ * <p>Setter for the field <code>network</code>.</p>
+ *
+ * @param bionet the bionet to set
+ */
+ public void setNetwork(BioNetwork bionet) {
+ this.network = bionet;
+ }
+
+ /**
+ * <p>getSetOfPackage.</p>
+ *
+ * @return the setOfPackage
+ */
+ public ArrayList<PackageParser> getSetOfPackage() {
+ return packages;
+ }
+
+ /**
+ * Add a package to this parser
+ *
+ * @param pkg the package to add
+ * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.JSBMLPackageReaderException if any.
+ */
+ public void addPackage(PackageParser pkg) throws JSBMLPackageReaderException {
+
+ if ((this.getModel().getLevel() <= 2 && pkg instanceof ReaderSBML2Compatible)
+ || (this.getModel().getLevel() > 2 && pkg instanceof ReaderSBML3Compatible)) {
+ this.getSetOfPackage().add(pkg);
+ } else {
+ throw new JSBMLPackageReaderException("Invalid SBML level and package Reader combination");
+ }
+
+ }
+
+ /**
+ * Set the {@link #packages} to a new list
+ *
+ * @param packages the ordered list of packages to set
+ * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.JSBMLPackageReaderException if any.
+ */
+ public void setPackages(ArrayList<PackageParser> packages) throws JSBMLPackageReaderException {
+ for (PackageParser pkg : packages) {
+ this.addPackage(pkg);
+ }
+ }
+
+ /**
+ * Launch the parsing of the jsbml model by the different packages
+ *
+ * @throws fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException if any.
+ */
+ public void parsePackageAdditionalData() throws Met4jSbmlReaderException {
+ for (PackageParser parser : this.getSetOfPackage()) {
+ parser.parseModel(model, this.getNetwork());
+ }
+ }
+
+ /**
+ * <p>Getter for the field <code>model</code>.</p>
+ *
+ * @return a {@link org.sbml.jsbml.Model} object.
+ */
+ public Model getModel() {
+ return model;
+ }
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/kegg/Kegg2BioNetwork.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/kegg/Kegg2BioNetwork.java
index a50cfa5ec06c69552b5beb2a730a94c5bd387b9a..eeb7b34c1b3ba3da95ca780f481b462b51af59a1 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/kegg/Kegg2BioNetwork.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/kegg/Kegg2BioNetwork.java
@@ -319,10 +319,27 @@ public class Kegg2BioNetwork {
for (String longGeneId : genes) {
String geneId = this.simplifyId(longGeneId);
- BioGene gene = new BioGene(geneId);
- BioProtein prot = new BioProtein(geneId);
- BioEnzyme enz = new BioEnzyme(geneId);
- network.add(gene, prot, enz);
+
+ BioGene gene = network.getGenesView().get(geneId);
+ if(gene == null)
+ {
+ gene = new BioGene(geneId);
+ network.add(gene);
+ }
+
+ BioProtein prot = network.getProteinsView().get(geneId);
+ if(prot == null)
+ {
+ prot = new BioProtein(geneId);
+ network.add(prot);
+ }
+
+ BioEnzyme enz = network.getEnzymesView().get(geneId);
+ if(enz == null) {
+ enz = new BioEnzyme(geneId);
+ network.add(enz);
+ }
+
network.affectGeneProduct(prot, gene);
network.affectSubUnit(enz, 1.0, prot);
network.affectEnzyme(reaction, enz);
@@ -346,19 +363,14 @@ public class Kegg2BioNetwork {
this.network.affectToCompartment(cpt, cpd);
}
if (child.getNodeName().equalsIgnoreCase("substrate")) {
- BioReactant lpart = new BioReactant(cpd, 1.0, cpt);
- ReactionAttributes.setConstant(lpart, false);
- network.affectLeft(reaction, lpart);
+ network.affectLeft(reaction, 1.0, cpt, cpd);
continue;
}
- BioReactant rpart = new BioReactant(cpd, 1.0, cpt);
- ReactionAttributes.setConstant(rpart, false);
- network.affectRight(reaction, rpart);
+ network.affectRight(reaction, 1.0, cpt, cpd);
}
}
}
-
network.affectToPathway(pathway, reaction);
}
}
@@ -397,7 +409,7 @@ public class Kegg2BioNetwork {
* @param substrateAndStoichio a String containing the coefficient (optional) and the cpd id
* @return a {@link BioReactant}
*/
- private BioReactant createReactant(String substrateAndStoichio, String reactionId) {
+ private void createReactant(String substrateAndStoichio, BioReaction reaction, Boolean rightSide) {
String stoichio;
String longCpdId;
BioMetabolite cpd;
@@ -413,7 +425,7 @@ public class Kegg2BioNetwork {
if (m.find()) {
// The stoichio is in the form 2n, we keep only 2.
stoichio = m.group(1);
- System.err.println("[met4j-io][Kegg2BioNetwork] Warning: in reaction " + reactionId +
+ System.err.println("[met4j-io][Kegg2BioNetwork] Warning: in reaction " + reaction.getId() +
" : changes the stoichiometric coefficient from " + tmp[0] + " to " + stoichio);
}
longCpdId = tmp[1];
@@ -426,7 +438,7 @@ public class Kegg2BioNetwork {
// Here we remove patterns like (n), (n +1)
if (longCpdId.matches(".*\\([^)]+\\)$")) {
String id2 = longCpdId.replaceAll("\\([^)]+\\)", "");
- System.err.println("[met4j-io][Kegg2BioNetwork] Warning: in reaction " + reactionId +
+ System.err.println("[met4j-io][Kegg2BioNetwork] Warning: in reaction " + reaction.getId() +
" : changes the id from " + longCpdId + " to " + id2);
longCpdId = id2;
}
@@ -446,10 +458,17 @@ public class Kegg2BioNetwork {
coeff = Double.parseDouble(stoichio);
} catch (NumberFormatException e) {
System.err.println("[met4j-io][Kegg2BioNetwork] Warning : The stoechiometry "
- + stoichio + " in the reaction " + reactionId + " is not a number, it is left as 1.0");
+ + stoichio + " in the reaction " + reaction.getId() + " is not a number, it is left as 1.0");
+ }
+
+ if(! rightSide){
+ this.network.affectLeft(reaction, coeff, cpt, cpd);
+ }
+ else {
+ this.network.affectRight(reaction, coeff, cpt, cpd);
}
- return new BioReactant(cpd, coeff, cpt);
+ return;
}
/**
@@ -518,13 +537,11 @@ public class Kegg2BioNetwork {
String[] prod = eq[1].split(" \\+ ");
for (String substrateAndStoichio : subs) {
- BioReactant lPart = createReactant(substrateAndStoichio, id);
- network.affectLeft(rxn, lPart);
+ createReactant(substrateAndStoichio, rxn, false);
}
for (String productAndStoechio : prod) {
- BioReactant rPart = createReactant(productAndStoechio, id);
- network.affectRight(rxn, rPart);
+ createReactant(productAndStoechio, rxn, true);
}
}
if (Data.get("ENZYME") != null) {
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java
index bde071692b8ee18b2a9034409de09f011618ace5..3a34207d426e1da8a09027092e736b8cdecdeb74 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/AbstractSetAttributesFromFile.java
@@ -50,6 +50,7 @@ import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+
/**
* <p>Abstract AbstractSetAttributesFromFile class.</p>
*
@@ -58,101 +59,79 @@ import java.util.regex.Pattern;
*/
public abstract class AbstractSetAttributesFromFile {
- private int colId = 0;
- private int colAttr = 1;
- private BioNetwork bn;
- private String fileIn;
- private String commentCharacter = "#";
- private int nSkip = 0;
- private String object = REACTION;
- private Boolean addPrefix = false;
- private Boolean addSuffix = false;
+ protected int colId = 0;
+ protected int colAttr = 1;
+ protected BioNetwork bn;
+ protected String fileIn;
+ protected String commentCharacter = "#";
+ protected int nSkip = 0;
+ protected EntityType entityType = EntityType.REACTION;
+ protected Boolean addPrefix = false;
+ protected Boolean addSuffix = false;
- private Set<String> ids;
+ protected Set<String> ids;
- /**
- * Constant <code>REACTION="R"</code>
- */
- public static final String REACTION = "R";
- /**
- * Constant <code>METABOLITE="M"</code>
- */
- public static final String METABOLITE = "M";
- /**
- * Constant <code>PROTEIN="P"</code>
- */
- public static final String PROTEIN = "P";
- /**
- * Constant <code>GENE="G"</code>
- */
- public static final String GENE = "G";
- /**
- * Constant <code>PATHWAY="Pa"</code>
- */
- public static final String PATHWAY = "Pa";
-
- private Set<String> objectIds;
+ protected Set<String> objectIds;
- private HashMap<String, String> idAttributeMap;
+ protected HashMap<String, String> idAttributeMap;
/**
* <p>Constructor for AbstractSetAttributesFromFile.</p>
*
- * @param colAttr : number of the attribute column
- * @param bn : BioNetwork
- * @param fileIn : tabulated file containing the ids and the attributes
- * @param c : comment character
- * @param o : object to set ("R" : reaction, "M" : metabolite, "G" : gene,
- * "P" : protein, "PA" : pathway)
- * @param p a {@link java.lang.Boolean} object.
- * @param nSkip a int.
- * @param s a {@link java.lang.Boolean} object.
- * @param colId a int.
+ * @param colId a int.
+ * @param colAttr : number of the attribute column
+ * @param bn : BioNetwork
+ * @param fileIn : tabulated file containing the ids and the attributes
+ * @param c : comment character
+ * @param nSkip a int.
+ * @param entityType a {@link EntityType}
+ * @param p a {@link Boolean} object.
+ * @param s a {@link Boolean} object.
*/
- public AbstractSetAttributesFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, String o,
+ public AbstractSetAttributesFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, EntityType entityType,
Boolean p, Boolean s) {
- this.setColId(colId);
- this.setColAttr(colAttr);
- this.setNetwork(bn);
- this.setFileIn(fileIn);
- this.setCommentCharacter(c);
- this.setnSkip(nSkip);
- this.setAddPrefix(p);
- this.setAddSuffix(s);
- this.setIdAttributeMap(new HashMap<String, String>());
+ this.colId = colId;
+ this.colAttr = colAttr;
+ this.bn = bn;
+ this.fileIn = fileIn;
+ this.commentCharacter = c;
+ this.nSkip = nSkip;
+ this.addPrefix = p;
+ this.addSuffix = s;
+ this.idAttributeMap = new HashMap<>();
this.ids = new HashSet<>();
- if (!o.equalsIgnoreCase(REACTION) && !o.equalsIgnoreCase(METABOLITE) && !o.equalsIgnoreCase(PROTEIN)
- && !o.equalsIgnoreCase(GENE) && !o.equalsIgnoreCase(PATHWAY)) {
- System.err.println("Bad identifier of object : " + o);
- System.err.println("Identifiers allowed : " + REACTION + " (reaction) " + METABOLITE + " (metabolite) "
- + PROTEIN + " (protein) " + GENE + " (gene) " + PATHWAY + " (pathway)");
- System.err.println(REACTION + " is defined as default");
- } else {
- this.setObject(o);
- }
+ this.entityType = entityType;
- if (this.getObject().equalsIgnoreCase(REACTION)) {
+ if (this.entityType.equals(EntityType.REACTION)) {
this.objectIds = bn.getReactionsView().getIds();
}
- if (this.getObject().equalsIgnoreCase(METABOLITE)) {
+ if (this.entityType.equals(EntityType.METABOLITE)) {
this.objectIds = bn.getMetabolitesView().getIds();
}
- if (this.getObject().equalsIgnoreCase(PROTEIN)) {
+ if (this.entityType.equals(EntityType.PROTEIN)) {
this.objectIds = bn.getProteinsView().getIds();
}
- if (this.getObject().equalsIgnoreCase(GENE)) {
+ if (this.entityType.equals(EntityType.GENE)) {
this.objectIds = bn.getGenesView().getIds();
}
- if (this.getObject().equalsIgnoreCase(PATHWAY)) {
+ if (this.entityType.equals(EntityType.PATHWAY)) {
this.objectIds = bn.getPathwaysView().getIds();
}
+ if (this.colId < 0) {
+ throw new IllegalArgumentException("The id column number must be positive");
+ }
+
+ if (this.colAttr < 0) {
+ throw new IllegalArgumentException("The attribute column number must be positive");
+ }
+
}
/**
@@ -161,22 +140,14 @@ public abstract class AbstractSetAttributesFromFile {
* @return a {@link java.lang.Boolean} object.
* @throws java.io.IOException if any.
*/
- public Boolean test() throws IOException {
+ public Boolean parseAttributeFile() throws IOException {
Boolean flag = true;
- if (this.colId < 0) {
- System.err.println("There is an error in the id column number");
- }
-
- if (this.colAttr < 0) {
- System.err.println("There is an error in the attribute column number");
- }
-
FileInputStream in;
BufferedReader br;
try {
- in = new FileInputStream(this.getFileIn());
+ in = new FileInputStream(this.fileIn);
InputStreamReader ipsr = new InputStreamReader(in);
br = new BufferedReader(ipsr);
} catch (Exception e) {
@@ -194,17 +165,7 @@ public abstract class AbstractSetAttributesFromFile {
flag = parseLine(ligne, nLines);
}
-
- br.close();
-
- if (flag == false) {
- System.err.println("Input file badly formatted");
- } else {
- System.err.println("The input file looks good and contains " + ids.size() + " entries");
- }
-
return flag;
-
}
protected Boolean parseLine(String line, int nLines) {
@@ -213,17 +174,26 @@ public abstract class AbstractSetAttributesFromFile {
line = line.replace("\n", "").replace("\r", "");
- if ((nLines > this.nSkip) && (! line.isEmpty())
- && (this.getCommentCharacter().equals("")
- || !line.matches("^" + this.getCommentCharacter() + ".*"))) {
+ if ((nLines > this.nSkip) && (!line.isEmpty())
+ && (this.commentCharacter.equals("")
+ || !line.matches("^" + this.commentCharacter + ".*"))) {
String[] tab = line.split("\\t");
- if (tab.length <= this.colId || tab.length <= this.colAttr) {
- System.err
- .println("********\n[Error]Bad number of columns line " + nLines + "\n********");
- flag = false;
- } else {
+ // We do not return an error if the length of the tab
+ // is less than the column index because when the final columns are empty,
+ // the split does not take into account them
+
+ Pattern pattern = Pattern.compile("\\t");
+ Matcher matcher = pattern.matcher(line);
+ long nbColumns = matcher.results().count() + 1;
+
+ if (nbColumns <= this.colId || nbColumns <= this.colAttr) {
+ System.err.println("********\n[Warning] Bad number of columns line " + nLines + "(" + nbColumns + ")\n********");
+ return false;
+ }
+
+ if (tab.length > this.colId && tab.length > this.colAttr) {
String attribute = tab[this.colAttr];
@@ -237,7 +207,7 @@ public abstract class AbstractSetAttributesFromFile {
// remove spaces
id = id.trim();
- if (this.getObject().equalsIgnoreCase(METABOLITE)) {
+ if (this.entityType.equals(EntityType.METABOLITE)) {
// To transform metabolite id like this cpd[c] in
// cpd_c
Pattern cpd_Pattern = Pattern.compile("^.*(\\[([^\\]]*)\\])$");
@@ -250,10 +220,10 @@ public abstract class AbstractSetAttributesFromFile {
}
}
- if (this.getObject().equalsIgnoreCase(METABOLITE) && this.addSuffix) {
+ if (this.entityType.equals(EntityType.METABOLITE) && this.addSuffix) {
Boolean presence = false;
- BioCollection<BioCompartment> compartmentsView = this.getNetwork().getCompartmentsView();
+ BioCollection<BioCompartment> compartmentsView = this.bn.getCompartmentsView();
// Checks if the suffix corresponds to a compartment
for (String compartmentId : compartmentsView.getIds()) {
@@ -280,7 +250,7 @@ public abstract class AbstractSetAttributesFromFile {
// +metaboliteId;
// }
- if (this.getNetwork().getMetabolitesView().containsId(metaboliteId)) {
+ if (this.bn.getMetabolitesView().containsId(metaboliteId)) {
this.getIdAttributeMap().put(metaboliteId, attribute);
presence = true;
}
@@ -303,10 +273,10 @@ public abstract class AbstractSetAttributesFromFile {
} else {
// id = id.replaceAll("[^A-Za-z0-9_]", "_");
- if (this.addPrefix && this.object.equalsIgnoreCase(REACTION)) {
+ if (this.addPrefix && this.entityType.equals(EntityType.REACTION)) {
if (!id.startsWith("R_"))
id = "R_" + id;
- } else if (this.addPrefix && this.object.equalsIgnoreCase(METABOLITE)) {
+ } else if (this.addPrefix && this.entityType.equals(EntityType.METABOLITE)) {
if (!id.startsWith("M_"))
id = "M_" + id;
}
@@ -352,150 +322,6 @@ public abstract class AbstractSetAttributesFromFile {
*/
public abstract Boolean setAttributes() throws IOException;
- /**
- * <p>Getter for the field <code>colId</code>.</p>
- *
- * @return the colId
- */
- public int getColId() {
- return colId;
- }
-
- /**
- * <p>Setter for the field <code>colId</code>.</p>
- *
- * @param colId the colId to set
- */
- public void setColId(int colId) {
- this.colId = colId;
- }
-
- /**
- * <p>Getter for the field <code>colAttr</code>.</p>
- *
- * @return the colAttr
- */
- public int getColAttr() {
- return colAttr;
- }
-
- /**
- * <p>Setter for the field <code>colAttr</code>.</p>
- *
- * @param colAttr the colAttr to set
- */
- public void setColAttr(int colAttr) {
- this.colAttr = colAttr;
- }
-
- /**
- * <p>getNetwork.</p>
- *
- * @return the network
- */
- public BioNetwork getNetwork() {
- return bn;
- }
-
- /**
- * <p>setNetwork.</p>
- *
- * @param bn the network to set
- */
- public void setNetwork(BioNetwork bn) {
- this.bn = bn;
- }
-
- /**
- * <p>Getter for the field <code>fileIn</code>.</p>
- *
- * @return the fileIn
- */
- public String getFileIn() {
- return fileIn;
- }
-
- /**
- * <p>Setter for the field <code>fileIn</code>.</p>
- *
- * @param fileIn the fileIn to set
- */
- public void setFileIn(String fileIn) {
- this.fileIn = fileIn;
- }
-
- /**
- * <p>Getter for the field <code>commentCharacter</code>.</p>
- *
- * @return the commentCharacter
- */
- public String getCommentCharacter() {
- return commentCharacter;
- }
-
- /**
- * <p>Setter for the field <code>commentCharacter</code>.</p>
- *
- * @param commentCharacter the commentCharacter to set
- */
- public void setCommentCharacter(String commentCharacter) {
- this.commentCharacter = commentCharacter;
- }
-
- /**
- * <p>Getter for the field <code>nSkip</code>.</p>
- *
- * @return the nSkip
- */
- public int getnSkip() {
- return nSkip;
- }
-
- /**
- * <p>Setter for the field <code>nSkip</code>.</p>
- *
- * @param nSkip the nSkip to set
- */
- public void setnSkip(int nSkip) {
- this.nSkip = nSkip;
- }
-
- /**
- * <p>Getter for the field <code>object</code>.</p>
- *
- * @return the object
- */
- public String getObject() {
- return object;
- }
-
- /**
- * <p>Setter for the field <code>object</code>.</p>
- *
- * @param object the object to set
- */
- public void setObject(String object) {
- this.object = object;
- }
-
- /**
- * <p>Setter for the field <code>addPrefix</code>.</p>
- *
- * @param p a {@link java.lang.Boolean} object.
- */
- public void setAddPrefix(Boolean p) {
- this.addPrefix = p;
- }
-
- /**
- * <p>Setter for the field <code>addSuffix</code>.</p>
- *
- * @param s a {@link java.lang.Boolean} object.
- */
- public void setAddSuffix(Boolean s) {
- this.addSuffix = s;
- }
-
/**
* <p>Getter for the field <code>idAttributeMap</code>.</p>
*
@@ -505,32 +331,4 @@ public abstract class AbstractSetAttributesFromFile {
return idAttributeMap;
}
- /**
- * <p>Setter for the field <code>idAttributeMap</code>.</p>
- *
- * @param idAttributeMap the idAttributeMap to set
- */
- public void setIdAttributeMap(HashMap<String, String> idAttributeMap) {
- this.idAttributeMap = idAttributeMap;
- }
-
- /**
- * <p>Getter for the field <code>addPrefix</code>.</p>
- *
- * @return a {@link java.lang.Boolean} object.
- */
- public Boolean getAddPrefix() {
- return addPrefix;
- }
-
- /**
- * <p>Getter for the field <code>addSuffix</code>.</p>
- *
- * @return a {@link java.lang.Boolean} object.
- */
- public Boolean getAddSuffix() {
- return addSuffix;
- }
-
-
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/reactant/ReactantAttributes.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java
similarity index 59%
rename from met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/reactant/ReactantAttributes.java
rename to met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java
index 479c12b4bb1125973e86612d006bc949432b6f4e..8b2ee8d9697b0e4364c24d26b54ad1583dd68b29 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/reactant/ReactantAttributes.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/EntityType.java
@@ -1,5 +1,5 @@
/*
- * Copyright INRAE (2020)
+ * Copyright INRAE (2022)
*
* contact-metexplore@inrae.fr
*
@@ -33,43 +33,8 @@
* knowledge of the CeCILL license and that you accept its terms.
*
*/
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
-package fr.inrae.toulouse.metexplore.met4j_io.annotations.reactant;
-
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant;
-import fr.inrae.toulouse.metexplore.met4j_io.annotations.GenericAttributes;
-
-/**
- * <p>ReactantAttributes class.</p>
- *
- * @author lcottret
- * @version $Id: $Id
- */
-public class ReactantAttributes extends GenericAttributes {
- /** Constant <code>IS_COFACTOR="is_cofactor"</code> */
- public static final String IS_COFACTOR = "is_cofactor";
-
- /**
- * get is cofactor attribute
- *
- * @param reactant a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant} object.
- * @return a {@link java.lang.Boolean} object.
- */
- public static Boolean getIsCofactor(BioReactant reactant) {
- if(reactant.getAttribute(IS_COFACTOR) == null) {
- return false;
- }
- return (Boolean) reactant.getAttribute(IS_COFACTOR);
-
- }
-
- /**
- * Set IsCofactor value
- *
- * @param reactant a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant} object.
- * @param b a boolean.
- */
- public static void setIsCofactor(BioReactant reactant, boolean b) {
- reactant.setAttribute(IS_COFACTOR, b);
- }
+public enum EntityType {
+ REACTION, METABOLITE, GENE, PROTEIN, PATHWAY
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFile.java
index b7c4741015425224a6eb538f7f7bdb16de4c627a..953ad109bb82a011b45564c2352b13a845b3523e 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFile.java
@@ -53,7 +53,7 @@ public class SetBoundsFromFile extends AbstractSetAttributesFromFile {
private BoundsType type;
public SetBoundsFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, BoundsType type) {
- super(colId, colAttr, bn, fileIn, c, nSkip, REACTION, p, false);
+ super(colId, colAttr, bn, fileIn, c, nSkip, EntityType.REACTION, p, false);
this.type = type;
}
@@ -78,12 +78,12 @@ public class SetBoundsFromFile extends AbstractSetAttributesFromFile {
* @return a {@link java.lang.Boolean} object.
* @throws java.io.IOException if any.
*/
- public Boolean setAttributes() throws IOException {
+ public Boolean setAttributes() {
- Boolean flag = true;
+ Boolean flag;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
@@ -97,7 +97,7 @@ public class SetBoundsFromFile extends AbstractSetAttributesFromFile {
for(String id : this.getIdAttributeMap().keySet()) {
n++;
Double bound = Double.parseDouble(this.getIdAttributeMap().get(id));
- BioReaction r = this.getNetwork().getReactionsView().get(id);
+ BioReaction r = this.bn.getReactionsView().get(id);
if(this.type.equals(BoundsType.LOWER)) {
ReactionAttributes.setLowerBound(r, new Flux(bound));
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFile.java
index 47e08ea297a5b794e6af26b7cda7608742ce5996..30615a88aa3f428d4561c03452b13752bdacbd38 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFile.java
@@ -37,7 +37,6 @@
package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
-import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
import java.io.IOException;
@@ -52,35 +51,44 @@ public class SetChargesFromFile extends AbstractSetAttributesFromFile {
/**
* <p>Constructor for SetChargesFromFile.</p>
*
- * @param colId a int.
+ * @param colId a int.
* @param colAttr a int.
- * @param bn a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork} object.
- * @param fileIn a {@link java.lang.String} object.
- * @param c a {@link java.lang.String} object.
- * @param nSkip a int.
- * @param p a {@link java.lang.Boolean} object.
- * @param s a {@link java.lang.Boolean} object.
+ * @param bn a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork} object.
+ * @param fileIn a {@link java.lang.String} object.
+ * @param c a {@link java.lang.String} object.
+ * @param nSkip a int.
+ * @param p a {@link java.lang.Boolean} object.
+ * @param s a {@link java.lang.Boolean} object.
*/
public SetChargesFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s) {
- super(colId, colAttr, bn, fileIn, c, nSkip, "M", p, s);
+ super(colId, colAttr, bn, fileIn, c, nSkip, EntityType.METABOLITE, p, s);
}
/**
* {@inheritDoc}
- *
+ * <p>
* Test the charge
*/
public Boolean testAttribute(String charge) {
- if(StringUtils.isInteger(charge)) {
- return true;
+
+ Boolean flag = true;
+
+ try {
+ Double val = Double.parseDouble(charge);
+ if(val%1 != 0) {
+ flag = false;
+ }
+ } catch (NumberFormatException e) {
+ flag = false;
}
- else {
- System.err.println(charge+ " no in good format (integer)");
- return false;
+
+ if(! flag) {
+ System.err.println("Error : the charge " + charge + " is not an integer");
}
+ return flag;
}
/**
@@ -89,38 +97,39 @@ public class SetChargesFromFile extends AbstractSetAttributesFromFile {
* @return a {@link java.lang.Boolean} object.
* @throws java.io.IOException if any.
*/
- public Boolean setAttributes() throws IOException {
+ public Boolean setAttributes() {
- Boolean flag = true;
+ Boolean flag;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
- if(!flag) {
+ if (!flag) {
return false;
}
int n = 0;
- for(String id : this.getIdAttributeMap().keySet()) {
+ for (String id : this.getIdAttributeMap().keySet()) {
n++;
String charge = this.getIdAttributeMap().get(id);
- try {
- this.getNetwork().getMetabolitesView().get(id).setCharge(Integer.parseInt(charge));
- } catch (NumberFormatException e) {
- System.err.println("Warning : the charge + \""+charge+"\" for the metabolite "+id+" is not an integer");
+ if(this.testAttribute(charge)) {
+ Double dbl = Double.parseDouble(charge);
+ this.bn.getMetabolitesView().get(id).setCharge(dbl.intValue());
+ }
+ else {
+ System.err.println("Warning : the charge + \"" + charge + "\" for the metabolite " + id + " is not an integer");
}
-
}
- System.err.println(n+" attributions");
+ System.err.println(n + " attributions");
return flag;
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFile.java
index 44991c87f520c40e3c68a40da132418b022fa6a3..17a618ecd7f377f999231cc049c12f425415e178 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFile.java
@@ -39,6 +39,9 @@ package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import java.io.IOException;
+import java.util.Arrays;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
/**
* <p>SetEcsFromFile class.</p>
@@ -47,32 +50,48 @@ import java.io.IOException;
* @version $Id: $Id
*/
public class SetEcsFromFile extends AbstractSetAttributesFromFile {
+ private final Pattern patternEC;
+
/**
* <p>Constructor for SetEcsFromFile.</p>
*
- * @param colId number of the column where are the reaction ids
+ * @param colId number of the column where are the reaction ids
* @param colAttr number of the column where are the gpr
- * @param bn BioNetwork
- * @param fileIn tabulated file
- * @param c comment string
- * @param nSkip number of lines to skip at the beginning of the file
- * @param p if true, to match the reactions in the sbml file, the reaction ids in the tabulated file are formatted in the palsson way
- * @param s a {@link java.lang.Boolean} object.
+ * @param bn BioNetwork
+ * @param fileIn tabulated file
+ * @param c comment string
+ * @param nSkip number of lines to skip at the beginning of the file
+ * @param p if true, to match the reactions in the sbml file, the reaction ids in the tabulated file are formatted in the palsson way
+ * @param s a {@link java.lang.Boolean} object.
*/
public SetEcsFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s) {
- super(colId, colAttr, bn, fileIn, c, nSkip, REACTION, p, s);
+ super(colId, colAttr, bn, fileIn, c, nSkip, EntityType.REACTION, p, s);
+
+ patternEC = Pattern.compile("(EC\\s*)*\\d{1}(\\.(\\d{0,3}|-)){0,3}");
}
/**
* {@inheritDoc}
- *
+ * <p>
* Test the ec
- * TODO : to complete
*/
public Boolean testAttribute(String ec) {
- return true;
+ if (ec.isEmpty())
+ return true;
+
+ if(ec.endsWith(";"))
+ return false;
+
+ String[] ecs = ec.split(";");
+
+ System.err.println("ec : "+ec+" l :"+ecs.length);
+
+ return Arrays.stream(ecs).allMatch(e -> {
+ Matcher m = patternEC.matcher(e);
+ return m.matches();
+ });
}
/**
@@ -86,28 +105,30 @@ public class SetEcsFromFile extends AbstractSetAttributesFromFile {
Boolean flag = true;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
- if(!flag) {
+ if (!flag) {
return false;
}
int n = 0;
- for(String id : this.getIdAttributeMap().keySet()) {
+ for (String id : this.getIdAttributeMap().keySet()) {
n++;
- String EC = this.getIdAttributeMap().get(id);
+ String ec = this.getIdAttributeMap().get(id);
- this.getNetwork().getReactionsView().get(id).setEcNumber(EC);
+ if(! ec.isEmpty()) {
+ this.bn.getReactionsView().get(id).setEcNumber(ec);
+ }
}
- System.err.println(n+" reactions processed");
+ System.err.println(n + " reactions processed");
return flag;
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFile.java
index effd5d5b3bc799fbd9b346e3e725d8d34770fc3e..e1f86bcfe43f8665429588eb9e0fb2ab640390b8 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFile.java
@@ -37,6 +37,7 @@
package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
import java.io.IOException;
@@ -62,7 +63,7 @@ public class SetFormulasFromFile extends AbstractSetAttributesFromFile {
*/
public SetFormulasFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s) {
- super(colId, colAttr, bn, fileIn, c, nSkip, "M", p, s);
+ super(colId, colAttr, bn, fileIn, c, nSkip, EntityType.METABOLITE, p, s);
}
@@ -72,7 +73,11 @@ public class SetFormulasFromFile extends AbstractSetAttributesFromFile {
* Test the name
*/
public Boolean testAttribute(String formula) {
- return true;
+ if(formula.isEmpty()) {
+ return true;
+ }
+
+ return StringUtils.checkMetaboliteFormula(formula);
}
/**
@@ -86,7 +91,7 @@ public class SetFormulasFromFile extends AbstractSetAttributesFromFile {
Boolean flag = true;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
@@ -103,7 +108,7 @@ public class SetFormulasFromFile extends AbstractSetAttributesFromFile {
String formula = this.getIdAttributeMap().get(id);
- this.getNetwork().getMetabolitesView().get(id).setChemicalFormula(formula);
+ this.bn.getMetabolitesView().get(id).setChemicalFormula(formula);
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFile.java
index f44322bfcc6e810cdf1963f251240dd542795d9d..26e4ff946b43ea641e82ac8ddf26e68b273985c9 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFile.java
@@ -40,7 +40,6 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.gpr.GPR;
-import fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.MalformedGeneAssociationStringException;
import java.io.IOException;
@@ -66,7 +65,7 @@ public class SetGprsFromFile extends AbstractSetAttributesFromFile {
*/
public SetGprsFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s) {
- super(colId, colAttr, bn, fileIn, c, nSkip, REACTION, p, s);
+ super(colId, colAttr, bn, fileIn, c, nSkip, EntityType.REACTION, p, s);
}
@@ -92,7 +91,7 @@ public class SetGprsFromFile extends AbstractSetAttributesFromFile {
Boolean flag = true;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
e.printStackTrace();
return false;
@@ -103,7 +102,7 @@ public class SetGprsFromFile extends AbstractSetAttributesFromFile {
}
- BioCollection<BioReaction> reactionsView = this.getNetwork().getReactionsView();
+ BioCollection<BioReaction> reactionsView = this.bn.getReactionsView();
for(String id : this.getIdAttributeMap().keySet()) {
@@ -112,7 +111,7 @@ public class SetGprsFromFile extends AbstractSetAttributesFromFile {
String gpr = this.getIdAttributeMap().get(id);
try {
- GPR.createGPRfromString(this.getNetwork(), reaction, gpr);
+ GPR.createGPRfromString(this.bn, reaction, gpr);
} catch (Exception e) {
e.printStackTrace();
System.err.println("GPR badly formatted for reaction "+reaction.getId());
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java
index 4747c0090360750591e0d9ace63378bcde64633e..7f66c2ed2be57693cdd0da487824078ddda05907 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFile.java
@@ -37,7 +37,6 @@
package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import java.io.IOException;
@@ -61,11 +60,11 @@ public class SetNamesFromFile extends AbstractSetAttributesFromFile {
* @param nSkip a int.
* @param p a {@link java.lang.Boolean} object.
* @param s a {@link java.lang.Boolean} object.
- * @param object a {@link java.lang.String} object.
+ * @param entityType a {@link EntityType} object.
*/
- public SetNamesFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s, String object) {
+ public SetNamesFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s, EntityType entityType) {
- super(colId, colAttr, bn, fileIn, c, nSkip, object, p, s);
+ super(colId, colAttr, bn, fileIn, c, nSkip, entityType, p, s);
}
@@ -89,7 +88,7 @@ public class SetNamesFromFile extends AbstractSetAttributesFromFile {
Boolean flag = true;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
@@ -108,20 +107,20 @@ public class SetNamesFromFile extends AbstractSetAttributesFromFile {
String name = this.getIdAttributeMap().get(id);
- if(this.getObject().equalsIgnoreCase(METABOLITE)) {
- object = this.getNetwork().getMetabolitesView().get(id);
+ if(this.entityType.equals(EntityType.METABOLITE)) {
+ object = this.bn.getMetabolitesView().get(id);
}
- else if(this.getObject().equalsIgnoreCase(GENE)) {
- object = this.getNetwork().getGenesView().get(id);
+ else if(this.entityType.equals(EntityType.GENE)) {
+ object = this.bn.getGenesView().get(id);
}
- else if(this.getObject().equalsIgnoreCase(PROTEIN)) {
- object = this.getNetwork().getProteinsView().get(id);
+ else if(this.entityType.equals(EntityType.PROTEIN)) {
+ object = this.bn.getProteinsView().get(id);
}
- else if(this.getObject().equalsIgnoreCase(PATHWAY)) {
- object = this.getNetwork().getPathwaysView().get(id);
+ else if(this.entityType.equals(EntityType.PATHWAY)) {
+ object = this.bn.getPathwaysView().get(id);
}
else {
- object = this.getNetwork().getReactionsView().get(id);
+ object = this.bn.getReactionsView().get(id);
}
object.setName(name);
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFile.java
index f38a7f317816b82d2d2ae9233279c5117789030e..faaaa5000cb76e264fa6eb51199557f2dc8d839e 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFile.java
@@ -78,7 +78,7 @@ public class SetPathwaysFromFile extends AbstractSetAttributesFromFile {
*/
public SetPathwaysFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s, String sep) {
- super(colId, colAttr, bn, fileIn, c, nSkip, REACTION, p, s);
+ super(colId, colAttr, bn, fileIn, c, nSkip, EntityType.REACTION, p, s);
this.sep = sep;
}
@@ -103,7 +103,7 @@ public class SetPathwaysFromFile extends AbstractSetAttributesFromFile {
Boolean flag = true;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
@@ -129,12 +129,12 @@ public class SetPathwaysFromFile extends AbstractSetAttributesFromFile {
String[] pathwayIds = pathwayIdsStr.split(Pattern.quote(sep));
- BioReaction rxn = this.getNetwork().getReactionsView().get(id);
+ BioReaction rxn = this.bn.getReactionsView().get(id);
- BioCollection<BioPathway> oldPathways = this.getNetwork().getPathwaysFromReaction(rxn);
+ BioCollection<BioPathway> oldPathways = this.bn.getPathwaysFromReaction(rxn);
for(BioPathway p : oldPathways) {
- this.getNetwork().removeReactionFromPathway(rxn, p);
+ this.bn.removeReactionFromPathway(rxn, p);
}
for (int i = 0; i < pathwayIds.length; i++) {
@@ -145,13 +145,13 @@ public class SetPathwaysFromFile extends AbstractSetAttributesFromFile {
pathwayId = pathwayId.replaceAll("[^A-Za-z0-9_-]", "_");
BioPathway pathway;
- if (this.getNetwork().getPathwaysView().containsId(pathwayId)) {
- pathway = this.getNetwork().getPathwaysView().get(pathwayId);
+ if (this.bn.getPathwaysView().containsId(pathwayId)) {
+ pathway = this.bn.getPathwaysView().get(pathwayId);
} else {
pathway = new BioPathway(pathwayId);
- this.getNetwork().add(pathway);
+ this.bn.add(pathway);
}
- this.getNetwork().affectToPathway(pathway, rxn);
+ this.bn.affectToPathway(pathway, rxn);
}
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java
index cb0ba72bc817d4721c849e9115e279e54461dfaf..c0572f52d2bdeb942c628e48753de2fb146155a7 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFile.java
@@ -39,7 +39,6 @@ package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioRef;
-import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
import fr.inrae.toulouse.metexplore.met4j_io.refs.IdentifiersOrg;
import java.io.IOException;
@@ -66,17 +65,17 @@ public class SetRefsFromFile extends AbstractSetAttributesFromFile {
* @param p a {@link java.lang.Boolean} object.
* @param s a {@link java.lang.Boolean} object.
* @param ref a {@link java.lang.String} object.
- * @param type a {@link java.lang.String} object.
+ * @param entityType a {@link EntityType} object.
*/
- public SetRefsFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s, String ref, String type) {
- super(colId, colAttr, bn, fileIn, c, nSkip, type, p, s);
+ public SetRefsFromFile(int colId, int colAttr, BioNetwork bn, String fileIn, String c, int nSkip, Boolean p, Boolean s, String ref, EntityType entityType) {
+ super(colId, colAttr, bn, fileIn, c, nSkip, entityType, p, s);
this.ref = ref;
}
/** {@inheritDoc} */
- public Boolean testAttribute(String charge) {
+ public Boolean testAttribute(String attribute) {
return true;
}
@@ -91,7 +90,7 @@ public class SetRefsFromFile extends AbstractSetAttributesFromFile {
Boolean flag = true;
try {
- flag = this.test();
+ flag = this.parseAttributeFile();
} catch (IOException e) {
return false;
}
@@ -103,7 +102,7 @@ public class SetRefsFromFile extends AbstractSetAttributesFromFile {
int n = 0;
if(! IdentifiersOrg.validIdentifiers.contains(ref)) {
- System.err.println("Warning : the identifier "+ref+" is not a valid id in identifiers.org, it will appear only in SBML notes");
+ System.err.println("Warning : the identifier "+ref+" is not a valid id in identifiers.org");
}
for(String id : this.getIdAttributeMap().keySet()) {
@@ -112,20 +111,20 @@ public class SetRefsFromFile extends AbstractSetAttributesFromFile {
BioEntity object;
n++;
- if(this.getObject().equalsIgnoreCase(METABOLITE)) {
- object = this.getNetwork().getMetabolitesView().get(id);
+ if(this.entityType.equals(EntityType.METABOLITE)) {
+ object = this.bn.getMetabolitesView().get(id);
}
- else if(this.getObject().equalsIgnoreCase(GENE)) {
- object = this.getNetwork().getGenesView().get(id);
+ else if(this.entityType.equals(EntityType.GENE)) {
+ object = this.bn.getGenesView().get(id);
}
- else if(this.getObject().equalsIgnoreCase(PROTEIN)) {
- object = this.getNetwork().getProteinsView().get(id);
+ else if(this.entityType.equals(EntityType.PROTEIN)) {
+ object = this.bn.getProteinsView().get(id);
}
- else if(this.getObject().equalsIgnoreCase(PATHWAY)) {
- object = this.getNetwork().getPathwaysView().get(id);
+ else if(this.entityType.equals(EntityType.PATHWAY)) {
+ object = this.bn.getPathwaysView().get(id);
}
else {
- object = this.getNetwork().getReactionsView().get(id);
+ object = this.bn.getReactionsView().get(id);
}
object.addRef(new BioRef("attributesTable", this.ref, this.getIdAttributeMap().get(id), 1));
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2Tab.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2Tab.java
index 06fe02247b61a066841ff1722b92558852acc7ba..63f2160cae77a505925db58bc4a30d4375527327 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2Tab.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2Tab.java
@@ -84,35 +84,40 @@ public class BioNetwork2Tab {
public void write() throws IOException {
FileWriter fw = new FileWriter(this.outputFile);
-
fw.write("#Id\tName\tFormulaIds\tFormulaNames\tEC\tpathways\tgpr\tlb\tub\n");
-
/**
* For ordering reactions in the file and thus making easy the tests and the versioning
*/
TreeMap<String, BioReaction> reactions = new TreeMap<String, BioReaction>(
this.network.getReactionsView().getMapView());
-
for(BioReaction r : reactions.values()) {
-
- String name = r.getName();
- String formulaIds = BioReactionUtils.getEquation(r, false, revSep, irrevSep, true);
- String formulaNames =BioReactionUtils.getEquation(r, true, revSep, irrevSep, true);
- String ec = r.getEcNumber() == null ? "NA" : r.getEcNumber();
- String pathways = BioReactionUtils.getPathwaysString(r, this.network,true, " ; ");
- String gpr = BioReactionUtils.getGPR(this.network, r);
- Flux lowerBound = ReactionAttributes.getLowerBound(r);
- String lb = lowerBound != null ? lowerBound.value.toString() : "NA";
- Flux upperBound = ReactionAttributes.getUpperBound(r);
- String ub = upperBound != null ? upperBound.value.toString() : "NA";
-
- fw.write(r.getId()+"\t"+name+"\t"+formulaIds+"\t"+formulaNames+"\t"+ec+"\t"
- + pathways + "\t" + gpr + "\t" + lb + "\t" +ub+"\n");
-
+ fw.write(this.getReactionLine(r));
}
-
fw.close();
}
+
+
+ /**
+ * Get reaction information in a String
+ * @param r a {@link BioReaction}
+ * @return a String
+ */
+ protected String getReactionLine(BioReaction r) {
+ String name = r.getName();
+ String formulaIds = BioReactionUtils.getEquation(r, false, revSep, irrevSep, true);
+ String formulaNames =BioReactionUtils.getEquation(r, true, revSep, irrevSep, true);
+ String ec = r.getEcNumber() == null ? "NA" : r.getEcNumber();
+ String pathways = BioReactionUtils.getPathwaysString(r, this.network,true, " ; ");
+ String gpr = BioReactionUtils.getGPR(this.network, r);
+ Flux lowerBound = ReactionAttributes.getLowerBound(r);
+ String lb = lowerBound != null ? lowerBound.value.toString() : "NA";
+ Flux upperBound = ReactionAttributes.getUpperBound(r);
+ String ub = upperBound != null ? upperBound.value.toString() : "NA";
+
+ return r.getId()+"\t"+name+"\t"+formulaIds+"\t"+formulaNames+"\t"+ec+"\t"
+ + pathways + "\t" + gpr + "\t" + lb + "\t" +ub+"\n";
+ }
+
}
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetwork.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetwork.java
index 3bcaa4bd97b7be085bd8d6245a18b846e3fe52eb..63622ba555fa64101a1e00123acd44ec2f8d187b 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetwork.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetwork.java
@@ -54,6 +54,8 @@ import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.isDouble;
+
/**
* <p>Tab2BioNetwork class.</p>
@@ -77,22 +79,26 @@ public class Tab2BioNetwork {
private BioNetwork bioNetwork;
private BioCompartment defaultCompartment;
+ private HashSet<String> reactions;
+
+ // To transform metabolite id like this cpd[c] in cpd_c
+ private Pattern cpdWithBracketsPattern = Pattern.compile("^.*(\\[([^\\]]*)\\])$");
/**
* <p>Constructor for Tab2BioNetwork.</p>
*
- * @param networkId a {@link java.lang.String} object.
- * @param colId a int.
- * @param colFormula a int.
- * @param formatReactionCobra a {@link java.lang.Boolean} object.
- * @param formatMetaboliteCobra a {@link java.lang.Boolean} object.
- * @param flagExternal a {@link java.lang.String} object.
- * @param irrReaction a {@link java.lang.String} object.
- * @param revReaction a {@link java.lang.String} object.
+ * @param networkId a {@link java.lang.String} object.
+ * @param colId a int.
+ * @param colFormula a int.
+ * @param formatReactionCobra a {@link java.lang.Boolean} object.
+ * @param formatMetaboliteCobra a {@link java.lang.Boolean} object.
+ * @param flagExternal a {@link java.lang.String} object.
+ * @param irrReaction a {@link java.lang.String} object.
+ * @param revReaction a {@link java.lang.String} object.
* @param addCompartmentFromMetaboliteSuffix a {@link java.lang.Boolean} object.
- * @param defaultCompartment a {@link java.lang.String} object.
- * @param nSkip a int.
+ * @param defaultCompartment a {@link java.lang.String} object.
+ * @param nSkip a int.
*/
public Tab2BioNetwork(String networkId, int colId, int colFormula, Boolean formatReactionCobra, Boolean formatMetaboliteCobra,
String flagExternal, String irrReaction, String revReaction,
@@ -113,6 +119,8 @@ public class Tab2BioNetwork {
this.defaultCompartment = new BioCompartment(this.defaultCompartmentId, this.defaultCompartmentId);
+ reactions = new HashSet<>();
+
}
/**
@@ -137,383 +145,326 @@ public class Tab2BioNetwork {
return false;
}
- String ligne;
+ String line;
int nLines = 0;
- Set<String> reactions = new HashSet<String>();
-
- while ((ligne = br.readLine()) != null) {
+ reactions.clear();
+ while ((line = br.readLine()) != null) {
nLines++;
- if (nLines > this.nSkip && !ligne.startsWith("#")) {
+ Boolean flagLine = this.testLine(line, nLines);
- String[] tab = ligne.split("\\t");
-
- if (tab.length < this.colId || tab.length < this.colFormula) {
- System.err.println("Bad number of columns line " + nLines);
- flag = false;
- } else {
- String id = tab[this.colId];
- String formula = tab[this.colFormula];
+ if (!flagLine) {
+ flag = false;
+ }
+ }
- // remove spaces
- id = id.trim();
- if (id.equals("")) {
- System.err.println("Reaction id empty line " + nLines);
- flag = false;
- }
+ if (flag == false) {
+ System.err.println("Input file badly formatted");
+ } else {
+ System.err.println("The input file looks good and contains " + reactions.size() + " reactions");
+ }
- if (reactions.contains(id)) {
- System.err.println("Duplicated reaction id : " + id + " line " + nLines);
- flag = false;
- } else {
- reactions.add(id);
- }
+ in.close();
- if (!formula.contains(this.irrReaction) && !formula.contains(this.revReaction)) {
- System.err.println("Reaction formula badly formatted line " + nLines + " : " + formula);
- flag = false;
- }
+ return flag;
+ }
- // in some palsson files, the compartment is specified at the beginning of the formula :
- // [c] : g3p + nad + pi <==> 13dpg + h + nadh
- Pattern compartment_Pattern = Pattern.compile("^(\\[.*\\] : ).*$");
- Matcher matcher = compartment_Pattern.matcher(formula);
- if (matcher.matches()) {
- String occurence = matcher.group(1);
+ /**
+ * Check if the line is correct
+ *
+ * @param line
+ * @param nLines
+ * @return
+ */
+ protected Boolean testLine(String line, int nLines) {
- formula = formula.replace(occurence, "");
- }
+ Boolean flag = true;
- String[] tabFormula;
- if (formula.contains(this.revReaction)) {
- tabFormula = formula.split(this.revReaction);
- } else {
- tabFormula = formula.split(this.irrReaction);
- }
+ if (nLines > this.nSkip && !line.startsWith("#")) {
- String leftString = tabFormula[0].trim();
+ String[] tab = line.split("\\t");
- String[] lefts = {};
+ Pattern pattern = Pattern.compile("\\t");
+ Matcher matcherTabulation = pattern.matcher(line);
+ long nbColumns = matcherTabulation.results().count() + 1;
- if (!leftString.equals("")) {
- lefts = leftString.split(" \\+ ");
- }
+ if (nbColumns <= this.colId || nbColumns <= this.colFormula) {
+ System.err.println("Bad number of columns line " + nLines);
+ flag = false;
+ } else {
+ String id = tab[this.colId];
+ String formula = tab[this.colFormula];
- String rightString;
+ // remove spaces
+ id = id.trim();
+ if (id.equals("")) {
+ System.err.println("Reaction id empty line " + nLines);
+ flag = false;
+ }
- if (tabFormula.length == 2) {
- rightString = tabFormula[1].trim();
- } else {
- rightString = "";
- }
+ if (reactions.contains(id)) {
+ System.err.println("Duplicated reaction id : " + id + " line " + nLines);
+ flag = false;
+ } else {
+ reactions.add(id);
+ }
+ if (!formula.contains(this.irrReaction) && !formula.contains(this.revReaction)) {
+ System.err.println("Reaction formula badly formatted line " + nLines + " : " + formula);
+ flag = false;
+ }
- String[] rights = {};
- if (!rightString.equals("")) {
- rights = rightString.split(" \\+ ");
- }
+ // in some palsson files, the compartment is specified at the beginning of the formula :
+ // [c] : g3p + nad + pi <==> 13dpg + h + nadh
+ Pattern compartment_Pattern = Pattern.compile("^(\\[.+\\]\\s*:\\s*).*$");
+ Matcher matcher = compartment_Pattern.matcher(formula);
- for (String cpdId : lefts) {
+ if (matcher.matches()) {
+ String occurence = matcher.group(1);
- cpdId = cpdId.trim();
+ formula = formula.replace(occurence, "");
+ }
- String sto = "1";
+ String[] tabFormula;
+ if (formula.contains(this.revReaction)) {
+ tabFormula = formula.split(this.revReaction);
+ } else {
+ tabFormula = formula.split(this.irrReaction);
+ }
- String[] t = cpdId.split(" ");
+ String leftString = tabFormula[0].trim();
- if (t.length > 2) {
- System.err.println("Some extra spaces present in metabolite " + cpdId + " line " + nLines + " : " + formula);
- flag = false;
- }
+ String[] lefts = {};
- if (t.length == 2) {
- sto = t[0];
- sto = sto.replace("(", "").replace(")", "").trim();
- cpdId = t[1].trim();
- }
+ if (!leftString.equals("")) {
+ lefts = leftString.split(" \\+ ");
+ }
+ String rightString;
- }
+ if (tabFormula.length == 2) {
+ rightString = tabFormula[1].trim();
+ } else {
+ rightString = "";
+ }
- for (String cpdId : rights) {
- cpdId = cpdId.trim();
+ String[] rights = {};
+ if (!rightString.equals("")) {
+ rights = rightString.split(" \\+ ");
+ }
- String sto = "1";
+ for (String cpdId : lefts) {
- String[] t = cpdId.split(" ");
+ cpdId = cpdId.trim();
- if (t.length > 2) {
- System.err.println("Some extra spaces present in metabolite " + cpdId + " line " + nLines + " : " + formula);
- }
+ String[] t = cpdId.split(" ");
- if (t.length == 2) {
- sto = t[0];
- sto = sto.replace("(", "").replace(")", "").trim();
- cpdId = t[1].trim();
- }
+ if (t.length > 2) {
+ System.err.println("Some extra spaces present in metabolite " + cpdId + " line " + nLines + " : " + formula);
+ flag = false;
}
-
}
- }
- }
- if (flag == false) {
- System.err.println("Input file badly formatted");
- } else {
- System.err.println("The input file looks good and contains " + reactions.size() + " reactions");
- }
+ for (String cpdId : rights) {
- in.close();
+ cpdId = cpdId.trim();
+
+ String[] t = cpdId.split(" ");
+ if (t.length > 2) {
+ System.err.println("Some extra spaces present in metabolite " + cpdId + " line " + nLines + " : " + formula);
+ flag = false;
+ }
+ }
+ }
+ }
return flag;
}
-
/**
- * Fill the network from formulas in the file
+ * Parses a line and create entities
*
- * @param fileIn a {@link java.lang.String} object.
- * @return a {@link java.lang.Boolean} object.
- * @throws java.io.IOException if any.
+ * @param line
+ * @param nLines
+ * @return true if everything ok
*/
- public Boolean createReactionsFromFile(String fileIn) throws IOException {
+ protected Boolean parseLine(String line, int nLines) {
Boolean flag = true;
- try {
- flag = this.testFile(fileIn);
- } catch (IOException e) {
- return false;
- }
-
- if (!flag) {
- return false;
- }
-
- FileInputStream in = new FileInputStream(fileIn);
- InputStreamReader ipsr = new InputStreamReader(in);
- BufferedReader br = new BufferedReader(ipsr);
- String ligne;
+ if (nLines > this.nSkip && !line.startsWith("#")) {
- int nLines = 0;
+ String[] tab = line.split("\\t");
-
- if (!this.addCompartmentFromMetaboliteSuffix) {
- this.bioNetwork.add(defaultCompartment);
- }
-
-
- while ((ligne = br.readLine()) != null) {
-
- nLines++;
-
- if (nLines > this.nSkip && !ligne.startsWith("#")) {
-
- String[] tab = ligne.split("\\t");
-
- String id = tab[this.colId].trim();
+ String id = tab[this.colId].trim();
// id = id.replaceAll("[^A-Za-z0-9_]", "_");
// id = StringUtils.sbmlEncode(id);
- String formula = tab[this.colFormula];
+ String formula = tab[this.colFormula];
- BioReaction reaction;
+ BioReaction reaction;
- String reactionId = id;
- if (this.formatReactionCobra) {
- reactionId = StringUtils.formatReactionIdCobra(id);
- }
+ String reactionId = id;
+ if (this.formatReactionCobra) {
+ reactionId = StringUtils.formatReactionIdCobra(id);
+ }
- reaction = new BioReaction(reactionId);
+ reaction = new BioReaction(reactionId);
- this.bioNetwork.add(reaction);
+ this.bioNetwork.add(reaction);
- // in some palsson files, the compartment is specified at the beginning of the formula :
- // [c] : g3p + nad + pi <==> 13dpg + h + nadh
- Pattern compartment_Pattern = Pattern.compile("^(\\[.*\\] : ).*$");
- Matcher matcher = compartment_Pattern.matcher(formula);
+ // in some palsson files, the compartment is specified at the beginning of the formula :
+ // [c] : g3p + nad + pi <==> 13dpg + h + nadh
+ Pattern compartment_Pattern = Pattern.compile("^(\\[(.+)\\]\\s*:\\s*).*$");
+ Matcher matcher = compartment_Pattern.matcher(formula);
- String compartmentId = "";
+ String compartmentId = "";
- if (matcher.matches()) {
- String occurence = matcher.group(1);
+ if (matcher.matches()) {
+ String occurence = matcher.group(1);
- String[] tabOcc = occurence.split(":");
+ //String[] tabOcc = occurence.split(":");
- compartmentId = tabOcc[0].replace("[", "").replace("]", "").trim();
+ //compartmentId = tabOcc[0].replace("[", "").replace("]", "").trim();
+ compartmentId = matcher.group(2);
- formula = formula.replace(occurence, "");
- }
+ formula = formula.replace(occurence, "");
+ }
- String[] tabFormula;
- if (formula.contains(this.revReaction)) {
- reaction.setReversible(true);
- tabFormula = formula.split(this.revReaction);
- } else {
- reaction.setReversible(false);
- tabFormula = formula.split(this.irrReaction);
- }
+ String[] tabFormula;
+ if (formula.contains(this.revReaction)) {
+ reaction.setReversible(true);
+ tabFormula = formula.split(this.revReaction);
+ } else {
+ reaction.setReversible(false);
+ tabFormula = formula.split(this.irrReaction);
+ }
- String leftString = tabFormula[0].trim();
+ String leftString = tabFormula[0].trim();
- List<String> lefts = new ArrayList<String>();
+ List<String> lefts = new ArrayList<>();
- if (!leftString.equals("")) {
- lefts = Arrays.asList(leftString.split(" \\+"));
- }
+ if (!leftString.equals("")) {
+ lefts = Arrays.asList(leftString.split(" \\+"));
+ }
- String rightString;
+ String rightString = tabFormula[1].trim();
- if (tabFormula.length == 2) {
- rightString = tabFormula[1].trim();
- } else {
- rightString = "";
- }
+ List<String> rights = new ArrayList<>();
- List<String> rights = new ArrayList<String>();
- if (!rightString.equals("")) {
- rights = Arrays.asList(rightString.split(" \\+ "));
- }
+ if (!rightString.equals("")) {
+ rights = Arrays.asList(rightString.split(" \\+ "));
+ }
- // To transform metabolite id like this cpd[c] in cpd_c
- Pattern cpd_Pattern = Pattern.compile("^.*(\\[([^\\]]*)\\])$");
+ for (String cpdId : lefts) {
+ parseReactant(reaction, compartmentId, cpdId, false);
+ }
- // To see if the id ends with _something
-// Pattern cpt_Pattern = Pattern.compile("^.*_([^_])*$");
+ for (String cpdId : rights) {
+ parseReactant(reaction, compartmentId, cpdId, true);
+ }
- // Flag to check if external metabolite ids have been created
-// Boolean flagExt = true;
-//
-// while (flagExt) {
-// flagExt = false;
+ }
+ return flag;
+ }
- for (String cpdId : lefts) {
+ /**
+ * Parse
+ * @param reaction
+ * @param compartmentId
+ * @param cpdId
+ * @param rightSide
+ */
+ private void parseReactant(BioReaction reaction, String compartmentId, String cpdId, Boolean rightSide) {
+ cpdId = cpdId.trim();
- cpdId = cpdId.trim();
+ String sto = "1";
- String sto = "1";
+ String[] t = cpdId.split(" ");
- String[] t = cpdId.split(" ");
+ if (t.length == 2) {
+ sto = t[0];
+ sto = sto.replace("(", "").replace(")", "").trim();
+ cpdId = t[1].trim();
+ }
- if (t.length == 2) {
- sto = t[0];
- sto = sto.replace("(", "").replace(")", "").trim();
- cpdId = t[1].trim();
- }
+ Matcher matcherCpd = cpdWithBracketsPattern.matcher(cpdId);
- Matcher matcherCpd = cpd_Pattern.matcher(cpdId);
+ boolean addCompartment = false;
- if (matcherCpd.matches()) {
- cpdId = cpdId.replace(matcherCpd.group(1), "_" + matcherCpd.group(2));
- } else {
- if (!compartmentId.equals("") && !leftString.equals("")) {
- cpdId = cpdId + "_" + compartmentId;
- }
- }
+ if (matcherCpd.matches()) {
+ cpdId = cpdId.replace(matcherCpd.group(1), "_" + matcherCpd.group(2));
+ addCompartment = true;
+ } else {
+ if (!compartmentId.equals("") ) {
+ addCompartment = true;
+ cpdId = cpdId + "_" + compartmentId;
+ }
+ }
- Double stoDouble = 1.0;
- if(fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.isDouble(sto)) {
- stoDouble = Double.parseDouble(sto);
- }
+ Double stoDouble = 1.0;
+ if (isDouble(sto)) {
+ stoDouble = Double.parseDouble(sto);
+ }
-// cpdId = cpdId.replaceAll("[^A-Za-z0-9_]", "_");
-
- BioReactant reactant = this.initReactant(cpdId, stoDouble);
-
- this.bioNetwork.affectLeft(reaction, reactant);
-
- // We create the corresponding external metabolite
-// if(rightString.equals("")) {
-// String cpdExternalId = cpdId+this.flagExternal;
-//
-// Matcher matcherCpt = cpt_Pattern.matcher(cpdId);
-//
-// // If the metabolite contains compartment id in its suffix, we replace
-// // it in the external metabolite id by the external suffix
-//
-// if(matcherCpt.matches()) {
-// String cptId = matcherCpt.group(1);
-// if(this.getBioNetwork().getCompartments().containsKey(cptId)) {
-// cpdExternalId = cpdId.replace("_"+cptId, this.flagExternal);
-// }
-// }
-//
-// rights.add(cpdExternalId);
-// }
- }
+ this.initReactant(reaction, cpdId, stoDouble, rightSide, addCompartment);
+ }
- for (String cpdId : rights) {
- cpdId = cpdId.trim();
+ /**
+ * Fill the network from formulas in the file
+ *
+ * @param fileIn a {@link java.lang.String} object.
+ * @return a {@link java.lang.Boolean} object.
+ * @throws java.io.IOException if any.
+ */
+ public Boolean createReactionsFromFile(String fileIn) throws IOException {
- String sto = "1";
+ Boolean flag;
- String[] t = cpdId.split(" ");
+ try {
+ flag = this.testFile(fileIn);
+ } catch (IOException e) {
+ return false;
+ }
- if (t.length == 2) {
- sto = t[0];
- sto = sto.replace("(", "").replace(")", "").trim();
- cpdId = t[1].trim();
- }
+ if (!flag) {
+ return false;
+ }
- Matcher matcherCpd = cpd_Pattern.matcher(cpdId);
+ FileInputStream in = new FileInputStream(fileIn);
+ InputStreamReader ipsr = new InputStreamReader(in);
+ BufferedReader br = new BufferedReader(ipsr);
+ String line;
- if (matcherCpd.matches()) {
- cpdId = cpdId.replace(matcherCpd.group(1), "_" + matcherCpd.group(2));
- } else {
- if (!compartmentId.equals("") && !rightString.equals("")) {
- cpdId = cpdId + "_" + compartmentId;
- }
- }
+ int nLines = 0;
-// cpdId = cpdId.replaceAll("[^A-Za-z0-9_]", "_");
+ if (!this.addCompartmentFromMetaboliteSuffix) {
+ this.bioNetwork.add(defaultCompartment);
+ }
- Double stoDouble = 1.0;
- if(fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.isDouble(sto)) {
- stoDouble = Double.parseDouble(sto);
- }
+ reactions.clear();
-// cpdId = cpdId.replaceAll("[^A-Za-z0-9_]", "_");
-
- BioReactant reactant = this.initReactant(cpdId, stoDouble);
-
- this.bioNetwork.affectRight(reaction, reactant);
-
- // We create the corresponding external metabolite
-// if(leftString.equals("")) {
-// String cpdExternalId = cpdId+this.flagExternal;
-//
-// Matcher matcherCpt = cpt_Pattern.matcher(cpdId);
-//
-// // If the metabolite contains compartment id in its suffix, we replace
-// // it in the external metabolite id by the external suffix
-//
-// if(matcherCpt.matches()) {
-// String cptId = matcherCpt.group(1);
-// if(this.getBioNetwork().getCompartments().containsKey(cptId)) {
-// cpdExternalId = cpdId.replace("_"+cptId, this.flagExternal);
-// }
-// }
-//
-// lefts.add(cpdExternalId);
-// flagExt=true;
-// }
-// }
- }
+ while ((line = br.readLine()) != null) {
- }
+ nLines++;
+ Boolean flagLine = this.parseLine(line, nLines);
+
+ if (!flagLine) {
+ flag = false;
+ }
}
br.close();
@@ -530,11 +481,11 @@ public class Tab2BioNetwork {
* @param cpdId
* @return
*/
- private BioReactant initReactant(String cpdId, Double coeff) {
+ private void initReactant(BioReaction reaction, String cpdId, Double coeff, Boolean rightSide, Boolean addCompartment) {
BioCompartment compartment = defaultCompartment;
- if (this.addCompartmentFromMetaboliteSuffix) {
+ if (this.addCompartmentFromMetaboliteSuffix || addCompartment) {
String[] t = cpdId.split("_");
String compartmentId = this.defaultCompartment.getId();
@@ -552,32 +503,41 @@ public class Tab2BioNetwork {
this.bioNetwork.add(compartment);
}
}
-
-
- if (this.formatMetaboliteCobra) {
- cpdId = StringUtils.formatMetaboliteIdCobra(cpdId, compartment.getId());
+ else {
+ if(! this.bioNetwork.contains(compartment)) {
+ this.bioNetwork.add(compartment);
}
+ }
- BioMetabolite cpd;
- BioCollection<BioMetabolite> metabolitesView = this.bioNetwork.getMetabolitesView();
- if (metabolitesView.containsId(cpdId)) {
- cpd = metabolitesView.get(cpdId);
- } else {
- cpd = new BioMetabolite(cpdId);
- this.bioNetwork.add(cpd);
- }
- this.bioNetwork.affectToCompartment(compartment, cpd);
+ if (this.formatMetaboliteCobra) {
+ cpdId = StringUtils.formatMetaboliteIdCobra(cpdId, compartment.getId());
+ }
- if (cpd.getId().endsWith(this.flagExternal)) {
- MetaboliteAttributes.setBoundaryCondition(cpd, true);
- } else {
- MetaboliteAttributes.setBoundaryCondition(cpd, false);
- }
+ BioMetabolite cpd;
+ BioCollection<BioMetabolite> metabolitesView = this.bioNetwork.getMetabolitesView();
+ if (metabolitesView.containsId(cpdId)) {
+ cpd = metabolitesView.get(cpdId);
+ } else {
+ cpd = new BioMetabolite(cpdId);
+ this.bioNetwork.add(cpd);
+ }
+ this.bioNetwork.affectToCompartment(compartment, cpd);
+
+ if (cpd.getId().endsWith(this.flagExternal)) {
+ MetaboliteAttributes.setBoundaryCondition(cpd, true);
+ } else {
+ MetaboliteAttributes.setBoundaryCondition(cpd, false);
+ }
+ if (!rightSide) {
+ this.bioNetwork.affectLeft(reaction, coeff, compartment, cpd);
+ } else {
+ this.bioNetwork.affectRight(reaction, coeff, compartment, cpd);
+ }
- return new BioReactant(cpd, coeff, compartment );
+ return;
}
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/reactant/ReactantAttributesTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/gpr/GPRTest.java
similarity index 58%
rename from met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/reactant/ReactantAttributesTest.java
rename to met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/gpr/GPRTest.java
index 9870a1cddd9328990295f42eed63946e1e8d7551..fdd871409aa0ed20f4e69cf0ece25fa5682d42c3 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/reactant/ReactantAttributesTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/gpr/GPRTest.java
@@ -1,5 +1,5 @@
/*
- * Copyright INRAE (2020)
+ * Copyright INRAE (2022)
*
* contact-metexplore@inrae.fr
*
@@ -34,56 +34,42 @@
*
*/
-package fr.inrae.toulouse.metexplore.met4j_io.annotations.reactant;
+package fr.inrae.toulouse.metexplore.met4j_io.annotations.gpr;
-import static org.junit.Assert.*;
-
-import org.junit.Before;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.MalformedGeneAssociationStringException;
import org.junit.Test;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant;
-import fr.inrae.toulouse.metexplore.met4j_io.annotations.GenericAttributes;
-
-public class ReactantAttributesTest {
-
- BioReactant r;
- BioCompartment c;
- BioMetabolite m;
-
- @Before
- public void init() {
- m = new BioMetabolite("m");
- c = new BioCompartment("c");
-
- r = new BioReactant(m, 1.0, c);
- }
-
- @Test
- public void testGetConstant() {
-
- assertFalse(ReactantAttributes.getConstant(r));
+import static org.junit.Assert.*;
- r.setAttribute(GenericAttributes.CONSTANT, false);
+public class GPRTest {
- assertFalse(ReactantAttributes.getConstant(r));
+ @Test
+ public void createGPRfromString() throws MalformedGeneAssociationStringException {
- r.setAttribute(GenericAttributes.CONSTANT, true);
+ BioNetwork network = new BioNetwork();
+ BioEnzyme e1 = new BioEnzyme("e1");
+ BioEnzyme e2 = new BioEnzyme("e2");
+ BioProtein p1 = new BioProtein("p1");
+ BioProtein p2 = new BioProtein("p2");
+ BioGene g1 = new BioGene("g1");
+ BioGene g2 = new BioGene("g2");
+ BioReaction r1 = new BioReaction("r1");
- assertTrue(ReactantAttributes.getConstant(r));
+ network.add(e1, e2, p1, p2, g1, g2, r1);
- }
+ network.affectGeneProduct(p1, g1);
+ network.affectSubUnit(e1, 1.0, p1);
+ network.affectEnzyme(r1, e1);
- @Test
- public void testSetConstant() {
+ GPR.createGPRfromString(network, r1, "G3 AND G4");
- ReactantAttributes.setConstant(r, false);
- assertFalse((Boolean) r.getAttribute(GenericAttributes.CONSTANT));
+ assertEquals(1, r1.getEnzymesView().size());
- ReactantAttributes.setConstant(r, true);
- assertTrue((Boolean) r.getAttribute(GenericAttributes.CONSTANT));
+ assertEquals(2, network.getGenesFromReactions(r1).size());
- }
+ assertTrue(network.getGenesFromReactions(r1).containsId("G3"));
+ assertTrue(network.getGenesFromReactions(r1).containsId("G4"));
-}
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetworkTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetworkTest.java
index af0bd86c0c85ff3607896bc29da01b4c55a329a7..a40074b221fb6fecaef309a7d98446923509fb9c 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetworkTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlToBioNetworkTest.java
@@ -78,7 +78,6 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.compartment.BioCompartmentType;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.compartment.CompartmentAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.network.NetworkAttributes;
-import fr.inrae.toulouse.metexplore.met4j_io.annotations.reactant.ReactantAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.Flux;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.SbmlAnnotation;
@@ -521,22 +520,16 @@ public class JsbmlToBioNetworkTest {
assertNotNull(m1Ref);
- assertTrue(ReactantAttributes.getConstant(m1Ref));
-
BioReactant m2Ref = parser.getNetwork().getRightReactants(reaction1).stream()
.filter((x) -> x.getPhysicalEntity().getId().compareTo("m2") == 0).findFirst().orElse(null);
assertNotNull(m2Ref);
- assertFalse(ReactantAttributes.getConstant(m2Ref));
-
BioReactant m1RefBis = parser.getNetwork().getRightReactants(reaction1).stream()
.filter((x) -> x.getPhysicalEntity().getId().compareTo("m1") == 0).findFirst().orElse(null);
assertNotNull(m1RefBis);
- assertFalse(ReactantAttributes.getConstant(m1RefBis));
-
// Test sbo term
String sboTerm = ReactionAttributes.getSboTerm(reaction1);
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFileTest.java
index 970e31d3ac0fe12320ee95c1155b83c46ddcc3d8..d04b90e7759dc4cc0053557637d057eba0b4abde 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFileTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetBoundsFromFileTest.java
@@ -40,7 +40,6 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.Flux;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.ReactionAttributes;
-import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import org.mockito.Mockito;
@@ -207,7 +206,7 @@ public class SetBoundsFromFileTest {
public void setLowerBounds() throws IOException {
SetBoundsFromFile c = Mockito.spy(new SetBoundsFromFile(0, 1, network, "", "#", 1, false, BoundsType.LOWER));
- Mockito.doReturn(true).when(c).test();
+ Mockito.doReturn(true).when(c).parseAttributeFile();
String line = "r1\t12.0\n";
@@ -229,7 +228,7 @@ public class SetBoundsFromFileTest {
public void setUpperBounds() throws IOException {
SetBoundsFromFile c = Mockito.spy(new SetBoundsFromFile(0, 1, network, "", "#", 1, false, BoundsType.UPPER));
- Mockito.doReturn(true).when(c).test();
+ Mockito.doReturn(true).when(c).parseAttributeFile();
String line = "r1\t12.0\n";
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..44283bda12234a0844b0f095528ad4aec06b49ed
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetChargesFromFileTest.java
@@ -0,0 +1,196 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetChargesFromFileTest {
+
+
+ private static BioNetwork network;
+ private static BioMetabolite m;
+ private static BioMetabolite m_cpd_c;
+
+
+ @BeforeClass
+ public static void init() {
+ network = new BioNetwork();
+ m = new BioMetabolite("m");
+ BioMetabolite m_cpd = new BioMetabolite("M_cpd");
+ BioMetabolite cpd_c = new BioMetabolite("cpd_c");
+ m_cpd_c = new BioMetabolite("M_cpd_c");
+
+ BioCompartment c = new BioCompartment("c");
+ network.add(m, m_cpd, cpd_c, c, m_cpd_c);
+
+ network.affectToCompartment(c, cpd_c, m_cpd_c);
+
+ }
+
+ @Test
+ public void testAttribute() {
+ SetChargesFromFile app = new SetChargesFromFile(1, 2, network, "", "#", 1, false, false);
+
+ assertTrue(app.testAttribute("2"));
+ assertTrue(app.testAttribute("2.0"));
+ assertFalse(app.testAttribute("NA"));
+ }
+
+
+ @Test
+ public void testParseLine() {
+ SetChargesFromFile app = new SetChargesFromFile(0, 1, network, "", "#", 0, false, false);
+ String line = "m\t2\n";
+
+ Boolean flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ assertTrue(app.getIdAttributeMap().containsKey("m"));
+
+ line = "something\t2\n";
+
+ flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ // A line with an absent metabolite is accepted but not registered in the map
+ assertFalse(app.getIdAttributeMap().containsKey("something"));
+
+ }
+
+ @Test
+ public void testParseLinePrefixMetabolite() {
+
+ SetChargesFromFile app = new SetChargesFromFile(0, 1, network, "", "#", 0, true, false);
+
+ String line = "cpd\t2\n";
+
+ Boolean flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ assertTrue(app.getIdAttributeMap().containsKey("M_cpd"));
+
+ }
+
+ @Test
+ public void testParseLineSuffixMetabolite() {
+
+ SetChargesFromFile app = new SetChargesFromFile(0, 1, network, "", "#", 0, false, true);
+
+ String line = "cpd\t2\n";
+
+ Boolean flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ assertTrue(app.getIdAttributeMap().containsKey("cpd_c"));
+
+ }
+
+ @Test
+ public void testParseLineCompartmentBracketsMetabolite() {
+
+ SetChargesFromFile app = new SetChargesFromFile(0, 1, network, "", "#", 0, false, false);
+
+ String line = "cpd[c]\t2\n";
+
+ Boolean flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ assertTrue(app.getIdAttributeMap().containsKey("cpd_c"));
+
+ app = new SetChargesFromFile(0, 1, network, "", "#", 0, false, true);
+
+ flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ assertFalse(app.getIdAttributeMap().containsKey("cpd_c"));
+ }
+
+
+ @Test
+ public void testParseLineSuffixPrefix() {
+
+ SetChargesFromFile app = new SetChargesFromFile(0, 1, network, "", "#", 0, true, true);
+
+ String line = "cpd\t2\n";
+
+ Boolean flag = app.parseLine(line, 1);
+ assertTrue(flag);
+
+ assertTrue(app.getIdAttributeMap().containsKey("M_cpd_c"));
+
+ flag = app.parseLine(line, 1);
+ assertFalse(flag);
+
+ }
+
+ @Test
+ public void setAttributes() throws IOException {
+
+ SetChargesFromFile app = Mockito.spy(new SetChargesFromFile(0, 1, network, "", "#", 0, true, true));
+
+ Mockito.doReturn(true).when(app).parseAttributeFile();
+ String line = "cpd\t2\n";
+
+ app.parseLine(line, 1);
+
+ Boolean flag = app.setAttributes();
+
+ assertTrue(flag);
+
+ assertEquals(2, m_cpd_c.getCharge(), 0.0);
+
+ }
+
+ @Test(expected = IllegalArgumentException.class)
+ public void constructorBadColumnId() throws IOException {
+ SetChargesFromFile app = Mockito.spy(new SetChargesFromFile(-1, 1, network, "", "#", 0, true, true));
+ }
+
+ @Test(expected = IllegalArgumentException.class)
+ public void constructorBadColumnAttribute() throws IOException {
+ SetChargesFromFile app = Mockito.spy(new SetChargesFromFile(1, -1, network, "", "#", 0, true, true));
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..ba0a9b1c01e7e862b24fe2af5d034a06e5aa80de
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetEcsFromFileTest.java
@@ -0,0 +1,144 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetEcsFromFileTest {
+
+
+ private SetEcsFromFile setEcsFromFile;
+ private BioNetwork network;
+ private BioReaction r;
+ private String line;
+
+ @Before
+ public void init() throws IOException {
+
+ network = new BioNetwork();
+ r = new BioReaction("r");
+ network.add(r);
+
+ line = "r\t1.2.3.5\n";
+
+ setEcsFromFile = Mockito.spy(new SetEcsFromFile(0, 1, network, "", "", 0, false, false));
+
+ Mockito.doReturn(true).when(setEcsFromFile).parseAttributeFile();
+
+
+ }
+
+ @Test
+ public void testAttributeNormal() {
+ String ec = "1.2.3.4";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+ ec = "1.2.3.134";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+ ec = "1.2.3.-";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+ ec = "1.2.3";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+ ec = "EC1.2.3.134";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+ ec = "EC 1.2.3.134";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+
+ ec = "1.2.3.4;1.4.32";
+ assertTrue(setEcsFromFile.testAttribute(ec));
+
+
+ }
+
+ @Test
+ public void testAttributeEmpty() {
+ String ec = "";
+
+ assertTrue(setEcsFromFile.testAttribute(ec));
+ }
+
+ @Test
+ public void testAttributeBadlyFormated() {
+ String ec = "NA";
+
+ assertFalse(setEcsFromFile.testAttribute(ec));
+
+ ec = "1.2.3.4|1.4.32";
+ assertFalse(setEcsFromFile.testAttribute(ec));
+
+ ec = "1.2.3.4;NA";
+ assertFalse(setEcsFromFile.testAttribute(ec));
+
+ ec = "1.2.3.4;";
+ assertFalse(setEcsFromFile.testAttribute(ec));
+ }
+
+ @Test
+ public void setAttributes() throws IOException {
+
+ Boolean flag = setEcsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setEcsFromFile.setAttributes();
+
+ assertEquals("1.2.3.5", r.getEcNumber());
+
+
+ }
+
+ @Test
+ public void setAttributeEmpty() throws IOException {
+ line = "r\t\ttruc\n";
+
+ Boolean flag = setEcsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setEcsFromFile.setAttributes();
+
+ assertEquals(null, r.getEcNumber());
+
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..b08d4ce310b537245369195f6d96b7db29f06397
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetFormulasFromFileTest.java
@@ -0,0 +1,130 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetFormulasFromFileTest {
+
+ private BioNetwork network;
+ private BioMetabolite metabolite;
+ private SetFormulasFromFile setFormulasFromFile;
+ private String line;
+
+ @Before
+ public void init() throws IOException {
+
+ network = new BioNetwork();
+ metabolite = new BioMetabolite("m");
+ network.add(metabolite);
+
+ setFormulasFromFile = Mockito.spy(new SetFormulasFromFile(0, 1, network, "", "#", 0, false, false));
+
+ Mockito.doReturn(true).when(setFormulasFromFile).parseAttributeFile();
+
+
+ line = "m\tCH3";
+ }
+
+
+ @Test
+ public void testAttribute() {
+
+ String s = "C2H3O6";
+
+ assertTrue(setFormulasFromFile.testAttribute(s));
+
+ s = "CH3O6";
+
+ assertTrue(setFormulasFromFile.testAttribute(s));
+
+ }
+
+ @Test
+ public void testAttributeEmpty() {
+
+ String s = "";
+
+ assertTrue(setFormulasFromFile.testAttribute(s));
+
+ }
+
+ @Test
+ public void testAttributeBadlyFormatted() {
+
+ String s = "tr";
+
+ assertFalse(setFormulasFromFile.testAttribute(s));
+
+ }
+
+ @Test
+ public void setAttributes() throws IOException {
+
+ Boolean flag = setFormulasFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setFormulasFromFile.setAttributes();
+
+ assertEquals("CH3", metabolite.getChemicalFormula());
+
+ }
+
+ @Test
+ public void setEmptyAttribute() throws IOException {
+
+ String line = "m\t\n";
+
+ Boolean flag = setFormulasFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setFormulasFromFile.setAttributes();
+
+ assertEquals(null, metabolite.getChemicalFormula());
+
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..d502a5725a39b74e7e636814ff19aac8c62dd9a9
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetGprsFromFileTest.java
@@ -0,0 +1,108 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+
+public class SetGprsFromFileTest {
+
+
+ private BioNetwork network;
+ private BioReaction reaction;
+ private SetGprsFromFile setGprsFromFile;
+
+ @Before
+ public void init() throws IOException {
+ network = new BioNetwork();
+ reaction = new BioReaction("r");
+ network.add(reaction);
+
+ setGprsFromFile = Mockito.spy(new SetGprsFromFile(0, 1, network, "", "", 0, false, false));
+
+ Mockito.doReturn(true).when(setGprsFromFile).parseAttributeFile();
+ }
+
+ @Test
+ public void testAttribute() {
+
+ assertTrue(setGprsFromFile.testAttribute("anything"));
+
+ }
+
+ @Test
+ public void setAttributes() throws IOException {
+
+ String line = "r\t(G1 and G2) or G3\n";
+
+ Boolean flag = setGprsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setGprsFromFile.setAttributes();
+
+ assertEquals(2, network.getEnzymesView().size());
+ assertEquals(3, network.getGenesView().size());
+ assertEquals(3, network.getProteinsView().size());
+ assertEquals(2, reaction.getEnzymesView().size());
+ }
+
+ @Test
+ public void setBadAttributes() throws IOException {
+
+ String line = "r\t(G1 and G2 or G3\n";
+
+ Boolean flag = setGprsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setGprsFromFile.setAttributes();
+
+ assertEquals(0, network.getEnzymesView().size());
+ assertEquals(0, network.getGenesView().size());
+ assertEquals(0, network.getProteinsView().size());
+ assertEquals(0, reaction.getEnzymesView().size());
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..2dbb97acbc3dbd435e5781db99a42be00d4f6b34
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetNamesFromFileTest.java
@@ -0,0 +1,171 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetNamesFromFileTest {
+
+ private BioNetwork network;
+ private BioReaction reaction;
+ private BioMetabolite metabolite;
+ private BioProtein protein;
+ private BioGene gene;
+ private BioPathway pathway;
+
+ @Before
+ public void init() {
+ network = new BioNetwork();
+ reaction = new BioReaction("r");
+ metabolite = new BioMetabolite("m");
+ protein = new BioProtein("p");
+ gene = new BioGene("g");
+ pathway = new BioPathway("pathway");
+
+ network.add(reaction, metabolite, protein, gene, pathway);
+
+
+ }
+
+
+ @Test
+ public void testAttribute() {
+ SetNamesFromFile setNamesFromFile = new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.REACTION);
+
+ assertTrue(setNamesFromFile.testAttribute("anything"));
+ }
+
+ @Test
+ public void setAttributesReaction() throws IOException {
+
+ SetNamesFromFile setNamesFromFile = Mockito.spy(new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.REACTION));
+ Mockito.doReturn(true).when(setNamesFromFile).parseAttributeFile();
+
+ String line = "r\tmyreaction\n";
+
+ Boolean flag = setNamesFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setNamesFromFile.setAttributes();
+
+ assertEquals("myreaction", reaction.getName());
+
+ }
+
+ @Test
+ public void setAttributesMetabolite() throws IOException {
+
+ SetNamesFromFile setNamesFromFile = Mockito.spy(new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.METABOLITE));
+ Mockito.doReturn(true).when(setNamesFromFile).parseAttributeFile();
+
+ String line = "m\tmymetabolite\n";
+
+ Boolean flag = setNamesFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setNamesFromFile.setAttributes();
+
+ assertEquals("mymetabolite", metabolite.getName());
+
+ }
+
+ @Test
+ public void setAttributesProtein() throws IOException {
+
+ SetNamesFromFile setNamesFromFile = Mockito.spy(new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.PROTEIN));
+ Mockito.doReturn(true).when(setNamesFromFile).parseAttributeFile();
+
+ String line = "p\tmyprotein\n";
+
+ Boolean flag = setNamesFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setNamesFromFile.setAttributes();
+
+ assertEquals("myprotein", protein.getName());
+
+ }
+
+ @Test
+ public void setAttributesGene() throws IOException {
+
+ SetNamesFromFile setNamesFromFile = Mockito.spy(new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.GENE));
+ Mockito.doReturn(true).when(setNamesFromFile).parseAttributeFile();
+
+ String line = "g\tmygene\n";
+
+ Boolean flag = setNamesFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setNamesFromFile.setAttributes();
+
+ assertEquals("mygene", gene.getName());
+
+ }
+
+ @Test
+ public void setAttributesPathway() throws IOException {
+
+ SetNamesFromFile setNamesFromFile = Mockito.spy(new SetNamesFromFile(0, 1, network, "", "", 0, false, false, EntityType.PATHWAY));
+ Mockito.doReturn(true).when(setNamesFromFile).parseAttributeFile();
+
+ String line = "pathway\tmypathway\n";
+
+ Boolean flag = setNamesFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setNamesFromFile.setAttributes();
+
+ assertEquals("mypathway", pathway.getName());
+
+ }
+
+
+
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8ded386a018a8ac8a725d46808ccdc5976e05b3d
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetPathwaysFromFileTest.java
@@ -0,0 +1,119 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioPathway;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetPathwaysFromFileTest {
+
+
+ private BioNetwork network;
+ private BioReaction reaction;
+ private SetPathwaysFromFile setPathwaysFromFile;
+ private BioReaction reaction2;
+
+ @Before
+ public void init() throws IOException {
+ network = new BioNetwork();
+ reaction = new BioReaction("r");
+ reaction2 = new BioReaction("r2");
+
+ network.add(reaction, reaction2);
+ setPathwaysFromFile = Mockito.spy(new SetPathwaysFromFile(0, 1, network, "", "", 0, false, false, ";"));
+
+ Mockito.doReturn(true).when(setPathwaysFromFile).parseAttributeFile();
+
+ }
+
+ @Test
+ public void testAttribute() {
+
+ assertTrue(setPathwaysFromFile.testAttribute("anything"));
+
+ }
+
+ @Test
+ public void setAttributes() throws IOException {
+
+ String line = "r\tp1";
+
+ Boolean flag = setPathwaysFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setPathwaysFromFile.setAttributes();
+
+ assertEquals(1, network.getPathwaysView().size());
+ assertTrue(network.getPathwaysView().containsId("p1"));
+
+ BioPathway p = network.getPathwaysView().get("p1");
+
+ assertEquals(1, network.getReactionsFromPathways(p).size());
+ assertTrue(network.getReactionsFromPathways(p).containsId("r"));
+
+ line = "r2\tp1;p2";
+
+ flag = setPathwaysFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setPathwaysFromFile.setAttributes();
+
+ assertEquals(2, network.getPathwaysView().size());
+
+ assertTrue(network.getPathwaysView().containsId("p1"));
+ assertTrue(network.getPathwaysView().containsId("p2"));
+
+ assertEquals(2, network.getReactionsFromPathways(p).size());
+
+ BioPathway p2 = network.getPathwaysView().get("p2");
+
+ assertEquals(1, network.getReactionsFromPathways(p2).size());
+
+ assertTrue(network.getReactionsFromPathways(p).containsId("r2"));
+
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..179d33846749f1c583a0e125c805f5fba0e589ba
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/attributes/SetRefsFromFileTest.java
@@ -0,0 +1,159 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.io.IOException;
+
+import static org.junit.Assert.*;
+
+public class SetRefsFromFileTest {
+
+
+ private BioNetwork network;
+ private BioReaction reaction;
+ private BioMetabolite metabolite;
+ private BioProtein protein;
+ private BioPathway pathway;
+ private BioGene gene;
+
+ @Before
+ public void init() {
+ network = new BioNetwork();
+ reaction = new BioReaction("r");
+ metabolite = new BioMetabolite("m");
+ protein = new BioProtein("p");
+ pathway = new BioPathway("pathway");
+ gene = new BioGene("g");
+
+ network.add(reaction, metabolite, protein, pathway, gene);
+ }
+
+ @Test
+ public void testAttribute() {
+ SetRefsFromFile setRefsFromFile = new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.REACTION);
+ assertTrue(setRefsFromFile.testAttribute("anything"));
+ }
+
+ @Test
+ public void setAttributesReaction() throws IOException {
+ SetRefsFromFile setRefsFromFile = Mockito.spy(new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.REACTION));
+ Mockito.doReturn(true).when(setRefsFromFile).parseAttributeFile();
+
+ String line = "r\trefValue";
+ Boolean flag = setRefsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setRefsFromFile.setAttributes();
+ System.err.println(reaction.getRefs());
+ BioRef refRef = new BioRef("attributeTable", "refTest", "refValue", 1);
+
+ assertTrue(reaction.getRefs().get("refTest").contains(refRef));
+
+ }
+
+ @Test
+ public void setAttributesMetabolite() throws IOException {
+ SetRefsFromFile setRefsFromFile = Mockito.spy(new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.METABOLITE));
+ Mockito.doReturn(true).when(setRefsFromFile).parseAttributeFile();
+
+ String line = "m\trefValue";
+ Boolean flag = setRefsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setRefsFromFile.setAttributes();
+ assertTrue(metabolite.getRefs().containsKey("refTest"));
+ BioRef refRef = new BioRef("attributeTable", "refTest", "refValue", 1);
+ assertTrue(metabolite.getRefs().get("refTest").contains(refRef));
+ }
+
+ @Test
+ public void setAttributesGene() throws IOException {
+ SetRefsFromFile setRefsFromFile = Mockito.spy(new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.GENE));
+ Mockito.doReturn(true).when(setRefsFromFile).parseAttributeFile();
+
+ String line = "g\trefValue";
+ Boolean flag = setRefsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setRefsFromFile.setAttributes();
+ assertTrue(gene.getRefs().containsKey("refTest"));
+ BioRef refRef = new BioRef("attributeTable", "refTest", "refValue", 1);
+ assertTrue(gene.getRefs().get("refTest").contains(refRef));
+ }
+
+ @Test
+ public void setAttributesProtein() throws IOException {
+ SetRefsFromFile setRefsFromFile = Mockito.spy(new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.PROTEIN));
+ Mockito.doReturn(true).when(setRefsFromFile).parseAttributeFile();
+
+ String line = "p\trefValue";
+ Boolean flag = setRefsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setRefsFromFile.setAttributes();
+ System.err.println(protein.getRefs());
+ assertTrue(protein.getRefs().containsKey("refTest"));
+ BioRef refRef = new BioRef("attributeTable", "refTest", "refValue", 1);
+ assertTrue(protein.getRefs().get("refTest").contains(refRef));
+ }
+
+ @Test
+ public void setAttributesPathway() throws IOException {
+ SetRefsFromFile setRefsFromFile = Mockito.spy(new SetRefsFromFile(0, 1, network, "", "", 0, false, false, "refTest", EntityType.PATHWAY));
+ Mockito.doReturn(true).when(setRefsFromFile).parseAttributeFile();
+
+ String line = "pathway\trefValue";
+ Boolean flag = setRefsFromFile.parseLine(line, 1);
+
+ assertTrue(flag);
+
+ setRefsFromFile.setAttributes();
+ assertTrue(pathway.getRefs().containsKey("refTest"));
+ BioRef refRef = new BioRef("attributeTable", "refTest", "refValue", 1);
+ assertTrue(pathway.getRefs().get("refTest").contains(refRef));
+ }
+
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2TabTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2TabTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..2b44d575af6f5ef1aafaeea2220c615e69a8f30a
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/BioNetwork2TabTest.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.network;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.Flux;
+import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.ReactionAttributes;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class BioNetwork2TabTest {
+
+ @Test
+ public void getReactionLine() {
+
+ BioReaction r = new BioReaction("r", "reaction");
+ BioMetabolite m1 = new BioMetabolite("m1", "metabolite1");
+ BioMetabolite m2 = new BioMetabolite("m2", "metabolite2");
+ BioCompartment c = new BioCompartment("c");
+ BioGene g = new BioGene("g1");
+ BioProtein p = new BioProtein("p1");
+ BioEnzyme e = new BioEnzyme("e1");
+ BioPathway pathway1 = new BioPathway("p1");
+ BioPathway pathway2 = new BioPathway("p2");
+
+ BioNetwork network = new BioNetwork();
+ network.add(r, m1, m2, c, g, p, e, pathway1, pathway2);
+ network.affectToCompartment(c, m1, m2);
+ network.affectGeneProduct(p, g);
+ network.affectSubUnit(e, 1.0, p);
+ network.affectEnzyme(r, e);
+ network.affectLeft(r, 1.0, c, m1);
+ network.affectRight(r, 1.0, c, m2);
+ network.affectToPathway(pathway1, r);
+ network.affectToPathway(pathway2, r);
+
+ ReactionAttributes.setLowerBound(r, new Flux(-10.0));
+ ReactionAttributes.setUpperBound(r, new Flux(10.0));
+
+ BioNetwork2Tab app = new BioNetwork2Tab(network, "", "<-->", "-->");
+
+ String testLine = app.getReactionLine(r);
+ String refLine = "r\treaction\tm1[c] <--> m2[c]\tmetabolite1[c] <--> metabolite2[c]\tNA\tp1 ; p2\tg1\t-10.0\t10.0\n";
+
+ assertEquals(refLine, testLine);
+
+ r.setReversible(false);
+ testLine = app.getReactionLine(r);
+ refLine = "r\treaction\tm1[c] --> m2[c]\tmetabolite1[c] --> metabolite2[c]\tNA\tp1 ; p2\tg1\t-10.0\t10.0\n";
+
+ assertEquals(refLine, testLine);
+ }
+}
\ No newline at end of file
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetworkTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetworkTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..97459633f336d9eee828b6c976f553ded0171237
--- /dev/null
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/tabulated/network/Tab2BioNetworkTest.java
@@ -0,0 +1,274 @@
+/*
+ * Copyright INRAE (2022)
+ *
+ * contact-metexplore@inrae.fr
+ *
+ * This software is a computer program whose purpose is to [describe
+ * functionalities and technical features of your software].
+ *
+ * This software is governed by the CeCILL license under French law and
+ * abiding by the rules of distribution of free software. You can use,
+ * modify and/ or redistribute the software under the terms of the CeCILL
+ * license as circulated by CEA, CNRS and INRIA at the following URL
+ * "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+ *
+ * As a counterpart to the access to the source code and rights to copy,
+ * modify and redistribute granted by the license, users are provided only
+ * with a limited warranty and the software's author, the holder of the
+ * economic rights, and the successive licensors have only limited
+ * liability.
+ *
+ * In this respect, the user's attention is drawn to the risks associated
+ * with loading, using, modifying and/or developing or reproducing the
+ * software by the user in light of its specific status of free software,
+ * that may mean that it is complicated to manipulate, and that also
+ * therefore means that it is reserved for developers and experienced
+ * professionals having in-depth computer knowledge. Users are therefore
+ * encouraged to load and test the software's suitability as regards their
+ * requirements in conditions enabling the security of their systems and/or
+ * data to be ensured and, more generally, to use and operate it in the
+ * same conditions as regards security.
+ *
+ * The fact that you are presently reading this means that you have had
+ * knowledge of the CeCILL license and that you accept its terms.
+ *
+ */
+
+package fr.inrae.toulouse.metexplore.met4j_io.tabulated.network;
+
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReactant;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+public class Tab2BioNetworkTest {
+
+ private Tab2BioNetwork app;
+
+ @Before
+ public void init() {
+ app = new Tab2BioNetwork("test", 0, 1,
+ false, false, "_b",
+ "->", "<->", false,
+ "c", 0);
+ }
+
+
+ @Test
+ public void testLine() {
+
+ String line = "r\tm1 + 2 m2 -> m3 + m4";
+
+ assertTrue(app.testLine(line, 1));
+ }
+
+ @Test
+ public void testLineIdEmpty() {
+ String line = " \tm1 + 2 m2 -> m3 + m4\n";
+
+ assertFalse(app.testLine(line, 1));
+ }
+
+ @Test
+ public void testBadFormulaLeft() {
+ String line = " \tm1 + 2 a m2 -> m3 + m4\n";
+
+ assertFalse(app.testLine(line, 1));
+ }
+
+ @Test
+ public void testBadFormulaRight() {
+ String line = " \tm1 + 2 m2 -> m3 m4\n";
+
+ assertFalse(app.testLine(line, 1));
+ }
+
+ @Test
+ public void testEmptyFormula() {
+ String line = "r\t\ttruc\n";
+
+ assertFalse(app.testLine(line, 1));
+ }
+
+ @Test
+ public void testFormulaWithoutArrow() {
+ String line = "r\ttruc + machin\n";
+
+ assertFalse(app.testLine(line, 1));
+ }
+
+ @Test
+ public void testBadNumberOfColumns() {
+
+ String line = "r\n";
+
+ assertFalse(app.testLine(line, 1));
+
+ }
+
+ @Test
+ public void testDuplicated() {
+
+ String line = "r\tm1 + 2 m2 <-> m3 + m4";
+ assertTrue(app.testLine(line, 1));
+ assertFalse(app.testLine(line, 1));
+
+ }
+
+ @Test
+ public void testFormulaWithCompartment() {
+ String line = "r\t[c] : m1 + 2 m2 <-> m3 + m4";
+ assertTrue(app.testLine(line, 1));
+ }
+
+ @Test
+ public void parseLine() {
+ String line = "r\tm1 + 2 m2 -> m3 + 3 m4";
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+
+ assertEquals(1, network.getReactionsView().size());
+ assertEquals(4, network.getMetabolitesView().size());
+ assertEquals(1, network.getCompartmentsView().size());
+ assertTrue(network.getReactionsView().containsId("r"));
+
+ BioReaction reaction = network.getReactionsView().get("r");
+
+ assertEquals(2, reaction.getLeftReactantsView().size());
+ assertEquals(2, reaction.getRightReactantsView().size());
+
+ BioReactant l1 = reaction.getLeftReactantsView().stream()
+ .filter(reactant -> reactant.getMetabolite().getId().equals("m2"))
+ .findFirst().get();
+
+ assertEquals(2, l1.getQuantity(), 0.0);
+
+ BioReactant r1 = reaction.getRightReactantsView().stream()
+ .filter(reactant -> reactant.getMetabolite().getId().equals("m4"))
+ .findFirst().get();
+
+ assertEquals(3, r1.getQuantity(), 0.0);
+
+ assertFalse(reaction.isReversible());
+
+ }
+
+ @Test
+ public void parseLineReversible() {
+ String line = "r\tm1 + 2 m2 <-> m3 + 3 m4";
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+ BioReaction reaction = network.getReactionsView().get("r");
+ assertTrue(reaction.isReversible());
+ }
+
+ @Test
+ public void parseLineEmptySide() {
+ String line = "r\t <-> ";
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+ assertEquals(1, network.getReactionsView().size());
+ assertEquals(0, network.getMetabolitesView().size());
+ }
+
+ @Test
+ public void parseLineWithCompartment() {
+ String line = "r\t[p] : m1 + 2 m2 -> m3 + 3 m4";
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+
+ assertEquals(1, network.getReactionsView().size());
+ assertEquals(4, network.getMetabolitesView().size());
+ assertEquals(1, network.getCompartmentsView().size());
+ assertTrue(network.getCompartmentsView().containsId("p"));
+
+ }
+
+ @Test
+ public void parseLineWithCompartments() {
+ String line = "r\tm1_c + 2 m2[p] -> m3_x + 3 m4_r";
+
+ app = new Tab2BioNetwork("test", 0, 1,
+ false, false, "_b",
+ "->", "<->", true,
+ "c", 0);
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+
+ assertEquals(1, network.getReactionsView().size());
+ assertEquals(4, network.getMetabolitesView().size());
+ assertEquals(4, network.getCompartmentsView().size());
+ assertTrue(network.getCompartmentsView().containsId("p"));
+ assertTrue(network.getCompartmentsView().containsId("c"));
+ assertTrue(network.getCompartmentsView().containsId("r"));
+ assertTrue(network.getCompartmentsView().containsId("x"));
+
+ }
+
+ @Test
+ public void parseLineWithFormatMetaboliteCobra() {
+ String line = "r\tm1_c + 2 m2[p] -> m3_x + 3 m4_r";
+
+ app = new Tab2BioNetwork("test", 0, 1,
+ false, true, "_b",
+ "->", "<->", true,
+ "c", 0);
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+
+ assertEquals(4, network.getMetabolitesView().size());
+ assertTrue(network.getMetabolitesView().containsId("M_m1_c"));
+ assertTrue(network.getMetabolitesView().containsId("M_m2_p"));
+ assertTrue(network.getMetabolitesView().containsId("M_m3_x"));
+ assertTrue(network.getMetabolitesView().containsId("M_m4_r"));
+ }
+
+ @Test
+ public void parseLineWithFormatReactionCobra() {
+ String line = "r\tm1_c + 2 m2[p] -> m3_x + 3 m4_r";
+
+ app = new Tab2BioNetwork("test", 0, 1,
+ true, true, "_b",
+ "->", "<->", true,
+ "c", 0);
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+ assertEquals(1, network.getReactionsView().size());
+
+ assertTrue(network.getReactionsView().containsId("R_r"));
+ }
+
+ @Test
+ public void parseSeveralLines() {
+
+ String line = "r\tm1 + 2 m2 <-> m3 + 3 m4";
+
+ app.parseLine(line, 1);
+
+ line = "r2\tm1 + 2 m2 <-> m3 + 3 m5";
+
+ app.parseLine(line, 1);
+
+ BioNetwork network = app.getBioNetwork();
+ assertEquals(2, network.getReactionsView().size());
+ assertEquals(5, network.getMetabolitesView().size());
+
+ }
+}
\ No newline at end of file
diff --git a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/AbstractSbmlSetAny.java b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/AbstractSbmlSetAny.java
index e1468903d26c38346e7821188a30707c49b180b9..c62e3ce2abc4d29dd7b6bb21380201e1d9a68e56 100644
--- a/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/AbstractSbmlSetAny.java
+++ b/met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/attributes/AbstractSbmlSetAny.java
@@ -36,6 +36,7 @@
package fr.inrae.toulouse.metexplore.met4j_toolbox.attributes;
+import fr.inrae.toulouse.metexplore.met4j_io.tabulated.attributes.EntityType;
import org.kohsuke.args4j.Option;
/**
@@ -58,8 +59,8 @@ public abstract class AbstractSbmlSetAny extends AbstractSbmlSet {
@Option(name="-s", usage="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites")
protected Boolean s=false;
- @Option(name="-o", usage="[R] Object type in the column id. R:reaction;M:metabolite;P:protein;G:gene")
- protected String o="R";
+ @Option(name="-o", usage="[REACTION] Object type in the column id : REACTION;METABOLITE;PROTEIN;GENE;PATHWAY")
+ protected EntityType o= EntityType.REACTION;
/**
* <p>Constructor for AbstractSbmlSetAny.</p>