From dbab29aefe57bf2bb25413331ec69b2bdf0e2e64 Mon Sep 17 00:00:00 2001
From: "piotr.gawron" <piotr.gawron@uni-new>
Date: Wed, 21 Sep 2016 12:59:16 +0200
Subject: [PATCH] clicking on reaction in submaps didn't work
---
CHANGELOG | 3 +-
.../services/search/data/FullAliasView.java | 1281 ++++++++---------
.../search/data/FullAliasViewFactory.java | 604 ++++----
.../java/lcsb/mapviewer/bean/SearchBean.java | 25 +-
.../resources/pfcomp/aliasSearchElement.xhtml | 9 +-
5 files changed, 935 insertions(+), 987 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 316bded663..2840325170 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -3,8 +3,9 @@ minerva (10.0.1) unstable; urgency=medium
* Bug fix: export to image
* Bug fix: trigger reaction and physical stimulation reactions are no
longer allowed (CellDesigner data model issue)
+ * Bug fix: clicking on reactions in submaps
- -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 16 Sep 2016 13:01:16 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 21 Sep 2016 13:01:16 +0200
minerva (10) stable; urgency=medium
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
index 3c828f6ed2..8268fbbb96 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
@@ -1,663 +1,618 @@
-package lcsb.mapviewer.services.search.data;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.services.search.IHeavyView;
-import lcsb.mapviewer.services.view.AnnotationView;
-import lcsb.mapviewer.services.view.DataMiningView;
-
-/**
- * Heavy {@link LightAliasView view} for alias representing data that should be
- * sent to client.
- *
- * @author Piotr Gawron
- *
- */
-public class FullAliasView extends LightAliasView implements IHeavyView {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(FullAliasView.class);
-
- /**
- * This class represents posttransational modification of the element.
- *
- * @author Piotr Gawron
- *
- */
- public static class PosttransationalModification implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the modification.
- */
- private String name;
-
- /**
- * Position where the modification occurred.
- */
- private String position;
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the position
- * @see #position
- */
- public String getPosition() {
- return position;
- }
-
- /**
- * @param position
- * the position to set
- * @see #position
- */
- public void setPosition(String position) {
- this.position = position;
- }
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Description.
- *
- * @see Element#notes
- */
- private String notes;
-
- /**
- * Type of the alias.
- *
- * @see Element#getStringType()
- */
- private String type;
-
- /**
- * Symbol of the element.
- *
- * @see Element#symbol
- */
- private String symbol;
-
- /**
- * Full name of the element.
- *
- * @see Element#fullName
- */
- private String fullName;
-
- /**
- * Abbreviation of the element.
- *
- * @see Element#abbreviation
- */
- private String abbreviation;
-
- /**
- * Formula describing the element.
- *
- * @see Element#formula
- */
- private String formula;
-
- /**
- * Charge of the element.
- *
- * @see Species#charge
- */
- private Integer charge;
-
- /**
- * Initial amount of species.
- *
- * @see Species#initialAmount
- */
- private Integer initialAmount = null;
-
- /**
- * Initial concentration of species.
- *
- * @see Species#initialConcentration
- */
- private Integer initialConcentration = null;
-
- /**
- * Is only substance units allowed in a species.
- *
- * @see Species#onlySubstanceUnits
- */
- private Boolean onlySubstanceUnits = null;
-
- /**
- * Name of the element.
- *
- * @see Element#name
- */
- private String name = "";
-
- /**
- * Name of the {@link Element#model}.
- */
- private String modelName;
-
- /**
- * Name of the {@link Alias#submodel}.
- */
- private String submodelName;
-
- /**
- * Id of the {@link Alias#submodel}.
- */
- private String submodelId;
-
- /**
- * List of synonyms of the element.
- *
- * @see Element#synonyms
- */
- private List<String> synonyms = new ArrayList<>();
-
- /**
- * List of former symbols used by the entity represented by this element.
- *
- * @see Element#formerSymbols
- */
- private List<String> formerSymbols = new ArrayList<>();
-
- /**
- * List of references for this element.
- *
- * @see Element#miriamData
- */
- private List<AnnotationView> references = new ArrayList<>();
-
- /**
- * List of other unstructurized feuters, specific for some subclases of Alias.
- *
- */
- private Map<String, Object> other = new HashMap<>();
-
- /**
- * Array with data mining entries.
- */
- private List<List<DataMiningView>> dataMining = new ArrayList<>();
-
- /**
- * List of data mining types.
- */
- private List<AnnotationView> dataMiningColumns = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param alias
- * original object from which this element is created
- * @param icon
- * string with icon that should be used to visualize this alias
- */
- protected FullAliasView(Alias alias, String icon) {
- super(alias, icon);
- setModelName(alias.getModel().getName());
- if (alias instanceof CompartmentAlias) {
- setName(((CompartmentAlias) alias).getTitle());
- }
- Element element = alias.getElement();
- if (element != null) {
- setAbbreviation(element.getAbbreviation());
- addFormerSymbols(element.getFormerSymbols());
- setFormula(element.getFormula());
- setFullName(element.getFullName());
- setName(element.getName());
- setNotes(element.getNotes());
- setSymbol(element.getSymbol());
- addSynonyms(element.getSynonyms());
- setType(element.getStringType());
- if (element instanceof Species) {
- Species species = (Species) element;
- setCharge(species.getCharge());
- setInitialAmount(species.getInitialAmount());
- setInitialConcentration(species.getInitialConcentration());
- setOnlySubstanceUnits(species.getOnlySubstanceUnits());
- if (alias.getSubmodel() != null && alias.getSubmodel().getSubmodel() != null) {
- setSubmodelName(alias.getSubmodel().getSubmodel().getName());
- setSubmodelId(alias.getSubmodel().getSubmodel().getId() + "");
- }
- }
- }
- }
-
- /**
- * Constructor that should be used only by the deserialization method.
- */
- protected FullAliasView() {
- }
-
- /**
- * Adds elements to {@link #synonyms} list.
- *
- * @param synonyms2
- * list of elements to add
- */
- private void addSynonyms(List<String> synonyms2) {
- synonyms.addAll(synonyms2);
- }
-
- /**
- * Adds elements to {@link #formerSymbols} list.
- *
- * @param formerSymbols2
- * list of elements to add
- */
- private void addFormerSymbols(List<String> formerSymbols2) {
- formerSymbols.addAll(formerSymbols2);
- }
-
- /**
- * @return the notes
- * @see #notes
- */
- public String getNotes() {
- return notes;
- }
-
- /**
- * @param notes
- * the notes to set
- * @see #notes
- */
- public void setNotes(String notes) {
- this.notes = notes;
- }
-
- /**
- * @return the symbol
- * @see #symbol
- */
- public String getSymbol() {
- return symbol;
- }
-
- /**
- * @param symbol
- * the symbol to set
- * @see #symbol
- */
- public void setSymbol(String symbol) {
- this.symbol = symbol;
- }
-
- /**
- * @return the fullName
- * @see #fullName
- */
- public String getFullName() {
- return fullName;
- }
-
- /**
- * @param fullName
- * the fullName to set
- * @see #fullName
- */
- public void setFullName(String fullName) {
- this.fullName = fullName;
- }
-
- /**
- * @return the abbreviation
- * @see #abbreviation
- */
- public String getAbbreviation() {
- return abbreviation;
- }
-
- /**
- * @param abbreviation
- * the abbreviation to set
- * @see #abbreviation
- */
- public void setAbbreviation(String abbreviation) {
- this.abbreviation = abbreviation;
- }
-
- /**
- * @return the formula
- * @see #formula
- */
- public String getFormula() {
- return formula;
- }
-
- /**
- * @param formula
- * the formula to set
- * @see #formula
- */
- public void setFormula(String formula) {
- this.formula = formula;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the synonyms
- * @see #synonyms
- */
- public List<String> getSynonyms() {
- return synonyms;
- }
-
- /**
- * @param synonyms
- * the synonyms to set
- * @see #synonyms
- */
- public void setSynonyms(List<String> synonyms) {
- this.synonyms = synonyms;
- }
-
- /**
- * @return the formerSymbols
- * @see #formerSymbols
- */
- public List<String> getFormerSymbols() {
- return formerSymbols;
- }
-
- /**
- * @param formerSymbols
- * the formerSymbols to set
- * @see #formerSymbols
- */
- public void setFormerSymbols(List<String> formerSymbols) {
- this.formerSymbols = formerSymbols;
- }
-
- /**
- * @return the references
- * @see #references
- */
- public List<AnnotationView> getReferences() {
- return references;
- }
-
- /**
- * @param references
- * the references to set
- * @see #references
- */
- public void setReferences(List<AnnotationView> references) {
- this.references = references;
- }
-
- /**
- * @return the other
- * @see #other
- */
- public Map<String, Object> getOther() {
- return other;
- }
-
- /**
- * Returns other (additional element) by the name.
- *
- * @param key
- * key identifing the feature.
- * @return other (additional element) by the name
- */
- public Object getOther(String key) {
- return other.get(key);
- }
-
- /**
- * @param other
- * the other to set
- * @see #other
- */
- public void setOther(Map<String, Object> other) {
- this.other = other;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * Adds elements to {@link #references} list.
- *
- * @param newReferences
- * list of elements to add
- */
- public void addReferences(List<AnnotationView> newReferences) {
- references.addAll(newReferences);
- }
-
- /**
- * @return the dataMining
- * @see #dataMining
- */
- public List<List<DataMiningView>> getDataMining() {
- return dataMining;
- }
-
- /**
- * @param dataMining
- * the dataMining to set
- * @see #dataMining
- */
- public void setDataMining(List<List<DataMiningView>> dataMining) {
- this.dataMining = dataMining;
- }
-
- /**
- * @return the dataMiningColumns
- * @see #dataMiningColumns
- */
- public List<AnnotationView> getDataMiningColumns() {
- return dataMiningColumns;
- }
-
- /**
- * @param dataMiningColumns
- * the dataMiningColumns to set
- * @see #dataMiningColumns
- */
- public void setDataMiningColumns(List<AnnotationView> dataMiningColumns) {
- this.dataMiningColumns = dataMiningColumns;
- }
-
- /**
- * Addsother (additional element) by the name.
- *
- * @param key
- * name of the feature
- * @param value
- * object representing data of the feature
- */
- public void addOther(String key, Object value) {
- other.put(key, value);
- }
-
- /**
- * @return the modelName
- * @see #modelName
- */
- public String getModelName() {
- return modelName;
- }
-
- /**
- * @param modelName
- * the modelName to set
- * @see #modelName
- */
- public void setModelName(String modelName) {
- this.modelName = modelName;
- }
-
- /**
- * @return the charge
- * @see #charge
- */
- public Integer getCharge() {
- return charge;
- }
-
- /**
- * @param charge
- * the charge to set
- * @see #charge
- */
- public void setCharge(Integer charge) {
- this.charge = charge;
- }
-
- /**
- * @return the initialAmount
- * @see #initialAmount
- */
- public Integer getInitialAmount() {
- return initialAmount;
- }
-
- /**
- * @param initialAmount
- * the initialAmount to set
- * @see #initialAmount
- */
- public void setInitialAmount(Integer initialAmount) {
- this.initialAmount = initialAmount;
- }
-
- /**
- * @return the initialConcentration
- * @see #initialConcentration
- */
- public Integer getInitialConcentration() {
- return initialConcentration;
- }
-
- /**
- * @param initialConcentration
- * the initialConcentration to set
- * @see #initialConcentration
- */
- public void setInitialConcentration(Integer initialConcentration) {
- this.initialConcentration = initialConcentration;
- }
-
- /**
- * @return the onlySubstanceUnits
- * @see #onlySubstanceUnits
- */
- public Boolean getOnlySubstanceUnits() {
- return onlySubstanceUnits;
- }
-
- /**
- * @param onlySubstanceUnits
- * the onlySubstanceUnits to set
- * @see #onlySubstanceUnits
- */
- public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
- this.onlySubstanceUnits = onlySubstanceUnits;
- }
-
- /**
- * @return the submodelName
- * @see #submodelName
- */
- public String getSubmodelName() {
- return submodelName;
- }
-
- /**
- * @param submodelName
- * the submodelName to set
- * @see #submodelName
- */
- public void setSubmodelName(String submodelName) {
- this.submodelName = submodelName;
- }
-
- /**
- * @return the submodelId
- * @see #submodelId
- */
- public String getSubmodelId() {
- return submodelId;
- }
-
- /**
- * @param submodelId
- * the submodelId to set
- * @see #submodelId
- */
- public void setSubmodelId(String submodelId) {
- this.submodelId = submodelId;
- }
-}
+package lcsb.mapviewer.services.search.data;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.layout.alias.CompartmentAlias;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.services.search.IHeavyView;
+import lcsb.mapviewer.services.view.AnnotationView;
+
+/**
+ * Heavy {@link LightAliasView view} for alias representing data that should be
+ * sent to client.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class FullAliasView extends LightAliasView implements IHeavyView {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(FullAliasView.class);
+
+ /**
+ * This class represents posttransational modification of the element.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public static class PosttransationalModification implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the modification.
+ */
+ private String name;
+
+ /**
+ * Position where the modification occurred.
+ */
+ private String position;
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the position
+ * @see #position
+ */
+ public String getPosition() {
+ return position;
+ }
+
+ /**
+ * @param position
+ * the position to set
+ * @see #position
+ */
+ public void setPosition(String position) {
+ this.position = position;
+ }
+ }
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Description.
+ *
+ * @see Element#notes
+ */
+ private String notes;
+
+ /**
+ * Type of the alias.
+ *
+ * @see Element#getStringType()
+ */
+ private String type;
+
+ /**
+ * Symbol of the element.
+ *
+ * @see Element#symbol
+ */
+ private String symbol;
+
+ /**
+ * Full name of the element.
+ *
+ * @see Element#fullName
+ */
+ private String fullName;
+
+ /**
+ * Abbreviation of the element.
+ *
+ * @see Element#abbreviation
+ */
+ private String abbreviation;
+
+ /**
+ * Formula describing the element.
+ *
+ * @see Element#formula
+ */
+ private String formula;
+
+ /**
+ * Charge of the element.
+ *
+ * @see Species#charge
+ */
+ private Integer charge;
+
+ /**
+ * Initial amount of species.
+ *
+ * @see Species#initialAmount
+ */
+ private Integer initialAmount = null;
+
+ /**
+ * Initial concentration of species.
+ *
+ * @see Species#initialConcentration
+ */
+ private Integer initialConcentration = null;
+
+ /**
+ * Is only substance units allowed in a species.
+ *
+ * @see Species#onlySubstanceUnits
+ */
+ private Boolean onlySubstanceUnits = null;
+
+ /**
+ * Name of the element.
+ *
+ * @see Element#name
+ */
+ private String name = "";
+
+ /**
+ * Name of the {@link Element#model}.
+ */
+ private String modelName;
+
+ /**
+ * Name of the {@link Alias#submodel}.
+ */
+ private String submodelName;
+
+ /**
+ * Id of the {@link Alias#submodel}.
+ */
+ private String submodelId;
+
+ /**
+ * List of synonyms of the element.
+ *
+ * @see Element#synonyms
+ */
+ private List<String> synonyms = new ArrayList<>();
+
+ /**
+ * List of former symbols used by the entity represented by this element.
+ *
+ * @see Element#formerSymbols
+ */
+ private List<String> formerSymbols = new ArrayList<>();
+
+ /**
+ * List of references for this element.
+ *
+ * @see Element#miriamData
+ */
+ private List<AnnotationView> references = new ArrayList<>();
+
+ /**
+ * List of other unstructurized feuters, specific for some subclases of Alias.
+ *
+ */
+ private Map<String, Object> other = new HashMap<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param alias
+ * original object from which this element is created
+ * @param icon
+ * string with icon that should be used to visualize this alias
+ */
+ protected FullAliasView(Alias alias, String icon) {
+ super(alias, icon);
+ setModelName(alias.getModel().getName());
+ if (alias instanceof CompartmentAlias) {
+ setName(((CompartmentAlias) alias).getTitle());
+ }
+ Element element = alias.getElement();
+ if (element != null) {
+ setAbbreviation(element.getAbbreviation());
+ addFormerSymbols(element.getFormerSymbols());
+ setFormula(element.getFormula());
+ setFullName(element.getFullName());
+ setName(element.getName());
+ setNotes(element.getNotes());
+ setSymbol(element.getSymbol());
+ addSynonyms(element.getSynonyms());
+ setType(element.getStringType());
+ if (element instanceof Species) {
+ Species species = (Species) element;
+ setCharge(species.getCharge());
+ setInitialAmount(species.getInitialAmount());
+ setInitialConcentration(species.getInitialConcentration());
+ setOnlySubstanceUnits(species.getOnlySubstanceUnits());
+ if (alias.getSubmodel() != null && alias.getSubmodel().getSubmodel() != null) {
+ setSubmodelName(alias.getSubmodel().getSubmodel().getName());
+ setSubmodelId(alias.getSubmodel().getSubmodel().getId() + "");
+ }
+ }
+ }
+ }
+
+ /**
+ * Constructor that should be used only by the deserialization method.
+ */
+ protected FullAliasView() {
+ }
+
+ /**
+ * Adds elements to {@link #synonyms} list.
+ *
+ * @param synonyms2
+ * list of elements to add
+ */
+ private void addSynonyms(List<String> synonyms2) {
+ synonyms.addAll(synonyms2);
+ }
+
+ /**
+ * Adds elements to {@link #formerSymbols} list.
+ *
+ * @param formerSymbols2
+ * list of elements to add
+ */
+ private void addFormerSymbols(List<String> formerSymbols2) {
+ formerSymbols.addAll(formerSymbols2);
+ }
+
+ /**
+ * @return the notes
+ * @see #notes
+ */
+ public String getNotes() {
+ return notes;
+ }
+
+ /**
+ * @param notes
+ * the notes to set
+ * @see #notes
+ */
+ public void setNotes(String notes) {
+ this.notes = notes;
+ }
+
+ /**
+ * @return the symbol
+ * @see #symbol
+ */
+ public String getSymbol() {
+ return symbol;
+ }
+
+ /**
+ * @param symbol
+ * the symbol to set
+ * @see #symbol
+ */
+ public void setSymbol(String symbol) {
+ this.symbol = symbol;
+ }
+
+ /**
+ * @return the fullName
+ * @see #fullName
+ */
+ public String getFullName() {
+ return fullName;
+ }
+
+ /**
+ * @param fullName
+ * the fullName to set
+ * @see #fullName
+ */
+ public void setFullName(String fullName) {
+ this.fullName = fullName;
+ }
+
+ /**
+ * @return the abbreviation
+ * @see #abbreviation
+ */
+ public String getAbbreviation() {
+ return abbreviation;
+ }
+
+ /**
+ * @param abbreviation
+ * the abbreviation to set
+ * @see #abbreviation
+ */
+ public void setAbbreviation(String abbreviation) {
+ this.abbreviation = abbreviation;
+ }
+
+ /**
+ * @return the formula
+ * @see #formula
+ */
+ public String getFormula() {
+ return formula;
+ }
+
+ /**
+ * @param formula
+ * the formula to set
+ * @see #formula
+ */
+ public void setFormula(String formula) {
+ this.formula = formula;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the synonyms
+ * @see #synonyms
+ */
+ public List<String> getSynonyms() {
+ return synonyms;
+ }
+
+ /**
+ * @param synonyms
+ * the synonyms to set
+ * @see #synonyms
+ */
+ public void setSynonyms(List<String> synonyms) {
+ this.synonyms = synonyms;
+ }
+
+ /**
+ * @return the formerSymbols
+ * @see #formerSymbols
+ */
+ public List<String> getFormerSymbols() {
+ return formerSymbols;
+ }
+
+ /**
+ * @param formerSymbols
+ * the formerSymbols to set
+ * @see #formerSymbols
+ */
+ public void setFormerSymbols(List<String> formerSymbols) {
+ this.formerSymbols = formerSymbols;
+ }
+
+ /**
+ * @return the references
+ * @see #references
+ */
+ public List<AnnotationView> getReferences() {
+ return references;
+ }
+
+ /**
+ * @param references
+ * the references to set
+ * @see #references
+ */
+ public void setReferences(List<AnnotationView> references) {
+ this.references = references;
+ }
+
+ /**
+ * @return the other
+ * @see #other
+ */
+ public Map<String, Object> getOther() {
+ return other;
+ }
+
+ /**
+ * Returns other (additional element) by the name.
+ *
+ * @param key
+ * key identifing the feature.
+ * @return other (additional element) by the name
+ */
+ public Object getOther(String key) {
+ return other.get(key);
+ }
+
+ /**
+ * @param other
+ * the other to set
+ * @see #other
+ */
+ public void setOther(Map<String, Object> other) {
+ this.other = other;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ /**
+ * Adds elements to {@link #references} list.
+ *
+ * @param newReferences
+ * list of elements to add
+ */
+ public void addReferences(List<AnnotationView> newReferences) {
+ references.addAll(newReferences);
+ }
+
+ /**
+ * Addsother (additional element) by the name.
+ *
+ * @param key
+ * name of the feature
+ * @param value
+ * object representing data of the feature
+ */
+ public void addOther(String key, Object value) {
+ other.put(key, value);
+ }
+
+ /**
+ * @return the modelName
+ * @see #modelName
+ */
+ public String getModelName() {
+ return modelName;
+ }
+
+ /**
+ * @param modelName
+ * the modelName to set
+ * @see #modelName
+ */
+ public void setModelName(String modelName) {
+ this.modelName = modelName;
+ }
+
+ /**
+ * @return the charge
+ * @see #charge
+ */
+ public Integer getCharge() {
+ return charge;
+ }
+
+ /**
+ * @param charge
+ * the charge to set
+ * @see #charge
+ */
+ public void setCharge(Integer charge) {
+ this.charge = charge;
+ }
+
+ /**
+ * @return the initialAmount
+ * @see #initialAmount
+ */
+ public Integer getInitialAmount() {
+ return initialAmount;
+ }
+
+ /**
+ * @param initialAmount
+ * the initialAmount to set
+ * @see #initialAmount
+ */
+ public void setInitialAmount(Integer initialAmount) {
+ this.initialAmount = initialAmount;
+ }
+
+ /**
+ * @return the initialConcentration
+ * @see #initialConcentration
+ */
+ public Integer getInitialConcentration() {
+ return initialConcentration;
+ }
+
+ /**
+ * @param initialConcentration
+ * the initialConcentration to set
+ * @see #initialConcentration
+ */
+ public void setInitialConcentration(Integer initialConcentration) {
+ this.initialConcentration = initialConcentration;
+ }
+
+ /**
+ * @return the onlySubstanceUnits
+ * @see #onlySubstanceUnits
+ */
+ public Boolean getOnlySubstanceUnits() {
+ return onlySubstanceUnits;
+ }
+
+ /**
+ * @param onlySubstanceUnits
+ * the onlySubstanceUnits to set
+ * @see #onlySubstanceUnits
+ */
+ public void setOnlySubstanceUnits(Boolean onlySubstanceUnits) {
+ this.onlySubstanceUnits = onlySubstanceUnits;
+ }
+
+ /**
+ * @return the submodelName
+ * @see #submodelName
+ */
+ public String getSubmodelName() {
+ return submodelName;
+ }
+
+ /**
+ * @param submodelName
+ * the submodelName to set
+ * @see #submodelName
+ */
+ public void setSubmodelName(String submodelName) {
+ this.submodelName = submodelName;
+ }
+
+ /**
+ * @return the submodelId
+ * @see #submodelId
+ */
+ public String getSubmodelId() {
+ return submodelId;
+ }
+
+ /**
+ * @param submodelId
+ * the submodelId to set
+ * @see #submodelId
+ */
+ public void setSubmodelId(String submodelId) {
+ this.submodelId = submodelId;
+ }
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java
index 23e02dfe95..7fd70377fc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasViewFactory.java
@@ -1,299 +1,305 @@
-package lcsb.mapviewer.services.search.data;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.primefaces.model.DefaultTreeNode;
-import org.primefaces.model.TreeNode;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import com.google.gson.Gson;
-
-import lcsb.mapviewer.annotation.data.Chebi;
-import lcsb.mapviewer.annotation.data.ChebiRelation;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
-import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.map.Element;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.graph.DataMiningType;
-import lcsb.mapviewer.model.map.layout.alias.Alias;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
-import lcsb.mapviewer.services.interfaces.IDataMiningService;
-import lcsb.mapviewer.services.overlay.ChebiTreeRow;
-import lcsb.mapviewer.services.search.ElementViewFactory;
-import lcsb.mapviewer.services.search.data.FullAliasView.PosttransationalModification;
-import lcsb.mapviewer.services.view.AnnotationView;
-import lcsb.mapviewer.services.view.AnnotationViewFactory;
-import lcsb.mapviewer.services.view.DataMiningView;
-import lcsb.mapviewer.services.view.DataMiningViewFactory;
-
-/**
- * Factory class for {@link LightAliasView} class.
- *
- * @author Piotr Gawron
- *
- */
-public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasView> {
-
- /**
- * How many rows with data mining information should be presented to the user.
- */
- private static final int MAX_MISSING_CONNECTIONS = 100;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(FullAliasViewFactory.class);
-
- /**
- * Factory used to create {@link AnnotationView} elements.
- */
- @Autowired
- private AnnotationViewFactory annotationViewFactory;
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector mc;
-
- /**
- * Factory object used for creation of {@link DataMiningView} elements.
- */
- @Autowired
- private DataMiningViewFactory dataMiningViewFactory;
-
- /**
- * Service that manages data mining information.
- */
- @Autowired
- private IDataMiningService dataMiningService;
-
- /**
- * Service accessing chebi database.
- */
- @Autowired
- private ChebiAnnotator chebiBackend;
-
- @Override
- public FullAliasView create(Alias alias) {
- return create(alias, null);
- }
-
- /**
- * Creates {@link FullAliasView} from given {@link Alias}.
- *
- * @param alias
- * alias for which view is created
- * @param icon
- * icon that should be assigned to the view
- * @return {@link FullAliasView} for given alias
- */
- public FullAliasView create(Alias alias, String icon) {
- FullAliasView result = new FullAliasView(alias, icon);
- Element element = alias.getElement();
- if (element != null) {
- result.addReferences(annotationViewFactory.createList(element.getMiriamData()));
- result.setDataMining(getDataMiningInformation(alias, MAX_MISSING_CONNECTIONS));
- AnnotationView structureView = annotationViewFactory.create(DataMiningType.STRUCTURE_ANALYSIS);
- result.getDataMiningColumns().add(structureView);
-
- AnnotationView textMiningView = annotationViewFactory.create(DataMiningType.TEXT_MINING);
- result.getDataMiningColumns().add(textMiningView);
- if (alias.getModel() != null) {
- for (DataMiningSet dms : alias.getModel().getDataMiningSets()) {
- if (DataMiningType.STRUCTURE_ANALYSIS.equals(dms.getType())) {
- if (dms.getSource() != null && !dms.getSource().isEmpty()) {
- structureView.setLink(dms.getSource());
- }
- if (dms.getName() != null && !dms.getName().isEmpty()) {
- structureView.setName(dms.getName());
- }
- structureView.setSummary(dms.getDescription());
-
- } else if (DataMiningType.TEXT_MINING.equals(dms.getType())) {
- if (dms.getSource() != null && !dms.getSource().isEmpty()) {
- textMiningView.setLink(dms.getSource());
- }
- if (dms.getName() != null && !dms.getName().isEmpty()) {
- textMiningView.setName(dms.getName());
- }
- textMiningView.setSummary(dms.getDescription());
- } else {
- throw new NotImplementedException(dms.getType() + " is not implemented.");
- }
- }
- }
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.CHEBI.equals(md.getDataType())) {
- try {
- Chebi chebi = chebiBackend.getChebiElementForChebiId(md);
- if (chebi != null) {
- result.addOther("chebiTree", chebi);
- } else {
- logger.warn("Invalid chebi identifier: " + md.getResource());
- }
- } catch (ChebiSearchException e) {
- logger.warn("Problem with accesing data about chebi: " + md.getResource(), e);
- }
- }
- }
- if (element instanceof Protein) {
- result.addOther("posttranslationalModifications", getPosttransationalModifications(alias));
- }
-
- }
- return result;
- }
-
- /**
- * Creates list of {@link PosttransationalModification} objects for object
- * alias.
- *
- * @param alias
- * alias of the object
- * @return list of {@link PosttransationalModification} objects for object
- * alias
- */
- private List<PosttransationalModification> getPosttransationalModifications(Alias alias) {
- List<PosttransationalModification> result = new ArrayList<PosttransationalModification>();
- Element species = alias.getElement();
- if (species instanceof Protein) {
- List<ModificationResidue> modifications = ((Protein) species).getModificationResidues();
- if (modifications.size() > 0) {
- for (ModificationResidue residue : modifications) {
- if (residue.getState() != null) {
- PosttransationalModification modification = new PosttransationalModification();
- modification.setName(residue.getState().getFullName());
- modification.setPosition(residue.getName());
- result.add(modification);
- }
- }
- }
- }
- return result;
- }
-
- @Override
- public String createGson(FullAliasView object) {
- return new Gson().toJson(object);
- }
-
- /**
- * Creates table for data mining information for given alias.
- *
- * @param alias
- * alias for which data mining information is added
- * @param maxMissingConnections
- * max elements that should be presented
- * @return html table with data mining information
- */
- protected List<List<DataMiningView>> getDataMiningInformation(Alias alias, int maxMissingConnections) {
- List<List<DataMiningView>> result = new ArrayList<List<DataMiningView>>();
- List<DataMiningView> enricoList = new ArrayList<DataMiningView>();
- List<DataMiningView> mariaList = new ArrayList<DataMiningView>();
- if (alias.getElement() == null || !(alias.getElement() instanceof Species)) {
- return result;
- }
- Species species = (Species) alias.getElement();
-
- if (dataMiningService != null) {
- Collection<DataMining> connections = dataMiningService.getMissingConnections(species);
- if (connections.size() > 0) {
- for (DataMining missingConnection : connections) {
- if (missingConnection.getType().equals(DataMiningType.STRUCTURE_ANALYSIS)) {
- if (enricoList.size() < maxMissingConnections) {
- DataMiningView view = dataMiningViewFactory.create(missingConnection);
- enricoList.add(view);
- }
- } else if (missingConnection.getType().equals(DataMiningType.TEXT_MINING)) {
- if (mariaList.size() < maxMissingConnections) {
- DataMiningView view = dataMiningViewFactory.create(missingConnection);
- mariaList.add(view);
- }
- } else {
- throw new InvalidArgumentException("Unknown type of missing connection: " + missingConnection.getType());
- }
- }
- }
- }
- int size = Math.max(mariaList.size(), enricoList.size());
- for (int i = 0; i < size; i++) {
- List<DataMiningView> row = new ArrayList<DataMiningView>();
- if (i < enricoList.size()) {
- row.add(enricoList.get(i));
- } else {
- row.add(null);
- }
- if (i < mariaList.size()) {
- row.add(mariaList.get(i));
- } else {
- row.add(null);
- }
- result.add(row);
- }
- return result;
- }
-
- /**
- * Creates empty {@link FullAliasView}.
- *
- * @return empty {@link FullAliasView}
- */
- public FullAliasView createEmpty() {
- return new FullAliasView();
- }
-
- /**
- * Creates {@link TreeNode} representing {@link Chebi} object. This object is
- * used by client side to represent data as a tree.
- *
- * @param chebi
- * object to be transforem
- * @return tree representing chebi element
- */
-
- protected TreeNode createTreeForChebi(Chebi chebi) {
- // create artificial root
-
- TreeNode root = new DefaultTreeNode(new ChebiTreeRow("root", "unknown", MiriamType.CHEBI.getDbHomepage(), ""), null);
- root.setExpanded(true);
- TreeNode lastElement = root;
- // create parents
- for (ChebiRelation relation : chebi.getIncomingChebi()) {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, relation.getId());
- ChebiTreeRow row = new ChebiTreeRow(relation.getName(), relation.getId(), mc.getUrlString(md), relation.getType());
- lastElement = new DefaultTreeNode(row, root);
- lastElement.setExpanded(true);
- }
-
- // create main chebi element
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, chebi.getChebiId());
- ChebiTreeRow row = new ChebiTreeRow(chebi.getName(), chebi.getChebiId(), mc.getUrlString(md), "");
-
- TreeNode element = new DefaultTreeNode(row, lastElement);
- element.setExpanded(true);
-
- // create children
-
- for (ChebiRelation relation : chebi.getOutgoingChebi()) {
- md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, relation.getId());
- row = new ChebiTreeRow(relation.getName(), relation.getId(), mc.getUrlString(md), relation.getType());
- new DefaultTreeNode(row, element);
- }
-
- return root;
- }
-
-}
+package lcsb.mapviewer.services.search.data;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.primefaces.model.DefaultTreeNode;
+import org.primefaces.model.TreeNode;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import com.google.gson.Gson;
+
+import lcsb.mapviewer.annotation.data.Chebi;
+import lcsb.mapviewer.annotation.data.ChebiRelation;
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.annotators.ChebiAnnotator;
+import lcsb.mapviewer.annotation.services.annotators.ChebiSearchException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.Element;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.graph.DataMining;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.graph.DataMiningType;
+import lcsb.mapviewer.model.map.layout.alias.Alias;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.fields.ModificationResidue;
+import lcsb.mapviewer.services.interfaces.IDataMiningService;
+import lcsb.mapviewer.services.overlay.ChebiTreeRow;
+import lcsb.mapviewer.services.search.ElementViewFactory;
+import lcsb.mapviewer.services.search.data.FullAliasView.PosttransationalModification;
+import lcsb.mapviewer.services.view.AnnotationView;
+import lcsb.mapviewer.services.view.AnnotationViewFactory;
+import lcsb.mapviewer.services.view.DataMiningView;
+import lcsb.mapviewer.services.view.DataMiningViewFactory;
+
+/**
+ * Factory class for {@link LightAliasView} class.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class FullAliasViewFactory extends ElementViewFactory<Alias, FullAliasView> {
+
+ /**
+ * How many rows with data mining information should be presented to the user.
+ */
+ private static final int MAX_MISSING_CONNECTIONS = 100;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(FullAliasViewFactory.class);
+
+ /**
+ * Factory used to create {@link AnnotationView} elements.
+ */
+ @Autowired
+ private AnnotationViewFactory annotationViewFactory;
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector mc;
+
+ /**
+ * Factory object used for creation of {@link DataMiningView} elements.
+ */
+ @Autowired
+ private DataMiningViewFactory dataMiningViewFactory;
+
+ /**
+ * Service that manages data mining information.
+ */
+ @Autowired
+ private IDataMiningService dataMiningService;
+
+ /**
+ * Service accessing chebi database.
+ */
+ @Autowired
+ private ChebiAnnotator chebiBackend;
+
+ @Override
+ public FullAliasView create(Alias alias) {
+ return create(alias, null);
+ }
+
+ /**
+ * Creates {@link FullAliasView} from given {@link Alias}.
+ *
+ * @param alias
+ * alias for which view is created
+ * @param icon
+ * icon that should be assigned to the view
+ * @return {@link FullAliasView} for given alias
+ */
+ public FullAliasView create(Alias alias, String icon) {
+ FullAliasView result = new FullAliasView(alias, icon);
+ Element element = alias.getElement();
+ if (element != null) {
+ result.addReferences(annotationViewFactory.createList(element.getMiriamData()));
+ result.addOther("dataMining", getDataMiningInformation(alias, MAX_MISSING_CONNECTIONS));
+
+ List<AnnotationView> columns = new ArrayList<>();
+ AnnotationView structureView = annotationViewFactory.create(DataMiningType.STRUCTURE_ANALYSIS);
+
+ AnnotationView textMiningView = annotationViewFactory.create(DataMiningType.TEXT_MINING);
+
+ columns.add(structureView);
+ columns.add(textMiningView);
+
+ result.addOther("dataMiningColumns", columns);
+
+ if (alias.getModel() != null) {
+ for (DataMiningSet dms : alias.getModel().getDataMiningSets()) {
+ if (DataMiningType.STRUCTURE_ANALYSIS.equals(dms.getType())) {
+ if (dms.getSource() != null && !dms.getSource().isEmpty()) {
+ structureView.setLink(dms.getSource());
+ }
+ if (dms.getName() != null && !dms.getName().isEmpty()) {
+ structureView.setName(dms.getName());
+ }
+ structureView.setSummary(dms.getDescription());
+
+ } else if (DataMiningType.TEXT_MINING.equals(dms.getType())) {
+ if (dms.getSource() != null && !dms.getSource().isEmpty()) {
+ textMiningView.setLink(dms.getSource());
+ }
+ if (dms.getName() != null && !dms.getName().isEmpty()) {
+ textMiningView.setName(dms.getName());
+ }
+ textMiningView.setSummary(dms.getDescription());
+ } else {
+ throw new NotImplementedException(dms.getType() + " is not implemented.");
+ }
+ }
+ }
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.CHEBI.equals(md.getDataType())) {
+ try {
+ Chebi chebi = chebiBackend.getChebiElementForChebiId(md);
+ if (chebi != null) {
+ result.addOther("chebiTree", chebi);
+ } else {
+ logger.warn("Invalid chebi identifier: " + md.getResource());
+ }
+ } catch (ChebiSearchException e) {
+ logger.warn("Problem with accesing data about chebi: " + md.getResource(), e);
+ }
+ }
+ }
+ if (element instanceof Protein) {
+ result.addOther("posttranslationalModifications", getPosttransationalModifications(alias));
+ }
+
+ }
+ return result;
+ }
+
+ /**
+ * Creates list of {@link PosttransationalModification} objects for object
+ * alias.
+ *
+ * @param alias
+ * alias of the object
+ * @return list of {@link PosttransationalModification} objects for object
+ * alias
+ */
+ private List<PosttransationalModification> getPosttransationalModifications(Alias alias) {
+ List<PosttransationalModification> result = new ArrayList<PosttransationalModification>();
+ Element species = alias.getElement();
+ if (species instanceof Protein) {
+ List<ModificationResidue> modifications = ((Protein) species).getModificationResidues();
+ if (modifications.size() > 0) {
+ for (ModificationResidue residue : modifications) {
+ if (residue.getState() != null) {
+ PosttransationalModification modification = new PosttransationalModification();
+ modification.setName(residue.getState().getFullName());
+ modification.setPosition(residue.getName());
+ result.add(modification);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String createGson(FullAliasView object) {
+ return new Gson().toJson(object);
+ }
+
+ /**
+ * Creates table for data mining information for given alias.
+ *
+ * @param alias
+ * alias for which data mining information is added
+ * @param maxMissingConnections
+ * max elements that should be presented
+ * @return html table with data mining information
+ */
+ protected List<List<DataMiningView>> getDataMiningInformation(Alias alias, int maxMissingConnections) {
+ List<List<DataMiningView>> result = new ArrayList<List<DataMiningView>>();
+ List<DataMiningView> enricoList = new ArrayList<DataMiningView>();
+ List<DataMiningView> mariaList = new ArrayList<DataMiningView>();
+ if (alias.getElement() == null || !(alias.getElement() instanceof Species)) {
+ return result;
+ }
+ Species species = (Species) alias.getElement();
+
+ if (dataMiningService != null) {
+ Collection<DataMining> connections = dataMiningService.getMissingConnections(species);
+ if (connections.size() > 0) {
+ for (DataMining missingConnection : connections) {
+ if (missingConnection.getType().equals(DataMiningType.STRUCTURE_ANALYSIS)) {
+ if (enricoList.size() < maxMissingConnections) {
+ DataMiningView view = dataMiningViewFactory.create(missingConnection);
+ enricoList.add(view);
+ }
+ } else if (missingConnection.getType().equals(DataMiningType.TEXT_MINING)) {
+ if (mariaList.size() < maxMissingConnections) {
+ DataMiningView view = dataMiningViewFactory.create(missingConnection);
+ mariaList.add(view);
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown type of missing connection: " + missingConnection.getType());
+ }
+ }
+ }
+ }
+ int size = Math.max(mariaList.size(), enricoList.size());
+ for (int i = 0; i < size; i++) {
+ List<DataMiningView> row = new ArrayList<DataMiningView>();
+ if (i < enricoList.size()) {
+ row.add(enricoList.get(i));
+ } else {
+ row.add(null);
+ }
+ if (i < mariaList.size()) {
+ row.add(mariaList.get(i));
+ } else {
+ row.add(null);
+ }
+ result.add(row);
+ }
+ return result;
+ }
+
+ /**
+ * Creates empty {@link FullAliasView}.
+ *
+ * @return empty {@link FullAliasView}
+ */
+ public FullAliasView createEmpty() {
+ return new FullAliasView();
+ }
+
+ /**
+ * Creates {@link TreeNode} representing {@link Chebi} object. This object is
+ * used by client side to represent data as a tree.
+ *
+ * @param chebi
+ * object to be transforem
+ * @return tree representing chebi element
+ */
+
+ protected TreeNode createTreeForChebi(Chebi chebi) {
+ // create artificial root
+
+ TreeNode root = new DefaultTreeNode(new ChebiTreeRow("root", "unknown", MiriamType.CHEBI.getDbHomepage(), ""), null);
+ root.setExpanded(true);
+ TreeNode lastElement = root;
+ // create parents
+ for (ChebiRelation relation : chebi.getIncomingChebi()) {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, relation.getId());
+ ChebiTreeRow row = new ChebiTreeRow(relation.getName(), relation.getId(), mc.getUrlString(md), relation.getType());
+ lastElement = new DefaultTreeNode(row, root);
+ lastElement.setExpanded(true);
+ }
+
+ // create main chebi element
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, chebi.getChebiId());
+ ChebiTreeRow row = new ChebiTreeRow(chebi.getName(), chebi.getChebiId(), mc.getUrlString(md), "");
+
+ TreeNode element = new DefaultTreeNode(row, lastElement);
+ element.setExpanded(true);
+
+ // create children
+
+ for (ChebiRelation relation : chebi.getOutgoingChebi()) {
+ md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, relation.getId());
+ row = new ChebiTreeRow(relation.getName(), relation.getId(), mc.getUrlString(md), relation.getType());
+ new DefaultTreeNode(row, element);
+ }
+
+ return root;
+ }
+
+}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java b/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java
index 6deb513adb..ccb0e1397f 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/SearchBean.java
@@ -12,7 +12,6 @@ import javax.faces.event.ActionEvent;
import org.apache.log4j.Logger;
import org.primefaces.event.SelectEvent;
-import org.primefaces.event.map.PointSelectEvent;
import org.primefaces.model.map.LatLng;
import lcsb.mapviewer.bean.MapBean.ClientMapData;
@@ -235,23 +234,6 @@ public class SearchBean extends AbstractMarkerManagerBean<SearchElementResult> i
/**
* This method is invoked by client when map is clicked.
*
- * @param event
- * click event with coordinates
- */
- public void mapClicked(final PointSelectEvent event) {
- logger.debug("Map clicked");
- addSessionParam(STRING_SEARCH_SESSION_PARAM + getCurrentMapId(), null);
- Point2D coord = mapBean.getTopModelMapData().getcConverter().toPoint(event.getLatLng());
- addSessionParam(COORDINATE_SEARCH_SESSION_PARAM + getCurrentMapId(), coord);
- addSessionParam(COORDINATE_SEARCH_MODEL_ID_SESSION_PARAM + getCurrentMapId(), getCurrentTopModel().getId());
-
- searchByCoordinates(coord, getCurrentTopModel());
- }
-
- /**
- * This method is invoked by client when map is clicked (any map except of the
- * main).
- *
* @param actionEvent
* event data
*/
@@ -327,7 +309,7 @@ public class SearchBean extends AbstractMarkerManagerBean<SearchElementResult> i
// find objects on the map
SearchElementResult result = searchService.searchByCoordinates(searchParams);
searchService.assignIcons(result, 0);
- super.addResult(result);
+ addResult(result);
// send markers to the map
refreshDataInJavascript(false);
@@ -415,6 +397,9 @@ public class SearchBean extends AbstractMarkerManagerBean<SearchElementResult> i
* @see #mapBean
*/
public MapBean getMapBean() {
+ if (mapBean == null) {
+ mapBean = findBean(MapBean.class);
+ }
return mapBean;
}
@@ -614,7 +599,7 @@ public class SearchBean extends AbstractMarkerManagerBean<SearchElementResult> i
* @return currently browsed map
*/
private Model getCurrentTopModel() {
- return mapBean.getCurrentTopModel();
+ return getMapBean().getCurrentTopModel();
}
/**
diff --git a/web/src/main/webapp/resources/pfcomp/aliasSearchElement.xhtml b/web/src/main/webapp/resources/pfcomp/aliasSearchElement.xhtml
index dc79b4d0bc..131d68e83d 100644
--- a/web/src/main/webapp/resources/pfcomp/aliasSearchElement.xhtml
+++ b/web/src/main/webapp/resources/pfcomp/aliasSearchElement.xhtml
@@ -106,11 +106,12 @@
</div>
</h:panelGroup>
- <p:panel header="Candidates" toggleable="true" rendered="#{((not empty cc.attrs.element.dataMining[0]) or (not empty cc.attrs.element.dataMining[1]))}" collapsed="true" style="font-size: 100%;width:100%" >
- <h:dataTable value="#{cc.attrs.element.dataMining}" var="candidateRow">
+ <p:panel header="Candidates" toggleable="true" rendered="#{not empty cc.attrs.element.other['dataMining']}" collapsed="true" style="font-size: 100%;width:100%" >
+
+ <h:dataTable value="#{cc.attrs.element.other['dataMining']}" var="candidateRow">
<h:column>
<f:facet name="header">
- <a href="#{cc.attrs.element.dataMiningColumns[0].link}" target="_blank">#{cc.attrs.element.dataMiningColumns[0].name}</a>
+ <a href="#{cc.attrs.element.other['dataMiningColumns'][0].link}" target="_blank">#{cc.attrs.element.other['dataMiningColumns'][0].name}</a>
</f:facet>
<ui:repeat var="suggestedElement" value="#{candidateRow[0].suggestedElements}">
@@ -124,7 +125,7 @@
</h:column>
<h:column>
- <f:facet name="header">#{cc.attrs.element.dataMiningColumns[1].name}</f:facet>
+ <f:facet name="header">#{cc.attrs.element.other['dataMiningColumns'][1].name}</f:facet>
<ui:repeat var="suggestedElement" value="#{candidateRow[1].suggestedElements}">
<h:panelGroup layout="block" rendered="#{empty suggestedElement.link}">
<h:outputText value="#{suggestedElement.name}" />,
--
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