diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index 534d8432b41e771f39fd170a54356001aa6cd48d..f7da34ff5dfc2d45ffe2881c0a8e5bd916aeb390 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -10,6 +10,7 @@ import java.util.Map;
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.comparator.StringComparator;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.map.BioEntity;
@@ -20,6 +21,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -60,6 +62,8 @@ public class ColorModelCommand extends ModelCommand {
*/
private ElementUtils eu = new ElementUtils();
+ private StringComparator stringComparator = new StringComparator();
+
/**
* Default constructor.
*
@@ -125,6 +129,9 @@ public class ColorModelCommand extends ModelCommand {
if (schema.getName() != null) {
return false;
}
+ if (!modelMatch(reaction.getModelData(), schema)) {
+ return false;
+ }
if (schema.getReactionIdentifier() != null
&& schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
@@ -150,6 +157,19 @@ public class ColorModelCommand extends ModelCommand {
return false;
}
+ private boolean modelMatch(ModelData model, ColorSchema schema) {
+ if (schema.getModelName() != null && !schema.getModelName().isEmpty()) {
+ if (model == null) {
+ logger.warn("Model of element is null...");
+ return false;
+ }
+ if (stringComparator.compare(model.getName(), schema.getModelName()) != 0) {
+ return false;
+ }
+ }
+ return true;
+ }
+
/**
* Applies color schema into the {@link Element}.
*
@@ -181,6 +201,9 @@ public class ColorModelCommand extends ModelCommand {
*/
protected boolean match(Element element, ColorSchema schema) {
if (element instanceof Species) {
+ if (!modelMatch(element.getModelData(), schema)) {
+ return false;
+ }
if (schema.getName() != null) {
if (!element.getName().equalsIgnoreCase(schema.getName())) {
return false;
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 6514aa1dc9b1550344228b8dfc1294502bfec864..d523a7c938e27f7168f6e8048cbb3e44e804c92f 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -362,4 +362,94 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
+ @Test
+ public void testReactionColoringWithModelNotMatching() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re4");
+ schema.setName(null);
+ schema.setModelName(model.getName() + "XXX");
+
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(0, map.values().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoringWithModelMatch() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re4");
+ schema.setName(null);
+ schema.setModelName(model.getName());
+
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(1, map.values().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasColoringWithModelNotMatching() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setName("CNC");
+ schema.setModelName(model.getName() + "XXX");
+
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(0, map.values().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasColoringWithModelMatch() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setName("CNC");
+ schema.setModelName(model.getName());
+
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(1, map.values().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
index 4b2c13e3e2ee5ed59bbd8ffeff5e72869170bfbb..e4a4b1f2e2e1dcfecfcefd5151066e4b4e7850df 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/ColorSchema.java
@@ -8,12 +8,13 @@ import java.util.List;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
/**
* Entry of coloring schema used for changing colors in the map. It allows to
- * identify some elements by use of the filters (by name, type, etcs.) and
- * contains information about the color that should be assigned to the fileter
+ * identify some elements by use of the filters (by name, type, etc.) and
+ * contains information about the color that should be assigned to the filter
* elements.
*
* @author Piotr Gawron
@@ -21,436 +22,449 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class ColorSchema implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Name of the {@link Element Element}. If null
- * then this field will be skiped.
- */
- private String name = null;
-
- /**
- * Identifier of the reaction to change the color.
- */
- private String reactionIdentifier = null;
-
- /**
- * Should the direction of highlighted reaction be reversed.
- */
- private Boolean reverseReaction = null;
-
- /**
- * Width of the line in the reaction.
- */
- private Double lineWidth = null;
-
- /**
- * In which compartments (identified by name) the element can occur.
- */
- private List<String> compartments = new ArrayList<String>();
-
- /**
- * What types of element should be identified by this entry.
- */
- private List<Class<? extends Element>> types = new ArrayList<>();
-
- /**
- * Value (-1..1 range) that is assigned to filtered elements (it will be
- * transformed into color later on). Only one of the {@link #value} and
- * {@link #color} can be set.
- */
- private Double value = null;
-
- /**
- * Color that is assigned to filtered elements. Only one of the {@link #value}
- * and {@link #color} can be set.
- */
- private Color color = null;
-
- /**
- * General identifier that identifies the element.
- */
- private String generalIdentifier = null;
-
- /**
- * List of specific identifiers that filter the elements.
- */
- private List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
-
- /**
- * Number of elements matched by this entry.
- */
- private int matches = 0;
-
- /**
- * Short description of the entry.
- */
- private String description;
-
- /**
- * Default constructor.
- */
- protected ColorSchema() {
- }
-
- /**
- * Initializes object by copying data from the parameter.
- *
- * @param original
- * original object used for initialization
- */
- protected ColorSchema(ColorSchema original) {
- this.setName(original.getName());
- this.setReactionIdentifier(original.getReactionIdentifier());
- this.setReverseReaction(original.getReverseReaction());
- this.setLineWidth(original.getLineWidth());
- this.addCompartments(original.getCompartments());
- this.addTypes(original.getTypes());
- this.setValue(original.getValue());
- this.setColor(original.getColor());
- this.setGeneralIdentifier(original.getGeneralIdentifier());
- this.addIdentifierColumns(original.getIdentifierColumns());
- this.setMatches(original.getMatches());
- this.setDescription(original.getDescription());
- }
-
- /**
- * Adds identifiers to {@link #identifierColumns} list.
- *
- * @param identifierColumnsList
- * list of pairs defining type of identifier and the identifier value
- */
- public void addIdentifierColumns(List<Pair<MiriamType, String>> identifierColumnsList) {
- for (Pair<MiriamType, String> pair : identifierColumnsList) {
- addIdentifierColumn(pair);
- }
-
- }
-
- /**
- * Adds class types to {@link #types} list.
- *
- * @param types2
- * list of classes to add
- */
- public void addTypes(List<Class<? extends Element>> types2) {
- for (Class<? extends Element> clazz : types2) {
- addType(clazz);
- }
- }
-
- /**
- * Adds compartment names to {@link #compartments} list.
- *
- * @param compartments2
- * elements to add
- */
- public void addCompartments(String[] compartments2) {
- for (String string : compartments2) {
- compartments.add(string);
- }
- }
-
- /**
- * Adds compartment names to {@link #compartments} list.
- *
- * @param compartments2
- * elements to add
- */
- public void addCompartments(Collection<String> compartments2) {
- for (String string : compartments2) {
- compartments.add(string);
- }
- }
-
- @Override
- public String toString() {
- StringBuilder result = new StringBuilder();
- result.append("[");
- if (name != null) {
- result.append(name + ",");
- }
- if (compartments.size() > 0) {
- result.append("(");
- for (String comp : compartments) {
- result.append(comp + ",");
- }
- result.append("),");
- }
- if (types.size() > 0) {
- result.append("(");
- for (Class<?> clazz : types) {
- result.append(clazz.getSimpleName() + ",");
- }
- result.append("),");
- }
- if (value != null) {
- result.append(value + ",");
- }
- if (color != null) {
- result.append(color + ",");
- }
- if (generalIdentifier != null) {
- result.append(generalIdentifier + ",");
- }
- if (types.size() > 0) {
- result.append("(");
- for (Pair<MiriamType, String> pair : identifierColumns) {
- result.append(pair.getLeft() + "-" + pair.getRight() + ",");
- }
- result.append("),");
- }
- result.append(matches + "]");
- return result.toString();
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- if (name == null) {
- this.name = null;
- } else {
- this.name = name.trim();
- }
- }
-
- /**
- * @return the compartments
- * @see #compartments
- */
- public List<String> getCompartments() {
- return compartments;
- }
-
- /**
- * @param compartments
- * the compartments to set
- * @see #compartments
- */
- public void setCompartments(List<String> compartments) {
- this.compartments = compartments;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public List<Class<? extends Element>> getTypes() {
- return types;
- }
-
- /**
- * @param types
- * the types to set
- * @see #types
- */
- public void setTypes(List<Class<? extends Element>> types) {
- this.types = types;
- }
-
- /**
- * @return the value
- * @see #value
- */
- public Double getValue() {
- return value;
- }
-
- /**
- * @param value
- * the value to set
- * @see #value
- */
- public void setValue(Double value) {
- this.value = value;
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the generalIdentifier
- * @see #generalIdentifier
- */
- public String getGeneralIdentifier() {
- return generalIdentifier;
- }
-
- /**
- * @param generalIdentifier
- * the generalIdentifier to set
- * @see #generalIdentifier
- */
- public void setGeneralIdentifier(String generalIdentifier) {
- this.generalIdentifier = generalIdentifier;
- }
-
- /**
- * @return the identifierColumns
- * @see #identifierColumns
- */
- public List<Pair<MiriamType, String>> getIdentifierColumns() {
- return identifierColumns;
- }
-
- /**
- * @param identifierColumns
- * the identifierColumns to set
- * @see #identifierColumns
- */
- public void setIdentifierColumns(List<Pair<MiriamType, String>> identifierColumns) {
- this.identifierColumns = identifierColumns;
- }
-
- /**
- * @return the matches
- * @see #matches
- */
- public int getMatches() {
- return matches;
- }
-
- /**
- * @param matches
- * the matches to set
- * @see #matches
- */
- public void setMatches(int matches) {
- this.matches = matches;
- }
-
- /**
- * Adds identifier to {@link #identifierColumns} list.
- *
- * @param pair
- * pair defining type of identifier and the identifier value
- */
- public void addIdentifierColumn(Pair<MiriamType, String> pair) {
- identifierColumns.add(pair);
-
- }
-
- /**
- * @return the reactionIdentifier
- * @see #reactionIdentifier
- */
- public String getReactionIdentifier() {
- return reactionIdentifier;
- }
-
- /**
- * @param reactionIdentifier
- * the reactionIdentifier to set
- * @see #reactionIdentifier
- */
- public void setReactionIdentifier(String reactionIdentifier) {
- this.reactionIdentifier = reactionIdentifier;
- }
-
- /**
- * @return the lineWidth
- * @see #lineWidth
- */
- public Double getLineWidth() {
- return lineWidth;
- }
-
- /**
- * @param lineWidth
- * the lineWidth to set
- * @see #lineWidth
- */
- public void setLineWidth(Double lineWidth) {
- this.lineWidth = lineWidth;
- }
-
- /**
- * @return the reverseReaction
- * @see #reverseReaction
- */
- public Boolean getReverseReaction() {
- return reverseReaction;
- }
-
- /**
- * @param reverseReaction
- * the reverseReaction to set
- * @see #reverseReaction
- */
- public void setReverseReaction(Boolean reverseReaction) {
- this.reverseReaction = reverseReaction;
- }
-
- /**
- * Adds compartment name to {@link #compartments}.
- *
- * @param name
- * compartment name
- */
- public void addCompartment(String name) {
- compartments.add(name);
- }
-
- /**
- * Adds class type to {@link #types} list.
- *
- * @param clazz
- * class to add
- */
- public void addType(Class<? extends Element> clazz) {
- this.types.add(clazz);
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * Creates a copy of this object.
- *
- * @return copy of the object
- */
- public abstract ColorSchema copy();
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Name of the {@link Element Element}. If null then this field will be skipped.
+ */
+ private String name = null;
+
+ /**
+ * Name of the {@link Model} to which this schema should be limited. If null
+ * then this field will be skipped.
+ */
+ private String modelName = null;
+
+ /**
+ * Identifier of the reaction to change the color.
+ */
+ private String reactionIdentifier = null;
+
+ /**
+ * Should the direction of highlighted reaction be reversed.
+ */
+ private Boolean reverseReaction = null;
+
+ /**
+ * Width of the line in the reaction.
+ */
+ private Double lineWidth = null;
+
+ /**
+ * In which compartments (identified by name) the element can occur.
+ */
+ private List<String> compartments = new ArrayList<String>();
+
+ /**
+ * What types of element should be identified by this entry.
+ */
+ private List<Class<? extends Element>> types = new ArrayList<>();
+
+ /**
+ * Value (-1..1 range) that is assigned to filtered elements (it will be
+ * transformed into color later on). Only one of the {@link #value} and
+ * {@link #color} can be set.
+ */
+ private Double value = null;
+
+ /**
+ * Color that is assigned to filtered elements. Only one of the {@link #value}
+ * and {@link #color} can be set.
+ */
+ private Color color = null;
+
+ /**
+ * General identifier that identifies the element.
+ */
+ private String generalIdentifier = null;
+
+ /**
+ * List of specific identifiers that filter the elements.
+ */
+ private List<Pair<MiriamType, String>> identifierColumns = new ArrayList<>();
+
+ /**
+ * Number of elements matched by this entry.
+ */
+ private int matches = 0;
+
+ /**
+ * Short description of the entry.
+ */
+ private String description;
+
+ /**
+ * Default constructor.
+ */
+ protected ColorSchema() {
+ }
+
+ /**
+ * Initializes object by copying data from the parameter.
+ *
+ * @param original
+ * original object used for initialization
+ */
+ protected ColorSchema(ColorSchema original) {
+ this.setName(original.getName());
+ this.setReactionIdentifier(original.getReactionIdentifier());
+ this.setReverseReaction(original.getReverseReaction());
+ this.setLineWidth(original.getLineWidth());
+ this.addCompartments(original.getCompartments());
+ this.addTypes(original.getTypes());
+ this.setValue(original.getValue());
+ this.setColor(original.getColor());
+ this.setGeneralIdentifier(original.getGeneralIdentifier());
+ this.addIdentifierColumns(original.getIdentifierColumns());
+ this.setMatches(original.getMatches());
+ this.setDescription(original.getDescription());
+ }
+
+ /**
+ * Adds identifiers to {@link #identifierColumns} list.
+ *
+ * @param identifierColumnsList
+ * list of pairs defining type of identifier and the identifier value
+ */
+ public void addIdentifierColumns(List<Pair<MiriamType, String>> identifierColumnsList) {
+ for (Pair<MiriamType, String> pair : identifierColumnsList) {
+ addIdentifierColumn(pair);
+ }
+
+ }
+
+ /**
+ * Adds class types to {@link #types} list.
+ *
+ * @param types2
+ * list of classes to add
+ */
+ public void addTypes(List<Class<? extends Element>> types2) {
+ for (Class<? extends Element> clazz : types2) {
+ addType(clazz);
+ }
+ }
+
+ /**
+ * Adds compartment names to {@link #compartments} list.
+ *
+ * @param compartments2
+ * elements to add
+ */
+ public void addCompartments(String[] compartments2) {
+ for (String string : compartments2) {
+ compartments.add(string);
+ }
+ }
+
+ /**
+ * Adds compartment names to {@link #compartments} list.
+ *
+ * @param compartments2
+ * elements to add
+ */
+ public void addCompartments(Collection<String> compartments2) {
+ for (String string : compartments2) {
+ compartments.add(string);
+ }
+ }
+
+ @Override
+ public String toString() {
+ StringBuilder result = new StringBuilder();
+ result.append("[");
+ if (name != null) {
+ result.append(name + ",");
+ }
+ if (compartments.size() > 0) {
+ result.append("(");
+ for (String comp : compartments) {
+ result.append(comp + ",");
+ }
+ result.append("),");
+ }
+ if (types.size() > 0) {
+ result.append("(");
+ for (Class<?> clazz : types) {
+ result.append(clazz.getSimpleName() + ",");
+ }
+ result.append("),");
+ }
+ if (value != null) {
+ result.append(value + ",");
+ }
+ if (color != null) {
+ result.append(color + ",");
+ }
+ if (generalIdentifier != null) {
+ result.append(generalIdentifier + ",");
+ }
+ if (types.size() > 0) {
+ result.append("(");
+ for (Pair<MiriamType, String> pair : identifierColumns) {
+ result.append(pair.getLeft() + "-" + pair.getRight() + ",");
+ }
+ result.append("),");
+ }
+ result.append(matches + "]");
+ return result.toString();
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ if (name == null) {
+ this.name = null;
+ } else {
+ this.name = name.trim();
+ }
+ }
+
+ /**
+ * @return the compartments
+ * @see #compartments
+ */
+ public List<String> getCompartments() {
+ return compartments;
+ }
+
+ /**
+ * @param compartments
+ * the compartments to set
+ * @see #compartments
+ */
+ public void setCompartments(List<String> compartments) {
+ this.compartments = compartments;
+ }
+
+ /**
+ * @return the types
+ * @see #types
+ */
+ public List<Class<? extends Element>> getTypes() {
+ return types;
+ }
+
+ /**
+ * @param types
+ * the types to set
+ * @see #types
+ */
+ public void setTypes(List<Class<? extends Element>> types) {
+ this.types = types;
+ }
+
+ /**
+ * @return the value
+ * @see #value
+ */
+ public Double getValue() {
+ return value;
+ }
+
+ /**
+ * @param value
+ * the value to set
+ * @see #value
+ */
+ public void setValue(Double value) {
+ this.value = value;
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the generalIdentifier
+ * @see #generalIdentifier
+ */
+ public String getGeneralIdentifier() {
+ return generalIdentifier;
+ }
+
+ /**
+ * @param generalIdentifier
+ * the generalIdentifier to set
+ * @see #generalIdentifier
+ */
+ public void setGeneralIdentifier(String generalIdentifier) {
+ this.generalIdentifier = generalIdentifier;
+ }
+
+ /**
+ * @return the identifierColumns
+ * @see #identifierColumns
+ */
+ public List<Pair<MiriamType, String>> getIdentifierColumns() {
+ return identifierColumns;
+ }
+
+ /**
+ * @param identifierColumns
+ * the identifierColumns to set
+ * @see #identifierColumns
+ */
+ public void setIdentifierColumns(List<Pair<MiriamType, String>> identifierColumns) {
+ this.identifierColumns = identifierColumns;
+ }
+
+ /**
+ * @return the matches
+ * @see #matches
+ */
+ public int getMatches() {
+ return matches;
+ }
+
+ /**
+ * @param matches
+ * the matches to set
+ * @see #matches
+ */
+ public void setMatches(int matches) {
+ this.matches = matches;
+ }
+
+ /**
+ * Adds identifier to {@link #identifierColumns} list.
+ *
+ * @param pair
+ * pair defining type of identifier and the identifier value
+ */
+ public void addIdentifierColumn(Pair<MiriamType, String> pair) {
+ identifierColumns.add(pair);
+
+ }
+
+ /**
+ * @return the reactionIdentifier
+ * @see #reactionIdentifier
+ */
+ public String getReactionIdentifier() {
+ return reactionIdentifier;
+ }
+
+ /**
+ * @param reactionIdentifier
+ * the reactionIdentifier to set
+ * @see #reactionIdentifier
+ */
+ public void setReactionIdentifier(String reactionIdentifier) {
+ this.reactionIdentifier = reactionIdentifier;
+ }
+
+ /**
+ * @return the lineWidth
+ * @see #lineWidth
+ */
+ public Double getLineWidth() {
+ return lineWidth;
+ }
+
+ /**
+ * @param lineWidth
+ * the lineWidth to set
+ * @see #lineWidth
+ */
+ public void setLineWidth(Double lineWidth) {
+ this.lineWidth = lineWidth;
+ }
+
+ /**
+ * @return the reverseReaction
+ * @see #reverseReaction
+ */
+ public Boolean getReverseReaction() {
+ return reverseReaction;
+ }
+
+ /**
+ * @param reverseReaction
+ * the reverseReaction to set
+ * @see #reverseReaction
+ */
+ public void setReverseReaction(Boolean reverseReaction) {
+ this.reverseReaction = reverseReaction;
+ }
+
+ /**
+ * Adds compartment name to {@link #compartments}.
+ *
+ * @param name
+ * compartment name
+ */
+ public void addCompartment(String name) {
+ compartments.add(name);
+ }
+
+ /**
+ * Adds class type to {@link #types} list.
+ *
+ * @param clazz
+ * class to add
+ */
+ public void addType(Class<? extends Element> clazz) {
+ this.types.add(clazz);
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * Creates a copy of this object.
+ *
+ * @return copy of the object
+ */
+ public abstract ColorSchema copy();
+
+ public String getModelName() {
+ return modelName;
+ }
+
+ public void setModelName(String modelName) {
+ this.modelName = modelName;
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 4104e98609257c909f66b8b30ac8347e1dd061e0..3e56dd04c2c760331cb683e5a3cbb1cb0bb3ad9a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -792,6 +792,8 @@ public class LayoutService implements ILayoutService {
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.NAME)) {
sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.MODEL_NAME)) {
+ sb.append(schema.getModelName() + "\t");
} else if (column.equals(ColorSchemaColumn.VALUE)) {
sb.append(schema.getValue() + "\t");
} else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
@@ -847,6 +849,8 @@ public class LayoutService implements ILayoutService {
sb.append("\t");
} else if (column.equals(ColorSchemaColumn.NAME)) {
sb.append(schema.getName() + "\t");
+ } else if (column.equals(ColorSchemaColumn.MODEL_NAME)) {
+ sb.append(schema.getModelName() + "\t");
} else if (column.equals(ColorSchemaColumn.VALUE)) {
sb.append(schema.getValue() + "\t");
} else if (column.equals(ColorSchemaColumn.COMPARTMENT)) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
index 2f358661b267053ed1a0db66055ad48d1d5e005c..0176a0da7e7e1832c80d4e7c0c93cde974ef9066 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java
@@ -157,6 +157,7 @@ public class ColorSchemaReader {
Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
Integer contigColumn = schemaColumns.get(ColorSchemaColumn.CONTIG);
Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
+ Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
Integer variantIdentifierColumn = schemaColumns.get(ColorSchemaColumn.VARIANT_IDENTIFIER);
Integer allelFrequencyColumn = schemaColumns.get(ColorSchemaColumn.ALLEL_FREQUENCY);
@@ -202,6 +203,9 @@ public class ColorSchemaReader {
if (nameColumn != null) {
processNameColumn(schema, values[nameColumn]);
}
+ if (modelNameColumn != null) {
+ processModelNameColumn(schema, values[modelNameColumn]);
+ }
if (compartmentColumn != null) {
processCompartmentColumn(schema, values[compartmentColumn]);
}
@@ -328,6 +332,12 @@ public class ColorSchemaReader {
schema.setName(content);
}
}
+ private void processModelNameColumn(ColorSchema schema, String content) {
+ if (!content.isEmpty()) {
+ schema.setModelName(content);
+ }
+ }
+
/**
* Sets proper compartment names to {@link ColorSchema} from cell content.
@@ -463,6 +473,7 @@ public class ColorSchemaReader {
Integer valueColumn = schemaColumns.get(ColorSchemaColumn.VALUE);
Integer colorColumn = schemaColumns.get(ColorSchemaColumn.COLOR);
Integer nameColumn = schemaColumns.get(ColorSchemaColumn.NAME);
+ Integer modelNameColumn = schemaColumns.get(ColorSchemaColumn.MODEL_NAME);
Integer identifierColumn = schemaColumns.get(ColorSchemaColumn.IDENTIFIER);
Integer reactionIdentifierColumn = schemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
Integer compartmentColumn = schemaColumns.get(ColorSchemaColumn.COMPARTMENT);
@@ -499,6 +510,9 @@ public class ColorSchemaReader {
if (nameColumn != null) {
processNameColumn(schema, values[nameColumn]);
}
+ if (modelNameColumn != null) {
+ processModelNameColumn(schema, values[modelNameColumn]);
+ }
if (valueColumn != null) {
schema.setValue(parseValueColumn(values[valueColumn], errorPrefix));
}
@@ -729,6 +743,9 @@ public class ColorSchemaReader {
if (schema.getName() != null) {
result.add(ColorSchemaColumn.NAME);
}
+ if (schema.getModelName() != null) {
+ result.add(ColorSchemaColumn.MODEL_NAME);
+ }
if (schema.getReactionIdentifier() != null) {
result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
index f852f697bcb65ecf669503a0bd3a3022d3010e0a..be39f1a333b1a6a9ec4e9834831ebf26574d978c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaXlsxReader.java
@@ -41,285 +41,302 @@ import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
*
*/
public class ColorSchemaXlsxReader {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ColorSchemaXlsxReader.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ColorSchemaXlsxReader.class);
- /**
- * @param fileName
- * file name
- * @param sheetName
- * sheet name.
- * @return list of ColorSchema.
- * @throws IOException
- * exception related to opening the input stream.
- * @throws InvalidColorSchemaException
- * invalid color schema exception.
- */
- public Collection<ColorSchema> readColorSchema(String fileName, String sheetName) throws IOException, InvalidColorSchemaException {
- ColorParser colorParser = new ColorParser();
- List<ColorSchema> result = new ArrayList<>();
- FileInputStream file = null;
- Workbook workbook = null;
+ /**
+ * @param fileName
+ * file name
+ * @param sheetName
+ * sheet name.
+ * @return list of ColorSchema.
+ * @throws IOException
+ * exception related to opening the input stream.
+ * @throws InvalidColorSchemaException
+ * invalid color schema exception.
+ */
+ public Collection<ColorSchema> readColorSchema(String fileName, String sheetName)
+ throws IOException, InvalidColorSchemaException {
+ ColorParser colorParser = new ColorParser();
+ List<ColorSchema> result = new ArrayList<>();
+ FileInputStream file = null;
+ Workbook workbook = null;
- try {
- file = new FileInputStream(fileName);
- // Using XSSF for xlsx format, for xls use HSSF
- // <-Interface, accepts both HSSF and XSSF.
- if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xls")) {
- workbook = new HSSFWorkbook(file);
- } else if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xlsx")) {
- workbook = new XSSFWorkbook(file);
- } else {
- throw new IllegalArgumentException("Received file does not have a standard excel extension.");
- }
- Sheet sheet = null;
- if (sheetName == null) {
- sheet = workbook.getSheetAt(0);
- } else {
- sheet = workbook.getSheet(sheetName);
- }
- DataFormat fmt = workbook.createDataFormat();
- CellStyle textStyle = workbook.createCellStyle();
- textStyle.setDataFormat(fmt.getFormat("@"));
+ try {
+ file = new FileInputStream(fileName);
+ // Using XSSF for xlsx format, for xls use HSSF
+ // <-Interface, accepts both HSSF and XSSF.
+ if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xls")) {
+ workbook = new HSSFWorkbook(file);
+ } else if (FilenameUtils.getExtension(fileName).equalsIgnoreCase("xlsx")) {
+ workbook = new XSSFWorkbook(file);
+ } else {
+ throw new IllegalArgumentException("Received file does not have a standard excel extension.");
+ }
+ Sheet sheet = null;
+ if (sheetName == null) {
+ sheet = workbook.getSheetAt(0);
+ } else {
+ sheet = workbook.getSheet(sheetName);
+ }
+ DataFormat fmt = workbook.createDataFormat();
+ CellStyle textStyle = workbook.createCellStyle();
+ textStyle.setDataFormat(fmt.getFormat("@"));
- Iterator<Row> rowIterator = sheet.iterator();
- Integer valueColumn = null;
- Integer colorColumn = null;
- Integer nameColumn = null;
- Integer identifierColumn = null;
- Integer reactionIdentifierColumn = null;
- Integer compartmentColumn = null;
- Integer typeColumn = null;
- Integer lineWidthColumn = null;
- Integer reverseReactionColumn = null;
- List<Pair<MiriamType, Integer>> foundCustomIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
- int lineIndex = 0;
- Map<ColorSchemaColumn, Integer> foundSchemaColumns = new HashMap<ColorSchemaColumn, Integer>();
- while (rowIterator.hasNext()) {
- Row row = rowIterator.next();
- Cell cell = row.getCell(0, Row.RETURN_BLANK_AS_NULL);
- if (cell == null) {
- continue;
- } else {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- if (cell.getStringCellValue().startsWith("#")) {
- continue;
- }
- }
- lineIndex++;
- if (lineIndex == 1) {
+ Iterator<Row> rowIterator = sheet.iterator();
+ Integer valueColumn = null;
+ Integer colorColumn = null;
+ Integer nameColumn = null;
+ Integer modelNameColumn = null;
+ Integer identifierColumn = null;
+ Integer reactionIdentifierColumn = null;
+ Integer compartmentColumn = null;
+ Integer typeColumn = null;
+ Integer lineWidthColumn = null;
+ Integer reverseReactionColumn = null;
+ List<Pair<MiriamType, Integer>> foundCustomIdentifiers = new ArrayList<Pair<MiriamType, Integer>>();
+ int lineIndex = 0;
+ Map<ColorSchemaColumn, Integer> foundSchemaColumns = new HashMap<ColorSchemaColumn, Integer>();
+ while (rowIterator.hasNext()) {
+ Row row = rowIterator.next();
+ Cell cell = row.getCell(0, Row.RETURN_BLANK_AS_NULL);
+ if (cell == null) {
+ continue;
+ } else {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ if (cell.getStringCellValue().startsWith("#")) {
+ continue;
+ }
+ }
+ lineIndex++;
+ if (lineIndex == 1) {
- Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
- for (MiriamType type : MiriamType.values()) {
- acceptableIdentifiers.put(type.getCommonName().toLowerCase(), type);
- }
+ Map<String, MiriamType> acceptableIdentifiers = new HashMap<String, MiriamType>();
+ for (MiriamType type : MiriamType.values()) {
+ acceptableIdentifiers.put(type.getCommonName().toLowerCase(), type);
+ }
- Iterator<Cell> cellIterator = row.cellIterator();
- int columnIndex = 0;
- while (cellIterator.hasNext()) {
- columnIndex++;
- sheet.setDefaultColumnStyle(columnIndex, textStyle);
- cell = cellIterator.next();
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String value = cell.getStringCellValue();
- boolean found = false;
- for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
- foundSchemaColumns.put(schemaColumn, columnIndex - 1);
- found = true;
- break;
- }
- }
- if (!found) {
- if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
- foundCustomIdentifiers.add(new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
- } else {
- String columnNames = "";
- for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
- columnNames += schemaColumn.getTitle() + ", ";
- }
- for (String string : acceptableIdentifiers.keySet()) {
- columnNames += ", " + string;
- }
- throw new InvalidColorSchemaException("Unknown column type: " + value + ". Acceptable column name: " + columnNames);
- }
- }
- }
- valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE);
- colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR);
- nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
- identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
- reactionIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
- compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
- typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
- lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
- reverseReactionColumn = foundSchemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
+ Iterator<Cell> cellIterator = row.cellIterator();
+ int columnIndex = 0;
+ while (cellIterator.hasNext()) {
+ columnIndex++;
+ sheet.setDefaultColumnStyle(columnIndex, textStyle);
+ cell = cellIterator.next();
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = cell.getStringCellValue();
+ boolean found = false;
+ for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
+ if (value.trim().equalsIgnoreCase(schemaColumn.getTitle())) {
+ foundSchemaColumns.put(schemaColumn, columnIndex - 1);
+ found = true;
+ break;
+ }
+ }
+ if (!found) {
+ if (acceptableIdentifiers.keySet().contains(value.toLowerCase())) {
+ foundCustomIdentifiers.add(
+ new Pair<MiriamType, Integer>(acceptableIdentifiers.get(value.toLowerCase()), columnIndex - 1));
+ } else {
+ String columnNames = "";
+ for (ColorSchemaColumn schemaColumn : ColorSchemaColumn.values()) {
+ columnNames += schemaColumn.getTitle() + ", ";
+ }
+ for (String string : acceptableIdentifiers.keySet()) {
+ columnNames += ", " + string;
+ }
+ throw new InvalidColorSchemaException(
+ "Unknown column type: " + value + ". Acceptable column name: " + columnNames);
+ }
+ }
+ }
+ valueColumn = foundSchemaColumns.get(ColorSchemaColumn.VALUE);
+ colorColumn = foundSchemaColumns.get(ColorSchemaColumn.COLOR);
+ nameColumn = foundSchemaColumns.get(ColorSchemaColumn.NAME);
+ modelNameColumn = foundSchemaColumns.get(ColorSchemaColumn.MODEL_NAME);
+ identifierColumn = foundSchemaColumns.get(ColorSchemaColumn.IDENTIFIER);
+ reactionIdentifierColumn = foundSchemaColumns.get(ColorSchemaColumn.REACTION_IDENTIFIER);
+ compartmentColumn = foundSchemaColumns.get(ColorSchemaColumn.COMPARTMENT);
+ typeColumn = foundSchemaColumns.get(ColorSchemaColumn.TYPE);
+ lineWidthColumn = foundSchemaColumns.get(ColorSchemaColumn.LINE_WIDTH);
+ reverseReactionColumn = foundSchemaColumns.get(ColorSchemaColumn.REVERSE_REACTION);
- if (valueColumn != null && colorColumn != null) {
- throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
- }
+ if (valueColumn != null && colorColumn != null) {
+ throw new InvalidColorSchemaException("Schema can contain only one of these two columns: ");
+ }
- if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0 && reactionIdentifierColumn == null) {
- throw new InvalidColorSchemaException("One of these columns is obligatory: name, identifier, reactionIdentifier");
- }
+ if (nameColumn == null && identifierColumn == null && foundCustomIdentifiers.size() == 0
+ && reactionIdentifierColumn == null) {
+ throw new InvalidColorSchemaException(
+ "One of these columns is obligatory: name, identifier, reactionIdentifier");
+ }
- if (valueColumn == null && colorColumn == null) {
- throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
- }
+ if (valueColumn == null && colorColumn == null) {
+ throw new InvalidColorSchemaException("Schema must contain one of these two columns: value, name");
+ }
- } else {
- ColorSchema schema = new GenericColorSchema();
- if (nameColumn != null) {
- schema.setName(row.getCell(nameColumn).getStringCellValue());
- }
- if (valueColumn != null) {
- try {
- cell = row.getCell(valueColumn);
- cell.setCellType(Cell.CELL_TYPE_STRING);
- schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
- } catch (Exception e) {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
- }
- if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
- throw new InvalidColorSchemaException(
- "[Line " + lineIndex + "] Value " + schema.getValue() + " out of range. Only values between -1 and 1 are allowed.");
- }
- }
- if (compartmentColumn != null) {
- String value = row.getCell(compartmentColumn).getStringCellValue();
- if (value != null) {
- String[] compartments = value.split(",");
- schema.addCompartments(compartments);
- }
- }
- if (typeColumn != null) {
- String value = row.getCell(typeColumn).getStringCellValue();
- if (value != null) {
- String[] types = value.split(",");
- for (String string : types) {
- SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
- if (mapping != null) {
- schema.addType(mapping.getModelClazz());
- } else {
- throw new InvalidColorSchemaException("Unknown class type: " + string + ".");
- }
- }
- }
- }
- if (colorColumn != null) {
- schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
- }
- if (reactionIdentifierColumn != null) {
- schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
- }
- if (lineWidthColumn != null) {
- cell = row.getCell(lineWidthColumn);
- cell.setCellType(Cell.CELL_TYPE_STRING);
- String value = cell.getStringCellValue();
- if (value != null && !value.trim().isEmpty()) {
- try {
- schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
- } catch (NumberFormatException e) {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
- }
- }
- }
- if (reverseReactionColumn != null) {
- cell = row.getCell(reverseReactionColumn);
- if (cell != null) {
- cell.setCellType(Cell.CELL_TYPE_STRING);
- schema.setReverseReaction("true".equalsIgnoreCase(cell.getStringCellValue()));
- }
- }
- if (identifierColumn != null) {
- cell = row.getCell(identifierColumn);
- if (cell != null && !cell.getStringCellValue().trim().isEmpty()) {
- MiriamConnector miriamConnector = new MiriamConnector();
- String value = cell.getStringCellValue().trim();
- if (miriamConnector.isValidIdentifier(value)) {
- schema.setGeneralIdentifier(value);
- } else {
- throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
- }
- }
- }
- for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
- cell = row.getCell(pair.getRight());
- if (cell != null) {
- schema.addIdentifierColumn(new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
- }
- }
+ } else {
+ ColorSchema schema = new GenericColorSchema();
+ if (nameColumn != null) {
+ schema.setName(row.getCell(nameColumn).getStringCellValue());
+ }
+ if (modelNameColumn != null) {
+ schema.setModelName(row.getCell(modelNameColumn).getStringCellValue());
+ }
+ if (valueColumn != null) {
+ try {
+ cell = row.getCell(valueColumn);
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ schema.setValue(Double.parseDouble(cell.getStringCellValue().replace(",", ".")));
+ } catch (Exception e) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Problem with parsing value for value column. Cell value" + cell);
+ }
+ if (schema.getValue() > 1 + Configuration.EPSILON || schema.getValue() < -1 - Configuration.EPSILON) {
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "] Value " + schema.getValue()
+ + " out of range. Only values between -1 and 1 are allowed.");
+ }
+ }
+ if (compartmentColumn != null) {
+ String value = row.getCell(compartmentColumn).getStringCellValue();
+ if (value != null) {
+ String[] compartments = value.split(",");
+ schema.addCompartments(compartments);
+ }
+ }
+ if (typeColumn != null) {
+ String value = row.getCell(typeColumn).getStringCellValue();
+ if (value != null) {
+ String[] types = value.split(",");
+ for (String string : types) {
+ SpeciesMapping mapping = SpeciesMapping.getMappingByString(string);
+ if (mapping != null) {
+ schema.addType(mapping.getModelClazz());
+ } else {
+ throw new InvalidColorSchemaException("Unknown class type: " + string + ".");
+ }
+ }
+ }
+ }
+ if (colorColumn != null) {
+ schema.setColor(colorParser.parse(row.getCell(colorColumn).getStringCellValue()));
+ }
+ if (reactionIdentifierColumn != null) {
+ schema.setReactionIdentifier(row.getCell(reactionIdentifierColumn).getStringCellValue());
+ }
+ if (lineWidthColumn != null) {
+ cell = row.getCell(lineWidthColumn);
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ String value = cell.getStringCellValue();
+ if (value != null && !value.trim().isEmpty()) {
+ try {
+ schema.setLineWidth(Double.parseDouble(value.replace(",", ".")));
+ } catch (NumberFormatException e) {
+ throw new InvalidColorSchemaException(
+ "[Line " + lineIndex + "] Problem with parsing value: \"" + value + "\"");
+ }
+ }
+ }
+ if (reverseReactionColumn != null) {
+ cell = row.getCell(reverseReactionColumn);
+ if (cell != null) {
+ cell.setCellType(Cell.CELL_TYPE_STRING);
+ schema.setReverseReaction("true".equalsIgnoreCase(cell.getStringCellValue()));
+ }
+ }
+ if (identifierColumn != null) {
+ cell = row.getCell(identifierColumn);
+ if (cell != null && !cell.getStringCellValue().trim().isEmpty()) {
+ MiriamConnector miriamConnector = new MiriamConnector();
+ String value = cell.getStringCellValue().trim();
+ if (miriamConnector.isValidIdentifier(value)) {
+ schema.setGeneralIdentifier(value);
+ } else {
+ throw new InvalidColorSchemaException("[Line " + lineIndex + "]" + " Invalid identifier: " + value);
+ }
+ }
+ }
+ for (Pair<MiriamType, Integer> pair : foundCustomIdentifiers) {
+ cell = row.getCell(pair.getRight());
+ if (cell != null) {
+ schema.addIdentifierColumn(new Pair<MiriamType, String>(pair.getLeft(), cell.getStringCellValue()));
+ }
+ }
- if ((schema.getValue() != null && schema.getColor() != null) || (schema.getValue() == null && schema.getColor() == null)) {
- throw new InvalidColorSchemaException("Value or Color is needed not both");
- }
+ if ((schema.getValue() != null && schema.getColor() != null)
+ || (schema.getValue() == null && schema.getColor() == null)) {
+ throw new InvalidColorSchemaException("Value or Color is needed not both");
+ }
- if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
- && schema.getReactionIdentifier() == null) {
- throw new InvalidColorSchemaException("One of these columns values is obligatory: name, identifier, reactionIdentifier");
- }
- result.add(schema);
- }
- }
- } finally {
- try {
- if (file != null) {
- file.close();
- }
- if (workbook != null) {
- workbook.close();
- }
- } catch (Exception e) {
+ if (schema.getName() == null && schema.getGeneralIdentifier() == null && foundCustomIdentifiers.size() == 0
+ && schema.getReactionIdentifier() == null) {
+ throw new InvalidColorSchemaException(
+ "One of these columns values is obligatory: name, identifier, reactionIdentifier");
+ }
+ result.add(schema);
+ }
+ }
+ } finally {
+ try {
+ if (file != null) {
+ file.close();
+ }
+ if (workbook != null) {
+ workbook.close();
+ }
+ } catch (Exception e) {
- }
- }
- return result;
+ }
+ }
+ return result;
- }
+ }
- /**
- * Returns list of columns that should be printed for given coloring schemas.
- *
- * @param schemas
- * list of schemas
- * @return list of columns that should be printed (were set in the coloring
- * schemas)
- */
- public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
- Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
- for (ColorSchema schema : schemas) {
- if (schema.getColor() != null) {
- result.add(ColorSchemaColumn.COLOR);
- }
- if (schema.getCompartments().size() > 0) {
- result.add(ColorSchemaColumn.COMPARTMENT);
- }
- if (schema.getGeneralIdentifier() != null || schema.getIdentifierColumns().size() > 0) {
- result.add(ColorSchemaColumn.IDENTIFIER);
- }
- if (schema.getLineWidth() != null) {
- result.add(ColorSchemaColumn.LINE_WIDTH);
- }
- if (schema.getName() != null) {
- result.add(ColorSchemaColumn.NAME);
- }
- if (schema.getReactionIdentifier() != null) {
- result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
- }
- if (schema.getReverseReaction() != null) {
- result.add(ColorSchemaColumn.REVERSE_REACTION);
- }
- if (schema.getTypes().size() > 0) {
- result.add(ColorSchemaColumn.TYPE);
- }
- if (schema.getValue() != null) {
- result.add(ColorSchemaColumn.VALUE);
- }
- }
- return result;
- }
+ /**
+ * Returns list of columns that should be printed for given coloring schemas.
+ *
+ * @param schemas
+ * list of schemas
+ * @return list of columns that should be printed (were set in the coloring
+ * schemas)
+ */
+ public Collection<ColorSchemaColumn> getSetColorSchemaColumns(Collection<ColorSchema> schemas) {
+ Set<ColorSchemaColumn> result = new HashSet<ColorSchemaColumn>();
+ for (ColorSchema schema : schemas) {
+ if (schema.getColor() != null) {
+ result.add(ColorSchemaColumn.COLOR);
+ }
+ if (schema.getCompartments().size() > 0) {
+ result.add(ColorSchemaColumn.COMPARTMENT);
+ }
+ if (schema.getGeneralIdentifier() != null || schema.getIdentifierColumns().size() > 0) {
+ result.add(ColorSchemaColumn.IDENTIFIER);
+ }
+ if (schema.getLineWidth() != null) {
+ result.add(ColorSchemaColumn.LINE_WIDTH);
+ }
+ if (schema.getName() != null) {
+ result.add(ColorSchemaColumn.NAME);
+ }
+ if (schema.getModelName() != null) {
+ result.add(ColorSchemaColumn.MODEL_NAME);
+ }
+ if (schema.getReactionIdentifier() != null) {
+ result.add(ColorSchemaColumn.REACTION_IDENTIFIER);
+ }
+ if (schema.getReverseReaction() != null) {
+ result.add(ColorSchemaColumn.REVERSE_REACTION);
+ }
+ if (schema.getTypes().size() > 0) {
+ result.add(ColorSchemaColumn.TYPE);
+ }
+ if (schema.getValue() != null) {
+ result.add(ColorSchemaColumn.VALUE);
+ }
+ }
+ return result;
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
index 6792e10ef5b0ebff44da960be6ad99a953e9ab1f..a5a4025546064af5b3c53c2b64941f900d7408b5 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/ColorSchemaColumn.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.services.utils.data;
import java.util.HashSet;
import java.util.Set;
-
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
@@ -16,136 +15,141 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
*/
public enum ColorSchemaColumn {
- /**
- * Name of the element.
- */
- NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Value that will be transformed into new color.
- *
- * @see ColorSchemaColumn#COLOR
- */
- VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * In which compartment the element should be located.
- */
- COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Class type of the element.
- */
- TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * New element/reaction color.
- */
- COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Identifier of the element.
- */
- IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Reaction identifier.
- */
- REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * New line width of the reaction.
- */
- LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
-
- /**
- * Position where gene variants starts.
- */
- POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Original DNA of the variant.
- */
- ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Alternative DNA of the variant.
- */
- ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Short description of the entry.
- */
- DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
-
- /**
- * Variant references.
- */
- REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * What's the {@link ReferenceGenomeType}.
- */
- REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * {@link ReferenceGenome#version Version} of the reference genome.
- */
- REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Contig where variant was observed.
- */
- CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
-
- /**
- * Should the direction of reaction be reversed.
- */
- REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }); //
-
- /**
- * Default constructor that creates enum entry.
- *
- * @param title
- * {@link #title}
- * @param types
- * list of {@link ColumnType types} where this column is allowed
- */
- ColorSchemaColumn(String title, ColorSchemaType[] types) {
- this.title = title;
- for (ColorSchemaType colorSchemaType : types) {
- this.types.add(colorSchemaType);
- }
- }
-
- /**
- * Human readable title used in input file.
- */
- private String title;
-
- /**
- * Set of types where column is allowed.
- */
- private Set<ColorSchemaType> types = new HashSet<>();
-
- /**
- *
- * @return {@link #title}
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * @return the types
- * @see #types
- */
- public Set<ColorSchemaType> getTypes() {
- return types;
- }
+ /**
+ * Name of the element.
+ */
+ NAME("name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Name of the element.
+ */
+ MODEL_NAME("model_name", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Value that will be transformed into new color.
+ *
+ * @see ColorSchemaColumn#COLOR
+ */
+ VALUE("value", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * In which compartment the element should be located.
+ */
+ COMPARTMENT("compartment", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Class type of the element.
+ */
+ TYPE("type", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * New element/reaction color.
+ */
+ COLOR("color", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Identifier of the element.
+ */
+ IDENTIFIER("identifier", new ColorSchemaType[] { ColorSchemaType.GENERIC, ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Reaction identifier.
+ */
+ REACTION_IDENTIFIER("reactionIdentifier", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * New line width of the reaction.
+ */
+ LINE_WIDTH("lineWidth", new ColorSchemaType[] { ColorSchemaType.GENERIC }), //
+
+ /**
+ * Position where gene variants starts.
+ */
+ POSITION("position", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Original DNA of the variant.
+ */
+ ORIGINAL_DNA("original_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Alternative DNA of the variant.
+ */
+ ALTERNATIVE_DNA("alternative_dna", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Short description of the entry.
+ */
+ DESCRIPTION("description", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT, ColorSchemaType.GENERIC }), //
+
+ /**
+ * Variant references.
+ */
+ REFERENCES("references", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * What's the {@link ReferenceGenomeType}.
+ */
+ REFERENCE_GENOME_TYPE("reference_genome_type", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * {@link ReferenceGenome#version Version} of the reference genome.
+ */
+ REFERENCE_GENOME_VERSION("reference_genome_version", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Contig where variant was observed.
+ */
+ CONTIG("contig", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ ALLEL_FREQUENCY("allel_frequency", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ VARIANT_IDENTIFIER("variant_identifier", new ColorSchemaType[] { ColorSchemaType.GENETIC_VARIANT }), //
+
+ /**
+ * Should the direction of reaction be reversed.
+ */
+ REVERSE_REACTION("reverseReaction", new ColorSchemaType[] { ColorSchemaType.GENERIC }); //
+
+ /**
+ * Default constructor that creates enum entry.
+ *
+ * @param title
+ * {@link #title}
+ * @param types
+ * list of {@link ColumnType types} where this column is allowed
+ */
+ ColorSchemaColumn(String title, ColorSchemaType[] types) {
+ this.title = title;
+ for (ColorSchemaType colorSchemaType : types) {
+ this.types.add(colorSchemaType);
+ }
+ }
+
+ /**
+ * Human readable title used in input file.
+ */
+ private String title;
+
+ /**
+ * Set of types where column is allowed.
+ */
+ private Set<ColorSchemaType> types = new HashSet<>();
+
+ /**
+ *
+ * @return {@link #title}
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * @return the types
+ * @see #types
+ */
+ public Set<ColorSchemaType> getTypes() {
+ return types;
+ }
}