diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index 0f045c0b3955b66629c5acc5b9b050e8a7bf4dcf..0476cd97063194b303b0c51104c52b4ab3b86242 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -123,7 +123,13 @@ public enum NoteField {
/**
* {@link Element#getSemanticZoomLevelVisibility()}.
*/
- SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", BioEntity.class, null); //
+ SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", BioEntity.class, null),
+
+ /**
+ * {@link Element#getSemanticZoomLevelVisibility()}.
+ */
+ TRANSPARENCY_ZOOM_LEVEL_VISIBILITY("TransparencyZoomLevelVisibility", Element.class, null),
+ ; //
/**
* Name used in the notes to distinguish fields.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index 0ca28cedefa8d160713502a582d9c8929628cb26..63db218c42e43a99d2256168cbd104262018d26e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -628,27 +628,41 @@ public class RestAnnotationParser extends XmlParser {
}
}
- /**
- * Assigns semanticZoomingLevel to the element from notes string.
- *
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
- */
- private void setSemanticZoomLevelVisibility(BioEntity element, String annotationString) {
- String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
- if (zoomLevelVisibility == null) {
- return;
- }
- if (element.getVisibilityLevel() == null || element.getVisibilityLevel().isEmpty()) {
- element.setVisibilityLevel(zoomLevelVisibility);
- } else if (!element.getVisibilityLevel().equals(zoomLevelVisibility)) {
- logger.warn(
- elementUtils.getElementTag(element) + " New " + NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
- + zoomLevelVisibility + "][" + element.getVisibilityLevel() + "]. Ignoring.");
- }
- }
+ /**
+ * Assigns semanticZoomingLevel to the element from notes string.
+ *
+ * @param element
+ * element to which data should be put to
+ * @param annotationString
+ * notes string
+ */
+ private void setSemanticZoomLevelVisibility(BioEntity element, String annotationString) {
+ String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
+ if (zoomLevelVisibility == null) {
+ return;
+ }
+ if (element.getVisibilityLevel() == null || element.getVisibilityLevel().isEmpty()) {
+ element.setVisibilityLevel(zoomLevelVisibility);
+ } else if (!element.getVisibilityLevel().equals(zoomLevelVisibility)) {
+ logger.warn(
+ elementUtils.getElementTag(element) + " New " + NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
+ + zoomLevelVisibility + "][" + element.getVisibilityLevel() + "]. Ignoring.");
+ }
+ }
+
+ private void setTransparencyZoomLevelVisibility(Element element, String annotationString) {
+ String transparencyZoomLevelVisibility = getParamByPrefix(annotationString, NoteField.TRANSPARENCY_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
+ if (transparencyZoomLevelVisibility == null) {
+ return;
+ }
+ if (element.getTransparencyLevel() == null || element.getTransparencyLevel().isEmpty()) {
+ element.setTransparencyLevel(transparencyZoomLevelVisibility);
+ } else if (!element.getTransparencyLevel().equals(transparencyZoomLevelVisibility)) {
+ logger.warn(
+ elementUtils.getElementTag(element) + " New " + NoteField.TRANSPARENCY_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
+ + transparencyZoomLevelVisibility + "][" + element.getVisibilityLevel() + "]. Ignoring.");
+ }
+ }
/**
* Assigns notes to the element from notes string. This might look strange.
@@ -719,6 +733,7 @@ public class RestAnnotationParser extends XmlParser {
setSubsystemToReaction(reaction, ann);
setGeneProteinReactionToReaction(reaction, ann);
} else if (object instanceof Element) {
+ setTransparencyZoomLevelVisibility((Element)object, ann);
setFullNameToSpecies((Element) object, ann);
setFormerSymbolsToSpecies((Element) object, ann);
if (object instanceof Species) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index a6f4b663a9292549d996eab2e7e4f1f33aef0abc..26242b8fb053fc896f3a7d09f6e612f38c9dc881 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -87,6 +87,18 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testParseTransparency() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/model_with_transparency.xml"));
+ assertFalse(model.getCompartments().get(0).getTransparencyLevel().isEmpty());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testOpenFromInvalidFile() throws Exception {
try {
diff --git a/converter-CellDesigner/testFiles/model_with_transparency.xml b/converter-CellDesigner/testFiles/model_with_transparency.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e14a7cd32740134a87699128f9d155cb9e94da56
--- /dev/null
+++ b/converter-CellDesigner/testFiles/model_with_transparency.xml
@@ -0,0 +1,273 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="15.0" y="73.0" w="137.0" h="153.0"/>
+<celldesigner:namePoint x="75.0" y="190.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca3" compartment="c3">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="176.0" y="30.0" w="203.0" h="129.0"/>
+<celldesigner:namePoint x="269.0" y="123.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca4" compartment="c4">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="443.0" y="69.0" w="149.0" h="178.0"/>
+<celldesigner:namePoint x="509.0" y="211.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca5" compartment="c5">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="197.0" y="219.0" w="186.0" h="129.0"/>
+<celldesigner:namePoint x="281.5" y="312.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="34.0" y="121.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="19.0" y="48.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2" compartmentAlias="ca3">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="233.0" y="57.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="57.0" y="27.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa3" species="s3" compartmentAlias="ca4">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="473.0" y="137.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="30.0" y="68.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa4" species="s4" compartmentAlias="ca5">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="277.0" y="263.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="80.0" y="44.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility:0
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c3" id="c3" name="c3" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility:1
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c3</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c4" id="c4" name="c4" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility:2
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c4</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+<compartment metaid="c5" id="c5" name="c5" size="1" units="volume" outside="default">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>TransparencyZoomLevelVisibility:3
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c5</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s1" compartment="c3" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s1" compartment="c4" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s1" compartment="c5" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
index 27d69c1334f94bb7dd427de18112a8d92362d4b1..b6d44ee2198f2e7e33f4d844a6b983cc3d40650e 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
@@ -1,11 +1,15 @@
package lcsb.mapviewer.commands;
+import java.util.HashSet;
+import java.util.Set;
+
import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
/**
* This {@link ModelCommand command} class allows to transform model into
@@ -16,46 +20,59 @@ import lcsb.mapviewer.model.map.model.Model;
*
*/
public class SetFixedHierarchyLevelCommand extends ModelCommand {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(SetFixedHierarchyLevelCommand.class);
- private Integer level;
-
- public SetFixedHierarchyLevelCommand(Model model, Integer level) {
- super(model);
- this.level = level;
- }
-
- @Override
- protected void undoImplementation() {
- throw new NotImplementedException();
- }
-
- @Override
- protected void executeImplementation() {
- if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
- throw new InvalidStateException("To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
- }
- if (level != null) {
- SemanticZoomLevelMatcher matcher = new SemanticZoomLevelMatcher();
- Model output = getModel();
- for (BioEntity bioEntity : output.getBioEntities()) {
- if (matcher.isVisible(level, bioEntity.getVisibilityLevel())) {
- bioEntity.setVisibilityLevel("0");
- } else {
- bioEntity.setVisibilityLevel(Integer.MAX_VALUE + "");
- }
- }
- }
-
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- @Override
- protected void redoImplementation() {
- throw new NotImplementedException();
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SetFixedHierarchyLevelCommand.class);
+ private Integer level;
+
+ public SetFixedHierarchyLevelCommand(Model model, Integer level) {
+ super(model);
+ this.level = level;
+ }
+
+ @Override
+ protected void undoImplementation() {
+ throw new NotImplementedException();
+ }
+
+ @Override
+ protected void executeImplementation() {
+ if (!ModelCommandStatus.CREATED.equals(getStatus()) && !ModelCommandStatus.UNDONE.equals(getStatus())) {
+ throw new InvalidStateException(
+ "To execute command, the command must be in CREATED or UNDONE state. " + getStatus() + " found.");
+ }
+ if (level != null) {
+ SemanticZoomLevelMatcher matcher = new SemanticZoomLevelMatcher();
+ Set<Model> models = new HashSet<>();
+ Model output = getModel();
+ models.add(output);
+ models.addAll(output.getSubmodels());
+ for (Model model : models) {
+ for (BioEntity bioEntity : model.getBioEntities()) {
+ if (matcher.isVisible(level, bioEntity.getVisibilityLevel())) {
+ bioEntity.setVisibilityLevel("0");
+ } else {
+ bioEntity.setVisibilityLevel(Integer.MAX_VALUE + "");
+ }
+ }
+ for (Element element : model.getElements()) {
+ if (matcher.isVisible(level, element.getTransparencyLevel())) {
+ element.setTransparencyLevel("0");
+ } else {
+ element.setTransparencyLevel(Integer.MAX_VALUE + "");
+ }
+ }
+ }
+ }
+
+ setStatus(ModelCommandStatus.EXECUTED);
+ }
+
+ @Override
+ protected void redoImplementation() {
+ throw new NotImplementedException();
+ }
}