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Commit f98d4cd1 authored by Piotr Gawron's avatar Piotr Gawron
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custom semantic zoom can control transparency levels

parent 6835036b
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2 merge requests!412changes from 12.1.0~beta.1 into master,!402Resolve "Custom semantic zoom - set transparency level"
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with 386 additions and 63 deletions
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+ 7
− 1
View file @ f98d4cd1
......@@ -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.
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+ 36
− 21
View file @ f98d4cd1
......@@ -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) {
......
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+ 12
− 0
View file @ f98d4cd1
......@@ -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 {
......
converter-CellDesigner/testFiles/model_with_transparency.xml 0 → 100644
+ 273
− 0
View file @ f98d4cd1
<?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>
model-command/src/main/java/lcsb/mapviewer/commands/SetFixedHierarchyLevelCommand.java
+ 58
− 41
View file @ f98d4cd1
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();
}
}
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