From 78efa4fea52a3cf85c3f2b8745fda9202c9d9041 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 8 May 2019 20:34:53 +0200
Subject: [PATCH] z-index can be passed as a parameter in cell designer file
---
.../model/celldesigner/LayerXmlParser.java | 2 +
.../celldesigner/annotation/ImportOnly.java | 13 +++
.../celldesigner/annotation/NoteField.java | 6 +-
.../annotation/RestAnnotationParser.java | 87 ++++++++++++-------
.../celldesigner/LayerXmlParserTest.java | 13 +++
.../annotation/RestAnnotationParserTest.java | 6 +-
.../layer_text_with_z_index.xml | 9 ++
.../model/graphics/PolylineData.java | 4 +
.../lcsb/mapviewer/model/map/BioEntity.java | 2 -
.../lcsb/mapviewer/model/map/Drawable.java | 2 +
.../model/map/layout/graphics/LayerOval.java | 7 +-
.../model/map/layout/graphics/LayerRect.java | 6 ++
.../model/map/layout/graphics/LayerText.java | 5 ++
.../mapviewer/model/map/species/Element.java | 5 +-
.../modelutils/map/ElementUtils.java | 15 +---
15 files changed, 131 insertions(+), 51 deletions(-)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java
create mode 100644 converter-CellDesigner/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index 8507bccf69..d84b7d7567 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -13,6 +13,7 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -522,6 +523,7 @@ public class LayerXmlParser {
}
}
}
+ new RestAnnotationParser().processNotes(result.getNotes(), result);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java
new file mode 100644
index 0000000000..3f62862dcf
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java
@@ -0,0 +1,13 @@
+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+@Retention(RUNTIME)
+@Target(FIELD)
+public @interface ImportOnly {
+
+}
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 6926d78e61..6b7826e7de 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
@@ -135,7 +135,11 @@ public enum NoteField {
*/
@Deprecated
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD("TransparencyZoomLevelVisibility", Element.class, null),
- ;
+
+ @ImportOnly
+ Z_INDEX("Z-Index", BioEntity.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 a2861c3f3e..94e0a5f499 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
@@ -23,9 +23,11 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
@@ -702,6 +704,24 @@ public class RestAnnotationParser {
}
}
+ private void setZIndex(Drawable element, String annotationString) {
+ String zIndex = getParamByPrefix(annotationString,
+ NoteField.Z_INDEX.getCommonName() + ":");
+ if (zIndex != null) {
+ try {
+ Integer z = Integer.valueOf(zIndex);
+ if (element.getZ() == null) {
+ element.setZ(z);
+ } else if (!element.getZ().equals(z)) {
+ logger.warn(elementUtils.getElementTag(element) + " New " + NoteField.Z_INDEX.getCommonName()
+ + " different than default [" + zIndex + "][" + element.getZ() + "]. Ignoring.");
+ }
+ } catch (NumberFormatException e) {
+ logger.warn("Invalid e index", e);
+ }
+ }
+ }
+
/**
* Assigns notes to the element from notes string. This might look strange. The
* idea is that sometimes we have notes from more then one source. And the data
@@ -739,7 +759,7 @@ public class RestAnnotationParser {
* @param object
* where the structural data should be put
*/
- public void processNotes(String notes, BioEntity object) {
+ public void processNotes(String notes, Drawable object) {
StringBuilder annotations = new StringBuilder();
String[] string = notes.split("\n");
@@ -758,38 +778,45 @@ public class RestAnnotationParser {
newNotes.append(string2 + "\n");
}
}
- object.setNotes(newNotes.toString().trim());
-
String ann = annotations.toString();
- setNotes(object, ann);
- setSymbol(object, ann);
- setSynonyms(object, ann);
- setSemanticZoomLevelVisibility(object, ann);
- setAbbreviation(object, ann);
- setFormula(object, ann);
- if (object instanceof Reaction) {
- Reaction reaction = (Reaction) object;
- setMechanicalConfidenceScoreToReaction(reaction, ann);
- setLowerBoundToReaction(reaction, ann);
- setUpperBoundToReaction(reaction, ann);
- 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) {
- setCharge((Species) object, ann);
+ setZIndex(object, ann);
+ if (object instanceof LayerText) {
+ ((LayerText) object).setNotes(newNotes.toString().trim());
+ }
+ if (object instanceof BioEntity) {
+ BioEntity bioEntity = (BioEntity) object;
+ bioEntity.setNotes(newNotes.toString().trim());
+
+ setNotes(bioEntity, ann);
+ setSymbol(bioEntity, ann);
+ setSynonyms(bioEntity, ann);
+ setSemanticZoomLevelVisibility(bioEntity, ann);
+ setAbbreviation(bioEntity, ann);
+ setFormula(bioEntity, ann);
+ if (object instanceof Reaction) {
+ Reaction reaction = (Reaction) object;
+ setMechanicalConfidenceScoreToReaction(reaction, ann);
+ setLowerBoundToReaction(reaction, ann);
+ setUpperBoundToReaction(reaction, ann);
+ 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) {
+ setCharge((Species) object, ann);
+ }
+ } else {
+ throw new NotImplementedException("Don't know how to process class: " + object.getClass());
}
- } else {
- throw new NotImplementedException("Don't know how to process class: " + object.getClass());
- }
- try {
- processRdfDescription(object);
- } catch (InvalidXmlSchemaException e) {
- String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
- logger.warn(warning);
+ try {
+ processRdfDescription(bioEntity);
+ } catch (InvalidXmlSchemaException e) {
+ String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
+ logger.warn(warning);
+ }
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
index bcbebd1dda..cd86511d35 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
@@ -391,6 +391,19 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testGetLayerTextWithZIndex() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ LayerText layer = parser.getLayerText(node);
+ assertEquals((Integer) 19, layer.getZ());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testParseInvalidLayerText() throws Exception {
try {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index 8954ef209f..ad764b200d 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -295,17 +295,19 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
for (NoteField field : NoteField.values()) {
boolean deprecated = false;
+ boolean importOnly = false;
try {
Field f = NoteField.class.getField(field.name());
if (f.isAnnotationPresent(Deprecated.class))
deprecated = true;
+ if (f.isAnnotationPresent(ImportOnly.class))
+ importOnly = true;
} catch (NoSuchFieldException | SecurityException e) {
}
- if (!deprecated) {
+ if (!deprecated && !importOnly) {
if (field.getClazz().isAssignableFrom(element.getClass())
-
|| CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
assertTrue("Export string doesn't contain info about: " + field.getCommonName(),
str.indexOf(field.getCommonName()) >= 0);
diff --git a/converter-CellDesigner/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml b/converter-CellDesigner/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml
new file mode 100644
index 0000000000..68185b6d00
--- /dev/null
+++ b/converter-CellDesigner/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml
@@ -0,0 +1,9 @@
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+Z-Index: 19
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
index c6579e150b..efb5eb7076 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineData.java
@@ -551,4 +551,8 @@ public class PolylineData implements Serializable, Drawable {
return 0;
}
+ @Override
+ public String getElementId() {
+ return toString();
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index b7ab37bcb5..9879bc60c5 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -196,8 +196,6 @@ public interface BioEntity extends Serializable, Drawable {
*/
Model getModel();
- String getElementId();
-
BioEntity copy();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/Drawable.java b/model/src/main/java/lcsb/mapviewer/model/map/Drawable.java
index 72c198d181..473fdeed72 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/Drawable.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/Drawable.java
@@ -37,5 +37,7 @@ public interface Drawable {
*/
void setZ(Integer z);
+ String getElementId();
+
double getSize();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java
index 4361ed2ada..88b9d684d2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerOval.java
@@ -276,7 +276,12 @@ public class LayerOval implements Serializable, Drawable {
@Override
public double getSize() {
- return width*height;
+ return width * height;
+ }
+
+ @Override
+ public String getElementId() {
+ return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
index 493d3ab9e7..e0a163b9f8 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
@@ -261,4 +261,10 @@ public class LayerRect implements Serializable, Drawable {
public double getSize() {
return width * height;
}
+
+ @Override
+ public String getElementId() {
+ return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
index af87c2ee02..d866c3e6e1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
@@ -372,4 +372,9 @@ public class LayerText implements Serializable, Drawable {
return width * height;
}
+ @Override
+ public String getElementId() {
+ return "x=" + x + ";y=" + y + "; w=" + width + ", h=" + height;
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index bef7a61fc7..9623aaa428 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -640,10 +640,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.fontSize = fontSize;
}
- /**
- * @return the elementId
- * @see #elementId
- */
+ @Override
public String getElementId() {
return elementId;
}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 932fb236d8..1998162145 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -11,8 +11,8 @@ import java.util.Set;
import org.apache.log4j.Logger;
import org.reflections.Reflections;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.Element;
@@ -57,7 +57,7 @@ public final class ElementUtils {
* tag for this element is created
* @return tag that identifies element
*/
- public String getElementTag(BioEntity element) {
+ public String getElementTag(Drawable element) {
return getElementTag(element, null);
}
@@ -72,15 +72,8 @@ public final class ElementUtils {
* null (in such situation it will be skipped in the tag)
* @return tag that identifies element
*/
- public String getElementTag(BioEntity element, Object annotator) {
- String id = null;
- if (element instanceof Element) {
- id = ((Element) element).getElementId();
- } else if (element instanceof Reaction) {
- id = ((Reaction) element).getIdReaction();
- } else {
- throw new NotImplementedException("Unknown class: " + element.getClass());
- }
+ public String getElementTag(Drawable element, Object annotator) {
+ String id = element.getElementId();
if (annotator != null) {
return "[" + annotator.getClass().getSimpleName() + "]\t[" + element.getClass().getSimpleName() + " " + id
+ "]\t";
--
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