From 0230122311629a1dc5b13fc030659ae270ffb023 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 16 Jun 2017 15:14:12 +0200
Subject: [PATCH] drawing of reactions for semantic zooming
---
.../annotation/RestAnnotationParserTest.java | 12 +
.../model/sbgnml/SbgnmlXmlExporter.java | 2 +-
.../model/sbgnml/SbgnmlXmlParser.java | 2 +-
.../graphics/AbstractImageGenerator.java | 23 +-
.../converter/graphics/ConverterParams.java | 35 +-
.../BioEntityConverter.java} | 40 +-
.../BioEntityConverterImpl.java} | 71 +--
.../bioEntity/element/ElementConverter.java | 17 +
.../BottomSquareCompartmentConverter.java | 4 +-
.../compartment/CompartmentConverter.java | 8 +-
.../LeftSquareCompartmentConverter.java | 4 +-
.../compartment/OvalCompartmentConverter.java | 4 +-
.../PathwayCompartmentConverter.java | 4 +-
.../RightSquareCompartmentConverter.java | 4 +-
.../SquareCompartmentConverter.java | 4 +-
.../TopSquareCompartmentConverter.java | 4 +-
.../element}/compartment/package-info.java | 2 +-
.../species/AntisenseRnaConverter.java | 4 +-
.../element}/species/ComplexConverter.java | 4 +-
.../element}/species/DegradedConverter.java | 4 +-
.../element}/species/DrugConverter.java | 4 +-
.../element}/species/GeneConverter.java | 4 +-
.../element}/species/IonConverter.java | 4 +-
.../element}/species/PhenotypeConverter.java | 4 +-
.../element}/species/ProteinConverter.java | 4 +-
.../element}/species/RnaConverter.java | 4 +-
.../SBGNNucleicAcidFeatureConverter.java | 4 +-
.../species/SimpleMoleculeConverter.java | 4 +-
.../element}/species/SpeciesConverter.java | 8 +-
.../element}/species/UnknownConverter.java | 4 +-
.../element}/species/package-info.java | 2 +-
.../reaction/ReactionConverter.java | 125 +++++-
.../reaction/package-info.java | 2 +-
.../converter/graphics/AllGraphicsTests.java | 4 +-
.../converter/graphics/ConverterTest.java | 9 +-
.../graphics/NormalImageGeneratorTest.java | 2 +-
.../species/AllSpeciesConverterTests.java | 2 +-
.../species/SpeciesConverterTest.java | 17 +-
.../reaction/AllReactionTests.java | 2 +-
.../reaction/ReactionConverterTest.java | 407 ++++++++++++++++++
.../reaction/ReactionConverterTest.java | 196 ---------
.../mapviewer/model/map/AnnotatedObject.java | 8 +-
.../model/map/reaction/Reaction.java | 15 +
.../mapviewer/model/map/species/Element.java | 14 +
44 files changed, 745 insertions(+), 356 deletions(-)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ElementConverter.java => bioEntity/BioEntityConverter.java} (50%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ElementConverterImpl.java => bioEntity/BioEntityConverterImpl.java} (62%)
create mode 100644 converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/BottomSquareCompartmentConverter.java (90%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/CompartmentConverter.java (92%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/LeftSquareCompartmentConverter.java (90%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/OvalCompartmentConverter.java (90%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/PathwayCompartmentConverter.java (89%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/RightSquareCompartmentConverter.java (91%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/SquareCompartmentConverter.java (91%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/TopSquareCompartmentConverter.java (90%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/compartment/package-info.java (59%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/AntisenseRnaConverter.java (93%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/ComplexConverter.java (94%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/DegradedConverter.java (92%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/DrugConverter.java (92%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/GeneConverter.java (93%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/IonConverter.java (92%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/PhenotypeConverter.java (91%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/ProteinConverter.java (96%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/RnaConverter.java (94%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/SBGNNucleicAcidFeatureConverter.java (93%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/SimpleMoleculeConverter.java (93%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/SpeciesConverter.java (95%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/UnknownConverter.java (91%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/package-info.java (65%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity}/reaction/ReactionConverter.java (74%)
rename converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/{ => bioEntity}/reaction/package-info.java (70%)
rename converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/AllSpeciesConverterTests.java (73%)
rename converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/{ => bioEntity/element}/species/SpeciesConverterTest.java (87%)
rename converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/{ => bioEntity}/reaction/AllReactionTests.java (74%)
create mode 100644 converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
delete mode 100644 converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java
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 ff04e70426..f8ab6d2d44 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
@@ -417,6 +417,18 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public String getSemanticZoomLevelVisibility() {
+ // TODO Auto-generated method stub
+ return null;
+ }
});
fail("Exception expected");
} catch (NotImplementedException e) {
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index c408b252ec..c6d7b70674 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -27,7 +27,7 @@ import org.sbgn.bindings.Sbgn;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index f808c488be..b66908389d 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -28,7 +28,7 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.graphics.species.SpeciesConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index c07d1422e6..e452e977f3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -16,8 +16,9 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
-import lcsb.mapviewer.converter.graphics.reaction.ReactionConverter;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -172,11 +173,11 @@ public abstract class AbstractImageGenerator {
* Should the visualization include hierarchical view or not.
*/
private boolean nested = false;
-
+
/**
* Should sbgn standard be used.
*/
- private boolean sbgn = false;
+ private boolean sbgn = false;
/**
* List of objects containging information about layouts visualized in the
@@ -561,7 +562,8 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param sbgn the sbgn to set
+ * @param sbgn
+ * the sbgn to set
* @see #sbgn
* @return object with all parameters
*/
@@ -738,7 +740,7 @@ public abstract class AbstractImageGenerator {
}
// get a converter for this compartment
- ElementConverterImpl converter = new ElementConverterImpl(compartment, colorExtractor);
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level);
if (nested) {
@@ -749,7 +751,7 @@ public abstract class AbstractImageGenerator {
// standard compartment (not the pathway)
if (nested || !(compartment instanceof PathwayCompartment)) {
try {
- converter.drawElement(compartment, graphics, compartmentParams, visibleLayouts);
+ converter.draw(compartment, graphics, compartmentParams, visibleLayouts);
} catch (Exception e) {
throw new DrawingException(eu.getElementTag(compartment) + "Problem with drawing element.", e);
}
@@ -825,14 +827,13 @@ public abstract class AbstractImageGenerator {
}
// at the beginning try to find an appropriate converter
- ElementConverterImpl converter = new ElementConverterImpl(species, sbgnFormat, colorExtractor);
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(species, sbgnFormat, colorExtractor);
double customScale = 1;
if (rescale) {
customScale = scale;
}
try {
- converter
- .drawElement(species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat), visibleLayouts);
+ converter.draw(species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat), visibleLayouts);
} catch (Exception e) {
throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
}
@@ -866,8 +867,8 @@ public abstract class AbstractImageGenerator {
if (!cross(reaction.getLines())) {
return;
}
- ReactionConverter converter = new ReactionConverter(colorExtractor);
- converter.drawReaction(reaction, graphics, sbgnFormat, visibleLayouts);
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
+ converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat), visibleLayouts);
}
/**
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
index c7499064c6..59577a9350 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
@@ -11,28 +11,33 @@ public class ConverterParams {
* Should the object be filled with the solid color. In other words it tells
* us if the object is not transparent.
*/
- private boolean fill = false;
+ private boolean fill = false;
/**
* At which level the object is visualized. It helps to deterimine font size.
* However it's possible that this value is not required.
*/
- private int level = 0;
+ private int level = 0;
/**
* What is the scale. It allows to adjust font size to be readable.
*/
- private double scale = 1;
+ private double scale = 1;
/**
* Should the text describing element be centered or not.
*/
- private boolean textCentered = false;
+ private boolean textCentered = false;
/**
* Should the map be displayed in SBGN format.
*/
- private boolean sbgnFormat = false;
+ private boolean sbgnFormat = false;
+
+ /**
+ * Is the semantic zooming filtered.
+ */
+ private boolean semanticZoomingOn = false;
/**
* @param fill
@@ -56,6 +61,17 @@ public class ConverterParams {
return this;
}
+ /**
+ * @param semanticZoomingOn
+ * the semanticZoomingOn to set
+ * @return object with all parameters
+ * @see #semanticZoomingOn
+ */
+ public ConverterParams semanticZoomingOn(final boolean semanticZoomingOn) {
+ this.semanticZoomingOn = semanticZoomingOn;
+ return this;
+ }
+
/**
* @param textCentered
* the textCentered to set
@@ -129,6 +145,14 @@ public class ConverterParams {
return sbgnFormat;
}
+ /**
+ * @return the semanticZoomingOn
+ * @see #semanticZoomingOn
+ */
+ public boolean isSemanticZoomingOn() {
+ return semanticZoomingOn;
+ }
+
@Override
public String toString() {
String result = "[" + this.getClass().getSimpleName() + "] " + //
@@ -136,6 +160,7 @@ public class ConverterParams {
"level:" + level + "," + //
"scale:" + scale + "," + //
"textCentered:" + textCentered + "," + //
+ "semanticZoomingOn:" + semanticZoomingOn + "," + //
"sbgnFormat:" + sbgnFormat;
return result;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
similarity index 50%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index d1992b796c..1d08111d03 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -1,23 +1,26 @@
-package lcsb.mapviewer.converter.graphics;
+package lcsb.mapviewer.converter.graphics.bioEntity;
import java.awt.Graphics2D;
import java.util.List;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Element;
/**
* This interface defines what operations should be possible to convert
- * {@link Element} into a graphics on Graphics2D object.
+ * {@link AnnotatedObject} into a graphics on Graphics2D object.
*
* @author Piotr Gawron
*
* @param <T>
* class of alias to convert
*/
-public interface ElementConverter<T extends Element> {
+public interface BioEntityConverter<T extends AnnotatedObject> {
/**
- * Alpha value (0..255) used for visualizing layout data that are normally
+ * Alpha value (0..255) used for visualizing overlay data that are normally
* visualized in javascript.
*/
int LAYOUT_ALPHA = 200;
@@ -25,49 +28,50 @@ public interface ElementConverter<T extends Element> {
/**
* This function draw representation of the alias on the graphics object.
*
- * @param alias
- * alias that should be drawn
+ * @param bioEntity
+ * {@link AnnotatedObject} that should be drawn
* @param graphics
- * where we want to draw alias
+ * where we want to draw bioEntity
* @param params
* visuzalization params (like, should the object be filled with
* solid color, etc.), for more information see
* {@link ConverterParams}
*
*/
- void drawElement(T alias, Graphics2D graphics, ConverterParams params);
+ void draw(T bioEntity, Graphics2D graphics, ConverterParams params);
/**
* This function draw representation of the alias on the graphics object.
*
- * @param alias
- * alias that should be drawn
+ * @param bioEntity
+ * {@link AnnotatedObject} that should be drawn
* @param graphics
- * where we want to draw alias
+ * where we want to draw bioEntity
* @param params
* visuzalization params (like, should the object be filled with
* solid color, etc.), for more information see
* {@link ConverterParams}
- * @param visualizedLayoutsColorSchemas
+ * @param visualizedOverlaysColorSchemas
* list of {@link ColorSchema} that were used for visualizing this
- * alias in different layouts that should be overlayed on the alias
+ * bioentity in different data overlays that should be overlayed on
+ * the alias
*
*/
- void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas);
+ void draw(T bioEntity, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedOverlaysColorSchemas);
/**
* This function will find proper font size to display text within it. Then it
* will print this text.
*
- * @param alias
- * alias with description to be drawn
+ * @param bioEntity
+ * bioEntity with description to be drawn
* @param graphics
* where the description should be drawn
* @param params
* parameters of visualization (centering, scale)
* @throws DrawingException
- * thrown when there is a problem with drawing alias
+ * thrown when there is a problem with drawing bioEntity
*/
- void drawText(T alias, Graphics2D graphics, ConverterParams params) throws DrawingException;
+ void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
similarity index 62%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index e96615f6ef..621c537345 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics;
+package lcsb.mapviewer.converter.graphics.bioEntity;
import java.awt.Graphics2D;
import java.util.List;
@@ -8,25 +8,29 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.graphics.compartment.BottomSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.LeftSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.OvalCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.PathwayCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.RightSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.SquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.compartment.TopSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.species.AntisenseRnaConverter;
-import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
-import lcsb.mapviewer.converter.graphics.species.DegradedConverter;
-import lcsb.mapviewer.converter.graphics.species.DrugConverter;
-import lcsb.mapviewer.converter.graphics.species.GeneConverter;
-import lcsb.mapviewer.converter.graphics.species.IonConverter;
-import lcsb.mapviewer.converter.graphics.species.PhenotypeConverter;
-import lcsb.mapviewer.converter.graphics.species.ProteinConverter;
-import lcsb.mapviewer.converter.graphics.species.RnaConverter;
-import lcsb.mapviewer.converter.graphics.species.SBGNNucleicAcidFeatureConverter;
-import lcsb.mapviewer.converter.graphics.species.SimpleMoleculeConverter;
-import lcsb.mapviewer.converter.graphics.species.UnknownConverter;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.BottomSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.LeftSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.OvalCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.PathwayCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.RightSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.SquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.TopSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AntisenseRnaConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DegradedConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DrugConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.GeneConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.IonConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.PhenotypeConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.RnaConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SBGNNucleicAcidFeatureConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.UnknownConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.compartment.OvalCompartment;
@@ -35,6 +39,7 @@ import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
@@ -59,13 +64,13 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
* @author Piotr Gawron
*
*/
-public class ElementConverterImpl implements ElementConverter<Element> {
+public class BioEntityConverterImpl implements BioEntityConverter<AnnotatedObject> {
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ElementConverterImpl.class.getName());
+ private static Logger logger = Logger.getLogger(BioEntityConverterImpl.class.getName());
/**
* Returns a converter for given element. If converter doesn't exist then
@@ -77,7 +82,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
* object that helps to convert overlay values into colors
* @return converter that can be applied for the given element
*/
- private ElementConverter<? extends Element> getConverterForElement(Element element, ColorExtractor colorExtractor) {
+ private BioEntityConverter<? extends AnnotatedObject> getConverterForElement(AnnotatedObject element, ColorExtractor colorExtractor) {
if (element == null) {
throw new InvalidArgumentException("element cannot be null");
}
@@ -123,6 +128,8 @@ public class ElementConverterImpl implements ElementConverter<Element> {
return new LeftSquareCompartmentConverter(colorExtractor);
} else if (element instanceof RightSquareCompartment) {
return new RightSquareCompartmentConverter(colorExtractor);
+ } else if (element instanceof Reaction) {
+ return new ReactionConverter(colorExtractor);
} else {
throw new NotImplementedException(new ElementUtils().getElementTag(element) + "Unknown element class");
}
@@ -132,7 +139,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
* Converter used for conversion of the {@link Element} given in constructor.
*/
@SuppressWarnings("rawtypes")
- private ElementConverter elementConverter = null;
+ private BioEntityConverter elementConverter = null;
/**
* Support constructor. Used in case of SBGN format display
@@ -144,7 +151,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
* @param sbgnFormat
* boolean value indicating if SBGN display format should be used
*/
- public ElementConverterImpl(final Element element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
+ public BioEntityConverterImpl(final AnnotatedObject element, final boolean sbgnFormat, ColorExtractor colorExtractor) {
// If element is a nucleic acid feature to be displayed in SBGN
if (sbgnFormat && (element instanceof AntisenseRna || element instanceof Rna || element instanceof Gene)) {
@@ -156,7 +163,7 @@ public class ElementConverterImpl implements ElementConverter<Element> {
// if we don't know which converter to use then throw an exception
if (elementConverter == null) {
- throw new InvalidArgumentException("Unknown converter for class: " + element.getClass() + ". Element id: " + element.getElementId());
+ throw new InvalidArgumentException(new ElementUtils().getElementTag(element) + "Unknown converter for class: " + element.getClass());
}
}
@@ -168,25 +175,25 @@ public class ElementConverterImpl implements ElementConverter<Element> {
* @param element
* {@link Element} for which this converter will be used
*/
- public ElementConverterImpl(final Element element, ColorExtractor colorExtractor) {
+ public BioEntityConverterImpl(final Element element, ColorExtractor colorExtractor) {
this(element, false, colorExtractor);
}
@SuppressWarnings("unchecked")
@Override
- public void drawElement(final Element element, final Graphics2D graphics, final ConverterParams params) {
- elementConverter.drawElement(element, graphics, params);
+ public void draw(final AnnotatedObject element, final Graphics2D graphics, final ConverterParams params) {
+ elementConverter.draw(element, graphics, params);
}
@SuppressWarnings("unchecked")
@Override
- public void drawText(final Element element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ public void drawText(final AnnotatedObject element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
elementConverter.drawText(element, graphics, params);
}
@SuppressWarnings("unchecked")
@Override
- public void drawElement(Element element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- elementConverter.drawElement(element, graphics, params, visualizedLayoutsColorSchemas);
+ public void draw(AnnotatedObject element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
new file mode 100644
index 0000000000..de6dae1ae8
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
@@ -0,0 +1,17 @@
+package lcsb.mapviewer.converter.graphics.bioEntity.element;
+
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * This interface defines what operations should be possible to convert
+ * {@link Element} into a graphics on Graphics2D object.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class of alias to convert
+ */
+public interface ElementConverter<T extends Element> extends BioEntityConverter<T> {
+
+}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
similarity index 90%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
index 07087ec3cd..c13cdbdaf2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/BottomSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
}
@Override
- public void drawElement(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final BottomSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
similarity index 92%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
index ce31fb93bb..93dd6f583e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Font;
@@ -14,7 +14,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.ElementConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;
@@ -175,8 +175,8 @@ public abstract class CompartmentConverter<T extends Compartment> implements Ele
}
@Override
- public void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- drawElement(alias, graphics, params);
+ public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ draw(alias, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
similarity index 90%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
index a3cac76c0b..513684d8ad 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/LeftSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
}
@Override
- public void drawElement(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final LeftSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
similarity index 90%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
index 3c385168fb..611eb3dead 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/OvalCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -47,7 +47,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
}
@Override
- public void drawElement(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final OvalCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/PathwayCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
similarity index 89%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/PathwayCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
index a3d6fd00ff..6d691cfab2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/PathwayCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -40,7 +40,7 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
private Color backgroundColor = Color.LIGHT_GRAY;
@Override
- public void drawElement(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final PathwayCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
similarity index 91%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
index 72099129b6..c1dbe6fa02 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/RightSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
}
@Override
- public void drawElement(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final RightSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
similarity index 91%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
index e67b330c23..169950485e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/SquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -59,7 +59,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
}
@Override
- public void drawElement(final SquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final SquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
similarity index 90%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
index b074e084f5..bdc72589df 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/TopSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
}
@Override
- public void drawElement(final TopSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final TopSquareCompartment alias, final Graphics2D graphics, final ConverterParams params) {
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java
similarity index 59%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java
index 238015b528..992fd5cbdd 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/compartment/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java
@@ -2,4 +2,4 @@
* Provides classes that draws different implemention of
* {@link Compartment} on the {@link Graphics2D}.
*/
-package lcsb.mapviewer.converter.graphics.compartment;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
similarity index 93%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index acc16bc98c..84d00dc02a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Font;
@@ -50,7 +50,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
@Override
- public void drawElement(final AntisenseRna alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final AntisenseRna alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getAntisenseRnaPath(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
similarity index 94%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
index 6a59e89cc6..345fb93944 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Font;
@@ -58,7 +58,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
@Override
- public void drawElement(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getState().equalsIgnoreCase("complexnoborder")) {
return;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
similarity index 92%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
index de6bcebb35..42152ef9f1 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DegradedConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -50,7 +50,7 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
}
@Override
- public void drawElement(final Degraded alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final Degraded alias, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
similarity index 92%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
index f55cf04258..4c412634f4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/DrugConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -68,7 +68,7 @@ public class DrugConverter extends SpeciesConverter<Drug> {
}
@Override
- public void drawElement(Drug alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(Drug alias, final Graphics2D graphics, final ConverterParams params) {
Shape a1 = getDrugShape(alias);
double offset = OFFSET_BETWEEN_BORDERS;
Shape a2 = new RoundRectangle2D.Double(
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
similarity index 93%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
index f5493ee149..514475cf86 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Font;
@@ -48,7 +48,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
}
@Override
- public void drawElement(final Gene alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final Gene alias, final Graphics2D graphics, final ConverterParams params) {
Shape shape = getGeneShape(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
similarity index 92%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
index fe8699ac72..733f3b7ddb 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -45,7 +45,7 @@ public class IonConverter extends SpeciesConverter<Ion> {
}
@Override
- public void drawElement(Ion alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(Ion alias, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(alias);
double x = getXCoord(alias, diameter);
double y = getYCoord(alias);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
similarity index 91%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
index 4ca043e210..0a6a2a059b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/PhenotypeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -44,7 +44,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
}
@Override
- public void drawElement(Phenotype alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(Phenotype alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getPhenotypePath(alias);
Color c = graphics.getColor();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
similarity index 96%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
index b3af8c09cb..0e794ffa6e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Font;
@@ -89,7 +89,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
}
@Override
- public void drawElement(final Protein alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final Protein alias, final Graphics2D graphics, final ConverterParams params) {
// Local variable setting the SBGN visualization
boolean sbgnFormat = params.isSbgnFormat();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
similarity index 94%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index 6b13ac398f..277a8afc65 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
@@ -5,7 +5,7 @@
* Object that helps to convert {@link ColorSchema} values into
* colors when drawing {@link Species}
*/
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Font;
@@ -55,7 +55,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
}
@Override
- public void drawElement(final Rna alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final Rna alias, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getRnaPath(alias);
Color c = graphics.getColor();
graphics.setColor(alias.getColor());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
similarity index 93%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
index 8dc25a7ffd..5412c1b961 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -64,7 +64,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
}
@Override
- public void drawElement(Species alias, Graphics2D graphics, ConverterParams params) {
+ public void draw(Species alias, Graphics2D graphics, ConverterParams params) {
// Unit of information text - multimer cardinality
String unitOfInformationText = null;
if (alias.getStatePrefix() != null && alias.getStateLabel() != null) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
similarity index 93%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
index ca287bfc97..8abca141bd 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -42,7 +42,7 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
}
@Override
- public void drawElement(final SimpleMolecule alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(final SimpleMolecule alias, final Graphics2D graphics, final ConverterParams params) {
int homodir;
if (params.isSbgnFormat()) {
// If the SBGN display mode is set, multimer is shown as two stacked
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
similarity index 95%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index cf3ca8313c..1f861eaef4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Font;
@@ -21,7 +21,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
-import lcsb.mapviewer.converter.graphics.ElementConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.species.Complex;
@@ -576,8 +576,8 @@ public abstract class SpeciesConverter<T extends Species> implements ElementConv
}
@Override
- public void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- drawElement(alias, graphics, params);
+ public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ draw(alias, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
similarity index 91%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
index 4d2045ebf9..e304953c08 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import java.awt.Color;
import java.awt.Graphics2D;
@@ -45,7 +45,7 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
}
@Override
- public void drawElement(Unknown alias, final Graphics2D graphics, final ConverterParams params) {
+ public void draw(Unknown alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getActivity()) {
int border = ACTIVITY_BORDER_DISTANCE;
alias.increaseBorder(border);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
similarity index 65%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/package-info.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
index 19c8857d76..2fb83e5d85 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
@@ -3,5 +3,5 @@
* {@link lcsb.mapviewer.db.model.map.species.Species Species} on the Graphics2D
* object.
*/
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
similarity index 74%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
index 2697266eb8..0060e3a9b3 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.reaction;
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
import java.awt.Color;
import java.awt.Font;
@@ -15,12 +15,19 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.AnnotatedObject;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
@@ -29,7 +36,11 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Thics class allows to draw reaction on the graphics2D.
@@ -37,7 +48,7 @@ import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
* @author Piotr Gawron
*
*/
-public class ReactionConverter {
+public class ReactionConverter implements BioEntityConverter<Reaction> {
/**
* When drawing operator this value defines radius of the joining operator
@@ -184,35 +195,34 @@ public class ReactionConverter {
}
}
- /**
- * Draw reaction on the graphics2D.
- *
- * @param reaction
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- * @param sbgnFormat
- * true if reaction is to be drawn in SBGN format
- */
- public void drawReaction(final Reaction reaction, final Graphics2D graphics, boolean sbgnFormat) {
+ @Override
+ public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params) {
Color color = graphics.getColor();
graphics.setColor(reaction.getReactants().get(0).getLine().getColor());
// first reactants
for (Reactant reactant : reaction.getReactants()) {
- drawReactant(graphics, reactant);
+ if (isVisible(reactant, params)) {
+ drawReactant(graphics, reactant);
+ }
}
// now products
for (Product product : reaction.getProducts()) {
- drawProduct(graphics, product);
+ if (isVisible(product, params)) {
+ drawProduct(graphics, product);
+ }
}
// draw modifiers
for (Modifier modifier : reaction.getModifiers()) {
- drawModifier(graphics, modifier);
+ if (isVisible(modifier, params)) {
+ drawModifier(graphics, modifier);
+ }
}
// and operators
for (NodeOperator operator : reaction.getOperators()) {
- drawOperator(graphics, operator, sbgnFormat);
+ if (isVisible(operator, params)) {
+ drawOperator(graphics, operator, params.isSbgnFormat());
+ }
}
// in the end we draw rectangle in the middle
@@ -220,6 +230,71 @@ public class ReactionConverter {
graphics.setColor(color);
}
+ private boolean isVisible(AbstractNode node, ConverterParams params) {
+ if (node instanceof NodeOperator) {
+ return isVisible((NodeOperator) node, params);
+ } else if (node instanceof ReactionNode) {
+ return isVisible(((ReactionNode) node).getElement(), params);
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + node.getClass());
+ }
+ }
+
+ private boolean isVisible(NodeOperator operator, ConverterParams params) {
+ boolean result = false;
+ if (operator.isModifierOperator() || operator.isReactantOperator()) {
+ for (AbstractNode input : operator.getInputs()) {
+ result |= isVisible(input, params);
+ }
+ } else if (operator.isProductOperator()) {
+ for (AbstractNode output : operator.getOutputs()) {
+ result |= isVisible(output, params);
+ }
+ } else {
+ throw new InvalidStateException("Unknown class state: " + operator);
+ }
+ return result;
+ }
+
+ private boolean isVisible(AnnotatedObject bioEntity, ConverterParams params) {
+ if (params.isSemanticZoomingOn()) {
+ boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
+ if (bioEntity instanceof Element) {
+ Compartment compartment = ((Element) bioEntity).getCompartment();
+ if (compartment != null) {
+ result &= isVisible(compartment, params);
+ }
+ if (bioEntity instanceof Species) {
+ Complex complex = ((Species) bioEntity).getComplex();
+ if (complex != null) {
+ result &= isVisible(complex, params);
+ }
+ }
+ }
+ return result;
+ }
+ return true;
+ }
+
+ private boolean matchLevel(int level, String semanticZoomLevelVisibility) {
+ if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
+ return true;
+ }
+ if (semanticZoomLevelVisibility.contains("{")) {
+ String strLevels = semanticZoomLevelVisibility.replace("{", "").replace("}", "");
+ String[] ranges = strLevels.split(",");
+ for (String string : ranges) {
+ if (Integer.valueOf(string).equals(level)) {
+ return true;
+ }
+ }
+ }
+ if (Integer.valueOf(semanticZoomLevelVisibility) <= level) {
+ return true;
+ }
+ return false;
+ }
+
/**
* Draw reaction on the graphics2D.
*
@@ -233,19 +308,19 @@ public class ReactionConverter {
* list of {@link ColorSchema} that were used for visualizing this
* alias in different layouts that should be overlayed on the alias
*/
- public void drawReaction(final Reaction reaction, final Graphics2D graphics, boolean sbgnFormat, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
if (visualizedLayoutsColorSchemas.size() == 0) {
- drawReaction(reaction, graphics, sbgnFormat);
+ draw(reaction, graphics, params);
} else if (visualizedLayoutsColorSchemas.size() == 1) {
if (visualizedLayoutsColorSchemas.get(0) == null) {
- drawReaction(reaction, graphics, sbgnFormat);
+ draw(reaction, graphics, params);
} else {
List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
for (AbstractNode node : reaction.getNodes()) {
oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
}
applyColorSchema(reaction, visualizedLayoutsColorSchemas.get(0));
- drawReaction(reaction, graphics, sbgnFormat);
+ draw(reaction, graphics, params);
for (Pair<AbstractNode, PolylineData> pair : oldData) {
pair.getLeft().setLine(pair.getRight());
}
@@ -258,14 +333,14 @@ public class ReactionConverter {
}
}
if (count == 0) {
- drawReaction(reaction, graphics, sbgnFormat);
+ draw(reaction, graphics, params);
} else {
List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
for (AbstractNode node : reaction.getNodes()) {
oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
}
applyColorSchema(reaction, DEFAULT_COLOR_SCHEMA);
- drawReaction(reaction, graphics, sbgnFormat);
+ draw(reaction, graphics, params);
for (Pair<AbstractNode, PolylineData> pair : oldData) {
pair.getLeft().setLine(pair.getRight());
}
@@ -448,4 +523,8 @@ public class ReactionConverter {
this.pointTransformation = pointTransformation;
}
+ @Override
+ public void drawText(Reaction bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+ }
+
}
\ No newline at end of file
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java
similarity index 70%
rename from converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/package-info.java
rename to converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java
index b03d32c941..d3b737737c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/reaction/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/package-info.java
@@ -3,5 +3,5 @@
* {@link lcsb.mapviewer.db.model.map.reaction.Reaction reactions} on the
* {@link java.awt.Graphics2D Graphics2D} object.
*/
-package lcsb.mapviewer.converter.graphics.reaction;
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
index 940247e162..9407853563 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AllGraphicsTests.java
@@ -1,9 +1,9 @@
package lcsb.mapviewer.converter.graphics;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AllSpeciesConverterTests;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.AllReactionTests;
import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
-import lcsb.mapviewer.converter.graphics.reaction.AllReactionTests;
-import lcsb.mapviewer.converter.graphics.species.AllSpeciesConverterTests;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
index 66e7eaa7ed..59f4964c75 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java
@@ -7,6 +7,7 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
@@ -26,10 +27,10 @@ public class ConverterTest {
public void test() {
try {
ColorExtractor colorExtractor = new ColorExtractor(Color.BLUE, Color.RED);
- new ElementConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
- new ElementConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
- new ElementConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
- new ElementConverterImpl(new RightSquareCompartment("id4"), colorExtractor);
+ new BioEntityConverterImpl(new BottomSquareCompartment("id1"), colorExtractor);
+ new BioEntityConverterImpl(new TopSquareCompartment("id2"), colorExtractor);
+ new BioEntityConverterImpl(new LeftSquareCompartment("id3"), colorExtractor);
+ new BioEntityConverterImpl(new RightSquareCompartment("id4"), colorExtractor);
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index 36d384f007..36d84707d1 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -15,7 +15,7 @@ import org.junit.Test;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.graphics.species.ComplexConverter;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/AllSpeciesConverterTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
similarity index 73%
rename from converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/AllSpeciesConverterTests.java
rename to converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
index f964383c73..69e9b97b05 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/AllSpeciesConverterTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AllSpeciesConverterTests.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
similarity index 87%
rename from converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
rename to converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index bc8c2b2eaf..1bdacdc9d7 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.species;
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@@ -15,6 +15,7 @@ import org.junit.Test;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -65,7 +66,7 @@ public class SpeciesConverterTest {
ProteinConverter rc = new ProteinConverter(colorExtractor);
GenericProtein alias = createAlias();
- rc.drawElement(alias, graphics, new ConverterParams());
+ rc.draw(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -79,7 +80,7 @@ public class SpeciesConverterTest {
List<ColorSchema> schemas = new ArrayList<>();
schemas.add(schema);
- rc.drawElement(alias2, graphics, new ConverterParams(), schemas);
+ rc.draw(alias2, graphics, new ConverterParams(), schemas);
int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -98,7 +99,7 @@ public class SpeciesConverterTest {
ProteinConverter rc = new ProteinConverter(colorExtractor);
GenericProtein alias = createAlias();
- rc.drawElement(alias, graphics, new ConverterParams());
+ rc.draw(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -112,14 +113,14 @@ public class SpeciesConverterTest {
List<ColorSchema> schemas = new ArrayList<>();
schemas.add(schema);
- rc.drawElement(alias2, graphics, new ConverterParams(), schemas);
+ rc.draw(alias2, graphics, new ConverterParams(), schemas);
int val2 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
graphics = bi.createGraphics();
- rc.drawElement(alias2, graphics, new ConverterParams(), new ArrayList<>());
+ rc.draw(alias2, graphics, new ConverterParams(), new ArrayList<>());
int val3 = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -139,7 +140,7 @@ public class SpeciesConverterTest {
ProteinConverter rc = new ProteinConverter(colorExtractor);
GenericProtein alias = createAlias();
- rc.drawElement(alias, graphics, new ConverterParams());
+ rc.draw(alias, graphics, new ConverterParams());
int val = bi.getRGB((int) alias.getCenterX(), (int) alias.getCenterY());
@@ -157,7 +158,7 @@ public class SpeciesConverterTest {
schema.setColor(Color.BLUE);
schemas.add(schema);
- rc.drawElement(alias2, graphics, new ConverterParams(), schemas);
+ rc.draw(alias2, graphics, new ConverterParams(), schemas);
int val2 = bi.getRGB((int) (alias.getX() + alias.getWidth() / 4), (int) alias.getCenterY());
int val3 = bi.getRGB((int) (alias.getCenterX()), (int) alias.getCenterY());
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/AllReactionTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java
similarity index 74%
rename from converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/AllReactionTests.java
rename to converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java
index 532c850e89..eb1ffeb4e9 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/AllReactionTests.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/AllReactionTests.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.graphics.reaction;
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
new file mode 100644
index 0000000000..6d2fe4eb5e
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -0,0 +1,407 @@
+package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
+
+import static org.junit.Assert.assertTrue;
+import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.FontMetrics;
+import java.awt.Graphics2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.reaction.AndOperator;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.OrOperator;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class ReactionConverterTest {
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawReactionWithLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(5.0);
+ rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output1 = outputStream.toByteArray();
+
+ Reaction reaction2 = createReaction(1.0);
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.BLACK);
+ schema.setLineWidth(5.0);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
+
+ outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output2 = outputStream.toByteArray();
+
+ // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+ // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ // Desktop.getDesktop().open(new File("tmp2.png"));
+
+ assertTrue(Arrays.equals(output1, output2));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawAfterDrawingReactionWithLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output1 = outputStream.toByteArray();
+
+ Reaction reaction2 = createReaction(1.0);
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.BLACK);
+ schema.setLineWidth(5.0);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), new ArrayList<>());
+
+ outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output2 = outputStream.toByteArray();
+
+ // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+ // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ // Desktop.getDesktop().open(new File("tmp2.png"));
+
+ assertTrue(Arrays.equals(output1, output2));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithFewLayouts() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bi.createGraphics();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(3.0);
+ rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output1 = outputStream.toByteArray();
+
+ Reaction reaction2 = createReaction(1.0);
+
+ bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ graphics = bi.createGraphics();
+
+ ColorSchema schema = new GenericColorSchema();
+ schema.setColor(Color.BLACK);
+ schema.setLineWidth(5.0);
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(schema);
+ schemas.add(schema);
+
+ rc.draw(reaction2, graphics, new ConverterParams().sbgnFormat(false), schemas);
+
+ outputStream = new ByteArrayOutputStream();
+ ImageIO.write(bi, "PNG", outputStream);
+ byte[] output2 = outputStream.toByteArray();
+
+ // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+ // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+ //
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ // Desktop.getDesktop().open(new File("tmp2.png"));
+
+ assertTrue(Arrays.equals(output1, output2));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ private Reaction createReaction(double lineWidth) {
+ Reaction result = new Reaction();
+
+ Modifier modifier = new Catalysis(new GenericProtein("s1"));
+ modifier.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 80)));
+ modifier.getLine().setWidth(lineWidth);
+
+ Reactant reactant = new Reactant(new GenericProtein("s2"));
+ reactant.setLine(new PolylineData(new Point2D.Double(90, 90), new Point2D.Double(10, 90)));
+ reactant.getLine().setWidth(lineWidth);
+ Product product = new Product(new GenericProtein("s3"));
+ product.setLine(new PolylineData(new Point2D.Double(200, 90), new Point2D.Double(110, 90)));
+ product.getLine().setWidth(lineWidth);
+ result.addModifier(modifier);
+ result.addProduct(product);
+ result.addReactant(reactant);
+ return result;
+ }
+
+ private Reaction createComplexReaction(double lineWidth) {
+ Reaction result = new Reaction();
+
+ Modifier modifier1 = new Catalysis(new GenericProtein("s1-1"));
+ modifier1.setLine(new PolylineData(new Point2D.Double(80, 20), new Point2D.Double(100, 40)));
+ modifier1.getLine().setWidth(lineWidth);
+
+ Modifier modifier2 = new Catalysis(new GenericProtein("s1-2"));
+ modifier2.setLine(new PolylineData(new Point2D.Double(120, 20), new Point2D.Double(100, 40)));
+ modifier2.getLine().setWidth(lineWidth);
+
+ AndOperator modifierOperator = new AndOperator();
+ modifierOperator.addInput(modifier1);
+ modifierOperator.addInput(modifier2);
+ modifierOperator.setLine(new PolylineData(new Point2D.Double(100, 40), new Point2D.Double(100, 80)));
+
+ Reactant reactant1 = new Reactant(new GenericProtein("s2-1"));
+ reactant1.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(10, 70)));
+ reactant1.getLine().setWidth(lineWidth);
+ Reactant reactant2 = new Reactant(new GenericProtein("s2-1"));
+ reactant2.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(10, 110)));
+ reactant2.getLine().setWidth(lineWidth);
+ OrOperator reactantOperator = new OrOperator();
+ reactantOperator.addInput(reactant1);
+ reactantOperator.addInput(reactant2);
+ reactantOperator.setLine(new PolylineData(new Point2D.Double(60, 90), new Point2D.Double(90, 90)));
+
+ Product product1 = new Product(new GenericProtein("s3-1"));
+ product1.setLine(new PolylineData(new Point2D.Double(200, 70), new Point2D.Double(130, 90)));
+ product1.getLine().setWidth(lineWidth);
+ Product product2 = new Product(new GenericProtein("s3-2"));
+ product2.setLine(new PolylineData(new Point2D.Double(200, 110), new Point2D.Double(130, 90)));
+ product2.getLine().setWidth(lineWidth);
+ SplitOperator productOperator = new SplitOperator();
+ productOperator.addOutput(product1);
+ productOperator.addOutput(product2);
+ productOperator.setLine(new PolylineData(new Point2D.Double(130, 90), new Point2D.Double(110, 90)));
+
+ result.addModifier(modifier1);
+ result.addModifier(modifier2);
+ result.addNode(modifierOperator);
+ result.addProduct(product1);
+ result.addProduct(product2);
+ result.addNode(productOperator);
+ result.addReactant(reactant1);
+ result.addReactant(reactant2);
+ result.addNode(reactantOperator);
+ return result;
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZooming() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(4)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndModifierOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getModifiers().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(3)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(3)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(3)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndModiferOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getModifiers().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(12)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndAllModifersOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getModifiers().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getModifiers().get(1).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(9)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ private Graphics2D createGraphicsMock() {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ FontMetrics fontMetrics = Mockito.mock(FontMetrics.class);
+ when(fontMetrics.getStringBounds(any(), any())).thenReturn(new Rectangle2D.Double());
+ when(graphics.getFontMetrics()).thenReturn(fontMetrics);
+ return graphics;
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(12)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawComplexReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = createGraphicsMock();
+ ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+ Reaction reaction = createComplexReaction(1.0);
+ reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(12)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java
deleted file mode 100644
index fa4a9c6b2b..0000000000
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/reaction/ReactionConverterTest.java
+++ /dev/null
@@ -1,196 +0,0 @@
-package lcsb.mapviewer.converter.graphics.reaction;
-
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.geom.Point2D;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.imageio.ImageIO;
-
-import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.modifier.Catalysis;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-
-public class ReactionConverterTest {
-
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testDrawReactionWithLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(5.0);
- rc.drawReaction(reaction, graphics, false);
-
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output1 = outputStream.toByteArray();
-
- Reaction reaction2 = createReaction(1.0);
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.BLACK);
- schema.setLineWidth(5.0);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
-
- rc.drawReaction(reaction2, graphics, false, schemas);
-
- outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output2 = outputStream.toByteArray();
-
- // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
- // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
- // Desktop.getDesktop().open(new File("tmp2.png"));
-
- assertTrue(Arrays.equals(output1, output2));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawAfterDrawingReactionWithLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(1.0);
- rc.drawReaction(reaction, graphics, false);
-
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output1 = outputStream.toByteArray();
-
- Reaction reaction2 = createReaction(1.0);
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.BLACK);
- schema.setLineWidth(5.0);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
-
- rc.drawReaction(reaction2, graphics, false, schemas);
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
- rc.drawReaction(reaction2, graphics, false, new ArrayList<>());
-
- outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output2 = outputStream.toByteArray();
-
- // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
- // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
- // Desktop.getDesktop().open(new File("tmp2.png"));
-
- assertTrue(Arrays.equals(output1, output2));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testDrawReactionWithFewLayouts() throws Exception {
- try {
- BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- Graphics2D graphics = bi.createGraphics();
- ReactionConverter rc = new ReactionConverter(colorExtractor);
-
- Reaction reaction = createReaction(3.0);
- rc.drawReaction(reaction, graphics, false);
-
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output1 = outputStream.toByteArray();
-
- Reaction reaction2 = createReaction(1.0);
-
- bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
- graphics = bi.createGraphics();
-
- ColorSchema schema = new GenericColorSchema();
- schema.setColor(Color.BLACK);
- schema.setLineWidth(5.0);
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(schema);
- schemas.add(schema);
-
- rc.drawReaction(reaction2, graphics, false, schemas);
-
- outputStream = new ByteArrayOutputStream();
- ImageIO.write(bi, "PNG", outputStream);
- byte[] output2 = outputStream.toByteArray();
-
- // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
- // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
- //
- // Desktop.getDesktop().open(new File("tmp.png"));
- // Desktop.getDesktop().open(new File("tmp2.png"));
-
- assertTrue(Arrays.equals(output1, output2));
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- private Reaction createReaction(double lineWidth) {
- Reaction result = new Reaction();
- Modifier modifier = new Catalysis();
- modifier.setLine(new PolylineData(new Point2D.Double(10, 20), new Point2D.Double(10, 100)));
- modifier.getLine().setWidth(lineWidth);
-
- Reactant reactant = new Reactant();
- reactant.setLine(new PolylineData(new Point2D.Double(100, 20), new Point2D.Double(100, 100)));
- reactant.getLine().setWidth(lineWidth);
- Product product = new Product();
- product.setLine(new PolylineData(new Point2D.Double(150, 20), new Point2D.Double(150, 100)));
- product.getLine().setWidth(lineWidth);
- result.addModifier(modifier);
- result.addProduct(product);
- result.addReactant(reactant);
- return result;
- }
-
-}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java b/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
index e13e3aa864..cca3829b52 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
@@ -126,13 +126,15 @@ public interface AnnotatedObject extends Serializable {
void setName(String name);
int getId();
-
/**
* Return human readable {@link String} representing class.
*
* @return human readable {@link String} representing class
*/
- public abstract String getStringType();
-
+ String getStringType();
+
+ void setSemanticZoomLevelVisibility(String zoomLevelVisibility);
+
+ String getSemanticZoomLevelVisibility();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 90c1e5cdc6..79059ab4cb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -180,6 +180,11 @@ public class Reaction implements AnnotatedObject {
*/
private String geneProteinReaction = null;
+ /**
+ * Zoom level visibility for semantic zooming.
+ */
+ private String zoomLevelVisibility;
+
/**
* Lists of all synonyms used for describing this element.
*/
@@ -867,4 +872,14 @@ public class Reaction implements AnnotatedObject {
this.synonyms.add(synonym);
}
+ @Override
+ public String getSemanticZoomLevelVisibility() {
+ return zoomLevelVisibility;
+ }
+
+ @Override
+ public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
+ this.zoomLevelVisibility = zoomLevelVisibility;
+ }
+
}
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 e624b92ffb..80530dda25 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
@@ -214,6 +214,11 @@ public abstract class Element implements AnnotatedObject, Serializable {
*/
private String fullName;
+ /**
+ * Zoom level visibility for semantic zooming.
+ */
+ private String zoomLevelVisibility;
+
/**
* Abbreviation associated with the element.
*/
@@ -1086,4 +1091,13 @@ public abstract class Element implements AnnotatedObject, Serializable {
dataMining.setElement(this);
}
+ @Override
+ public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
+ this.zoomLevelVisibility = zoomLevelVisibility;
+ }
+
+ public String getSemanticZoomLevelVisibility(){
+ return this.zoomLevelVisibility;
+ }
+
}
\ No newline at end of file
--
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