diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
index 9a7e8d6fe33c600b4c321c5af9e2ed88da9654b8..80d2c2f7a7d76259ebfd9e032514fb1d70abf7be 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/cache/WebPageDownloader.java
@@ -4,7 +4,6 @@ import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
-import java.net.ConnectException;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
@@ -85,8 +84,8 @@ public class WebPageDownloader {
urlConn.setRequestMethod("GET");
urlConn.addRequestProperty("User-Agent", "minerva-framework");
try {
- urlConn.connect();
- code = urlConn.getResponseCode();
+ urlConn.connect();
+ code = urlConn.getResponseCode();
} catch (FileNotFoundException e) {
code = HttpURLConnection.HTTP_NOT_FOUND;
} catch (IOException e) {
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Configuration.java b/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
index 4db91ad32b813654ab30e0ec872690109f6c1398..8afe7171c40f77edb086d39c1258edee4c7be199 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Configuration.java
@@ -67,6 +67,10 @@ public final class Configuration {
* Where the main webpgae is located.
*/
public static final String MAIN_PAGE = "/index.xhtml";
+
+ /**
+ * Name of the cookie for authentication token.
+ */
public static final String AUTH_TOKEN = "MINERVA_AUTH_TOKEN";
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
index db00f59da024510942394ca4db3cf790efa3d0f4..f9ec3e0770b7e80ca0f178a8dded4d8d3aa8dcf8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
@@ -5,6 +5,8 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
/**
* Describes structural information that appears in the cell designer notes.
@@ -116,7 +118,12 @@ public enum NoteField {
/**
* {@link Species#charge}.
*/
- CHARGE("Charge", CellDesignerSpecies.class, null); //
+ CHARGE("Charge", CellDesignerSpecies.class, null), //
+
+ /**
+ * {@link Element#getSemanticZoomLevelVisibility()}.
+ */
+ SEMANTIC_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelVisibility", AnnotatedObject.class, null); //
/**
* Name used in the notes to distinguish fields.
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index b46d75a00ff20d1f8623ba227e437b44f9d5ce6c..a1ab11fc4ad10cb3e8b74f6fb9e6b0196013f9b4 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -562,6 +562,28 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ /**
+ * Assigns semanticZoomingLevel to the element from notes string.
+ *
+ * @param element
+ * element to which data should be put to
+ * @param annotationString
+ * notes string
+ */
+ private void setSemanticZoomLevelVisibility(AnnotatedObject element, String annotationString) {
+ String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
+ if (zoomLevelVisibility == null) {
+ return;
+ }
+ if (element.getSemanticZoomLevelVisibility() == null) {
+ element.setSemanticZoomLevelVisibility(zoomLevelVisibility);
+ } else if (!element.getSemanticZoomLevelVisibility().equals(zoomLevelVisibility)) {
+ logger.warn(
+ elementUtils.getElementTag(element) + " New " + NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
+ + zoomLevelVisibility + "][" + element.getSemanticZoomLevelVisibility() + "]. Ignoring.");
+ }
+ }
+
/**
* Assigns notes to the element from notes string. This might look strange.
* The idea is that sometimes we have notes from more then one source. And the
@@ -620,6 +642,7 @@ public class RestAnnotationParser extends XmlParser {
setNotes(object, ann);
setSymbol(object, ann);
setSynonyms(object, ann);
+ setSemanticZoomLevelVisibility(object, ann);
setAbbreviation(object, ann);
setFormula(object, ann);
if (object instanceof Reaction) {
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 ff04e704263c0441452fe77f708ad972460e4c8f..f8ab6d2d441325298cd4f0bc6455476c01aca300 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 c408b252ec46ad4dbd0e6197bca23debb212647c..c6d7b706742e0c5560469a846910d2ecf5059124 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 f808c488be0611e3ff65a0cf13b43012b0691453..b66908389d19846ae461ed243800a41f0bb81577 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 c07d1422e660e6c34342af7f1f7b2e48106d7678..16e997154b53d5419fbf41c379f9d409dd39ac33 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 +16,8 @@ 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.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 +172,16 @@ public abstract class AbstractImageGenerator {
* Should the visualization include hierarchical view or not.
*/
private boolean nested = false;
-
+
+ /**
+ * Should the visualization include semantic zoom view or not.
+ */
+ private boolean semanticZoom = false;
+
/**
* Should sbgn standard be used.
*/
- private boolean sbgn = false;
+ private boolean sbgn = false;
/**
* List of objects containging information about layouts visualized in the
@@ -208,6 +213,17 @@ public abstract class AbstractImageGenerator {
return this;
}
+ /**
+ * @param semanticZoom
+ * semanticZoom to set
+ * @return object with all parameters
+ * @see #semanticZoom
+ */
+ public Params semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
+
/**
* @param scale
* scale to set
@@ -561,7 +577,8 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param sbgn the sbgn to set
+ * @param sbgn
+ * the sbgn to set
* @see #sbgn
* @return object with all parameters
*/
@@ -659,13 +676,13 @@ public abstract class AbstractImageGenerator {
// compartment/complexes)
if (element instanceof Species) {
if (((Species) element).getComplex() == null) {
- drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+ drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
}
}
}
// draw all reactions
for (Reaction reaction : params.getModel().getSortedReactions()) {
- drawReaction(reaction, params.getVisibleLayoutsForElement(reaction));
+ drawReaction(reaction, params.getVisibleLayoutsForElement(reaction), params);
}
// draw all compartments
for (Compartment compartment : params.getModel().getSortedCompartments()) {
@@ -738,8 +755,8 @@ public abstract class AbstractImageGenerator {
}
// get a converter for this compartment
- ElementConverterImpl converter = new ElementConverterImpl(compartment, colorExtractor);
- ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level);
+ BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
+ ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).semanticZoomingOn(params.semanticZoom);
if (nested) {
compartmentParams.fill(fill).scale(Math.max(scale, 1));
@@ -749,7 +766,7 @@ 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);
}
@@ -769,7 +786,7 @@ public abstract class AbstractImageGenerator {
for (Element element : result) {
// if a child is a standard species
if (element instanceof Species) {
- drawSpecies((Species) element, params.getVisibleLayoutsForElement(element));
+ drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
} else if (element instanceof Compartment) {
drawCompartment((Compartment) element, nested, params.getVisibleLayoutsForElement(element), params);
} else {
@@ -793,10 +810,12 @@ public abstract class AbstractImageGenerator {
* object to be drawn
* @param visibleLayouts
* list of {@link ColorSchema} used for coloring species in layouts
+ * @param params
+ * list of all params to create apropriate image
* @throws DrawingException
* thrown when there was a problem with drawing a {@link Species}
*/
- protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts) throws DrawingException {
+ protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
// The displaying of species is indicated by values of VisibilityLevel. If
// VisibilityLevel is big enough, then it is
@@ -825,14 +844,16 @@ 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).semanticZoomingOn(params.semanticZoom),
+ visibleLayouts);
} catch (Exception e) {
throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
}
@@ -847,7 +868,7 @@ public abstract class AbstractImageGenerator {
// depending on current zoom level, children are drawn or not
if (complex.getTransparencyLevel() <= level) {
for (Species a : complex.getElements()) {
- drawSpecies(a, visibleLayouts);
+ drawSpecies(a, visibleLayouts, params);
}
}
}
@@ -861,13 +882,15 @@ public abstract class AbstractImageGenerator {
* object to be drawn
* @param visibleLayouts
* list of {@link ColorSchema} used for coloring reaction in layouts
+ * @param params
+ * list of all params to create apropriate image
*/
- protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts) {
+ protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) {
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).semanticZoomingOn(params.semanticZoom).level(level), 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 c7499064c6533d5b85cc5d0cd9b06365da434c17..59577a9350b052778edde539029263c7bb881727 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/ElementConverter.java
deleted file mode 100644
index d1992b796ce8c4c30531713a9f4e9451cfd89a05..0000000000000000000000000000000000000000
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ElementConverter.java
+++ /dev/null
@@ -1,73 +0,0 @@
-package lcsb.mapviewer.converter.graphics;
-
-import java.awt.Graphics2D;
-import java.util.List;
-
-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.
- *
- * @author Piotr Gawron
- *
- * @param <T>
- * class of alias to convert
- */
-public interface ElementConverter<T extends Element> {
- /**
- * Alpha value (0..255) used for visualizing layout data that are normally
- * visualized in javascript.
- */
- int LAYOUT_ALPHA = 200;
-
- /**
- * This function draw representation of the alias on the graphics object.
- *
- * @param alias
- * alias that should be drawn
- * @param graphics
- * where we want to draw alias
- * @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);
-
- /**
- * This function draw representation of the alias on the graphics object.
- *
- * @param alias
- * alias that should be drawn
- * @param graphics
- * where we want to draw alias
- * @param params
- * visuzalization params (like, should the object be filled with
- * solid color, etc.), for more information see
- * {@link ConverterParams}
- * @param visualizedLayoutsColorSchemas
- * list of {@link ColorSchema} that were used for visualizing this
- * alias in different layouts that should be overlayed on the alias
- *
- */
- void drawElement(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas);
-
- /**
- * 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 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
- */
- void drawText(T alias, Graphics2D graphics, ConverterParams params) throws DrawingException;
-
-}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
index d9e35b48dfd43e10d49d4a9e2c4a9a7a61bb8f05..5e44baf42537fb87f7051a0005efa08c45a86f97 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
@@ -57,21 +57,25 @@ public class MapGenerator {
* Do we want to generate images in hierarchical view or normal.
*
*/
- private boolean nested = false;
+ private boolean nested = false;
+ /**
+ * Do we want to generate images with semantic zoom view or not.
+ */
+ private boolean semanticZoom = false;
/**
* Should we remove empty elements in nested view.
*
*/
- private boolean removeEmpty = false;
+ private boolean removeEmpty = false;
/**
* Callback function that update progress information.
*
*/
- private IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
+ private IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
/**
* Zoom factor on the lowest level.
@@ -135,6 +139,17 @@ public class MapGenerator {
return this;
}
+ /**
+ * @param semanticZoom
+ * the semanticZoom to set
+ * @see #nested
+ * @return full {@link MapGeneratorParams} object
+ */
+ public MapGeneratorParams semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
+
/**
* @return the removeEmpty
* @see #removeEmpty
@@ -326,6 +341,8 @@ public class MapGenerator {
imgParams.height(TILE_SIZE * TILES_CACHE_NUM);
imgParams.model(params.model);
imgParams.sbgn(params.sbgn);
+ imgParams.level(i);
+ imgParams.semanticZoom(params.semanticZoom);
if (params.nested) {
imgParams.level(i).nested(params.nested);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
new file mode 100644
index 0000000000000000000000000000000000000000..0f3fbea1f767125d5922bbed62ae53ee300e4999
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -0,0 +1,253 @@
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import java.awt.Graphics2D;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
+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.reaction.AbstractNode;
+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.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+
+/**
+ * This interface defines what operations should be possible to convert
+ * {@link AnnotatedObject} into a graphics on Graphics2D object.
+ *
+ * @author Piotr Gawron
+ *
+ * @param <T>
+ * class of alias to convert
+ */
+public abstract class BioEntityConverter<T extends AnnotatedObject> {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(BioEntityConverter.class);
+
+ /**
+ * Alpha value (0..255) used for visualizing overlay data that are normally
+ * visualized in javascript.
+ */
+ public static final int LAYOUT_ALPHA = 200;
+
+ /**
+ * This function draw representation of the alias on the graphics object.
+ *
+ * @param bioEntity
+ * {@link AnnotatedObject} that should be drawn
+ * @param graphics
+ * 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}
+ *
+ */
+ public void draw(T bioEntity, Graphics2D graphics, ConverterParams params) {
+ draw(bioEntity, graphics, params, new ArrayList<>());
+ }
+
+ /**
+ * This function draw representation of the alias on the graphics object.
+ *
+ * @param bioEntity
+ * {@link AnnotatedObject} that should be drawn
+ * @param graphics
+ * 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 visualizedOverlaysColorSchemas
+ * list of {@link ColorSchema} that were used for visualizing this
+ * bioentity in different data overlays that should be overlayed on
+ * the alias
+ *
+ */
+ public abstract 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 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 bioEntity
+ */
+ public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+
+ /**
+ * Checks if {@link AbstractNode} is visible according to visualization given
+ * in params.
+ *
+ * @param node
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
+ protected 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());
+ }
+ }
+
+ /**
+ * Checks if {@link NodeOperator} is visible according to visualization given
+ * in params.
+ *
+ * @param operator
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
+ protected 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;
+ }
+
+ /**
+ * Checks if {@link AnnotatedObject} is visible according to visualization
+ * given in params.
+ *
+ * @param bioEntity
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
+ protected 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);
+ }
+ }
+ } else if (bioEntity instanceof Reaction) {
+ if (!isAnyProductVisible(((Reaction) bioEntity).getProducts(), params)) {
+ result = false;
+ } else if (!isAnyReactantVisible(((Reaction) bioEntity).getReactants(), params)) {
+ result = false;
+ }
+
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + bioEntity.getClass());
+ }
+
+ return result;
+ }
+ return true;
+ }
+
+ /**
+ * Checks if at least one reactant is visible.
+ *
+ * @param reactants
+ * list of reactants
+ * @param params
+ * params against which check is run
+ * @return true if at least one reactant is visible
+ */
+ private boolean isAnyReactantVisible(List<Reactant> reactants, ConverterParams params) {
+ boolean result = false;
+ for (Reactant reactant : reactants) {
+ if (isVisible(reactant, params)) {
+ result = true;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Checks if at least one product is visible.
+ *
+ * @param products
+ * list of products
+ * @param params
+ * params against which check is run
+ * @return true if at least one product is visible
+ */
+ private boolean isAnyProductVisible(List<Product> products, ConverterParams params) {
+ boolean result = false;
+ for (Product product : products) {
+ if (isVisible(product, params)) {
+ result = true;
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Checks if level belongs to the range defined in
+ * semanticZoomLevelVisibility.
+ *
+ * @param level
+ * level to ve checked
+ * @param semanticZoomLevelVisibility
+ * range of levels to be checked
+ * @return true if level is in the range
+ */
+ protected 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;
+ }
+
+}
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 e96615f6ef559df3540a69e0ad871d6760fa35bd..bb68987a1ce1d12af1161f848bfea2622930a5ce 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 extends 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 +175,24 @@ 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 drawText(final AnnotatedObject element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ if (isVisible(element, params)) {
+ elementConverter.drawText(element, graphics, params);
+ }
}
@SuppressWarnings("unchecked")
@Override
- public void drawText(final Element element, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
- elementConverter.drawText(element, graphics, params);
+ public void draw(AnnotatedObject element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ if (isVisible(element, params)) {
+ elementConverter.draw(element, graphics, params, visualizedLayoutsColorSchemas);
+ }
}
- @SuppressWarnings("unchecked")
- @Override
- public void drawElement(Element element, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
- elementConverter.drawElement(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 0000000000000000000000000000000000000000..1bec6b8f64c1e7350cac580ae3b56077b7a5b273
--- /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 abstract class 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 07087ec3cda0e74b620bdda4b2b59ed1a0e90fe5..c13cdbdaf24231be3974fe5bc902b7caaf22072b 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 91%
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 ce31fb93bb7d3440fb7c0aeb93c28c7a37cc4e09..555a06d3d0e4ffb5246bc36d5b137c9c9b8d79c6 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;
@@ -31,7 +31,7 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
* class for which the comparator is created
*
*/
-public abstract class CompartmentConverter<T extends Compartment> implements ElementConverter<T> {
+public abstract class CompartmentConverter<T extends Compartment> extends ElementConverter<T> {
/**
* Default class logger.
@@ -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 a3cac76c0bfe0a722fcc95c45f004c942ce9431e..513684d8ad9e028c08f8e0d7f84f2034f43caebf 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 3c385168fb6c31a65aa5eff8c7e1873afa43b57d..611eb3deade2953f84cf4eaaf47b024479cb04c5 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 a3d6fd00ffdb31571a81b3acd9e92cc60a7c9554..6d691cfab2def72d712c1f44930ae194b5f151e9 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 72099129b6492cce9758c90f0e32d4e25c0d44cf..c1dbe6fa02feade3f0bdbb25f31a667a0442a376 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 e67b330c239c03743dc7cb27accd089e80a8efc3..169950485e06c1e1e55659969a56d0093a2cacf4 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 b074e084f5a04ee262d697be3c8896df9cf3f0fc..bdc72589df5e084cef1f4954297159415bf597af 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 238015b528866ec59541387f040aa29e41c1b991..992fd5cbdd9dfdfd4011f20370be4540a06eab61 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/bioEntity/element/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..2a4ce8bf838bfe86d594989af69d186381caa8e7
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java
@@ -0,0 +1,5 @@
+/**
+ * Provides classes that draws {@link lcsb.mapviewer.model.map.species.Element
+ * Elements} on the Graphics2D object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.element;
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 acc16bc98c697e1728e5f007131d20e9e1fc7698..84d00dc02a8c969fcc03de52697d7d17a7f988cb 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 6a59e89cc68ad9229d7118f5df8ebefaac3a4695..345fb9394478a769db5eb1ffeee759a457a08b7f 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 de6bcebb35da9439fd6481b637120d3c3532410d..42152ef9f1c518e85485ab9c268049202831b667 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 f55cf04258bfecf782c8c28dd94e6fddad6b9fc8..4c412634f46f78414c63f1a7426463cd1aaeb92d 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 f5493ee149bf9f9270bc0b25eeb205ca0bcf3b2b..514475cf86205411fc334f3dc88b411aecde5443 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 fe8699ac7232e1d7468cc45a52834fb9c2309c89..733f3b7ddb0dcf1f165360352c9e603854b8db3f 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 4ca043e2104412058387ac522854ba0350a028f6..0a6a2a059b9bd3d4cf9024797bd17d88c112b949 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 b3af8c09cb91bea6ed909a61ab5a3a002e12a1c3..0e794ffa6e425ca2af04a2a9d87c185b3728ebb3 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 6b13ac398f659d0b965f6f2d8797e720511443e4..277a8afc651d80665eaf652fd9d4dae4622926b4 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 8dc25a7ffdc7ca1c1062f006dcc39fc15f75612b..5412c1b961a4f388bf754aea9e8452528312722c 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 ca287bfc971da7cc9ab21e0174bc187887b99543..8abca141bd11232bed19933a0737079b56a8c016 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 94%
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 cf3ca8313cb36184ca0b76ab1da5090fe3f8ac53..73cb492d1e5dbf4873b41fb636622ca5add02b16 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;
@@ -37,7 +37,7 @@ import lcsb.mapviewer.model.map.species.Species;
* @author Piotr Gawron
*
*/
-public abstract class SpeciesConverter<T extends Species> implements ElementConverter<T> {
+public abstract class SpeciesConverter<T extends Species> extends ElementConverter<T> {
/**
* PI value.
@@ -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 4d2045ebf9b86289bebdfb842b970ed688d1f31c..e304953c08b75d94805cb84ae052e4c912611228 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/bioEntity/element/species/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..bb5eba0424d844789420b16d4b88a0c4c8962213
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
@@ -0,0 +1,6 @@
+/**
+ * Provides classes that draws
+ * {@link lcsb.mapviewer.db.model.map.species.Species Species} on the Graphics2D
+ * object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
new file mode 100644
index 0000000000000000000000000000000000000000..128760d664f8f39309c72c3a0713eb13dcd171fc
--- /dev/null
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/package-info.java
@@ -0,0 +1,5 @@
+/**
+ * Provides classes that draws {@link lcsb.mapviewer.model.map.AnnotatedObject
+ * BioEntites} on the Graphics2D object.
+ */
+package lcsb.mapviewer.converter.graphics.bioEntity;
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 86%
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 2697266eb836e792f109627dfb8afde82d028b29..1881210ae7ea63ec35a9382d0950bafea12cfc9d 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;
@@ -17,6 +17,9 @@ import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.Pair;
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;
@@ -37,7 +40,7 @@ import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
* @author Piotr Gawron
*
*/
-public class ReactionConverter {
+public class ReactionConverter extends BioEntityConverter<Reaction> {
/**
* When drawing operator this value defines radius of the joining operator
@@ -184,35 +187,34 @@ 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
@@ -220,32 +222,20 @@ public class ReactionConverter {
graphics.setColor(color);
}
- /**
- * 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
- * @param visualizedLayoutsColorSchemas
- * 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) {
+ @Override
+ 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 +248,14 @@ 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 +438,8 @@ 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 b03d32c941ee5fe702e8d7f4c90dea7e9e647549..d3b737737c9fcfe6f3b63b74d9496584f2c6f67a 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/main/java/lcsb/mapviewer/converter/graphics/species/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/package-info.java
deleted file mode 100644
index 19c8857d76af552ecc6677e4120e7f498e72c447..0000000000000000000000000000000000000000
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/species/package-info.java
+++ /dev/null
@@ -1,7 +0,0 @@
-/**
- * Provides classes that draws aliases of
- * {@link lcsb.mapviewer.db.model.map.species.Species Species} on the Graphics2D
- * object.
- */
-package lcsb.mapviewer.converter.graphics.species;
-
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 940247e162a4ea2ab262dbc9012f928d5fcf0a06..712c9d780cc68a7801c4536f6d38d703ec5d54e6 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
@@ -1,19 +1,18 @@
package lcsb.mapviewer.converter.graphics;
-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;
import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.converter.graphics.bioEntity.AllBioEntityTests;
+import lcsb.mapviewer.converter.graphics.geometry.AllGeometryTests;
+import lcsb.mapviewer.converter.graphics.placefinder.AllPlaceFinderTest;
+
@RunWith(Suite.class)
-@SuiteClasses({ AllGeometryTests.class, //
+@SuiteClasses({ //
+ AllBioEntityTests.class, //
+ AllGeometryTests.class, //
AllPlaceFinderTest.class, //
- AllReactionTests.class, //
- AllSpeciesConverterTests.class, //
ConverterTest.class, //
ImageGeneratorsTest.class, //
MapGeneratorTest.class, //
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 66e7eaa7edd963b522a6713a7e7c66d0bd7ad385..59f4964c758ef2dd761a65abd1d6196885e54d99 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 36d384f0070428c4f17bd8681ab851e7a1fa8a9b..36d84707d1901ea6c5e5a23e32f1f975708fcbef 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/bioEntity/AllBioEntityTests.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..4feec5c7d2f55a7a9f1e0888bc0ac822acb149ef
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/AllBioEntityTests.java
@@ -0,0 +1,18 @@
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AllSpeciesConverterTests;
+import lcsb.mapviewer.converter.graphics.bioEntity.reaction.AllReactionTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ //
+ AllSpeciesConverterTests.class, //
+ AllReactionTests.class, //
+ BioEntityConverterImplTest.class//
+})
+public class AllBioEntityTests {
+
+}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..8ba25ceb5b694c44954955c85a691d880e1aa439
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
@@ -0,0 +1,98 @@
+package lcsb.mapviewer.converter.graphics.bioEntity;
+
+import static org.mockito.Matchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+
+import org.junit.After;
+import org.junit.AfterClass;
+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.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;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class BioEntityConverterImplTest {
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN);
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndReactantOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+ Reaction reaction = createReaction(1.0);
+ reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+
+ BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(0)).draw(any(GeneralPath.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDrawReactionWithSemanticZoomingAndProductOff() throws Exception {
+ try {
+ Graphics2D graphics = Mockito.mock(Graphics2D.class);
+
+ Reaction reaction = createReaction(1.0);
+ reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+
+ BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
+ rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+
+ verify(graphics, times(0)).draw(any(GeneralPath.class));
+
+ } 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;
+ }
+
+}
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 f964383c73143a290d137f3c480472d4585ad1fc..69e9b97b05c9d7cd6406a6a214914ee29c84da1a 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 bc8c2b2eaf147564f64e636c39878aee078b08c5..1bdacdc9d7ea94ec4328ca4f6305873286000a4a 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 532c850e89d8ab6200a64dd06d859fd0c5690b00..eb1ffeb4e95d059ab4f43d9ce91824429a3ae726 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 0000000000000000000000000000000000000000..4623a640195498ae168413bdec83498a2e4ebc6b
--- /dev/null
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -0,0 +1,404 @@
+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.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.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 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 fa4a9c6b2b145e8f3f3ea2f6b450c254a06d6f96..0000000000000000000000000000000000000000
--- 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 e13e3aa8648abd1b1ab023b1545aa4a151d6615b..2a9ec585d0e782d016f3e629837005049d058213 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/AnnotatedObject.java
@@ -125,14 +125,32 @@ public interface AnnotatedObject extends Serializable {
*/
void setName(String name);
+ /**
+ * Returns database identifier of the object.
+ *
+ * @return database identifier of the object
+ */
int getId();
-
/**
* Return human readable {@link String} representing class.
*
* @return human readable {@link String} representing class
*/
- public abstract String getStringType();
-
+ String getStringType();
+
+ /**
+ * Sets semantic zoom level visibility.
+ *
+ * @param zoomLevelVisibility
+ * semantic zoom level visibility
+ */
+ void setSemanticZoomLevelVisibility(String zoomLevelVisibility);
+
+ /**
+ * Returns semantic zoom level visibility.
+ *
+ * @return semantic zoom level visibility
+ */
+ String getSemanticZoomLevelVisibility();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
index be5a84f3f9c1349ebe938d52cf86d0de5402f740..3dbbeab40d75cdde78a7c11d1c4e4ed5b54a397d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/OvalCompartment.java
@@ -38,6 +38,12 @@ public class OvalCompartment extends Compartment {
super(original);
}
+ /**
+ * Default constructor.
+ *
+ * @param elementId
+ * identifier of the compartment
+ */
public OvalCompartment(String elementId) {
super();
setElementId(elementId);
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 90c1e5cdc6b7efd6fa4076858312a6f7513941ee..c1eb4a094427f36cfe14e5d45f7f4061489c688e 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.
*/
@@ -231,7 +236,7 @@ public class Reaction implements AnnotatedObject {
name = original.getName();
reversible = original.reversible;
kineticLaw = original.kineticLaw;
- miriamDataSet = new HashSet<MiriamData>();
+ miriamDataSet = new HashSet<>();
for (MiriamData md : original.getMiriamData()) {
miriamDataSet.add(new MiriamData(md));
}
@@ -244,10 +249,11 @@ public class Reaction implements AnnotatedObject {
upperBound = original.getUpperBound();
subsystem = original.getSubsystem();
geneProteinReaction = original.getGeneProteinReaction();
- synonyms = new ArrayList<String>();
+ synonyms = new ArrayList<>();
for (String synonym : original.getSynonyms()) {
synonyms.add(synonym);
}
+ setSemanticZoomLevelVisibility(original.getSemanticZoomLevelVisibility());
}
@@ -867,4 +873,14 @@ 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 e624b92ffb386407e46def4e5e20c34d7e050c8b..386c2995adde11c9d6870a8b9b243c87ee696007 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 +1091,14 @@ public abstract class Element implements AnnotatedObject, Serializable {
dataMining.setElement(this);
}
+ @Override
+ public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
+ this.zoomLevelVisibility = zoomLevelVisibility;
+ }
+
+ @Override
+ public String getSemanticZoomLevelVisibility() {
+ return this.zoomLevelVisibility;
+ }
+
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
index 62875191ca8a99293cb0a87b49e0f4069b891554..237aee82abc42b6d8ce6711067084fcf8006b1b2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Species.java
@@ -168,6 +168,7 @@ public abstract class Species extends Element {
homodimer = original.getHomodimer();
positionToCompartment = original.getPositionToCompartment();
hypothetical = original.getHypothetical();
+ setSemanticZoomLevelVisibility(original.getSemanticZoomLevelVisibility());
// don't copy reaction nodes
}
diff --git a/persist/src/db/11/fix_db_20170616.sql b/persist/src/db/11/fix_db_20170616.sql
new file mode 100644
index 0000000000000000000000000000000000000000..1123f0a8a930fa1bc6fe1b2a40857a0d6621103b
--- /dev/null
+++ b/persist/src/db/11/fix_db_20170616.sql
@@ -0,0 +1,3 @@
+-- semantic zooming
+alter table element_table add column zoomlevelvisibility character varying default null;
+alter table reaction_table add column zoomlevelvisibility character varying default null;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
index 1374985424da145d3af1a72412c0597c673b5152..80caa2d0fdf8af75475909a5233562ddf1e074ea 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeController.java
@@ -6,7 +6,6 @@ import org.springframework.web.bind.annotation.CookieValue;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
import lcsb.mapviewer.api.BaseController;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index d3182f0880ec74f8d3d52d341dc7fa57b0e51e41..1f5526d0370ff3831445b04e5a2d1af8f2437ee5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -17,8 +17,6 @@ import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.RequestParam;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
@@ -266,19 +264,19 @@ public class ProjectRestImpl extends BaseRestImpl {
Double minY = originalModel.getHeight();
Double maxX = 0.0;
Double maxY = 0.0;
- Path2D polygon = cc.latLngToPolygon(polygonString);
-
- PathIterator pathIter = polygon.getPathIterator(null);
- while (!pathIter.isDone()) {
- final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
- if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
- minX = Math.min(minX, segment[0]);
- maxX = Math.max(maxX, segment[0]);
- minY = Math.min(minY, segment[1]);
- maxY = Math.max(maxY, segment[1]);
- }
- pathIter.next();
+ Path2D polygon = cc.latLngToPolygon(polygonString);
+
+ PathIterator pathIter = polygon.getPathIterator(null);
+ while (!pathIter.isDone()) {
+ final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
+ if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
+ minX = Math.min(minX, segment[0]);
+ maxX = Math.max(maxX, segment[0]);
+ minY = Math.min(minY, segment[1]);
+ maxY = Math.max(maxY, segment[1]);
}
+ pathIter.next();
+ }
maxX = Math.min(originalModel.getWidth(), maxX);
maxY = Math.min(originalModel.getHeight(), maxY);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
index 95cdfe87f7512719d1860a4c7bda61f9cb2dc170..427b20fb2a8c6fc641c77a781ff8c19080ee73a8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalController.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.api.projects.chemicals;
-import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index f7ec8bcfb8c201cc49df0a229cd872e8491b07b8..75f01d1125cadac9bd7edb37bcf0020f62d3f3d4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -21,8 +21,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.persist.dao.map.ReactionDao;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
index 9f8bd3fe86291062473e0240e67a49eef7a7cfa1..2c96827f476b4a9a847018358401e3b5b0995976 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
@@ -68,7 +68,7 @@ public class BioEntitiesController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList", method = { RequestMethod.GET, RequestMethod.POST },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public String[] getSuggestedQueryList( //
+ public String[] getSuggestedQueryList(//
@PathVariable(value = "projectId") String projectId, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token//
) throws SecurityException {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index c1305c14372b227c0cbbe080b7237a8ffc2152d3..3529d79e687dcd402cc7727327db39c31385ba4c 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.api.projects.models.bioEntities.reactions;
-import java.awt.geom.PathIterator;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
index a17deb36691a28a079d48478b158aaa848a707cc..50f9b691892db89ac0941f0c54abe744bf448191 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java
@@ -16,27 +16,21 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
-public class PublicationsRestImpl extends BaseRestImpl{
+public class PublicationsRestImpl extends BaseRestImpl {
Logger logger = Logger.getLogger(PublicationsRestImpl.class);
@@ -158,7 +152,8 @@ public class PublicationsRestImpl extends BaseRestImpl{
this.factory = factory;
}
- public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString, Integer length) throws SecurityException, QueryException {
+ public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString, Integer length)
+ throws SecurityException, QueryException {
List<Model> models = getModels(projectId, modelId, token);
Integer start = Math.max(0, Integer.valueOf(startString));
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
index 45a4ada00d1e377fb5074471b13441b6bf8ae353..815d1b9aff25e37ad4bc32f9c02f300313ac4f16 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayController.java
@@ -90,7 +90,7 @@ public class OverlayController extends BaseController {
}
@RequestMapping(value = "/projects/{projectId}/overlays/", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public LayoutView addOverlay( //
+ public LayoutView addOverlay(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@PathVariable(value = "projectId") String projectId, //
@RequestParam(value = "name") String name, //
@@ -103,7 +103,7 @@ public class OverlayController extends BaseController {
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.DELETE }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> removeOverlay( //
+ public Map<String, Object> removeOverlay(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId //
@@ -112,7 +112,7 @@ public class OverlayController extends BaseController {
}
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}", method = { RequestMethod.PATCH }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public LayoutView updateOverlay( //
+ public LayoutView updateOverlay(//
@RequestBody String body, //
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId, //
@@ -125,7 +125,7 @@ public class OverlayController extends BaseController {
@RequestMapping(value = "/projects/{projectId}/overlays/{overlayId}:downloadSource", method = { RequestMethod.GET },
produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getOverlaySource( //
+ public ResponseEntity<byte[]> getOverlaySource(//
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "overlayId") String overlayId //
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 9544bbeb5b86719879c212700278259070095e89..ed690aaad7e343d312adb59129a0ee2b7889f400 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -38,8 +38,6 @@ import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.data.FullAliasView;
-import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
import lcsb.mapviewer.services.search.data.LightReactionView;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index eea455176c321f0b3e8fc651fc288a3196ff29fa..212e7360c7dcd0c7e1849862b1e3126a30c488ac 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -636,6 +636,9 @@ public class ProjectService implements IProjectService {
IProgressUpdater.MAX_PROGRESS * imgCounter / finalSize + progress / finalSize, params);
}
});
+ if (layout.getTitle().contains(BuildInLayout.SEMANTIC.getTitle())) {
+ imgParams.semanticZoom(params.isSemanticZoom());
+ }
generator.generateMapImages(imgParams);
}
counter++;
@@ -704,18 +707,21 @@ public class ProjectService implements IProjectService {
if (params.isNetworkLayoutAsDefault()) {
buildInLayouts.add(BuildInLayout.NORMAL);
for (BuildInLayout buildInLayout : BuildInLayout.values()) {
- if (!buildInLayout.equals(BuildInLayout.NORMAL)) {
+ if (!buildInLayout.equals(BuildInLayout.NORMAL) && !buildInLayout.equals(BuildInLayout.SEMANTIC)) {
buildInLayouts.add(buildInLayout);
}
}
} else {
buildInLayouts.add(BuildInLayout.NESTED);
for (BuildInLayout buildInLayout : BuildInLayout.values()) {
- if (!buildInLayout.equals(BuildInLayout.NESTED)) {
+ if (!buildInLayout.equals(BuildInLayout.NESTED) && !buildInLayout.equals(BuildInLayout.SEMANTIC)) {
buildInLayouts.add(buildInLayout);
}
}
}
+ if (params.isSemanticZoom()) {
+ buildInLayouts.add(BuildInLayout.SEMANTIC);
+ }
// reverse the order of build in layouts, so we can insert them at the
// beginning of list of layouts (the order will be the same)
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
index 67952223b4b70e21706c1bfe295064caf50a8c1e..43cc0ff508433a0296c7596093d257bcbe3460a1 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -7,7 +7,6 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.search.data.FullAliasView;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightReactionView;
import lcsb.mapviewer.services.view.AuthenticationToken;
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
index 704b6abb7a4b58ec875a78a72196aa057df606db..bc59fb9104b9321272dececad18ec75e053a8afc 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
@@ -4,7 +4,6 @@ import java.util.Collection;
import java.util.List;
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.user.BasicPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
index e1a59f32d37cb373563a3aa7e40ed93aa5860aa1..ee446efa7ec86b8158848196155c4a4fb1941df7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/SearchResultFactory.java
@@ -1,26 +1,16 @@
package lcsb.mapviewer.services.search;
import java.util.Collection;
-import java.util.HashSet;
import java.util.List;
-import java.util.Set;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.data.TargetType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Gene;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.GeneRow;
@@ -62,10 +52,10 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
* {@link lcsb.mapviewer.services.view.AnnotationView} elements.
*/
@Autowired
- private AnnotationViewFactory annotationViewFactory;
+ private AnnotationViewFactory annotationViewFactory;
@Autowired
- private ElementMatcher elementMatcher;
+ private ElementMatcher elementMatcher;
/**
* Returns detailed information about element respective to the set of targets
@@ -114,12 +104,10 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
return null;
}
-
protected boolean elementMatch(TargetView target, Element element) {
return elementMatcher.elementMatch(target, element);
}
-
/**
* @return the annotationViewFactory
* @see #annotationViewFactory
@@ -137,7 +125,6 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
this.annotationViewFactory = annotationViewFactory;
}
-
/**
* @return the elementMatcher
* @see #elementMatcher
@@ -146,9 +133,9 @@ public abstract class SearchResultFactory<T, S extends ISearchResultView> extend
return elementMatcher;
}
-
/**
- * @param elementMatcher the elementMatcher to set
+ * @param elementMatcher
+ * the elementMatcher to set
* @see #elementMatcher
*/
public void setElementMatcher(ElementMatcher elementMatcher) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
index 7edaee16379296a7511c59557ccdcb652ddc5ba4..21df2ed92d971e0160604b9b9f9b859b8075fdcf 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -59,6 +59,7 @@ public class CreateProjectParams {
* Is the project a complex multi-file project.
*/
private boolean complex;
+ private boolean semanticZoom;
/**
* List of zip entries in the complex model definition.
@@ -722,4 +723,13 @@ public class CreateProjectParams {
return this;
}
+ public CreateProjectParams semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
+
+ public boolean isSemanticZoom() {
+ return this.semanticZoom;
+ }
+
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
index 13011324b3e60a4f273d4a3e8fe6cef6be72938a..3bdf5704f793378735a463ae359cb91e99cd36fe 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
@@ -32,6 +32,7 @@ public enum BuildInLayout { //
* Standard visualization with hierarchical view.
*/
NESTED("Pathways and compartments", "_nested", null, true),
+ SEMANTIC("Semantic zoom", "_semantic", null, false),
/**
* Clean visualization (with colors reset to black and white).
*/
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
index bafe1cd65ace628698072d51d347e9bc89035db9..0e08e4a105f21283040a4609fe99c885458f1cfb 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
@@ -209,6 +209,8 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
*/
private String sbgnFormat = "false";
+ private String semanticOverlay = "false";
+
/**
* List of zip entries corresponding to
* {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} files in the
@@ -664,6 +666,7 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
params.addZipEntry(submodel);
}
params.sbgnFormat("true".equalsIgnoreCase(sbgnFormat));
+ params.semanticZoom("true".equalsIgnoreCase(semanticOverlay));
params.networkLayoutAsDefault("true".equalsIgnoreCase(networkLayoutAsDefault));
projectService.createProject(params);
projectService.updateClassAnnotatorTreeForUser(
@@ -1485,4 +1488,21 @@ public class ProjectBean extends AbstractManagedBean implements Serializable {
this.newProjectOrganism = newProjectOrganism;
}
+ /**
+ * @return the semanticOverlay
+ * @see #semanticOverlay
+ */
+ public String getSemanticOverlay() {
+ return semanticOverlay;
+ }
+
+ /**
+ * @param semanticOverlay
+ * the semanticOverlay to set
+ * @see #semanticOverlay
+ */
+ public void setSemanticOverlay(String semanticOverlay) {
+ this.semanticOverlay = semanticOverlay;
+ }
+
}
diff --git a/web/src/main/webapp/admin/projects.xhtml b/web/src/main/webapp/admin/projects.xhtml
index a036465233728e14a31fb7ed97666ede4951fb0d..ba3c03ba04460b79659a3220a86625450d5ff672 100644
--- a/web/src/main/webapp/admin/projects.xhtml
+++ b/web/src/main/webapp/admin/projects.xhtml
@@ -303,6 +303,10 @@ configurations of the source file are discussed in <a href="#{request.context
<p:selectBooleanCheckbox value="#{projectMB.networkLayoutAsDefault}" />
<cc:helpButton helpText='If this checkbox is checked, the default overlay in User panel will present pure network. If the checkbox is unchecked then default overlay will present pathways and compartments view.'/>
+ <h:outputText value="Semantic zooming: " />
+ <p:selectBooleanCheckbox value="#{projectMB.semanticOverlay}" />
+ <cc:helpButton helpText=''/>
+
</h:panelGrid>
<center>
<p:commandButton value="Submit" icon="ui-icon-disk" actionListener="#{projectMB.createProject}" onclick="PF('addProjectDialog').hide();" update=":projectForm:projectDataTable"/>