From f49f6cc3355d7166914fd5ded743ca26b8c04b63 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Mon, 17 Mar 2025 17:09:22 +0100
Subject: [PATCH] export pathway
---
.../celldesigner/CellDesignerXmlParser.java | 2 +-
.../model/celldesigner/LayerXmlParser.java | 61 +++-
.../CellDesignerTestFunctions.java | 15 +
.../celldesigner/LayerXmlParserTest.java | 5 +-
.../model/celldesigner/ProjectExportTest.java | 15 +
.../graphics/AbstractImageGenerator.java | 333 ++++++------------
.../converter/model/sbml/SbmlLayerParser.java | 3 +-
.../mapviewer/converter/ProjectFactory.java | 4 +-
.../model/map/model/ModelComparator.java | 12 +-
.../wikipathway/xml/ModelContructor.java | 14 +-
.../services/impl/ProjectService.java | 12 -
11 files changed, 219 insertions(+), 257 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index a732c0d83e..6f6a521c4d 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -734,7 +734,7 @@ public class CellDesignerXmlParser extends Converter {
result.append(speciesCollectionXmlParser.geneCollectionToXmlString(genes));
result.append(speciesCollectionXmlParser.rnaCollectionToXmlString(rnas));
result.append(speciesCollectionXmlParser.antisenseRnaCollectionToXmlString(antisenseRnas));
- result.append(layerParser.layerCollectionToXml(model.getLayers()));
+ result.append(layerParser.layerCollectionToXml(model.getLayers(), model.getCompartments()));
result.append("</celldesigner:extension>\n");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index 592a89b005..affddd6eaa 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.geometry.ColorParser;
@@ -7,6 +8,8 @@ import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
@@ -28,7 +31,9 @@ import java.awt.geom.Point2D;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
/**
* Parser used for parsing CellDesigner xml to get {@link Layer} object.
@@ -81,7 +86,7 @@ public class LayerXmlParser {
* @param layers collection of layers
* @return xml node representing layers collection
*/
- public String layerCollectionToXml(final Collection<Layer> layers) {
+ public String layerCollectionToXml(final Collection<Layer> layers, final Collection<Compartment> compartments) {
for (final Layer layer : layers) {
if (NumberUtils.isParsable(layer.getLayerId())) {
problematicIdCounter = Math.max(problematicIdCounter, Integer.parseInt(layer.getLayerId()));
@@ -89,8 +94,25 @@ public class LayerXmlParser {
}
StringBuilder result = new StringBuilder();
result.append("<celldesigner:listOfLayers>");
+ boolean compartmentsAdded = false;
+ Set<PathwayCompartment> pathways = new HashSet<>();
+ for (Compartment compartment : compartments) {
+ if (compartment instanceof PathwayCompartment) {
+ pathways.add((PathwayCompartment) compartment);
+ }
+ }
for (final Layer layer : layers) {
- result.append(layerToXml(layer));
+ if (layer.getName().equals(CreateHierarchyCommand.PATHWAY_LAYER_NAME)) {
+ compartmentsAdded = true;
+ result.append(layerToXml(layer, pathways));
+ } else {
+ result.append(layerToXml(layer, new HashSet<>()));
+ }
+ }
+ if (!compartmentsAdded) {
+ Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
+ result.append(layerToXml(layer, pathways));
}
result.append("</celldesigner:listOfLayers>\n");
return result.toString();
@@ -275,7 +297,7 @@ public class LayerXmlParser {
* @param layer object to be transformed into xml
* @return CellDesigner xml representation for the layer
*/
- String layerToXml(final Layer layer) {
+ String layerToXml(final Layer layer, final Set<PathwayCompartment> pathways) {
StringBuilder result = new StringBuilder();
String id = layer.getLayerId();
if (!NumberUtils.isParsable(id)) {
@@ -293,6 +315,9 @@ public class LayerXmlParser {
for (final LayerImage layerImage : layer.getImages()) {
result.append(layerImageToXml(layerImage));
}
+ for (final PathwayCompartment pathway : pathways) {
+ result.append(pathwayToXml(pathway));
+ }
result.append("</celldesigner:listOfTexts>\n");
result.append("<celldesigner:listOfSquares>\n");
@@ -579,4 +604,34 @@ public class LayerXmlParser {
return result.toString();
}
+ String pathwayToXml(final PathwayCompartment pathway) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerSpeciesAlias>");
+ result.append("<celldesigner:layerNotes>\n");
+ String notes = pathway.getName();
+ if (notes == null) {
+ notes = "";
+ }
+ if (commonParser.getNotesXmlContent(pathway.getNotes()) != null) {
+ notes += "\n" + commonParser.getNotesXmlContent(pathway.getNotes());
+ }
+ if (pathway.getFillColor() != null && !pathway.getFillColor().equals(Color.WHITE)) {
+ notes += "\nBackgroundColor:" + new ColorParser().colorToHtml(pathway.getFillColor());
+ }
+ if (!pathway.getBorderColor().equals(Color.LIGHT_GRAY)) {
+ notes += "\nBorderColor:" + new ColorParser().colorToHtml(pathway.getBorderColor());
+ }
+ result.append(notes);
+ result.append("\n</celldesigner:layerNotes>");
+ result.append("<celldesigner:paint color=\"" + XmlParser.colorToString(pathway.getFontColor()) + "\"/>");
+ result.append("<celldesigner:bounds x=\"" + pathway.getX() + "\" ");
+ result.append(" y=\"" + pathway.getY() + "\" ");
+ result.append(" w=\"" + pathway.getWidth() + "\" ");
+ result.append(" h=\"" + pathway.getHeight() + "\"/>");
+ result.append("<celldesigner:font size=\"" + pathway.getFontSize().intValue() + "\"/>");
+ result.append("</celldesigner:layerSpeciesAlias>\n");
+ return result.toString();
+ }
+
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
index 379d507b56..9140a5181f 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
@@ -16,6 +16,7 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
@@ -169,6 +170,20 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
return compartment;
}
+ protected PathwayCompartment createPathway() {
+ final PathwayCompartment pathwayCompartment = new PathwayCompartment("art0");
+ pathwayCompartment.setName(faker.science().element());
+ assignCoordinates(13, 14, 100, 120, pathwayCompartment);
+ pathwayCompartment.setNameVerticalAlign(VerticalAlign.TOP);
+ pathwayCompartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
+ pathwayCompartment.setNameX(pathwayCompartment.getX() + 10);
+ pathwayCompartment.setNameY(pathwayCompartment.getY() + 10);
+ pathwayCompartment.setNameWidth(pathwayCompartment.getWidth() - 20);
+ pathwayCompartment.setNameHeight(pathwayCompartment.getHeight() - 20);
+
+ return pathwayCompartment;
+ }
+
protected static LayerText createText() {
final LayerText layerText = new LayerText();
layerText.setX(256.0);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
index e6fcbd17d9..ad1b8ef7b2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
@@ -25,6 +25,7 @@ import org.w3c.dom.Node;
import java.awt.Color;
import java.awt.geom.Rectangle2D;
import java.util.Collection;
+import java.util.HashSet;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -53,7 +54,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
assertNotNull(layers);
assertEquals(1, layers.size());
- xmlString = parser.layerCollectionToXml(layers);
+ xmlString = parser.layerCollectionToXml(layers, new HashSet<>());
node = getNodeFromXmlString(xmlString);
Collection<Layer> layers2 = parser.parseLayers(node);
assertNotNull(layers2);
@@ -119,7 +120,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
Layer layer = parser.getLayer(node);
assertNotNull(layer);
- xmlString = parser.layerToXml(layer);
+ xmlString = parser.layerToXml(layer, new HashSet<>());
node = getNodeFromXmlString(xmlString);
Layer layers2 = parser.getLayer(node);
assertNotNull(layers2);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
index fb3eb9eaab..adbeeabe2a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
@@ -8,6 +8,7 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectComparator;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
@@ -239,4 +240,18 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
testSerializationOverZip(project);
}
+ @Test
+ public void testWithPathway() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(126);
+ model.setHeight(148);
+ PathwayCompartment pathway = createPathway();
+ model.addElement(pathway);
+
+ project.addModel(model);
+
+ testSerializationOverZip(project);
+ }
+
}
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 df9a04f21c..3a08e727ca 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
@@ -1,24 +1,6 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.geom.Line2D;
-import java.awt.geom.Rectangle2D;
-import java.io.File;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.nio.file.FileStore;
-import java.nio.file.Files;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.MimeType;
@@ -35,7 +17,6 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -46,6 +27,21 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.geom.Line2D;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.FileStore;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.List;
/**
* This class is responsible for creation of the image from the model. It's an
@@ -78,9 +74,8 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry;
* from graphics2D and save it into separate files</li>
* </ul>
* </p>
- *
+ *
* @author Piotr Gawron
- *
*/
public abstract class AbstractImageGenerator {
@@ -99,13 +94,13 @@ public abstract class AbstractImageGenerator {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Class that allows to check if element is visible (or transparent) when
* drawing. It's used to filter out invisible elements when drawing
* semantic/hierarchy view.
*/
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+ private final SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
* On which level in hierarchical view we should visualize map.
*/
@@ -145,11 +140,8 @@ public abstract class AbstractImageGenerator {
* {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
* params}.
*
- * @param params
- * list of all params to create appropriate image
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- *
+ * @param params list of all params to create appropriate image
+ * @throws DrawingException thrown when there was a problem with drawing a map
*/
protected AbstractImageGenerator(final Params params) {
this.params = params;
@@ -167,18 +159,15 @@ public abstract class AbstractImageGenerator {
* This method creates a graphics object for different implementations of
* canvas with fixed width and height.
*
- * @param width
- * width of the canvas (graphics2d) to be created
- * @param height
- * height of the canvas (graphics2d) to be created
+ * @param width width of the canvas (graphics2d) to be created
+ * @param height height of the canvas (graphics2d) to be created
*/
protected abstract void createImageObject(final double width, final double height);
/**
* Draw a model into {@link #getGraphics()} object.
- *
- * @throws DrawingException
- * thrown when there is a problem with drawing
+ *
+ * @throws DrawingException thrown when there is a problem with drawing
*/
protected void draw() throws DrawingException {
if (isDrawn()) {
@@ -248,21 +237,8 @@ public abstract class AbstractImageGenerator {
}
private List<Drawable> getDrawables() {
- boolean isOriginallyVisible = false;
- for (Layer layer : params.getModel().getLayers()) {
- if (Objects.deepEquals(layer.getName(), CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- isOriginallyVisible = layer.isVisible();
- layer.setVisible(true);
- }
- }
List<Drawable> drawables = new ArrayList<>(params.getModel().getDrawables(true));
drawables.sort(BioEntity.Z_INDEX_COMPARATOR);
- for (Layer layer : params.getModel().getLayers()) {
- if (Objects.deepEquals(layer.getName(), CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- // revert change that was required to obtain drawables with text layer
- layer.setVisible(isOriginallyVisible);
- }
- }
return drawables;
}
@@ -300,10 +276,8 @@ public abstract class AbstractImageGenerator {
/**
* This method draw a {@link Compartment} on a graphics.
*
- * @param compartment
- * object that we want to draw
- * @throws DrawingException
- * thrown when there was a problem with drawing {@link Compartment}
+ * @param compartment object that we want to draw
+ * @throws DrawingException thrown when there was a problem with drawing {@link Compartment}
*/
protected void drawCompartment(final Compartment compartment) throws DrawingException {
// get a converter for this compartment
@@ -328,10 +302,8 @@ public abstract class AbstractImageGenerator {
/**
* This method draw a {@link Species} on a graphics.
*
- * @param species
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Species}
+ * @param species object to be drawn
+ * @throws DrawingException thrown when there was a problem with drawing a {@link Species}
*/
protected void drawSpecies(final Species species) throws DrawingException {
if (!cross(species.getBorder())) {
@@ -368,10 +340,8 @@ public abstract class AbstractImageGenerator {
/**
* This method draw a reaction on a graphics.
*
- * @param reaction
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Reaction}
+ * @param reaction object to be drawn
+ * @throws DrawingException thrown when there was a problem with drawing a {@link Reaction}
*/
protected void drawReaction(final Reaction reaction) throws DrawingException {
if (!cross(reaction.getLines())) {
@@ -385,8 +355,7 @@ public abstract class AbstractImageGenerator {
/**
* Checks if one of the lines in parameter cross the frame.
*
- * @param lines
- * list of lines to check
+ * @param lines list of lines to check
* @return true if the cross point exist, false otherwise
*/
private boolean cross(final List<Line2D> lines) {
@@ -402,8 +371,7 @@ public abstract class AbstractImageGenerator {
* Checks if the rectangle in the parameters cross the fram in which we are
* currently draw image.
*
- * @param rect
- * rectangle to check
+ * @param rect rectangle to check
* @return true if rectangle check the frame, false otherwise
*/
protected boolean cross(final Rectangle2D rect) {
@@ -418,8 +386,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param graphics
- * the graphics to set
+ * @param graphics the graphics to set
*/
protected void setGraphics(final Graphics2D graphics) {
this.graphics = graphics;
@@ -428,12 +395,9 @@ public abstract class AbstractImageGenerator {
/**
* Saves generated image into file.
*
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param fileName file where the images should be saved
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void saveToFile(final String fileName) throws IOException, DrawingException {
if (!isDrawn()) {
@@ -446,24 +410,18 @@ public abstract class AbstractImageGenerator {
/**
* Saves generated image from {@link #getGraphics()} into file.
*
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param fileName file where the images should be saved
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
protected abstract void saveToFileImplementation(final String fileName) throws IOException;
/**
* Saves generated image into {@link OutputStream}.
*
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @throws IOException thrown when there is problem with output stream
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void saveToOutputStream(final OutputStream os) throws IOException, DrawingException {
if (!isDrawn()) {
@@ -476,32 +434,22 @@ public abstract class AbstractImageGenerator {
* Saves generated image from {@link #getGraphics()} into {@link OutputStream}
* .
*
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @throws IOException thrown when there is problem with output stream
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
protected abstract void saveToOutputStreamImplementation(final OutputStream os) throws IOException;
/**
* Saves part of the generated image file.
*
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param fileName file where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void savePartToFile(final int x, final int y, final int width, final int height, final String fileName)
throws IOException, DrawingException {
@@ -525,42 +473,29 @@ public abstract class AbstractImageGenerator {
/**
* Saves part of the generated image from {@link #getGraphics()} into file.
*
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
+ * @param fileName file where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
*/
protected abstract void savePartToFileImplementation(final int x, final int y, final int width, final int height,
- final String fileName) throws IOException;
+ final String fileName) throws IOException;
/**
* Saves part of the generated image into {@link OutputStream}.
*
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void savePartToOutputStream(final int x, final int y, final int width, final int height,
- final OutputStream os) throws IOException, DrawingException {
+ final OutputStream os) throws IOException, DrawingException {
if (!isDrawn()) {
draw();
}
@@ -571,23 +506,16 @@ public abstract class AbstractImageGenerator {
* Saves part of the generated image from {@link #getGraphics()} into
* {@link OutputStream}.
*
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
protected abstract void savePartToOutputStreamImplementation(final int x, final int y, final int width,
- final int height, final OutputStream os) throws IOException;
+ final int height, final OutputStream os) throws IOException;
/**
* Returns name of the format to which this graphic converter will transform.
@@ -600,8 +528,7 @@ public abstract class AbstractImageGenerator {
* Returns {@link MimeType} that should be used for files generated by this
* image generator.
*
- * @return {@link MimeType} that should be used for files generated by this
- * image generator
+ * @return {@link MimeType} that should be used for files generated by this image generator
*/
public abstract MimeType getMimeType();
@@ -620,8 +547,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param sbgnFormat
- * the sbgnFormat to set
+ * @param sbgnFormat the sbgnFormat to set
*/
protected void sbgnFormat(final boolean sbgnFormat) {
this.sbgnFormat = sbgnFormat;
@@ -636,8 +562,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param drawn
- * the drawn to set
+ * @param drawn the drawn to set
* @see #drawn
*/
private void setDrawn(final boolean drawn) {
@@ -653,8 +578,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param params
- * the params to set
+ * @param params the params to set
* @see #params
*/
protected void setParams(final Params params) {
@@ -665,7 +589,6 @@ public abstract class AbstractImageGenerator {
* This class contains a list of params that are used for drawing.
*
* @author Piotr Gawron
- *
*/
public static class Params {
@@ -740,9 +663,8 @@ public abstract class AbstractImageGenerator {
* single layout. In this map we have pairs between {@link Element}/
* {@link Reaction} and {@link DataOverlayEntry} used to visualize the
* element.
- *
*/
- private List<List<Pair<? extends BioEntity, DataOverlayEntry>>> visibleDataOverlays = new ArrayList<>();
+ private final List<List<Pair<? extends BioEntity, DataOverlayEntry>>> visibleDataOverlays = new ArrayList<>();
/**
* Color that should be used for drawing overlays with minimum value.
@@ -759,8 +681,7 @@ public abstract class AbstractImageGenerator {
private Color neutralColor = Color.WHITE;
/**
- * @param scale
- * scale to set
+ * @param scale scale to set
* @return object with all parameters
* @see #scale
*/
@@ -770,8 +691,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param scale
- * scale to set
+ * @param scale scale to set
* @return object with all parameters
* @see #scale
*/
@@ -781,9 +701,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param x
- * x coordinate to be set
+ * @param x x coordinate to be set
* @return object with all parameters
* @see #x
*/
@@ -793,8 +711,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param x
- * x coordinate to be set
+ * @param x x coordinate to be set
* @return object with all parameters
* @see #x
*/
@@ -804,8 +721,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param y
- * y coordinate to be set
+ * @param y y coordinate to be set
* @return object with all parameters
* @see #y
*/
@@ -815,8 +731,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param y
- * y coordinate to be set
+ * @param y y coordinate to be set
* @return object with all parameters
* @see #y
*/
@@ -826,8 +741,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param width
- * width to set
+ * @param width width to set
* @return object with all parameters
* @see #width
*/
@@ -837,8 +751,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param width
- * width to set
+ * @param width width to set
* @return object with all parameters
* @see #width
*/
@@ -848,9 +761,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param height
- * height to set
+ * @param height height to set
* @return object with all parameters
* @see #height
*/
@@ -860,8 +771,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param height
- * height to set
+ * @param height height to set
* @return object with all parameters
* @see #height
*/
@@ -871,9 +781,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param background
- * background flag to set
+ * @param background background flag to set
* @return object with all parameters
* @see #background
*/
@@ -883,9 +791,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param nested
- * nested flag to set
+ * @param nested nested flag to set
* @return object with all parameters
* @see #nested
*/
@@ -895,9 +801,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param model
- * model to set
+ * @param model model to set
* @return object with all parameters
* @see #model
*/
@@ -913,9 +817,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param level
- * level to set
+ * @param level level to set
* @return object with all parameters
* @see #level
*/
@@ -927,8 +829,7 @@ public abstract class AbstractImageGenerator {
/**
* Sets {@link #level} parameter from {@link String}.
*
- * @param zoomLevel
- * new {@link #level} value
+ * @param zoomLevel new {@link #level} value
* @return object with all parameters
*/
public Params level(final String zoomLevel) {
@@ -941,7 +842,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return scale value
* @see #scale
*/
@@ -950,7 +850,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return x coordinate value
* @see #x
*/
@@ -959,7 +858,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return y coordinate value
* @see #y
*/
@@ -968,7 +866,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return width value
* @see #width
*/
@@ -977,7 +874,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return height value
* @see #height
*/
@@ -986,7 +882,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return model object
* @see #model
*/
@@ -995,7 +890,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return background value
* @see #background
*/
@@ -1004,7 +898,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return nested value
* @see #nested
*/
@@ -1033,10 +926,9 @@ public abstract class AbstractImageGenerator {
* contains mapping between {@link Element}/{@link Reaction} and
* {@link DataOverlayEntry} used for coloring specific element.
*
- * @param map
- * layout data containing mapping between {@link Element}/
- * {@link Reaction} and {@link DataOverlayEntry} used for coloring
- * specific element
+ * @param map layout data containing mapping between {@link Element}/
+ * {@link Reaction} and {@link DataOverlayEntry} used for coloring
+ * specific element
*/
public void addVisibleDataOverlay(final List<Pair<? extends BioEntity, DataOverlayEntry>> map) {
visibleDataOverlays.add(map);
@@ -1050,12 +942,9 @@ public abstract class AbstractImageGenerator {
* Returns list with {@link DataOverlayEntry} used to visualize the specific
* object in data overlays visualized in the JavaScript.
*
- * @param object
- * object ({@link Element} or {@link Reaction}) for which we return
- * list of {@link DataOverlayEntry} in different layouts
- * @return list with {@link DataOverlayEntry} used to visualize the specific
- * object in data overlays visualized in the JavaScript
- * @see #visibleDataOverlays
+ * @param object object ({@link Element} or {@link Reaction}) for which we return
+ * list of {@link DataOverlayEntry} in different layouts
+ * @return list with {@link DataOverlayEntry} used to visualize the specific object in data overlays visualized in the JavaScript
*/
public List<List<DataOverlayEntry>> getVisibleDataOverlaysForElement(final BioEntity object) {
List<List<DataOverlayEntry>> result = new ArrayList<>();
@@ -1075,8 +964,7 @@ public abstract class AbstractImageGenerator {
* Returns {@link Color} that should be used for drawing overlays with
* maximum value.
*
- * @return {@link Color} that should be used for drawing overlays with
- * maximum value
+ * @return {@link Color} that should be used for drawing overlays with maximum value
*/
public Color getMaxColor() {
return maxColor;
@@ -1090,16 +978,14 @@ public abstract class AbstractImageGenerator {
* Returns {@link Color} that should be used for drawing overlays with
* minimum value.
*
- * @return {@link Color} that should be used for drawing overlays with
- * minimum value
+ * @return {@link Color} that should be used for drawing overlays with minimum value
*/
public Color getMinColor() {
return minColor;
}
/**
- * @param minColor
- * minColor to set
+ * @param minColor minColor to set
* @return object with all parameters
* @see #minColor
*/
@@ -1109,8 +995,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param maxColor
- * maxColor to set
+ * @param maxColor maxColor to set
* @return object with all parameters
* @see #maxColor
*/
@@ -1120,8 +1005,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param simpleColor
- * simpleColor to set
+ * @param simpleColor simpleColor to set
* @return object with all parameters
* @see #simpleColor
*/
@@ -1139,10 +1023,9 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
+ * @param sbgn the sbgn to set
* @return object with all parameters
+ * @see #sbgn
*/
public Params sbgn(final boolean sbgn) {
this.sbgn = sbgn;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java
index 82e31e6801..894be0c3f4 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.converter.model.sbml;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -22,7 +21,7 @@ public class SbmlLayerParser extends SbmlBioEntityParser {
Layer layer = new Layer();
layer.setLayerId(1);
layer.setZ(1);
- layer.setName(CreateHierarchyCommand.TEXT_LAYER_NAME);
+ layer.setName("text");
SbmlModelUtils sbmlModelUtils = new SbmlModelUtils(sbmlModel);
Layout layout = sbmlModelUtils.getLayout();
if (layout != null) {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index 6a4939e969..fd05cbb417 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -178,7 +178,9 @@ public class ProjectFactory {
addModelFileToZip(project.getTopModel(), project.getTopModel().getName() + "." + converter.getFileExtensions().get(0), converter, zos);
for (ModelData model : project.getModels()) {
if (model != project.getTopModelData()) {
- addModelFileToZip(model.getModel(), ZipEntryFileFactory.SUBMODEL_DIRECTORY + model.getName() + "." + converter.getFileExtensions().get(0), converter, zos);
+ addModelFileToZip(model.getModel(),
+ ZipEntryFileFactory.SUBMODEL_DIRECTORY + model.getName() + "." + converter.getFileExtensions().get(0), converter,
+ zos);
}
}
Model mapping = createMappingModel(project.getModels());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index 3b56cb0799..f31d8915ff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -27,6 +27,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
import java.util.Calendar;
import java.util.Collection;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Map;
import java.util.Set;
@@ -112,7 +113,16 @@ public class ModelComparator extends Comparator<Model> {
int status = compareElements(arg0.getElements(), arg1.getElements());
if (status != 0) {
- logger.debug("Set of elements different");
+ Set<String> model0ids = new HashSet<>();
+ Set<String> model1ids = new HashSet<>();
+
+ for (Element element : arg0.getElements()) {
+ model0ids.add(element.getElementId());
+ }
+ for (Element element : arg1.getElements()) {
+ model1ids.add(element.getElementId());
+ }
+ logger.debug("Set of elements different: {}, {}", model1ids, model0ids);
return status;
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
index f20dc52948..f6bf6a4c3d 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
@@ -106,7 +106,7 @@ public class ModelContructor {
*/
private static final double EPSILON = 1e-6;
/**
- * List of {@link Shape#shape shapes} that are not supported to be part of a
+ * List of shapes that are not supported to be part of a
* {@link Complex complex}.
*/
private static final Set<GpmlShape> INALID_COMPLEX_SHAPE_CHILDREN = new HashSet<>();
@@ -1252,7 +1252,7 @@ public class ModelContructor {
}
if (complex.getName() == null || (complex.getName().isEmpty())) {
for (final Layer layer : model.getLayers()) {
- if (layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
+ if (!layer.getName().equals(CreateHierarchyCommand.PATHWAY_LAYER_NAME)) {
LayerText toRemove = null;
for (final LayerText lt : layer.getTexts()) {
if (complex.contains(lt)) {
@@ -1297,7 +1297,7 @@ public class ModelContructor {
for (final Compartment compartment : model.getCompartments()) {
if (compartment.getName() == null || compartment.getName().isEmpty()) {
for (final Layer layer : model.getLayers()) {
- if (layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
+ if (!layer.getName().equals(CreateHierarchyCommand.PATHWAY_LAYER_NAME)) {
LayerText toRemove = null;
for (final LayerText lt : layer.getTexts()) {
if (compartment.contains(lt)) {
@@ -1322,12 +1322,6 @@ public class ModelContructor {
}
}
- /**
- * Creates list of {@link LayerLine} in the model from gpml model.
- *
- * @param graph gpml model
- * @return list of {@link LayerLine}
- */
private Collection<PolylineData> createLines(final Graph graph) {
final List<PolylineData> result = new ArrayList<PolylineData>();
for (final PolylineData pd : graph.getLines()) {
@@ -1398,7 +1392,7 @@ public class ModelContructor {
layer.setVisible(true);
layer.setLayerId(1);
layer.setZ(1);
- layer.setName(CreateHierarchyCommand.TEXT_LAYER_NAME);
+ layer.setName("text");
}
}
}
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 11e01fb110..51c76d2285 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -41,7 +41,6 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundImageLayer;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundStatus;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -58,7 +57,6 @@ import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.ProjectLogEntryDao;
import lcsb.mapviewer.persist.dao.ProjectLogEntryProperty;
import lcsb.mapviewer.persist.dao.ProjectProperty;
-import lcsb.mapviewer.persist.dao.graphics.LayerProperty;
import lcsb.mapviewer.persist.dao.map.ModelProperty;
import lcsb.mapviewer.persist.dao.user.UserAnnotationSchemaDao;
import lcsb.mapviewer.services.interfaces.ICommentService;
@@ -602,16 +600,6 @@ public class ProjectService implements IProjectService {
self.createSimpleProject(params);
}
- Map<LayerProperty, Object> layerFilter = new HashMap<>();
- layerFilter.put(LayerProperty.PROJECT_ID, params.getProjectId());
- List<Layer> layers = layerService.getAll(layerFilter, Pageable.unpaged()).getContent();
- for (final Layer layer : layers) {
- if (!layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- layer.setVisible(false);
- layerService.update(layer);
- }
- }
-
self.updateProjectStatus(params.getProjectId(), ProjectStatus.UPLOADING_TO_DB, 0.0);
self.addBuiltInBackgrounds(params);
--
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