From 0206ddb1c57b73f75a801626e8a5d626ff35610b Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Fri, 14 Mar 2025 16:55:26 +0100
Subject: [PATCH] export data overlays
---
.../CellDesignerTestFunctions.java | 32 ++++
.../model/celldesigner/ProjectExportTest.java | 52 +++++-
.../converter/ColorSchemaWriter.java | 167 ++++++++++++++++++
.../mapviewer/converter/ProjectFactory.java | 22 ++-
.../converter/zip/ZipEntryFileFactory.java | 48 +++--
.../mapviewer/model/ProjectComparator.java | 10 ++
.../model/overlay/DataOverlayComparator.java | 59 +++++++
.../overlay/DataOverlayEntryComparator.java | 107 +++++++++++
.../modelutils/map/ClassNameComparator.java | 7 +-
.../modelutils/map/ElementUtils.java | 57 +++---
10 files changed, 492 insertions(+), 69 deletions(-)
create mode 100644 converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java
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 24e3bebbca..c6f6b59e96 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
@@ -1,6 +1,7 @@
package lcsb.mapviewer.converter.model.celldesigner;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
import lcsb.mapviewer.converter.ConverterParams;
@@ -38,9 +39,13 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.BindingRegion;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.GenericDataOverlayEntry;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Rule;
+import org.mockito.internal.util.collections.Sets;
import java.awt.Canvas;
import java.awt.Color;
@@ -117,6 +122,7 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
protected static GenericProtein createProtein() {
final GenericProtein protein = new GenericProtein("id" + (idCounter++));
+ protein.setName(faker.science().element());
protein.setActivity(true);
protein.setFontSize(4);
protein.setStateLabel("xxx");
@@ -323,4 +329,30 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
}
+ protected DataOverlay createDataOverlay() {
+ DataOverlay dataOverlay = new DataOverlay();
+ dataOverlay.setPublic(faker.bool().bool());
+ dataOverlay.setName(faker.name().fullName());
+ dataOverlay.setDescription(faker.lorem().sentence());
+ return dataOverlay;
+ }
+
+ protected DataOverlayEntry createDataOverlayEntry() {
+ DataOverlayEntry entry = new GenericDataOverlayEntry();
+ entry.setName(faker.text().text(4).toUpperCase());
+ entry.setDescription(faker.lorem().sentence());
+ entry.setModelName(faker.witcher().monster());
+ entry.setCompartments(Sets.newSet(faker.witcher().potion(), faker.witcher().potion()));
+ entry.setElementId(faker.witcher().sign());
+ entry.setLineWidth(faker.number().randomDouble(2, 1, 3));
+ if (Math.random() < 0.5) {
+ entry.setColor(new ColorParser().parse(faker.color().hex()));
+ } else {
+ entry.setValue(faker.number().randomDouble(2, -1, 1));
+ }
+ entry.setReverseReaction(faker.bool().bool());
+ return entry;
+ }
+
+
}
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 1f5034282d..4f29ab512c 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
@@ -14,6 +14,9 @@ import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.GenericDataOverlayEntry;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -26,6 +29,7 @@ import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
public class ProjectExportTest extends CellDesignerTestFunctions {
@@ -115,8 +119,50 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
testSerializationOverZip(project);
}
+ @Test
+ public void testDataOverlay() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ model.addElement(protein);
+ project.addModel(model);
+
+ DataOverlay overlay = createDataOverlay();
+ overlay.setPublic(true);
+ overlay.addEntry(createDataOverlayEntry());
+ overlay.addEntry(createDataOverlayEntry());
+
+ project.addDataOverlay(overlay);
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testPrivateDataOverlay() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ model.addElement(protein);
+ project.addModel(model);
+
+ DataOverlay overlay = createDataOverlay();
+ overlay.setPublic(false);
+ DataOverlayEntry entry = new GenericDataOverlayEntry();
+ entry.setName(protein.getName());
+ entry.setValue(faker.number().randomDouble(2, -1, 1));
+
+ project.addDataOverlay(overlay);
+
+ testSerializationOverZip(project, false);
+ }
private void testSerializationOverZip(final Project project) throws Exception {
+ testSerializationOverZip(project, true);
+ }
+
+ private void testSerializationOverZip(final Project project, final boolean shouldBeTheSame) throws Exception {
File tempFile = File.createTempFile("CD-", ".zip");
try (FileOutputStream outputStream = new FileOutputStream(tempFile)) {
byte[] data = projectFactory.project2zip(project);
@@ -132,7 +178,11 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
clearModelFromZ(model);
}
- assertEquals(0, projectComparator.compare(project, project2));
+ if (shouldBeTheSame) {
+ assertEquals(0, projectComparator.compare(project, project2));
+ } else {
+ assertNotEquals(0, projectComparator.compare(project, project2));
+ }
}
private ComplexZipConverterParams createDefaultParams(final File tempFile) throws IOException {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java
new file mode 100644
index 0000000000..543cf68ed1
--- /dev/null
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java
@@ -0,0 +1,167 @@
+package lcsb.mapviewer.converter;
+
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.DataOverlayType;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class ColorSchemaWriter {
+
+ private static final Map<String, Class<? extends BioEntity>> speciesMapping;
+
+ static {
+ speciesMapping = new HashMap<>();
+ speciesMapping.put("protein", Protein.class);
+ speciesMapping.put("gene", Gene.class);
+ speciesMapping.put("complex", Complex.class);
+ speciesMapping.put("simple_molecule", SimpleMolecule.class);
+ speciesMapping.put("ion", Ion.class);
+ speciesMapping.put("phenotype", Phenotype.class);
+ speciesMapping.put("drug", Drug.class);
+ speciesMapping.put("rna", Rna.class);
+ speciesMapping.put("antisense_rna", AntisenseRna.class);
+ speciesMapping.put("unknown", Unknown.class);
+ speciesMapping.put("degraded", Degraded.class);
+ }
+
+ /**
+ * Object that parses colors from string.
+ */
+ private final ColorParser colorParser = new ColorParser();
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger();
+
+ public String entriesToStringTable(final Set<DataOverlayEntry> entries) {
+ List<ColorSchemaColumn> columns = new ArrayList<>();
+ for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
+ if (column.getTypes().contains(DataOverlayType.GENERIC)) {
+ columns.add(column);
+ }
+ }
+
+ StringBuilder builder = new StringBuilder();
+ builder.append(getHeader(columns));
+ for (DataOverlayEntry entry : entries) {
+ builder.append("\n").append(getRow(entry, columns));
+ }
+
+ return builder.toString();
+ }
+
+ private String getRow(final DataOverlayEntry entry, final List<ColorSchemaColumn> columns) {
+ StringBuilder row = new StringBuilder();
+ int counter = 0;
+ for (ColorSchemaColumn column : columns) {
+ if (counter > 0) {
+ row.append("\t");
+ }
+ counter++;
+ String data = "";
+ switch (column) {
+ case COLOR:
+ if (entry.getColor() != null) {
+ data = new ColorParser().colorToHtml(entry.getColor());
+ }
+ break;
+ case NAME:
+ if (entry.getName() != null) {
+ data = entry.getName();
+ }
+ break;
+ case ELEMENT_IDENTIFIER:
+ if (entry.getElementId() != null) {
+ data = entry.getElementId();
+ }
+ break;
+ case MAP_NAME:
+ if (entry.getModelName() != null) {
+ data = entry.getModelName();
+ }
+ break;
+ case LINE_WIDTH:
+ if (entry.getLineWidth() != null) {
+ data = entry.getLineWidth().toString();
+ }
+ break;
+ case VALUE:
+ if (entry.getValue() != null) {
+ data = entry.getValue().toString();
+ }
+ break;
+ case REVERSE_REACTION:
+ if (entry.getReverseReaction() != null) {
+ data = entry.getReverseReaction().toString();
+ }
+ break;
+ case COMPARTMENT:
+ data = StringUtils.join(entry.getCompartments(), ",");
+ break;
+ case DESCRIPTION:
+ if (entry.getDescription() != null) {
+ data = entry.getDescription().replace("\t", " ").replace("\n", " ");
+ }
+ break;
+ default:
+ data = "";
+ break;
+ }
+ row.append(data);
+ }
+ return row.toString();
+ }
+
+ private String getHeader(final List<ColorSchemaColumn> columns) {
+ StringBuilder header = new StringBuilder();
+ for (ColorSchemaColumn column : columns) {
+ if (header.length() > 0) {
+ header.append("\t");
+ }
+ header.append(column.toString());
+ }
+ return header.toString();
+ }
+
+ public String overlayToString(final DataOverlay overlay) {
+ String metaData = overlayMetaData(overlay);
+
+ String content = metaData + entriesToStringTable(overlay.getEntries());
+ return content;
+ }
+
+ private String overlayMetaData(final DataOverlay overlay) {
+ StringBuilder metaData = new StringBuilder();
+ if (overlay.getName() != null) {
+ metaData.append("#" + ZipEntryFileFactory.LAYOUT_HEADER_PARAM_NAME + "=" + overlay.getName() + "\n");
+ }
+ if (overlay.getDescription() != null) {
+ metaData.append("#" + ZipEntryFileFactory.LAYOUT_HEADER_PARAM_DESCRIPTION + "=" + overlay.getDescription().replace("\n", " ") + "\n");
+ }
+
+ return metaData.toString();
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index 51e60b8766..ea388b84d9 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -6,6 +6,7 @@ import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.InconsistentModelException;
@@ -27,6 +28,7 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.overlay.DataOverlay;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -175,28 +177,42 @@ 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(), "submaps/" + 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());
- addModelFileToZip(mapping, "submaps/mapping." + converter.getFileExtensions().get(0), converter, zos);
+ addModelFileToZip(mapping, ZipEntryFileFactory.SUBMODEL_DIRECTORY + "mapping." + converter.getFileExtensions().get(0), converter, zos);
for (ModelData model : project.getModels()) {
addGlyphsToZip(model.getModel(), zos);
}
+ for (DataOverlay overlay : project.getDataOverlays()) {
+ if (overlay.isPublic()) {
+ addDataOverlayToZip(overlay, zos);
+ }
+ }
+
} catch (IOException ioe) {
throw new ConverterException(ioe);
}
return byteArrayOutputStream.toByteArray();
}
+ private void addDataOverlayToZip(final DataOverlay overlay, final ZipOutputStream zos) throws IOException {
+ ColorSchemaWriter writer = new ColorSchemaWriter();
+ ZipEntry entry = new ZipEntry(ZipEntryFileFactory.LAYOUT_DIRECTORY + overlay.getId() + "_" + overlay.getName());
+ zos.putNextEntry(entry);
+ zos.write(writer.overlayToString(overlay).getBytes());
+ zos.closeEntry();
+ }
+
private void addGlyphsToZip(final Model model, final ZipOutputStream zos) throws IOException {
for (Element element : model.getElements()) {
if (element.getGlyph() != null) {
UploadedFileEntry uploadedFileEntry = element.getGlyph().getFile();
- ZipEntry entry = new ZipEntry("glyphs/" + new File(uploadedFileEntry.getOriginalFileName()).getName());
+ ZipEntry entry = new ZipEntry(ZipEntryFileFactory.GLYPHS_DIRECTORY + new File(uploadedFileEntry.getOriginalFileName()).getName());
zos.putNextEntry(entry);
zos.write(uploadedFileEntry.getFileContent());
zos.closeEntry();
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
index 317842d763..8bc71e00b2 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
@@ -1,23 +1,21 @@
package lcsb.mapviewer.converter.zip;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-import lcsb.mapviewer.common.TextFileUtils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
/**
* Factory class used to create {@link ZipEntryFile} objects.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ZipEntryFileFactory {
/**
@@ -39,7 +37,7 @@ public class ZipEntryFileFactory {
* Directory in a zip file where information about submodels is stored. These
* entries should be by default transformed into {@link ModelZipEntryFile}.
*/
- private static final String SUBMODEL_DIRECTORY = "submaps/";
+ public static final String SUBMODEL_DIRECTORY = "submaps/";
/**
* Directory in a zip file where information about
* {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} is stored. These
@@ -51,24 +49,24 @@ public class ZipEntryFileFactory {
* {@link lcsb.mapviewer.model.map.layout.graphics.Glyph} is stored. These
* entries should be by default transformed into {@link GlyphZipEntryFile}.
*/
- private static final String GLYPHS_DIRECTORY = "glyphs/";
+ public static final String GLYPHS_DIRECTORY = "glyphs/";
/**
* Directory in a zip file where information about
* {@link lcsb.mapviewer.model.map.layout.Layout Layout} is stored. These
* entries should be by default transformed into {@link LayoutZipEntryFile}.
*/
- private static final String LAYOUT_DIRECTORY = "layouts/";
+ public static final String LAYOUT_DIRECTORY = "layouts/";
/**
* Name of the parameter in {@link LayoutZipEntryFile file describing layout}
* corresponding to the {@link LayoutZipEntryFile#name layout name}.
*/
- private static final String LAYOUT_HEADER_PARAM_NAME = "NAME";
+ public static final String LAYOUT_HEADER_PARAM_NAME = "NAME";
/**
* Name of the parameter in {@link LayoutZipEntryFile file describing layout}
* corresponding to the {@link LayoutZipEntryFile#description layout
* description}.
*/
- private static final String LAYOUT_HEADER_PARAM_DESCRIPTION = "DESCRIPTION";
+ public static final String LAYOUT_HEADER_PARAM_DESCRIPTION = "DESCRIPTION";
/**
* Default class logger.
*/
@@ -78,14 +76,11 @@ public class ZipEntryFileFactory {
/**
* Generates instance of {@link ZipEntryFile} representing entry in the zip file
* with pre-parsed structural data (like: type, name, description, etc).
- *
- * @param entry
- * {@link ZipEntry entry} in the {@link ZipFile}
- * @param zipFile
- * original {@link ZipFile}
+ *
+ * @param entry {@link ZipEntry entry} in the {@link ZipFile}
+ * @param zipFile original {@link ZipFile}
* @return {@link ZipEntryFile} for the given {@link ZipEntry}
- * @throws IOException
- * thrown when there is a problem with accessing zip file
+ * @throws IOException thrown when there is a problem with accessing zip file
*/
public ZipEntryFile createZipEntryFile(final ZipEntry entry, final ZipFile zipFile) throws IOException {
if (entry.isDirectory()) {
@@ -142,14 +137,11 @@ public class ZipEntryFileFactory {
/**
* Creates {@link LayoutZipEntryFile layout entry} from input stream and given
* name of the layout.
- *
- * @param name
- * name of the layout
- * @param inputStream
- * stream where data is stored
+ *
+ * @param name name of the layout
+ * @param inputStream stream where data is stored
* @return {@link LayoutZipEntryFile} processed from input data
- * @throws IOException
- * thrown when there is problem with accessing input data
+ * @throws IOException thrown when there is problem with accessing input data
*/
public LayoutZipEntryFile createLayoutZipEntryFile(final String name, final InputStream inputStream) throws IOException {
LayoutZipEntryFile result = new LayoutZipEntryFile();
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
index 776c2556b7..c11a06102d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
@@ -8,6 +8,8 @@ import lcsb.mapviewer.model.map.layout.graphics.GlyphComparator;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelDataComparator;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayComparator;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -19,6 +21,7 @@ public class ProjectComparator extends Comparator<Project> {
private final ModelComparator modelComparator;
private final SetComparator<ModelData> modelDataSetComparator;
+ private final SetComparator<DataOverlay> dataOverlaySetComparator;
private final SetComparator<Glyph> glyphSetComparator;
public ProjectComparator(final double epsilon) {
@@ -26,6 +29,7 @@ public class ProjectComparator extends Comparator<Project> {
modelComparator = new ModelComparator(epsilon);
modelDataSetComparator = new SetComparator<>(new ModelDataComparator(epsilon));
glyphSetComparator = new SetComparator<>(new GlyphComparator());
+ dataOverlaySetComparator = new SetComparator<>(new DataOverlayComparator(epsilon));
}
public ProjectComparator() {
@@ -51,6 +55,12 @@ public class ProjectComparator extends Comparator<Project> {
return modelDataSetComparator.compare(arg0.getModels(), arg1.getModels());
}
+ int status = dataOverlaySetComparator.compare(new HashSet<>(arg0.getDataOverlays()), new HashSet<>(arg1.getDataOverlays()));
+ if (status != 0) {
+ logger.debug("Data overlays different");
+ return status;
+ }
+
return 0;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java
new file mode 100644
index 0000000000..5937141f60
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java
@@ -0,0 +1,59 @@
+package lcsb.mapviewer.model.overlay;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+import java.util.HashSet;
+
+public class DataOverlayComparator extends Comparator<DataOverlay> {
+
+ private final SetComparator<DataOverlayEntry> dataOverlayEntrySetComparator;
+
+ public DataOverlayComparator(final double epsilon) {
+ super(DataOverlay.class, true);
+ this.dataOverlayEntrySetComparator = new SetComparator<>(new DataOverlayEntryComparator(epsilon));
+ }
+
+ public DataOverlayComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(final DataOverlay arg0, final DataOverlay arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ int status = stringComparator.compare(arg0.getName(), arg1.getName());
+ if (status != 0) {
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getDescription(), arg1.getDescription());
+ if (status != 0) {
+ logger.debug("Description different: {}, {}", arg0.getDescription(), arg1.getDescription());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ if (status != 0) {
+ logger.debug("GenomeVersion different: {}, {}", arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ if (status != 0) {
+ logger.debug("GenomeVersion different: {}, {}", arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ return status;
+ }
+
+ status = dataOverlayEntrySetComparator.compare(new HashSet<>(arg0.getEntries()), new HashSet<>(arg1.getEntries()));
+ if (status != 0) {
+ logger.debug("Entries different");
+ return status;
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java
new file mode 100644
index 0000000000..8ab3b2deef
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java
@@ -0,0 +1,107 @@
+package lcsb.mapviewer.model.overlay;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.ColorComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamDataComparator;
+import lcsb.mapviewer.modelutils.map.ClassNameComparator;
+
+public class DataOverlayEntryComparator extends Comparator<DataOverlayEntry> {
+
+ private final SetComparator<MiriamData> miriamDataSetComparator = new SetComparator<>(new MiriamDataComparator());
+
+ private final SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
+ private final SetComparator<Class<? extends BioEntity>> classSetComparator = new SetComparator<>(new ClassNameComparator<>());
+
+ private final ColorComparator colorComparator = new ColorComparator();
+ private final BooleanComparator booleanComparator = new BooleanComparator();
+ private final DoubleComparator doubleComparator;
+
+ public DataOverlayEntryComparator(final double epsilon) {
+ super(DataOverlayEntry.class);
+ doubleComparator = new DoubleComparator(epsilon);
+ }
+
+ public DataOverlayEntryComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(final DataOverlayEntry arg0, final DataOverlayEntry arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ int status = stringComparator.compare(arg0.getName(), arg1.getName());
+ if (status != 0) {
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getDescription(), arg1.getDescription());
+ if (status != 0) {
+ logger.debug("Description different: {}, {}", arg0.getDescription(), arg1.getDescription());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getElementId(), arg1.getElementId());
+ if (status != 0) {
+ logger.debug("ElementId different: {}, {}", arg0.getElementId(), arg1.getElementId());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getModelName(), arg1.getModelName());
+ if (status != 0) {
+ logger.debug("ModelName different: {}, {}", arg0.getModelName(), arg1.getModelName());
+ return status;
+ }
+
+ status = colorComparator.compare(arg0.getColor(), arg1.getColor());
+ if (status != 0) {
+ logger.debug("Color different: {}, {}", arg0.getColor(), arg1.getColor());
+ return status;
+ }
+
+ status = miriamDataSetComparator.compare(arg0.getMiriamData(), arg1.getMiriamData());
+ if (status != 0) {
+ logger.debug("MiriamData different: {}, {}", arg0.getMiriamData(), arg1.getMiriamData());
+ return status;
+ }
+
+ status = stringSetComparator.compare(arg0.getCompartments(), arg1.getCompartments());
+ if (status != 0) {
+ logger.debug("Compartments different: {}, {}", arg0.getCompartments(), arg1.getCompartments());
+ return status;
+ }
+
+ status = doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
+ if (status != 0) {
+ logger.debug("LineWidth different: {}, {}", arg0.getLineWidth(), arg1.getLineWidth());
+ return status;
+ }
+
+ status = booleanComparator.compare(arg0.getReverseReaction(), arg1.getReverseReaction());
+ if (status != 0) {
+ logger.debug("ReverseReaction different: {}, {}", arg0.getReverseReaction(), arg1.getReverseReaction());
+ return status;
+ }
+
+ status = doubleComparator.compare(arg0.getValue(), arg1.getValue());
+ if (status != 0) {
+ logger.debug("Value different: {}, {}", arg0.getValue(), arg1.getValue());
+ return status;
+ }
+
+ status = classSetComparator.compare(arg0.getTypes(), arg1.getTypes());
+ if (status != 0) {
+ logger.debug("Types different: {}, {}", arg0.getTypes(), arg1.getTypes());
+ return status;
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
index f88c513a5b..a25bcd8764 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
@@ -4,14 +4,13 @@ import java.util.Comparator;
/**
* Class used to compare classes using class names (SimpleName).
- *
+ *
* @author Piotr Gawron
- *
*/
-public class ClassNameComparator implements Comparator<Class<?>> {
+public class ClassNameComparator<T> implements Comparator<Class<? extends T>> {
@Override
- public int compare(final Class<?> o1, final Class<?> o2) {
+ public int compare(final Class<? extends T> o1, final Class<? extends T> o2) {
return o1.getSimpleName().compareTo(o2.getSimpleName());
}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 019eb8ff2f..d47c340960 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -1,5 +1,15 @@
package lcsb.mapviewer.modelutils.map;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.reflections.Reflections;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@ -11,22 +21,10 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.reflections.Reflections;
-
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
/**
* Class with some util method for {@link BioEntity} objects.
- *
+ *
* @author Piotr Gawron
- *
*/
public final class ElementUtils {
@@ -52,23 +50,21 @@ public final class ElementUtils {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
- * @param elementClasses
- * the elementClasses to set
+ * @param elementClasses the elementClasses to set
* @see #elementClasses
*/
- protected static void setElementClasses(final Map<String, Class<? extends Element>> elementClasses) {
+ static void setElementClasses(final Map<String, Class<? extends Element>> elementClasses) {
ElementUtils.elementClasses = elementClasses;
}
/**
- * @param reactionClasses
- * the reactionClasses to set
+ * @param reactionClasses the reactionClasses to set
* @see #reactionClasses
*/
- protected static void setReactionClasses(final Map<String, Class<? extends Reaction>> reactionClasses) {
+ static void setReactionClasses(final Map<String, Class<? extends Reaction>> reactionClasses) {
ElementUtils.reactionClasses = reactionClasses;
}
@@ -76,8 +72,7 @@ public final class ElementUtils {
* This method return tag that identifies {@link BioEntity}. This tag should
* be used in warning messages.
*
- * @param element
- * tag for this element is created
+ * @param element tag for this element is created
* @return tag that identifies element
*/
public String getElementTag(final Drawable element) {
@@ -88,11 +83,9 @@ public final class ElementUtils {
* This method return tag that identifies {@link BioEntity}. This tag should
* be used in warning messages.
*
- * @param element
- * tag for this element is created
- * @param annotator
- * this object identifies class that will produce warning. it can be
- * null (in such situation it will be skipped in the tag)
+ * @param element tag for this element is created
+ * @param annotator this object identifies class that will produce warning. it can be
+ * null (in such situation it will be skipped in the tag)
* @return tag that identifies element
*/
public String getElementTag(final Drawable element, final Object annotator) {
@@ -182,8 +175,7 @@ public final class ElementUtils {
* Returns list of classes that extends {@link Element} class, but don't have
* children (leaves in the hierarchy tree).
*
- * @return list of classes that extends {@link Element} class, but don't have
- * children (leaves in the hierarchy tree)
+ * @return list of classes that extends {@link Element} class, but don't have children (leaves in the hierarchy tree)
*/
public List<Class<? extends Element>> getAvailableElementSubclasses() {
List<Class<? extends Element>> result = new ArrayList<>();
@@ -191,14 +183,14 @@ public final class ElementUtils {
refreshClasses();
}
result.addAll(elementClasses.values());
- Collections.sort(result, new ClassNameComparator());
+ Collections.sort(result, new ClassNameComparator<>());
return result;
}
/**
* Refresh list of known implementation of {@link Element} class.
*/
- protected void refreshClasses() {
+ private void refreshClasses() {
bioEntityClassByStringName = new HashMap<>();
List<Class<? extends Element>> tmp = new ArrayList<>();
@@ -270,8 +262,7 @@ public final class ElementUtils {
/**
* Returns a {@link Class} that extends {@link BioEntity} for a given name.
*
- * @param name
- * name of the class
+ * @param name name of the class
* @return {@link Class} that extends {@link BioEntity} for a given name
*/
public Class<?> getClassByName(final String name) {
--
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