From 3136d0b6609706c6bf421a5fc793c8acc63267b6 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 20 Mar 2018 17:07:53 +0100
Subject: [PATCH] default colors added
---
.../common/geometry/ColorParser.java | 105 +++++++++---------
.../model/sbml/SbmlBioEntityParser.java | 7 ++
.../model/sbml/species/ElementColorEnum.java | 81 ++++++++++++++
.../sbml/species/SbmlSpeciesParserTest.java | 18 ++-
4 files changed, 159 insertions(+), 52 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
diff --git a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
index f78e460818..76ee7ad305 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
@@ -14,61 +14,64 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
*/
public class ColorParser {
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
- /**
- * Length of the string describing color in rgb: "#RRGGBB".
- */
- private static final int COLOR_STRING_LENGTH = 7;
+ /**
+ * Length of the string describing color in RGB: "#RRGGBB".
+ */
+ private static final int COLOR_STRING_LENGTH = 7;
- /**
- * Where starts description of red color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_RED = 1;
+ /**
+ * Where starts description of red color in string representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_RED = 1;
- /**
- * Where starts description of green color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_GREEN = 3;
+ /**
+ * Where starts description of green color in string representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_GREEN = 3;
- /**
- * Where starts description of blue color in stirng representing color.
- */
- private static final int COLOR_SUBSTRING_START_BLUE = 5;
+ /**
+ * Where starts description of blue color in string representing color.
+ */
+ private static final int COLOR_SUBSTRING_START_BLUE = 5;
- /**
- * Extracts {@link Color} from input {@link String}.
- *
- * @param string
- * text to process
- * @return {@link Color} obtained from input text
- */
- public Color parse(String string) {
- if (string.charAt(0) != '#') {
- string = "#" + string;
- }
- if (string.length() != COLOR_STRING_LENGTH) {
- throw new InvalidArgumentException("Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
- } else {
- return new Color(Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
- Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
- }
- }
+ /**
+ * Extracts {@link Color} from input {@link String}.
+ *
+ * @param string
+ * text to process
+ * @return {@link Color} obtained from input text
+ */
+ public Color parse(String string) {
+ if (string.charAt(0) != '#') {
+ string = "#" + string;
+ }
+ if (string.length() != COLOR_STRING_LENGTH) {
+ throw new InvalidArgumentException(
+ "Invalid color value: " + string + ". Correct format: #xxxxxx (where x is a hex value)");
+ } else {
+ return new Color(
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_RED, COLOR_SUBSTRING_START_GREEN), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_GREEN, COLOR_SUBSTRING_START_BLUE), HEX_BASE), //
+ Integer.valueOf(string.substring(COLOR_SUBSTRING_START_BLUE, COLOR_STRING_LENGTH), HEX_BASE));
+ }
+ }
- /**
- * Converts color into list of atributes.
- *
- * @param color color to convert
- * @return map with list of color attributes
- */
- public Map<String, Object> colorToMap(Color color) {
- Map<String, Object> result = new HashMap<>();
- result.put("alpha", color.getAlpha());
- result.put("rgb", color.getRGB());
- return result;
- }
+ /**
+ * Converts color into list of attributes.
+ *
+ * @param color
+ * color to convert
+ * @return map with list of color attributes
+ */
+ public Map<String, Object> colorToMap(Color color) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("alpha", color.getAlpha());
+ result.put("rgb", color.getRGB());
+ return result;
+ }
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index 7ba0246982..e9926b9ed9 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -15,8 +15,10 @@ import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.converter.model.sbml.species.ElementColorEnum;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.species.Element;
public class SbmlBioEntityParser extends XmlParser {
Logger logger = Logger.getLogger(SbmlBioEntityParser.class);
@@ -55,6 +57,11 @@ public class SbmlBioEntityParser extends XmlParser {
}
String notes = extractNotes(sbmlElement);
result.setNotes(notes);
+
+ if (result instanceof Element) {
+ Element element = (Element) result;
+ element.setColor(ElementColorEnum.getColorByClass(element.getClass()));
+ }
}
private String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
new file mode 100644
index 0000000000..7dd12ee398
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/ElementColorEnum.java
@@ -0,0 +1,81 @@
+package lcsb.mapviewer.converter.model.sbml.species;
+
+import java.awt.Color;
+
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.model.map.compartment.OvalCompartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+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.Element;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.IonChannelProtein;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.ReceptorProtein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.TruncatedProtein;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+public enum ElementColorEnum {
+ ANTISENSE_RNA(AntisenseRna.class, "#ff6666"), //
+ COMPLEX(Complex.class, "#f7f7f7"), //
+ DEGRADED(Degraded.class, "#ffcccc"), //
+ DRUG(Drug.class, "#ff00ff"), //
+ ELEMENT(Element.class, "#000000"), //
+ GENE(Gene.class, "#ffff66"), //
+ GENERIC_PROTEIN(GenericProtein.class, "ccffcc"), //
+ TRUNCATED_PROTEIN(TruncatedProtein.class, "#ffcccc"), //
+ ION(Ion.class, "#9999ff"), //
+ ION_CHANNEL(IonChannelProtein.class, "#ccffff"), //
+ OVAL_COMPARTMENT(OvalCompartment.class, "#cccc00"), //
+ PHENOTYPE(Phenotype.class, "#cc99ff"), //
+ RECEPTOR(ReceptorProtein.class, "#ffffcc"), //
+ RNA(Rna.class, "#66ff66"), //
+ SIMPLE_MOLECULE(SimpleMolecule.class, "#ccff66"), //
+ SQUARE_COMPARTMENT(SquareCompartment.class, "#cccc00"), //
+ UNKNOWN(Unknown.class, "#cccccc"), //
+ ;
+
+ private Class<? extends Element> clazz;
+ private Color color;
+
+ ColorParser colorParser = new ColorParser();
+
+ private ElementColorEnum(Class<? extends Element> clazz, String color) {
+ this.clazz = clazz;
+ if (color != null) {
+ this.color = colorParser.parse(color);
+ }
+ }
+
+ public static Color getColorByClass(Class<? extends Element> clazz) {
+ Color result = null;
+ for (ElementColorEnum type : ElementColorEnum.values()) {
+ if (type.getClazz().equals(clazz)) {
+ result = type.getColor();
+ }
+ }
+ if (result == null) {
+ for (ElementColorEnum type : ElementColorEnum.values()) {
+ if (type.getClazz().isAssignableFrom(clazz)) {
+ result = type.getColor();
+ }
+ }
+ }
+ return result;
+ }
+
+ public Class<? extends Element> getClazz() {
+ return clazz;
+ }
+
+ public Color getColor() {
+ return color;
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
index 2a049eecec..3951251a80 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.sbml.species;
+import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
@@ -7,6 +8,7 @@ import java.io.FileNotFoundException;
import org.apache.log4j.Logger;
import org.junit.Test;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.sbml.SbmlParser;
@@ -30,11 +32,14 @@ public class SbmlSpeciesParserTest {
Logger logger = Logger.getLogger(SbmlSpeciesParserTest.class);
SbmlParser parser = new SbmlParser();
+ ColorParser colorParser = new ColorParser();
+
@Test
public void testParseAntisenseRna() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/antisense_rna.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof AntisenseRna);
+ assertEquals(ElementColorEnum.ANTISENSE_RNA.getColor(), element.getColor());
}
@Test
@@ -42,6 +47,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/complex.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Complex);
+ assertEquals(ElementColorEnum.COMPLEX.getColor(), element.getColor());
}
@Test
@@ -49,6 +55,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/degraded.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Degraded);
+ assertEquals(ElementColorEnum.DEGRADED.getColor(), element.getColor());
}
@Test
@@ -56,6 +63,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/drug.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Drug);
+ assertEquals(ElementColorEnum.DRUG.getColor(), element.getColor());
}
@Test
@@ -63,6 +71,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/gene.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Gene);
+ assertEquals(ElementColorEnum.GENE.getColor(), element.getColor());
}
@Test
@@ -70,6 +79,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/generic_protein.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof GenericProtein);
+ assertEquals(ElementColorEnum.GENERIC_PROTEIN.getColor(), element.getColor());
}
@Test
@@ -77,6 +87,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/ion_channel.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof IonChannelProtein);
+ assertEquals(ElementColorEnum.ION_CHANNEL.getColor(), element.getColor());
}
@Test
@@ -84,6 +95,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/ion.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Ion);
+ assertEquals(ElementColorEnum.ION.getColor(), element.getColor());
}
@Test
@@ -91,6 +103,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/phenotype.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Phenotype);
+ assertEquals(ElementColorEnum.PHENOTYPE.getColor(), element.getColor());
}
@Test
@@ -98,6 +111,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/receptor.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof ReceptorProtein);
+ assertEquals(ElementColorEnum.RECEPTOR.getColor(), element.getColor());
}
@Test
@@ -105,6 +119,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/rna.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Rna);
+ assertEquals(ElementColorEnum.RNA.getColor(), element.getColor());
}
@Test
@@ -112,6 +127,7 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/small_molecule.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof SimpleMolecule);
+ assertEquals(ElementColorEnum.SIMPLE_MOLECULE.getColor(), element.getColor());
}
@Test
@@ -126,6 +142,6 @@ public class SbmlSpeciesParserTest {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/unknown_species.xml"));
Element element = model.getElementByElementId("s1");
assertTrue(element instanceof Unknown);
+ assertEquals(ElementColorEnum.UNKNOWN.getColor(), element.getColor());
}
-
}
--
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