diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
index 9ab997e868bebcff00247ca3cd39fbfccda4ce15..642041780bcd2a957fe3c3a961979805c9bf87ac 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
@@ -96,7 +96,7 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
result.setLineOuterWidth(XmlParser.getNodeAttr("outerWidth", node));
result.setLineInnerWidth(XmlParser.getNodeAttr("innerWidth", node));
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
- result.setColor(getCommonParser().getColor(node));
+ result.setFillColor(getCommonParser().getColor(node));
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
// not handled
continue;
@@ -176,7 +176,7 @@ public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartmen
sb.append("innerWidth=\"" + compartment.getInnerWidth() + "\"/>\n");
sb.append("<celldesigner:paint ");
- sb.append("color=\"" + XmlParser.colorToString(compartment.getColor()) + "\" scheme=\"Color\"/>\n");
+ sb.append("color=\"" + XmlParser.colorToString(compartment.getFillColor()) + "\" scheme=\"Color\"/>\n");
sb.append("</celldesigner:compartmentAlias>\n");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
index 8c11c5182f25088c1d613d3c67fc520451d741be..7eacf6d90da2d92f19de406007c68bf9a4e84684 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
@@ -142,7 +142,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
result.setWidth(view.getBoxSize().width);
result.setHeight(view.getBoxSize().height);
result.setLineWidth(view.getSingleLine().getWidth());
- result.setColor(view.getColor());
+ result.setFillColor(view.getColor());
} else if (!state.equalsIgnoreCase("complexnoborder")) {
throw new InvalidXmlSchemaException("No view (" + state + ") in ComplexAlias for " + result.getElementId());
}
@@ -228,13 +228,13 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
sb.append("<celldesigner:innerPosition x=\"" + complex.getX() + "\" y=\"" + complex.getY() + "\"/>");
sb.append("<celldesigner:boxSize width=\"" + complex.getWidth() + "\" height=\"" + complex.getHeight() + "\"/>");
sb.append("<celldesigner:singleLine width=\"" + complex.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(complex.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(complex.getFillColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:usualView>\n");
sb.append("<celldesigner:briefView>");
sb.append("<celldesigner:innerPosition x=\"" + complex.getX() + "\" y=\"" + complex.getY() + "\"/>");
sb.append("<celldesigner:boxSize width=\"" + complex.getWidth() + "\" height=\"" + complex.getHeight() + "\"/>");
sb.append("<celldesigner:singleLine width=\"" + complex.getWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(complex.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(complex.getFillColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:briefView>\n");
sb.append(createStructuralStateTag(complex));
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index eb6732861b5a0a78a43082cad9f4a29d035775a3..47c94d6ecdbcabca803738e71a68c3ee257f33c3 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -121,7 +121,7 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
result.setWidth(view.getBoxSize().width);
result.setHeight(view.getBoxSize().height);
result.setLineWidth(view.getSingleLine().getWidth());
- result.setColor(view.getColor());
+ result.setFillColor(view.getColor());
} else {
throw new InvalidXmlSchemaException(errorPrefix + "No view in Alias");
}
@@ -220,13 +220,13 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(species.getFillColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:usualView>\n");
sb.append("<celldesigner:briefView>");
sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("<celldesigner:paint color=\"" + XmlParser.colorToString(species.getFillColor()) + "\" scheme=\"Color\"/>");
sb.append("</celldesigner:briefView>\n");
if (species.getStateLabel() != null || species.getStatePrefix() != null) {
sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
index 1d7fd45b3a2230cefe813835d29d75adcc02a24b..42e01bae253caae28e3f1312885074a3f986e2ca 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
@@ -127,7 +127,7 @@ public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
assertEquals(522.0, alias.getWidth(), 1e-6);
assertEquals(392.5, alias.getNamePoint().getX(), 1e-6);
assertEquals(196.5, alias.getNamePoint().getY(), 1e-6);
- assertEquals(0xffcccc00, alias.getColor().getRGB());
+ assertEquals(0xffcccc00, alias.getFillColor().getRGB());
}
@Test
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index fcc383be6082580f2306d4e6be98410b1064480d..5b3809f9d7bb96e6a02fc9a8a3e81c22b6e024b4 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -1513,7 +1513,7 @@ public class SbgnmlXmlParser {
compartment.setX(new Double(glyph.getBbox().getX()));
compartment.setY(new Double(glyph.getBbox().getY()));
compartment.setThickness(1.0);
- compartment.setColor(COMPARTMENT_COLOR);
+ compartment.setFillColor(COMPARTMENT_COLOR);
if (glyph.getLabel() != null && glyph.getLabel().getBbox() != null) {
compartment.setNamePoint(glyph.getLabel().getBbox().getX(), glyph.getLabel().getBbox().getY());
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
index 8f67f5ba6ee3e1340be97f7fb7484164df45ea34..006764b2084cd5fb8521d4b39547b555ee054ff2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java
@@ -53,7 +53,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
Area a1 = new Area(
new Rectangle2D.Double(0.0, compartment.getY(), compartment.getWidth(), compartment.getHeight()));
- Color c1 = compartment.getColor();
+ Color c1 = compartment.getFillColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
index b33f237530a7ee6338bebb0513eb84fbaf566b24..ae887428b0b646a53094c2b225bb1f01e52fbb3f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java
@@ -53,7 +53,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
compartment.getHeight());
Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
- Color c1 = compartment.getColor();
+ Color c1 = compartment.getFillColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
index 9732dffbf7fec5f39fdfb78314292a46ec0bd1d1..137197ae938e5e2f59b44f9b599830616cb00557 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
@@ -56,7 +56,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
Shape s3 = getShape(compartment);
compartment.increaseBorder(compartment.getThickness());
- Color c1 = compartment.getColor();
+ Color c1 = compartment.getFillColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
index b2741dec632d71976311a9060a06d9291883834e..2a33cb022c279fb3e815a1362cc17122a519e395 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
@@ -43,7 +43,7 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
compartment.getHeight());
Color color = compartment.getFontColor();
- Color backgroundColor = compartment.getColor();
+ Color backgroundColor = compartment.getFillColor();
// fill the background
boolean fill = !isTransparent(compartment, params);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
index 53bf786fe92f04c4ace23596455fc75d491bdeaf..4d7e1f657dba0c2c40b579580bf754e2be6f8fe4 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java
@@ -53,7 +53,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
Area a1 = new Area(
new Rectangle2D.Double(compartment.getX(), 0.0, compartment.getWidth(), compartment.getHeight()));
- Color c1 = compartment.getColor();
+ Color c1 = compartment.getFillColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
index f7b4fb6127572ef9e2feee2b26d03a67e7f36e1b..fc9ea262ff8e2db2e2d998cf73518f2b7e1541ba 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
@@ -70,7 +70,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
Shape s3 = getShape(compartment);
compartment.increaseBorder(compartment.getThickness());
- Color c1 = compartment.getColor();
+ Color c1 = compartment.getFillColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
index f24d5b112aeb1c0310bb5d5f1c8441fa35010275..144bcbaa9a555063b9783cf094c83e1cd07f7dd5 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
@@ -51,7 +51,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
compartment.getHeight() - compartment.getThickness());
Area a1 = new Area(new Rectangle2D.Double(0.0, 0.0, compartment.getWidth(), compartment.getHeight()));
- Color c1 = compartment.getColor();
+ Color c1 = compartment.getFillColor();
Color c2 = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), HIGH_ALPHA_LEVEL);
if (c1.equals(Color.WHITE)) {
c1 = Color.BLACK;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
index 1acd6b1f197dd5c87fc12b9fa5940ab0d33f0e1d..26f6127d3a5e95cfd637a6b544bac9682a2c2d57 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
@@ -43,7 +43,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
protected void drawImpl(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getAntisenseRnaPath(antisenseRna);
Color c = graphics.getColor();
- graphics.setColor(antisenseRna.getColor());
+ graphics.setColor(antisenseRna.getFillColor());
graphics.fill(path);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
index 7a91e5485a2907c63f3928490a00193a94e018f4..009b375c60e7ca6c0b020762d08779179273c099 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
@@ -83,7 +83,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
Color c = graphics.getColor();
Stroke stroke = graphics.getStroke();
- graphics.setColor(complex.getColor());
+ graphics.setColor(complex.getFillColor());
graphics.fill(path);
graphics.setColor(c);
graphics.setStroke(getBorderLine(complex));
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
index 888cd469a597d70d97d653c1f62f9668a5e0c6f3..f3fa0d94b71ac711aa1d6b0ae04acb9aafdb7bb0 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
@@ -65,7 +65,7 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
a1.exclusiveOr(new Area(path));
Color c = graphics.getColor();
- graphics.setColor(degraded.getColor());
+ graphics.setColor(degraded.getFillColor());
graphics.fill(a1);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
index 3d59e0381861ef72c8e283c43202538c577d3124..85ba4f8090549af248c89013458791b8af270b7a 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
@@ -71,7 +71,7 @@ public class DrugConverter extends SpeciesConverter<Drug> {
RECTANGLE_CORNER_ARC_SIZE,
RECTANGLE_CORNER_ARC_SIZE);
Color c = graphics.getColor();
- graphics.setColor(drug.getColor());
+ graphics.setColor(drug.getFillColor());
graphics.fill(a1);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
index f14871e30a6b454b4bcca991d68f20bdcf8f3ff6..50798c1057906c28cb525fae3d2fa8685bcfbea2 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
@@ -43,7 +43,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
protected void drawImpl(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
Shape shape = getGeneShape(gene);
Color c = graphics.getColor();
- graphics.setColor(gene.getColor());
+ graphics.setColor(gene.getFillColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
index ffe8c75cfd8ed46de948fbfa84574d635037ba8c..c1be7c92c14e0b4948988a04aa5961a62998471b 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
@@ -46,7 +46,7 @@ public class IonConverter extends SpeciesConverter<Ion> {
double y = getYCoord(ion);
Shape shape = new Ellipse2D.Double(x, y, diameter, diameter);
Color c = graphics.getColor();
- graphics.setColor(ion.getColor());
+ graphics.setColor(ion.getFillColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
index a2ed8af2c6abd01bb0510b849d5eed166828c06c..36c65d1ab1fbe9c2266d72d6ac450626b17b6974 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
@@ -42,7 +42,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
GeneralPath path = getPhenotypePath(phenotype);
Color c = graphics.getColor();
- graphics.setColor(phenotype.getColor());
+ graphics.setColor(phenotype.getFillColor());
graphics.fill(path);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
index 4ebc97efca6c927136d6d10bb452dd57ce5318a2..641609c1141cf4b7751471ecc884ea318298b5f1 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
@@ -149,7 +149,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
shape = getDefaultAliasShape(protein);
}
Color c = graphics.getColor();
- graphics.setColor(protein.getColor());
+ graphics.setColor(protein.getFillColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index 0182f77db36ebc7925a72a5cfee13641032162a7..0050a2b52200f3b5f67c6baeb2f3ec16f596b121 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
@@ -49,7 +49,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
protected void drawImpl(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getRnaPath(rna);
Color c = graphics.getColor();
- graphics.setColor(rna.getColor());
+ graphics.setColor(rna.getFillColor());
graphics.fill(path);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
index e5b42d58b58dd3a9f7d6ee431091f0872e95ea96..e38e738ddb2cf3c49d1e47f0cf954e07179a02c9 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
@@ -92,7 +92,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
Shape shape = getShape(species);
Color c = graphics.getColor();
- graphics.setColor(species.getColor());
+ graphics.setColor(species.getFillColor());
graphics.fill(shape);
graphics.setColor(c);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
index a72c5318eab94975c116ebd0fa4f113fbfd0e47a..92251e33c3018a09794e0fe7bf860a4a43760065 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
@@ -73,7 +73,7 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
Shape shape = new Ellipse2D.Double(simpleMolecule.getX(), simpleMolecule.getY(), simpleMolecule.getWidth(),
simpleMolecule.getHeight());
Color c = graphics.getColor();
- graphics.setColor(simpleMolecule.getColor());
+ graphics.setColor(simpleMolecule.getFillColor());
graphics.fill(shape);
graphics.setColor(c);
Stroke stroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
index 0dd8e7577f9ef6d84095263f9e952ad240b75ba3..bcf30e4d9fa4b3ddf424b0a7a3ecb5ed2b5071ef 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
@@ -56,7 +56,7 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
Shape shape = new Ellipse2D.Double(unknown.getX(), unknown.getY(), unknown.getWidth(), unknown.getHeight());
Color c = graphics.getColor();
- graphics.setColor(unknown.getColor());
+ graphics.setColor(unknown.getFillColor());
graphics.fill(shape);
graphics.setColor(c);
drawText(unknown, graphics, params);
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java
index 5f0c137114c71c6f6f27823191b6fc63d1202634..e8f7b76419a3ef71e21fb1a5feac191efcdb95ee 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverterTest.java
@@ -35,7 +35,7 @@ public class PathwayCompartmentConverterTest extends GraphicsTestFunctions {
pathway.setY(10);
pathway.setWidth(100);
pathway.setHeight(200);
- pathway.setColor(Color.BLUE);
+ pathway.setFillColor(Color.BLUE);
pathway.setTransparencyLevel("12");
model.addElement(pathway);
@@ -57,7 +57,7 @@ public class PathwayCompartmentConverterTest extends GraphicsTestFunctions {
pathway.setY(10);
pathway.setWidth(100);
pathway.setHeight(200);
- pathway.setColor(Color.BLUE);
+ pathway.setFillColor(Color.BLUE);
model.addElement(pathway);
converter.draw(pathway, graphics, new ConverterParams().nested(true));
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java
index acd62dd9725dcde9a89e35908b53b12234e8d99b..c9f52b80ab08b69085bff00551bf14f38621f535 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverterTest.java
@@ -73,7 +73,7 @@ public class ComplexConverterTest extends GraphicsTestFunctions {
protein.setY(20);
protein.setWidth(100);
protein.setHeight(80);
- protein.setColor(Color.WHITE);
+ protein.setFillColor(Color.WHITE);
return protein;
}
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 294eb975e2b031067128ab3816e92e7258843fde..6f6da10ab7b260ee900f314576309d98380d8589 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
@@ -146,7 +146,7 @@ public class SbmlBioEntityParser {
if (result instanceof Element) {
Element element = (Element) result;
- element.setColor(ElementColorEnum.getColorByClass(element.getClass()));
+ element.setFillColor(ElementColorEnum.getColorByClass(element.getClass()));
}
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
index 427a0d119e566eff3b859b198b046b49448c4fe8..f127c2b6e494ff5d604fe6c33dad78d955159315 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -45,7 +45,7 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
@Override
protected LocalStyle createStyle(T element) {
LocalStyle result = super.createStyle(element);
- ColorDefinition color = getColorDefinition(element.getColor());
+ ColorDefinition color = getColorDefinition(element.getFillColor());
result.getGroup().setFill(color.getId());
result.getGroup().setFontSize(element.getFontSize().shortValue());
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index e4fe38ff9aacc118374a3d904972c105dbadbf0c..7b372369bddf7d76e6dcf79bd146227abcf98a52 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -115,7 +115,7 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
if (style.getGroup().isSetFill()) {
Color backgroundColor = getColorByColorDefinition(style.getGroup().getFill());
- elementWithLayout.setColor(backgroundColor);
+ elementWithLayout.setFillColor(backgroundColor);
}
if (style.getGroup().isSetFontSize()) {
elementWithLayout.setFontSize(style.getGroup().getFontSize());
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
index d4d47b95c9de55ae5253051d4b1a90dfc657bcfb..74f1a4c743979253b94f9e58d10671a5a3684340 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -97,7 +97,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
LocalStyle style = super.createStyle(element);
style.getGroup().setStrokeWidth(element.getThickness());
style.getGroup().setFill(null);
- style.getGroup().setStroke(getColorDefinition(element.getColor()).getId());
+ style.getGroup().setStroke(getColorDefinition(element.getFillColor()).getId());
if (element instanceof OvalCompartment) {
Ellipse ellipse = new Ellipse();
ellipse.setAbsoluteRx(false);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
index a15250b9414bce32e5dbb7d5fd866079fdf9c4af..b59fd170a4c89c71ee69a896d42573345de9d0ed 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
@@ -80,7 +80,7 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
if (!style.getGroup().isSetFill() && style.getGroup().isSetStroke()) {
Color backgroundColor = getColorByColorDefinition(style.getGroup().getStroke());
- elementWithLayout.setColor(backgroundColor);
+ elementWithLayout.setFillColor(backgroundColor);
}
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 6a2c07c77127c0aabfe643620122fcb181d75c57..a4a3c387bbaf3cbeac013c60850320cba7a0a095 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -243,7 +243,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
public void testColorParsing() throws Exception {
Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
for (Element element : model.getElements()) {
- element.setColor(Color.BLUE);
+ element.setFillColor(Color.BLUE);
}
Model model2 = getModelAfterSerializing(model);
assertEquals(0, comparator.compare(model, model2));
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 46380cbe56baf49eff03844759c89ab4c3f5331d..b0b30e37fe6034c336bb77e6ba08b96e05cdf0e4 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
@@ -27,7 +27,7 @@ public class SbmlSpeciesParserTest {
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());
+ assertEquals(ElementColorEnum.ANTISENSE_RNA.getColor(), element.getFillColor());
}
@Test
@@ -35,7 +35,7 @@ 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());
+ assertEquals(ElementColorEnum.COMPLEX.getColor(), element.getFillColor());
}
@Test
@@ -43,7 +43,7 @@ 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());
+ assertEquals(ElementColorEnum.DEGRADED.getColor(), element.getFillColor());
}
@Test
@@ -51,7 +51,7 @@ 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());
+ assertEquals(ElementColorEnum.DRUG.getColor(), element.getFillColor());
}
@Test
@@ -59,7 +59,7 @@ 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());
+ assertEquals(ElementColorEnum.GENE.getColor(), element.getFillColor());
}
@Test
@@ -67,7 +67,7 @@ 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());
+ assertEquals(ElementColorEnum.GENERIC_PROTEIN.getColor(), element.getFillColor());
}
@Test
@@ -75,7 +75,7 @@ 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());
+ assertEquals(ElementColorEnum.ION_CHANNEL.getColor(), element.getFillColor());
}
@Test
@@ -83,7 +83,7 @@ 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());
+ assertEquals(ElementColorEnum.ION.getColor(), element.getFillColor());
}
@Test
@@ -91,7 +91,7 @@ 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());
+ assertEquals(ElementColorEnum.PHENOTYPE.getColor(), element.getFillColor());
}
@Test
@@ -99,7 +99,7 @@ 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());
+ assertEquals(ElementColorEnum.RECEPTOR.getColor(), element.getFillColor());
}
@Test
@@ -107,7 +107,7 @@ 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());
+ assertEquals(ElementColorEnum.RNA.getColor(), element.getFillColor());
}
@Test
@@ -115,7 +115,7 @@ 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());
+ assertEquals(ElementColorEnum.SIMPLE_MOLECULE.getColor(), element.getFillColor());
}
@Test
@@ -130,7 +130,7 @@ 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());
+ assertEquals(ElementColorEnum.UNKNOWN.getColor(), element.getFillColor());
}
@Test
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index 961ad55116ab5c3f59ae45bce51ccf5a9ded2c60..136bffd3d332ce19a6a4403b29e24ceb7a3c726d 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -158,10 +158,10 @@ public class ColorModelCommand extends ModelCommand {
*/
private void applyColor(Element element, ColorSchema schema) throws InvalidColorSchemaException {
if (element instanceof Species) {
- if (!element.getColor().equals(Color.WHITE)) {
+ if (!element.getFillColor().equals(Color.WHITE)) {
throw new InvalidColorSchemaException("At least two rows try to set color to element: " + element.getName());
}
- element.setColor(colorExtractor.getNormalizedColor(schema));
+ element.setFillColor(colorExtractor.getNormalizedColor(schema));
}
}
@@ -338,7 +338,7 @@ public class ColorModelCommand extends ModelCommand {
private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
for (Element element : result.getElements()) {
- element.setColor(Color.WHITE);
+ element.setFillColor(Color.WHITE);
element.setGlyph(null);
}
for (Reaction reaction : result.getReactions()) {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 09e86f7372fcaaa78ac78a44f9f65261c855bf99..7170fbbaf8a4443a436f1818a17ab2a4874fa6d7 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -168,7 +168,7 @@ public class CreateHierarchyCommand extends ModelCommand {
compartment.setWidth(text.getWidth());
compartment.setHeight(text.getHeight());
compartment.setFontColor(text.getColor());
- compartment.setColor(text.getBackgroundColor());
+ compartment.setFillColor(text.getBackgroundColor());
compartment.setName(extractNameFromText(text.getNotes()));
compartment.setNotes(extractNotesFromText(text.getNotes()));
compartment.setZ(text.getZ());
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
index 8b3f9ec7b2d9b326e42107c89ddf97353a64edbb..3dd913e80018992015140548ef798e0d1d2255ac 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommand.java
@@ -42,8 +42,8 @@ public class ChangeElementColorCommand extends ChangeElementPropertyCommand<Colo
includeInAffectedRegion(getAlias());
- setOldValue(getAlias().getColor());
- getAlias().setColor((Color) getNewValue());
+ setOldValue(getAlias().getFillColor());
+ getAlias().setFillColor((Color) getNewValue());
includeInAffectedRegion(getAlias());
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index b60c45de521652b7c3e32f0b3467655e182b3362..27bc0c97551bdad1207ef677656d05e0a8b33965 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -50,7 +50,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schemas.add(schema);
ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas, colorExtractor);
- assertFalse(Color.RED.equals(coloredModel.getElementByElementId("sa14").getColor()));
+ assertFalse(Color.RED.equals(coloredModel.getElementByElementId("sa14").getFillColor()));
factory.execute();
@@ -58,7 +58,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
assertFalse(comparator.compare(model, coloredModel) == 0);
- assertEquals(Color.RED, coloredModel.getElementByElementId("sa14").getColor());
+ assertEquals(Color.RED, coloredModel.getElementByElementId("sa14").getFillColor());
}
@Test
@@ -172,9 +172,9 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
assertFalse(
- coloredModel2.getElementByElementId("sa2").getColor().equals(model2.getElementByElementId("sa2").getColor()));
+ coloredModel2.getElementByElementId("sa2").getFillColor().equals(model2.getElementByElementId("sa2").getFillColor()));
assertFalse(
- coloredModel3.getElementByElementId("sa2").getColor().equals(model2.getElementByElementId("sa2").getColor()));
+ coloredModel3.getElementByElementId("sa2").getFillColor().equals(model2.getElementByElementId("sa2").getFillColor()));
}
@Test
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
index bf3b226e508bb75d44c548ac6ec324385a8c9f33..c80c333bafe3277305e7f01ebc5aa50cf7ade320 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/properties/ChangeElementColorCommandTest.java
@@ -30,9 +30,9 @@ public class ChangeElementColorCommandTest extends CommandTestFunctions {
public void testChangeAliasColor() throws Exception {
Element alias = model.getElementByElementId("alias_id");
ChangeElementColorCommand command = new ChangeElementColorCommand(model, alias, Color.PINK);
- assertFalse(alias.getColor().equals(Color.PINK));
+ assertFalse(alias.getFillColor().equals(Color.PINK));
command.execute();
- assertTrue(alias.getColor().equals(Color.PINK));
+ assertTrue(alias.getFillColor().equals(Color.PINK));
}
@Test
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
index 73b490dae3d9f52a8a11dcce2c2e4f1f101e5bf4..887bef49548405663899777bbc663e9dde6113c7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
@@ -111,7 +111,7 @@ public class Compartment extends Element {
thickness = DEFAULT_COMPARTMENT_THICKNESS;
outerWidth = DEFAULT_OUTER_BORDER_WIDTH;
innerWidth = DEFAULT_INNER_BORDER_WIDTH;
- setColor(DEFAULT_COLOR);
+ setFillColor(DEFAULT_COLOR);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
index dfd70ecebdab71b65ef7e5d157a80a68f4f59a60..54e13a257bb9392d9407ef29070281a82d681b13 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/PathwayCompartment.java
@@ -38,7 +38,7 @@ public class PathwayCompartment extends Compartment {
public PathwayCompartment(String elementId) {
super();
setElementId(elementId);
- setColor(Color.LIGHT_GRAY);
+ setFillColor(Color.LIGHT_GRAY);
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 631dc6a158080de5cd6cb5a4df7e2e2ea4b85515..d9d3fa49bf8e86f347572e39cfed877615900aed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -146,12 +146,20 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Color of the font.
*/
+ @Column(nullable = false)
private Color fontColor = Color.BLACK;
/**
* Color of filling.
*/
- private Color color;
+ @Column(nullable = false)
+ private Color fillColor;
+
+ /**
+ * Color of filling.
+ */
+ @Column(nullable = false)
+ private Color borderColor;
/**
* From which level element should be visible.
@@ -252,7 +260,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
width = original.getWidth();
height = original.getHeight();
fontSize = original.getFontSize();
- color = original.getColor();
+ fillColor = original.getFillColor();
fontColor = original.getFontColor();
for (SearchIndex searchIndex : original.getSearchIndexes()) {
searchIndexes.add(searchIndex.copy());
@@ -289,7 +297,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
width = 0.0;
height = 0.0;
fontSize = DEFAULT_FONT_SIZE;
- color = Color.white;
+ fillColor = Color.white;
}
/**
@@ -499,7 +507,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public void setY(Double y) {
this.y = y;
- } /**
+ }
+
+ /**
* Makes a copy of the element.
*
* @return copy of the element
@@ -650,7 +660,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public Compartment getCompartment() {
return compartment;
- } @Override
+ }
+
+ @Override
public String getVisibilityLevel() {
return visibilityLevel;
}
@@ -667,18 +679,22 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
formerCompartment.removeElement(this);
}
this.compartment = compartment;
- } @Override
+ }
+
+ @Override
public void setVisibilityLevel(String visibilityLevel) {
this.visibilityLevel = visibilityLevel;
}
/**
* @return the color
- * @see #color
+ * @see #fillColor
*/
- public Color getColor() {
- return color;
- } @Override
+ public Color getFillColor() {
+ return fillColor;
+ }
+
+ @Override
public void setVisibilityLevel(Integer visibilityLevel) {
if (visibilityLevel == null) {
this.visibilityLevel = null;
@@ -690,10 +706,10 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* @param color
* the color to set
- * @see #color
+ * @see #fillColor
*/
- public void setColor(Color color) {
- this.color = color;
+ public void setFillColor(Color color) {
+ this.fillColor = color;
}
/**
@@ -793,7 +809,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public void setFullName(String fullName) {
this.fullName = fullName;
- } @XmlTransient
+ }
+
+ @XmlTransient
@Override
public Model getModel() {
return model.getModel();
@@ -805,7 +823,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public List<String> getFormerSymbols() {
return formerSymbols;
- } /**
+ }
+
+ /**
* @param model
* the model to set
* @see #model
@@ -929,7 +949,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public List<String> getSynonyms() {
return synonyms;
- } /**
+ }
+
+ /**
* @return the formula
* @see #formula
*/
@@ -944,7 +966,9 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
*/
public void setSynonyms(List<String> synonyms) {
this.synonyms = synonyms;
- } /**
+ }
+
+ /**
* @param formula
* the formula to set
* @see #formula
@@ -1057,19 +1081,12 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.glyph = glyph;
}
+ public Color getBorderColor() {
+ return borderColor;
+ }
-
-
-
-
-
-
-
-
-
-
-
-
-
+ public void setBorderColor(Color borderColor) {
+ this.borderColor = borderColor;
+ }
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 6c3485ab989596209f64b487d8373b96dfa854c9..47e258e9d383f06936967286e3ced6e9ea4608a6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -106,9 +106,9 @@ public class ElementComparator extends Comparator<Element> {
return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
}
- if (colorComparator.compare(arg0.getColor(), arg1.getColor()) != 0) {
- logger.debug("Color different: " + arg0.getColor() + ", " + arg1.getColor());
- return colorComparator.compare(arg0.getColor(), arg1.getColor());
+ if (colorComparator.compare(arg0.getFillColor(), arg1.getFillColor()) != 0) {
+ logger.debug("Color different: " + arg0.getFillColor() + ", " + arg1.getFillColor());
+ return colorComparator.compare(arg0.getFillColor(), arg1.getFillColor());
}
// this should be somehow modified, because it can create a situation where
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
index 744def3b480acd51751056b0c961e44a048a4995..d5a334daad7c66bb52bd9b41ba901b8ed518f264 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/compartment/CompartmentComparatorTest.java
@@ -87,7 +87,7 @@ public class CompartmentComparatorTest extends ModelTestFunctions {
result.setWidth(4);
result.setHeight(5);
result.setFontSize(9.0);
- result.setColor(Color.BLUE);
+ result.setFillColor(Color.BLUE);
result.setVisibilityLevel("14");
result.setThickness(998);
result.setOuterWidth(45);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
index 66936298e41e17e375c5ebbb27df899ddb985413..fc3664671864565e576a5505a21a59b773071143 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ElementSubmodelConnectionComparatorTest.java
@@ -108,7 +108,7 @@ public class ElementSubmodelConnectionComparatorTest extends ModelTestFunctions
private Element createElement() {
Element protein = new GenericProtein("protein_id");
- protein.setColor(Color.BLACK);
+ protein.setFillColor(Color.BLACK);
return protein;
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
index 196210dedfe8090877afdae03295eb9d84240433..69d3cdf7e9377b1e7496c287dc68cc23a0b0d5c1 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ComplexComparatorTest.java
@@ -49,7 +49,7 @@ public class ComplexComparatorTest extends ModelTestFunctions {
result.setWidth(4);
result.setHeight(5);
result.setFontSize(9.0);
- result.setColor(Color.BLUE);
+ result.setFillColor(Color.BLUE);
result.setVisibilityLevel("14");
Species protein = new GenericProtein("S");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
index 48d6f03c0ecae0e29998f108e4c5aca3b14b6084..40e258071dc6648e8139d281a74c97a45fdc2e0f 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
@@ -64,7 +64,7 @@ public class ElementComparatorTest extends ModelTestFunctions {
sa1 = new GenericProtein("id2");
sa2 = new GenericProtein("id2");
- sa2.setColor(Color.BLUE);
+ sa2.setFillColor(Color.BLUE);
assertTrue(comparator.compare(sa1, sa2) != 0);
sa1 = new GenericProtein("id2");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
index df3283922c40509780b493fda1ad2d7c48a3abed..dc72c66471f1cbdb97433c3c3c3ef9c172eea518 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/SpeciesComparatorTest.java
@@ -54,7 +54,7 @@ public class SpeciesComparatorTest extends ModelTestFunctions {
result.setWidth(4);
result.setHeight(5);
result.setFontSize(9.0);
- result.setColor(Color.BLUE);
+ result.setFillColor(Color.BLUE);
result.setVisibilityLevel(14);
result.setStateLabel("123");
result.setStatePrefix("1234");
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 f8a1a67c3bd28930db8c17856c65953a9bc34ef3..bfea9a18e21dea3cc8e988d513e1264f8deda3f3 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -240,7 +240,7 @@ public class ModelContructor {
alias.setY(rec.getY());
alias.setWidth((int) rec.getWidth());
alias.setHeight((int) rec.getHeight());
- alias.setColor(DEFAULT_COMPLEX_ALIAS_COLOR);
+ alias.setFillColor(DEFAULT_COMPLEX_ALIAS_COLOR);
data.id2alias.put(group.getGraphId(), alias);
model.addElement(alias);
@@ -479,7 +479,7 @@ public class ModelContructor {
alias.setY(rec.getY());
alias.setWidth((int) rec.getWidth());
alias.setHeight((int) rec.getHeight());
- alias.setColor(gpmlElement.getFillColor());
+ alias.setFillColor(gpmlElement.getFillColor());
return alias;
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 929b4db2df6037cbc4e4a98c480e97d671286437..af1a751a67e6e49fa5fd1f2dca63e3f845258874 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -410,9 +410,9 @@ public class ModelToGPML {
dataNodes.append(" <Comment>" + sa.getNotes() + "</Comment>\n");
dataNodes.append(biopaxParser.toReferenceXml(sa.getMiriamData()));
- String red = Integer.toHexString(sa.getColor().getRed());
- String green = Integer.toHexString(sa.getColor().getGreen());
- String blue = Integer.toHexString(sa.getColor().getBlue());
+ String red = Integer.toHexString(sa.getFillColor().getRed());
+ String green = Integer.toHexString(sa.getFillColor().getGreen());
+ String blue = Integer.toHexString(sa.getFillColor().getBlue());
if (red.length() == 1) {
red = "0" + red;
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index 2569ea3c2ffd790fc279b5de562d91a5146d02bc..6ca53968c42ad10c8f1745bed83f9e7df115a490 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -123,8 +123,8 @@ public class ComplexReactionToModelTest extends WikipathwaysTestFunctions {
Element redAlias = model.getElementByElementId("d9620");
Element blackAlias = model.getElementByElementId("d046f");
- assertFalse(Color.BLACK.equals(redAlias.getColor()));
- assertTrue(Color.WHITE.equals(blackAlias.getColor()));
+ assertFalse(Color.BLACK.equals(redAlias.getFillColor()));
+ assertTrue(Color.WHITE.equals(blackAlias.getFillColor()));
assertEquals(1, getWarnings().size());
}
diff --git a/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191024__element_border_color.sql b/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191024__element_border_color.sql
new file mode 100644
index 0000000000000000000000000000000000000000..8c7ab82dc6eef343c46b32a0b41a9ab4b6f5c698
--- /dev/null
+++ b/persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191024__element_border_color.sql
@@ -0,0 +1,9 @@
+alter table element_table rename column color to fill_color;
+alter table element_table add column border_color bytea default E'\\xaced00057372000e6a6176612e6177742e436f6c6f7201a51783108f337502000546000666616c70686149000576616c75654c0002637374001b4c6a6176612f6177742f636f6c6f722f436f6c6f7253706163653b5b00096672676276616c75657400025b465b00066676616c756571007e0002787000000000ff010101707070';
+update element_table set border_color=E'\\xaced00057372000e6a6176612e6177742e436f6c6f7201a51783108f337502000546000666616c70686149000576616c75654c0002637374001b4c6a6176612f6177742f636f6c6f722f436f6c6f7253706163653b5b00096672676276616c75657400025b465b00066676616c756571007e0002787000000000ff010101707070';
+update element_table set border_color=font_color where element_type_db='PATHWAY';
+update element_table set border_color=fill_color where element_type_db in
+ ('BOTTOM_SQUARE_COMPARTMENT', 'LEFT_SQUARE_COMPARTMENT', 'OVAL_COMPARTMENT', 'RIGHT_SQUARE_COMPARTMENT', 'SQUARE_COMPARTMENT', 'TOP_SQUARE_COMPARTMENT');
+alter table element_table alter column border_color set not null;
+update element_table set fill_color=E'\\xaced00057372000e6a6176612e6177742e436f6c6f7201a51783108f337502000546000666616c70686149000576616c75654c0002637374001b4c6a6176612f6177742f636f6c6f722f436f6c6f7253706163653b5b00096672676276616c75657400025b465b00066676616c756571007e0002787000000000ff010101707070' where fill_color is null;
+alter table element_table alter column fill_color set not null;
diff --git a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
index 798fa15e868747d459cc52314aa6a107fc4d00c4..2e7ac370ae1756070880293cfe54dba818a8225f 100644
--- a/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java
@@ -199,7 +199,7 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
factory.execute();
- assertFalse(model.getElementByElementId("sa1").getColor().equals(Color.WHITE));
+ assertFalse(model.getElementByElementId("sa1").getFillColor().equals(Color.WHITE));
}
@Test