diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
index a8b145747ac0df7284850bf1f1d19e0bf001dc80..0dd861759ebbcbea498fbb73f27a239f150dc443 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java
@@ -72,6 +72,22 @@ public abstract class BioEntityConverter<T extends BioEntity> {
draw(bioEntity, graphics, params, new ArrayList<>());
}
+ /**
+ * This function draw {@link BioEntity} on the {@link Graphics2D} object.
+ *
+ * @param bioEntity
+ * {@link BioEntity} that should be drawn
+ * @param graphics
+ * where we want to draw bioEntity
+ * @param params
+ * visualization params (like, should the object be filled with solid
+ * color, etc.), for more information see {@link ConverterParams}
+ * @throws DrawingException
+ * thrown when there is a problem with drawing {@link BioEntity}
+ *
+ */
+ protected abstract void drawImpl(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+
/**
* This function draw representation of the alias on the graphics object.
*
@@ -90,7 +106,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* thrown when there is a problem with drawing {@link BioEntity}
*
*/
- public abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params,
+ protected abstract void draw(T bioEntity, Graphics2D graphics, ConverterParams params,
List<ColorSchema> visualizedOverlaysColorSchemas)
throws DrawingException;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
index f4e895661fc3764c7c552dd8ead11b4f0f35b402..2153b4333e32168ce51092239f70c94b04ef2a14 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java
@@ -199,4 +199,10 @@ public class BioEntityConverterImpl extends BioEntityConverter<BioEntity> {
}
}
+ @SuppressWarnings("unchecked")
+ @Override
+ protected void drawImpl(BioEntity bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+ elementConverter.draw(bioEntity, graphics, params);
+ }
+
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
index 3f108b2a44be7c966ab56962e5be117d25049e45..9a6e85e6ec4dc2e086e3f672619f5c62289017d6 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java
@@ -1,6 +1,16 @@
package lcsb.mapviewer.converter.graphics.bioEntity.element;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
+
+import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.species.Element;
/**
@@ -14,4 +24,37 @@ import lcsb.mapviewer.model.map.species.Element;
*/
public abstract class ElementConverter<T extends Element> extends BioEntityConverter<T> {
+ @Override
+ public final void draw(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException {
+ if (bioEntity.getGlyph() != null) {
+ drawGlyph(bioEntity, graphics);
+ } else {
+ super.draw(bioEntity, graphics, params);
+ }
+ }
+
+ /**
+ * Draws a {@link Glyph} for given bioEntity.
+ *
+ * @param bioEntity
+ * element that should be visualized as a {@link Glyph}
+ * @param graphics
+ * {@link Graphics2D} where we are drawing
+ * @throws DrawingException
+ * thrown when there is a problem with drawing
+ */
+ private void drawGlyph(T bioEntity, Graphics2D graphics) throws DrawingException {
+ try {
+ Image img = ImageIO.read(new ByteArrayInputStream(bioEntity.getGlyph().getFile().getFileContent()));
+ graphics.drawImage(img,
+ bioEntity.getX().intValue(), bioEntity.getY().intValue(),
+ (int) (bioEntity.getX() + bioEntity.getWidth()), (int) (bioEntity.getY() + bioEntity.getHeight()),
+ 0, 0, img.getWidth(null), img.getHeight(null),
+ null);
+ } catch (IOException e) {
+ throw new DrawingException(
+ "Problem with processing glyph file: " + bioEntity.getGlyph().getFile().getOriginalFileName(), e);
+ }
+ }
+
}
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 06b04ff84b2f6ea3c51119fdec84b8ba16681965..49fda869361dfbd4e28bddee5e012d4030e7e992 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
@@ -45,7 +45,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
}
@Override
- public void draw(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ protected void drawImpl(final BottomSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
index 9c6769776f5d52b9075eed3e27aed8fc118b7cc8..2c9b32cc9002685b3ead55f5a0c90aa2bdc26d9f 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java
@@ -179,7 +179,7 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
@Override
public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- draw(alias, graphics, params);
+ drawImpl(alias, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
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 fa24065489db34bf30435c41a29d6211c356cf60..860079d2f74b2d7fbfd0a70834194181f469f8ca 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
@@ -45,7 +45,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
}
@Override
- public void draw(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ protected void drawImpl(final LeftSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java
index 07addb7e2a37f86c74902ae87fc744bdd9179f97..d52073e682881cea7b6abbae43935ee00e3afb8c 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
@@ -48,7 +48,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
}
@Override
- public void draw(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ protected void drawImpl(final OvalCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java
index 8da05b92fa64ac1fc318a5c1a91fcf8ac5d34cda..87bcb8fb020b110d439e748454b136d7358b63b6 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
@@ -36,7 +36,7 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
}
@Override
- public void draw(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params)
+ protected void drawImpl(final PathwayCompartment compartment, final Graphics2D graphics, final ConverterParams params)
throws DrawingException {
// keep the old values of colors and line
Color oldColor = graphics.getColor();
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 4431113ae6628a1bd5b8854ad6ab206f7ce89f1a..d9116520e2d3cecc6271a0ecb1b9d8e14946aecc 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
@@ -45,7 +45,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
}
@Override
- public void draw(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ protected void drawImpl(final RightSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java
index a524860740d51594dc4747eb38baca0670d35b06..ab6de2d9a5504f9010c1de06e78d475f4f0d4f4f 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
@@ -61,7 +61,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
}
@Override
- public void draw(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ protected void drawImpl(final SquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
// keep the old values of color and line type
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java
index c30a6ae45e326246542ded0b5a3680ef01e25076..a1a53b8b3be44b2ad42e32ddbe0ba5268d3673d3 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
@@ -45,7 +45,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
}
@Override
- public void draw(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
+ protected void drawImpl(final TopSquareCompartment compartment, final Graphics2D graphics, final ConverterParams params) throws DrawingException {
Color oldColor = graphics.getColor();
Stroke oldStroke = graphics.getStroke();
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 136e148f57d3389cf509eaa179a851f0c694a219..3b4b395ac87b1abaffa2069131616149e4f4c3a6 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
@@ -44,7 +44,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
}
@Override
- public void draw(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final AntisenseRna antisenseRna, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getAntisenseRnaPath(antisenseRna);
Color c = graphics.getColor();
graphics.setColor(antisenseRna.getColor());
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 bf7e9ff809a48c077225e540cc456967f7188888..f8651b9659f5932f2ed442ca56d4c15e4555b771 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
@@ -57,7 +57,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
}
@Override
- public void draw(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getState().equalsIgnoreCase("complexnoborder")) {
return;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
index e51b68f673a024cbc99b54c845ddfe615c4f2d5f..6e9372c56b9fbbe902bf21658c1c8eb6af2b7436 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
@@ -49,7 +49,7 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
}
@Override
- public void draw(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final Degraded degraded, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(degraded);
double x = getXCoord(degraded, diameter);
double y = getYCoord(degraded);
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 e21d696918e9ba811ed39984f6a715db05c27605..f917d41fcefc584a52b0777c7d1a51abfb8c9d8d 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
@@ -67,7 +67,7 @@ public class DrugConverter extends SpeciesConverter<Drug> {
}
@Override
- public void draw(Drug drug, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(Drug drug, final Graphics2D graphics, final ConverterParams params) {
Shape a1 = getDrugShape(drug);
double offset = OFFSET_BETWEEN_BORDERS;
Shape a2 = new RoundRectangle2D.Double(
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 2877c47e251f6c0072e261749c6352846053c23e..5f3e6682417ba3c38bfe601b46958cde744c054b 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> {
}
@Override
- public void draw(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final Gene gene, final Graphics2D graphics, final ConverterParams params) {
Shape shape = getGeneShape(gene);
Color c = graphics.getColor();
graphics.setColor(gene.getColor());
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 d4ff6fccbae66537cf1610423b7fd827624ad325..0b938b0996af830f811059429017c45041e3492b 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
@@ -42,7 +42,7 @@ public class IonConverter extends SpeciesConverter<Ion> {
}
@Override
- public void draw(Ion ion, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(Ion ion, final Graphics2D graphics, final ConverterParams params) {
double diameter = getDiameter(ion);
double x = getXCoord(ion, diameter);
double y = getYCoord(ion);
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 5d73019e9a7222f39d8a9a72de859ac5c65d9aef..7cd37307323963793183f61023e3466523de5727 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> {
}
@Override
- public void draw(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(Phenotype phenotype, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getPhenotypePath(phenotype);
Color c = graphics.getColor();
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 4649301841932a723db74b1e18dc7d7aa3fa692d..26148f80091ba04c270ca15d925433749ddb76c3 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
@@ -87,7 +87,7 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
}
@Override
- public void draw(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final Protein protein, final Graphics2D graphics, final ConverterParams params) {
// Local variable setting the SBGN visualization
boolean sbgnFormat = params.isSbgnFormat();
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
index c66fada0f4568f32e76f2634a9a3c49c9973b01d..c36bf559ea53d37821fc7e5443b129288da01f50 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
@@ -50,7 +50,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
}
@Override
- public void draw(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final Rna rna, final Graphics2D graphics, final ConverterParams params) {
GeneralPath path = getRnaPath(rna);
Color c = graphics.getColor();
graphics.setColor(rna.getColor());
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 4c7ead26d0252f9cdf1ba15f791a9ae9b6af86ef..c62e51d3afae344158c36ac961049b2cbed40f40 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
@@ -63,7 +63,7 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
}
@Override
- public void draw(Species species, Graphics2D graphics, ConverterParams params) {
+ protected void drawImpl(Species species, Graphics2D graphics, ConverterParams params) {
// Unit of information text - multimer cardinality
String unitOfInformationText = null;
if (species.getStatePrefix() != null && species.getStateLabel() != null) {
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 ef50bcde90f1830b18c40e53e2a890cbf040fdd7..9fb6eab78dd74d9caaa59463f0b8ae18b1bd3bbe 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
@@ -42,7 +42,7 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
}
@Override
- public void draw(final SimpleMolecule simpleMolecule, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final SimpleMolecule simpleMolecule, final Graphics2D graphics, final ConverterParams params) {
int homodir;
if (params.isSbgnFormat()) {
// If the SBGN display mode is set, multimer is shown as two stacked
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
index 980ac89b8315020b225cf2080019aa219c482a3b..2aca0689bd3218657dd18a39a0442a7fa7a15124 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
@@ -498,7 +498,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
@Override
public void draw(T species, Graphics2D graphics, ConverterParams params,
List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
- draw(species, graphics, params);
+ drawImpl(species, graphics, params);
Color oldColor = graphics.getColor();
int count = 0;
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 1135513a8c3ac2648376801ff49ff75dc0cf163d..14e17a446350b08b5d75dfebff9d265ffa909e91 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
@@ -44,7 +44,7 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
}
@Override
- public void draw(Unknown unknown, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(Unknown unknown, final Graphics2D graphics, final ConverterParams params) {
if (unknown.getActivity()) {
int border = ACTIVITY_BORDER_DISTANCE;
unknown.increaseBorder(border);
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
index 72540779895b8b695b7872408c3bd0f19601db2c..910e87eb8e91cd4581c712dfa26fbc5c477a14f7 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
@@ -35,7 +35,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
/**
- * Thics class allows to draw reaction on the graphics2D.
+ * This class allows to draw reaction on the graphics2D.
*
* @author Piotr Gawron
*
@@ -196,7 +196,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
@Override
- public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params) {
+ protected void drawImpl(final Reaction reaction, final Graphics2D graphics, final ConverterParams params) {
Color color = graphics.getColor();
graphics.setColor(reaction.getReactants().get(0).getLine().getColor());
// first reactants
@@ -231,19 +231,19 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
@Override
- public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
+ public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
if (visualizedLayoutsColorSchemas.size() == 0) {
- draw(reaction, graphics, params);
+ drawImpl(reaction, graphics, params);
} else if (visualizedLayoutsColorSchemas.size() == 1) {
if (visualizedLayoutsColorSchemas.get(0) == null) {
- draw(reaction, graphics, params);
+ drawImpl(reaction, graphics, params);
} else {
List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
for (AbstractNode node : reaction.getNodes()) {
oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
}
applyColorSchema(reaction, visualizedLayoutsColorSchemas.get(0));
- draw(reaction, graphics, params);
+ drawImpl(reaction, graphics, params);
for (Pair<AbstractNode, PolylineData> pair : oldData) {
pair.getLeft().setLine(pair.getRight());
}
@@ -256,14 +256,14 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
}
}
if (count == 0) {
- draw(reaction, graphics, params);
+ drawImpl(reaction, graphics, params);
} else {
List<Pair<AbstractNode, PolylineData>> oldData = new ArrayList<>();
for (AbstractNode node : reaction.getNodes()) {
oldData.add(new Pair<AbstractNode, PolylineData>(node, node.getLine()));
}
applyColorSchema(reaction, DEFAULT_COLOR_SCHEMA);
- draw(reaction, graphics, params);
+ drawImpl(reaction, graphics, params);
for (Pair<AbstractNode, PolylineData> pair : oldData) {
pair.getLeft().setLine(pair.getRight());
}
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
index d44d12eefa6f4a8162467e4debc206eb89ff566c..50fabb870e6ef87e738182be7461de64b522c630 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java
@@ -7,16 +7,24 @@ import static org.mockito.ArgumentMatchers.anyBoolean;
import static org.mockito.ArgumentMatchers.anyInt;
import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.argThat;
+import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import java.awt.Color;
+import java.awt.Desktop;
import java.awt.Graphics2D;
+import java.awt.Image;
import java.awt.geom.Point2D;
import java.awt.image.BufferedImage;
+import java.awt.image.ImageObserver;
+import java.io.File;
+import java.nio.file.Files;
import java.util.ArrayList;
import java.util.List;
+import javax.imageio.ImageIO;
+
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
@@ -26,8 +34,10 @@ import org.mockito.Mockito;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.converter.graphics.geometry.ArrowTransformation;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.field.BindingRegion;
@@ -369,6 +379,32 @@ public class SpeciesConverterTest {
}
}
+ @Test
+ public void testDrawAliasWithGlyph() throws Exception {
+ try {
+ BufferedImage bi = new BufferedImage(200, 200, BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = Mockito.spy(bi.createGraphics());
+ ProteinConverter rc = new ProteinConverter(colorExtractor);
+
+ GenericProtein alias = createProtein();
+ Glyph glyph = new Glyph();
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setOriginalFileName("test");
+ byte[] fileContent = Files.readAllBytes(new File("testFiles/glyph.png").toPath());
+
+ file.setFileContent(fileContent);
+ glyph.setFile(file);
+ alias.setGlyph(glyph);
+ rc.draw(alias, graphics, new ConverterParams());
+
+ verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(),
+ anyInt(), anyInt(), nullable(ImageObserver.class));
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
private GenericProtein createProtein() {
GenericProtein protein = new GenericProtein("id");
protein.setName("NAME_OF_THE_ELEMENT");
diff --git a/converter-graphics/testFiles/glyph.png b/converter-graphics/testFiles/glyph.png
new file mode 100644
index 0000000000000000000000000000000000000000..a29b0dfdd7bb45af5ef280121fe0115694eb384e
Binary files /dev/null and b/converter-graphics/testFiles/glyph.png differ