From 6b6354cf6714f0520fe58d0c7a75963fe68fd81d Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 29 Jun 2017 14:49:15 +0200
Subject: [PATCH] fill parameter removed from drawinf parameters (it's computed
on demand)
---
.../graphics/AbstractImageGenerator.java | 8 ++---
.../converter/graphics/ConverterParams.java | 35 +++----------------
.../bioEntity/BioEntityConverter.java | 8 +++--
.../BottomSquareCompartmentConverter.java | 8 +++--
.../compartment/CompartmentConverter.java | 25 ++++++-------
.../LeftSquareCompartmentConverter.java | 9 ++---
.../compartment/OvalCompartmentConverter.java | 5 +--
.../PathwayCompartmentConverter.java | 5 +--
.../RightSquareCompartmentConverter.java | 9 ++---
.../SquareCompartmentConverter.java | 5 +--
.../TopSquareCompartmentConverter.java | 10 +++---
11 files changed, 54 insertions(+), 73 deletions(-)
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index afd349aacb..e61ab7b630 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -755,17 +755,13 @@ public abstract class AbstractImageGenerator {
ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).nested(params.nested);
if (params.nested) {
- compartmentParams.fill(fill).scale(Math.max(scale, 1));
+ compartmentParams.scale(Math.max(scale, 1));
}
// we draw compartment only when we have hierarchical view or it's
// standard compartment (not the pathway)
if (params.nested || !(compartment instanceof PathwayCompartment)) {
- try {
- converter.draw(compartment, graphics, compartmentParams, visibleLayouts);
- } catch (Exception e) {
- throw new DrawingException(eu.getElementTag(compartment) + "Problem with drawing element.", e);
- }
+ converter.draw(compartment, graphics, compartmentParams, visibleLayouts);
}
// If compartment should be filled, then we could skip drawing the inside
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
index 7efaa3e51b..91932eae2e 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
@@ -7,45 +7,29 @@ package lcsb.mapviewer.converter.graphics;
*
*/
public class ConverterParams {
- /**
- * Should the object be filled with the solid color. In other words it tells
- * us if the object is not transparent.
- */
- private boolean fill = false;
/**
* At which level the object is visualized. It helps to deterimine font size.
* However it's possible that this value is not required.
*/
- private int level = 0;
+ private int level = 0;
/**
* What is the scale. It allows to adjust font size to be readable.
*/
- private double scale = 1;
+ private double scale = 1;
/**
* Should the text describing element be centered or not.
*/
- private boolean textCentered = false;
+ private boolean textCentered = false;
/**
* Should the map be displayed in SBGN format.
*/
- private boolean sbgnFormat = false;
-
- private boolean nested = false;
+ private boolean sbgnFormat = false;
- /**
- * @param fill
- * the fill to set
- * @return object with all parameters
- * @see #fill
- */
- public ConverterParams fill(final boolean fill) {
- this.fill = fill;
- return this;
- }
+ private boolean nested = false;
/**
* @param scale
@@ -110,14 +94,6 @@ public class ConverterParams {
return this;
}
- /**
- * @return the fill
- * @see #fill
- */
- public boolean isFill() {
- return fill;
- }
-
/**
* @return the scale
* @see #scale
@@ -153,7 +129,6 @@ public class ConverterParams {
@Override
public String toString() {
String result = "[" + this.getClass().getSimpleName() + "] " + //
- "fill:" + fill + "," + //
"level:" + level + "," + //
"scale:" + scale + "," + //
"textCentered:" + textCentered + "," + //
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 2bf39b74d6..3c0969d891 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
@@ -41,7 +41,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
@SuppressWarnings("unused")
private final Logger logger = Logger.getLogger(BioEntityConverter.class);
- private SemanticZoomLevelMatcher semanticZoomLevelMatcher = new SemanticZoomLevelMatcher();
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
* Alpha value (0..255) used for visualizing overlay data that are normally
@@ -160,7 +160,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
*/
protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
if (params.isNested()) {
- boolean result = semanticZoomLevelMatcher.isVisible(params.getLevel(), bioEntity.getVisibilityLevel());
+ boolean result = zoomLevelMatcher.isVisible(params.getLevel(), bioEntity.getVisibilityLevel());
if (bioEntity instanceof Element) {
Compartment compartment = ((Element) bioEntity).getCompartment();
if (compartment != null) {
@@ -186,6 +186,10 @@ public abstract class BioEntityConverter<T extends BioEntity> {
return true;
}
+ protected boolean isTransparent(Element bioEntity, ConverterParams params) {
+ return zoomLevelMatcher.isTransparent(params.getLevel(), bioEntity.getTransparencyLevel());
+ }
+
/**
* Checks if at least one reactant is visible.
*
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 c13cdbdaf2..b2af327cf2 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
@@ -14,6 +14,7 @@ import lcsb.mapviewer.converter.graphics.ConverterParams;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import org.apache.log4j.Logger;
@@ -61,7 +62,8 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
}
// fill the background
- if (params.isFill()) {
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(c1);
} else {
Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
@@ -76,7 +78,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
graphics.setStroke(LineType.SOLID.getStroke());
graphics.draw(s3);
graphics.setColor(c2);
- if (params.isFill()) {
+ if (fill) {
graphics.fill(a1);
}
// restore color and line type
@@ -84,7 +86,7 @@ public class BottomSquareCompartmentConverter extends CompartmentConverter<Botto
graphics.setStroke(oldStroke);
// draw description
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, params);
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 7e3a88ad40..4db51f040b 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
@@ -35,58 +35,56 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
*/
public abstract class CompartmentConverter<T extends Compartment> extends ElementConverter<T> {
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
-
/**
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CompartmentConverter.class.getName());
+ private static Logger logger = Logger.getLogger(CompartmentConverter.class.getName());
/**
* Default font size.
*/
- private static final int DEFAULT_FONT_SIZE = 10;
+ private static final int DEFAULT_FONT_SIZE = 10;
/**
* Alpha level for inside of the transparent compartments.
*/
- public static final int DEFAULT_ALPHA_LEVEL = 8;
+ public static final int DEFAULT_ALPHA_LEVEL = 8;
/**
* Class used for transformation of lines.
*/
- private LineTransformation lineTransformation = new LineTransformation();
+ private LineTransformation lineTransformation = new LineTransformation();
/**
* Class used for transformation of ellipses.
*/
- private EllipseTransformation ellipseTransformation = new EllipseTransformation();
+ private EllipseTransformation ellipseTransformation = new EllipseTransformation();
/**
* Default alpha level for transparent compartments.
*/
- private static int alphaLevel = DEFAULT_ALPHA_LEVEL;
+ private static int alphaLevel = DEFAULT_ALPHA_LEVEL;
/**
* Default alpha level for semi-transparent borders.
*/
- protected static final int HIGH_ALPHA_LEVEL = 127;
+ protected static final int HIGH_ALPHA_LEVEL = 127;
/**
* Class used for finding place to draw desciption of the compartment.
*/
- private PlaceFinder placeFinder;
+ private PlaceFinder placeFinder;
/**
* Object used for synchronization when accessing {@link #placeFinder}.
*/
- private String placeFinderSynchronization = "";
+ private String placeFinderSynchronization = "";
/**
* Object that helps to convert {@link ColorSchema} values into colors.
*/
- private ColorExtractor colorExtractor;
+ private ColorExtractor colorExtractor;
/**
* Default constructor.
@@ -107,8 +105,7 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
"Dimension of the alias must be bigger than 0. Alias id: " + alias.getElementId() + " (name: \"" + alias.getName() + "\")");
}
Rectangle2D border = alias.getBorder();
- if (zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel())
- && !zoomLevelMatcher.isTransparent(params.getLevel(), alias.getTransparencyLevel())) {
+ if (isVisible(alias, params) && !isTransparent(alias, params)) {
synchronized (placeFinderSynchronization) {
if (placeFinder == null || placeFinder.getModel() != alias.getModelData()) {
placeFinder = new PlaceFinder(alias.getModelData().getModel());
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 513684d8ad..e6767a608f 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
@@ -29,7 +29,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
+ private static Logger logger = Logger.getLogger(LeftSquareCompartmentConverter.class.getName());
/**
* Default constructor.
@@ -61,7 +61,8 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
}
// fill the background
- if (params.isFill()) {
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(c1);
} else {
Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
@@ -76,7 +77,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
graphics.setStroke(LineType.SOLID.getStroke());
graphics.draw(s3);
graphics.setColor(c2);
- if (params.isFill()) {
+ if (fill) {
graphics.fill(a1);
}
@@ -85,7 +86,7 @@ public class LeftSquareCompartmentConverter extends CompartmentConverter<LeftSqu
graphics.setStroke(oldStroke);
// draw description
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, params);
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 611eb3dead..ea5a579a5a 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
@@ -68,7 +68,8 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
a1.subtract(new Area(s3));
// fill the background
- if (params.isFill()) {
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(c1);
} else {
Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
@@ -90,7 +91,7 @@ public class OvalCompartmentConverter extends CompartmentConverter<OvalCompartme
graphics.setStroke(oldStroke);
// draw description
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, params);
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 6d691cfab2..b9ff85306f 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
@@ -50,7 +50,8 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
Color color = alias.getColor();
// fill the background
- if (params.isFill()) {
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(backgroundColor);
} else {
Color bgAlphaColor = new Color(0, 0, 0, getAlphaLevel());
@@ -68,7 +69,7 @@ public class PathwayCompartmentConverter extends CompartmentConverter<PathwayCom
graphics.setStroke(oldStroke);
// draw description of the compartment
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, 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 c1dbe6fa02..92303a36f8 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
@@ -30,7 +30,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
+ private static Logger logger = Logger.getLogger(RightSquareCompartmentConverter.class.getName());
/**
* Default constructor.
@@ -61,7 +61,8 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
}
// fill the background
- if (params.isFill()) {
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(c1);
} else {
Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
@@ -76,7 +77,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
graphics.setStroke(LineType.SOLID.getStroke());
graphics.draw(s3);
graphics.setColor(c2);
- if (params.isFill()) {
+ if (fill) {
graphics.fill(a1);
}
// restore color and line type
@@ -89,7 +90,7 @@ public class RightSquareCompartmentConverter extends CompartmentConverter<RightS
alias.getNamePoint().setLocation(x, y);
// draw description
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, params);
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 169950485e..c19e0deb0c 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
@@ -80,7 +80,8 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
a1.subtract(new Area(s3));
// fill the background
- if (params.isFill()) {
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(c1);
} else {
Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
@@ -102,7 +103,7 @@ public class SquareCompartmentConverter extends CompartmentConverter<SquareCompa
graphics.setStroke(oldStroke);
// draw description
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, params);
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 bdc72589df..33a325562f 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
@@ -30,7 +30,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
+ private static Logger logger = Logger.getLogger(TopSquareCompartmentConverter.class.getName());
/**
* Default constructor.
@@ -58,7 +58,9 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
c1 = Color.BLACK;
}
- if (params.isFill()) {
+ // fill the background
+ boolean fill = !isTransparent(alias, params);
+ if (fill) {
graphics.setColor(c1);
} else {
Color bgAlphaColor = new Color(c1.getRed(), c1.getGreen(), c1.getBlue(), getAlphaLevel());
@@ -72,7 +74,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
graphics.setStroke(LineType.SOLID.getStroke());
graphics.draw(s3);
graphics.setColor(c2);
- if (params.isFill()) {
+ if (fill) {
graphics.fill(a1);
}
@@ -80,7 +82,7 @@ public class TopSquareCompartmentConverter extends CompartmentConverter<TopSquar
graphics.setColor(oldColor);
graphics.setStroke(oldStroke);
// draw description
- if (params.isFill()) {
+ if (fill) {
Point2D tmpPoint = alias.getNamePoint();
alias.setNamePoint(alias.getCenter());
drawText(alias, graphics, params);
--
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