From f2eb5642a74807db8ab635cf77e0743d733a74a0 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 29 Jun 2017 16:00:28 +0200
Subject: [PATCH] simplification of abstract methods syntax (unnecessary params
removed)
---
.../graphics/AbstractImageGenerator.java | 47 ++++++++-----------
1 file changed, 19 insertions(+), 28 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 16b964e447..0f4115b9e9 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
@@ -679,20 +679,20 @@ public abstract class AbstractImageGenerator {
// compartment/complexes)
if (element instanceof Species) {
if (((Species) element).getComplex() == null && element.getCompartment() == null) {
- drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
+ drawSpecies((Species) element);
}
}
}
// draw all reactions
for (Reaction reaction : params.getModel().getSortedReactions()) {
- drawReaction(reaction, params.getVisibleLayoutsForElement(reaction), params);
+ drawReaction(reaction);
}
// draw all compartments
for (Compartment compartment : params.getModel().getSortedCompartments()) {
// draw only compartment that don't have parents (aren't included in any
// compartment/complexes)
if (compartment.getCompartment() == null) {
- drawCompartment(compartment, params.getVisibleLayoutsForElement(compartment), params);
+ drawCompartment(compartment);
}
}
@@ -731,14 +731,10 @@ public abstract class AbstractImageGenerator {
*
* @param compartment
* object that we want to draw
- * @param visibleLayouts
- * list of {@link ColorSchema} used for coloring element in layouts
- * @param params
- * list of all params to create apropriate image
* @throws DrawingException
* thrown when there was a problem with drawing {@link Compartment}
*/
- protected void drawCompartment(final Compartment compartment, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
+ protected void drawCompartment(final Compartment compartment) throws DrawingException {
// get a converter for this compartment
BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
ConverterParams compartmentParams = new ConverterParams().level(level).nested(params.nested);
@@ -750,7 +746,7 @@ public abstract class AbstractImageGenerator {
// we draw compartment only when we have hierarchical view or it's
// standard compartment (not the pathway)
if (params.nested || !(compartment instanceof PathwayCompartment)) {
- converter.draw(compartment, graphics, compartmentParams, visibleLayouts);
+ converter.draw(compartment, graphics, compartmentParams, params.getVisibleLayoutsForElement(compartment));
}
// If compartment should be filled, then we could skip drawing the inside
@@ -762,12 +758,12 @@ public abstract class AbstractImageGenerator {
Collections.sort(result, Element.SIZE_COMPARATOR);
// draw all children of this compartment
- for (Element element : result) {
+ for (Element child : result) {
// if a child is a standard species
- if (element instanceof Species) {
- drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
- } else if (element instanceof Compartment) {
- drawCompartment((Compartment) element, params.getVisibleLayoutsForElement(element), params);
+ if (child instanceof Species) {
+ drawSpecies((Species) child);
+ } else if (child instanceof Compartment) {
+ drawCompartment((Compartment) child);
} else {
// if a child is not a compartment or a species then we have a
// problem
@@ -788,14 +784,10 @@ public abstract class AbstractImageGenerator {
*
* @param species
* object to be drawn
- * @param visibleLayouts
- * list of {@link ColorSchema} used for coloring species in layouts
- * @param params
- * list of all params to create apropriate image
* @throws DrawingException
* thrown when there was a problem with drawing a {@link Species}
*/
- protected void drawSpecies(final Species species, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
+ protected void drawSpecies(final Species species) throws DrawingException {
/**
* Last conditions in this 'ifs' provides the certainty of visibility of
@@ -827,7 +819,9 @@ public abstract class AbstractImageGenerator {
if (rescale) {
customScale = scale;
}
- converter.draw(species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested), visibleLayouts);
+ converter.draw(
+ species, graphics, new ConverterParams().scale(customScale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
+ params.getVisibleLayoutsForElement(species));
// if the species is a complex then we may want to draw children
// objects
@@ -838,8 +832,8 @@ public abstract class AbstractImageGenerator {
if (!complex.getState().equalsIgnoreCase("brief")) {
// depending on current zoom level, children are drawn or not
if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
- for (Species a : complex.getElements()) {
- drawSpecies(a, visibleLayouts, params);
+ for (Species child : complex.getElements()) {
+ drawSpecies(child);
}
}
}
@@ -851,18 +845,15 @@ public abstract class AbstractImageGenerator {
*
* @param reaction
* object to be drawn
- * @param visibleLayouts
- * list of {@link ColorSchema} used for coloring reaction in layouts
- * @param params
- * list of all params to create apropriate image
* @throws DrawingException
*/
- protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) throws DrawingException {
+ protected void drawReaction(final Reaction reaction) throws DrawingException {
if (!cross(reaction.getLines())) {
return;
}
BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
- converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), visibleLayouts);
+ converter.draw(
+ reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), params.getVisibleLayoutsForElement(reaction));
}
/**
--
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