From e34439f2beae4221af3dc6e7de7683423be47324 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 28 Jun 2017 18:09:49 +0200
Subject: [PATCH] either pathways and compartments or custom semantic zoom view
isi accessible when generating project
---
.../lcsb/mapviewer/run/LegendGenerator.java | 2 +-
.../graphics/AbstractImageGenerator.java | 23 ++-------------
.../converter/graphics/ConverterParams.java | 25 +++++++---------
.../converter/graphics/MapGenerator.java | 21 +-------------
.../bioEntity/BioEntityConverter.java | 2 +-
.../bioEntity/BioEntityConverterImplTest.java | 4 +--
.../reaction/ReactionConverterTest.java | 16 +++++-----
.../services/impl/ProjectService.java | 29 +++++++++----------
.../services/utils/data/BuildInLayout.java | 4 +--
9 files changed, 42 insertions(+), 84 deletions(-)
diff --git a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
index 9df1420f0e..df75ffdad6 100644
--- a/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
+++ b/console/src/main/java/lcsb/mapviewer/run/LegendGenerator.java
@@ -160,7 +160,7 @@ public class LegendGenerator {
Model copy = new CopyCommand(model).execute();
PngImageGenerator generator = new PngImageGenerator(new Params()
- .scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(2).semanticZoom(true));
+ .scale(ZOOM_FACTOR).x(lo.startX).y(lo.startY).width(lo.width).height(lo.height).model(copy).level(1).nested(true));
generator.saveToFile(fileName);
Desktop.getDesktop().open(new File(fileName));
}
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 19fe2746b3..3d4e0aefa3 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
@@ -175,11 +175,6 @@ public abstract class AbstractImageGenerator {
*/
private boolean nested = false;
- /**
- * Should the visualization include semantic zoom view or not.
- */
- private boolean semanticZoom = false;
-
/**
* Should sbgn standard be used.
*/
@@ -215,17 +210,6 @@ public abstract class AbstractImageGenerator {
return this;
}
- /**
- * @param semanticZoom
- * semanticZoom to set
- * @return object with all parameters
- * @see #semanticZoom
- */
- public Params semanticZoom(boolean semanticZoom) {
- this.semanticZoom = semanticZoom;
- return this;
- }
-
/**
* @param scale
* scale to set
@@ -754,7 +738,7 @@ public abstract class AbstractImageGenerator {
// get a converter for this compartment
BioEntityConverterImpl converter = new BioEntityConverterImpl(compartment, colorExtractor);
- ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).semanticZoomingOn(params.semanticZoom);
+ ConverterParams compartmentParams = new ConverterParams().textCentered(fill).level(level).nested(params.nested);
if (params.nested) {
compartmentParams.fill(fill).scale(Math.max(scale, 1));
@@ -855,8 +839,7 @@ public abstract class AbstractImageGenerator {
}
try {
converter.draw(
- species, graphics,
- new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).semanticZoomingOn(params.semanticZoom),
+ species, graphics, new ConverterParams().scale(customScale).textCentered(rescale).level(level).sbgnFormat(sbgnFormat).nested(params.nested),
visibleLayouts);
} catch (Exception e) {
throw new DrawingException(eu.getElementTag(species) + "Problem with drawing element.", e);
@@ -894,7 +877,7 @@ public abstract class AbstractImageGenerator {
return;
}
BioEntityConverterImpl converter = new BioEntityConverterImpl(reaction, sbgnFormat, colorExtractor);
- converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).semanticZoomingOn(params.semanticZoom).level(level), visibleLayouts);
+ converter.draw(reaction, graphics, new ConverterParams().sbgnFormat(sbgnFormat).nested(params.nested).level(level), visibleLayouts);
}
/**
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 59577a9350..7efaa3e51b 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
@@ -34,10 +34,7 @@ public class ConverterParams {
*/
private boolean sbgnFormat = false;
- /**
- * Is the semantic zooming filtered.
- */
- private boolean semanticZoomingOn = false;
+ private boolean nested = false;
/**
* @param fill
@@ -62,13 +59,13 @@ public class ConverterParams {
}
/**
- * @param semanticZoomingOn
- * the semanticZoomingOn to set
+ * @param nested
+ * the nested to set
* @return object with all parameters
- * @see #semanticZoomingOn
+ * @see #nested
*/
- public ConverterParams semanticZoomingOn(final boolean semanticZoomingOn) {
- this.semanticZoomingOn = semanticZoomingOn;
+ public ConverterParams nested(final boolean nested) {
+ this.nested = nested;
return this;
}
@@ -146,11 +143,11 @@ public class ConverterParams {
}
/**
- * @return the semanticZoomingOn
- * @see #semanticZoomingOn
+ * @return the nested
+ * @see #nested
*/
- public boolean isSemanticZoomingOn() {
- return semanticZoomingOn;
+ public boolean isNested() {
+ return nested;
}
@Override
@@ -160,7 +157,7 @@ public class ConverterParams {
"level:" + level + "," + //
"scale:" + scale + "," + //
"textCentered:" + textCentered + "," + //
- "semanticZoomingOn:" + semanticZoomingOn + "," + //
+ "nested:" + nested + "," + //
"sbgnFormat:" + sbgnFormat;
return result;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
index 5e44baf425..697177d051 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/MapGenerator.java
@@ -58,10 +58,6 @@ public class MapGenerator {
*
*/
private boolean nested = false;
- /**
- * Do we want to generate images with semantic zoom view or not.
- */
- private boolean semanticZoom = false;
/**
* Should we remove empty elements in nested view.
*
@@ -139,17 +135,6 @@ public class MapGenerator {
return this;
}
- /**
- * @param semanticZoom
- * the semanticZoom to set
- * @see #nested
- * @return full {@link MapGeneratorParams} object
- */
- public MapGeneratorParams semanticZoom(boolean semanticZoom) {
- this.semanticZoom = semanticZoom;
- return this;
- }
-
/**
* @return the removeEmpty
* @see #removeEmpty
@@ -342,11 +327,7 @@ public class MapGenerator {
imgParams.model(params.model);
imgParams.sbgn(params.sbgn);
imgParams.level(i);
- imgParams.semanticZoom(params.semanticZoom);
-
- if (params.nested) {
- imgParams.level(i).nested(params.nested);
- }
+ imgParams.nested(params.nested);
PngImageGenerator generator = new PngImageGenerator(imgParams);
for (int cx = 0; cx < TILES_CACHE_NUM; cx++) {
for (int cy = 0; cy < TILES_CACHE_NUM; cy++) {
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 fc23fb911c..30a411a810 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
@@ -156,7 +156,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
* @return true if object is visible
*/
protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
- if (params.isSemanticZoomingOn()) {
+ if (params.isNested()) {
boolean result = semanticZoomLevelMatcher.isVisible(params.getLevel(), bioEntity.getVisibilityLevel());
if (bioEntity instanceof Element) {
Compartment compartment = ((Element) bioEntity).getCompartment();
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
index 9141204ccf..206b3f332f 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java
@@ -49,7 +49,7 @@ public class BioEntityConverterImplTest {
reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(0)).draw(any(GeneralPath.class));
@@ -67,7 +67,7 @@ public class BioEntityConverterImplTest {
reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(0)).draw(any(GeneralPath.class));
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
index 8d17b603ca..2606bb7c83 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java
@@ -264,7 +264,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(1.0);
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(4)).draw(any(GeneralPath.class));
@@ -281,7 +281,7 @@ public class ReactionConverterTest {
Reaction reaction = createReaction(1.0);
reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(3)).draw(any(GeneralPath.class));
@@ -298,7 +298,7 @@ public class ReactionConverterTest {
Reaction reaction = createReaction(1.0);
reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(3)).draw(any(GeneralPath.class));
@@ -315,7 +315,7 @@ public class ReactionConverterTest {
Reaction reaction = createReaction(1.0);
reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(3)).draw(any(GeneralPath.class));
@@ -332,7 +332,7 @@ public class ReactionConverterTest {
Reaction reaction = createComplexReaction(1.0);
reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(12)).draw(any(GeneralPath.class));
@@ -350,7 +350,7 @@ public class ReactionConverterTest {
Reaction reaction = createComplexReaction(1.0);
reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
reaction.getModifiers().get(1).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(9)).draw(any(GeneralPath.class));
@@ -375,7 +375,7 @@ public class ReactionConverterTest {
Reaction reaction = createComplexReaction(1.0);
reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(12)).draw(any(GeneralPath.class));
@@ -392,7 +392,7 @@ public class ReactionConverterTest {
Reaction reaction = createComplexReaction(1.0);
reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
- rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
+ rc.draw(reaction, graphics, new ConverterParams().nested(true).level(10));
verify(graphics, times(12)).draw(any(GeneralPath.class));
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index c502dcc853..ed54015542 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -648,7 +648,6 @@ public class ProjectService implements IProjectService {
MapGeneratorParams imgParams = generator.new MapGeneratorParams()
.directory(directory).sbgn(params.isSbgnFormat()).nested(layout.isHierarchicalView()).updater(updater);
if (layout.getTitle().contains(BuildInLayout.SEMANTIC.getTitle())) {
- imgParams.semanticZoom(params.isSemanticZoom());
if (Character.isDigit(layout.getTitle().charAt(layout.getTitle().length() - 1))) {
output = prepareSemanticZoomModel(model, layout.getTitle().replaceAll("[^0-9.]", ""));
}
@@ -728,24 +727,20 @@ public class ProjectService implements IProjectService {
model.setTileSize(MapGenerator.TILE_SIZE);
List<BuildInLayout> buildInLayouts = new ArrayList<>();
+ BuildInLayout nested = null;
+ if (params.isSemanticZoom()) {
+ nested = BuildInLayout.SEMANTIC;
+ } else {
+ nested = BuildInLayout.NESTED;
+ }
if (params.isNetworkLayoutAsDefault()) {
buildInLayouts.add(BuildInLayout.NORMAL);
- for (BuildInLayout buildInLayout : BuildInLayout.values()) {
- if (!buildInLayout.equals(BuildInLayout.NORMAL) && !buildInLayout.equals(BuildInLayout.SEMANTIC)) {
- buildInLayouts.add(buildInLayout);
- }
- }
+ buildInLayouts.add(nested);
} else {
- buildInLayouts.add(BuildInLayout.NESTED);
- for (BuildInLayout buildInLayout : BuildInLayout.values()) {
- if (!buildInLayout.equals(BuildInLayout.NESTED) && !buildInLayout.equals(BuildInLayout.SEMANTIC)) {
- buildInLayouts.add(buildInLayout);
- }
- }
- }
- if (params.isSemanticZoom()) {
- buildInLayouts.add(BuildInLayout.SEMANTIC);
+ buildInLayouts.add(nested);
+ buildInLayouts.add(BuildInLayout.NORMAL);
}
+ buildInLayouts.add(BuildInLayout.CLEAN);
// reverse the order of build in layouts, so we can insert them at the
// beginning of list of layouts (the order will be the same)
@@ -972,7 +967,9 @@ public class ProjectService implements IProjectService {
}
Model originalModel = createModel(params, project);
- new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel), generator.computeZoomFactor(originalModel)).execute();
+ if (!params.isSemanticZoom()) {
+ new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel), generator.computeZoomFactor(originalModel)).execute();
+ }
addUsers(project, params);
createImages(originalModel, params);
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
index 3bdf5704f7..c0edc377be 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/data/BuildInLayout.java
@@ -31,8 +31,8 @@ public enum BuildInLayout { //
/**
* Standard visualization with hierarchical view.
*/
- NESTED("Pathways and compartments", "_nested", null, true),
- SEMANTIC("Semantic zoom", "_semantic", null, false),
+ NESTED("Pathways and compartments", "_nested", null, true), //
+ SEMANTIC("Semantic zoom", "_semantic", null, true),
/**
* Clean visualization (with colors reset to black and white).
*/
--
GitLab