From 05944698d30e07c1add2b8b4ebd5dd5ac5fa3f95 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 28 Jun 2017 17:40:07 +0200
Subject: [PATCH] semantic zooming and hierarchy visualizaion are unified on
the model level
---
.../annotation/RestAnnotationParser.java | 10 ++--
.../annotation/RestAnnotationParserTest.java | 12 +++--
.../graphics/AbstractImageGenerator.java | 34 +++++++-----
.../bioEntity/BioEntityConverter.java | 2 +-
.../bioEntity/SemanticZoomLevelMatcher.java | 11 +++-
.../compartment/CompartmentConverter.java | 28 +++++-----
.../element/species/ComplexConverter.java | 12 +++--
.../element/species/SpeciesConverter.java | 5 +-
.../graphics/placefinder/PlaceFinder.java | 40 ++++++++------
.../graphics/NormalImageGeneratorTest.java | 6 +--
.../graphics/PdfImageGeneratorTest.java | 6 +--
.../bioEntity/BioEntityConverterImplTest.java | 4 +-
.../reaction/ReactionConverterTest.java | 16 +++---
.../placefinder/AllPlaceFinderTest.java | 16 +++---
.../commands/CreateHierarchyCommand.java | 12 ++---
.../mapviewer/commands/CopyCommandTest.java | 6 +--
.../commands/CreateHierarchyCommandTest.java | 25 +++++----
.../lcsb/mapviewer/model/map/BioEntity.java | 12 ++++-
.../model/map/reaction/Reaction.java | 38 ++++++--------
.../map/reaction/ReactionComparator.java | 7 ++-
.../mapviewer/model/map/species/Element.java | 52 +++++++------------
.../model/map/species/ElementComparator.java | 10 +---
.../CompartmentComparatorTest.java | 2 +-
.../model/map/reaction/ReactionTest.java | 13 ++---
.../map/species/ComplexComparatorTest.java | 2 +-
.../model/map/species/ElementTest.java | 2 +-
persist/src/db/11/fix_db_20170628.sql | 8 +++
.../services/impl/ProjectService.java | 6 +--
.../services/impl/SearchService.java | 5 +-
.../services/search/data/FullAliasView.java | 9 ++--
.../search/data/FullReactionView.java | 6 +--
31 files changed, 225 insertions(+), 192 deletions(-)
create mode 100644 persist/src/db/11/fix_db_20170628.sql
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index ca09d6630b..97cbe2c445 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -129,7 +129,7 @@ public class RestAnnotationParser extends XmlParser {
sb.append(createEntry(NoteField.PANTHER, filterMiriam(data, MiriamType.PANTHER), forceFullInfo));
sb.append(createEntry(NoteField.DESCRIPTION, null, forceFullInfo));
sb.append(createEntry(NoteField.ABBREVIATION, element.getAbbreviation(), forceFullInfo));
- sb.append(createEntry(NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY, element.getSemanticZoomLevelVisibility(), forceFullInfo));
+ sb.append(createEntry(NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY, element.getVisibilityLevel(), forceFullInfo));
sb.append(createEntry(NoteField.CHARGED_FORMULA, element.getFormula(), forceFullInfo));
if (element instanceof Species) {
sb.append(createEntry(NoteField.CHARGE, ((Species) element).getCharge(), forceFullInfo));
@@ -640,12 +640,12 @@ public class RestAnnotationParser extends XmlParser {
if (zoomLevelVisibility == null) {
return;
}
- if (element.getSemanticZoomLevelVisibility() == null) {
- element.setSemanticZoomLevelVisibility(zoomLevelVisibility);
- } else if (!element.getSemanticZoomLevelVisibility().equals(zoomLevelVisibility)) {
+ if (element.getVisibilityLevel() == null || element.getVisibilityLevel().isEmpty()) {
+ element.setVisibilityLevel(zoomLevelVisibility);
+ } else if (!element.getVisibilityLevel().equals(zoomLevelVisibility)) {
logger.warn(
elementUtils.getElementTag(element) + " New " + NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + " different than default ["
- + zoomLevelVisibility + "][" + element.getSemanticZoomLevelVisibility() + "]. Ignoring.");
+ + zoomLevelVisibility + "][" + element.getVisibilityLevel() + "]. Ignoring.");
}
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
index f396388cca..f9d45fd607 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
@@ -428,16 +428,22 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
}
@Override
- public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
+ public void setVisibilityLevel(String zoomLevelVisibility) {
// TODO Auto-generated method stub
-
+
}
@Override
- public String getSemanticZoomLevelVisibility() {
+ public String getVisibilityLevel() {
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ public void setVisibilityLevel(Integer zoomLevelVisibility) {
+ // TODO Auto-generated method stub
+
+ }
});
fail("Exception expected");
} catch (NotImplementedException e) {
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 14ed133d42..19fe2746b3 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
@@ -17,6 +17,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.converter.graphics.layer.LayerConverter;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
@@ -67,6 +68,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*
*/
public abstract class AbstractImageGenerator {
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
* Model is drawn as a partial image (x,y,width,height parameters of
@@ -78,32 +80,32 @@ public abstract class AbstractImageGenerator {
* TODO maybe more effecient (and safe) solution would be to include text
* desciption as parts of the object border
*/
- private static final int SINGLE_FRAME_MARGIN = 100;
+ private static final int SINGLE_FRAME_MARGIN = 100;
/**
* On which level in hierarchical view we should visualize map.
*/
- private int level = Integer.MAX_VALUE;
+ private int level = Integer.MAX_VALUE;
/**
* Zoom factor of the drawing.
*/
- private double scale = 1;
+ private double scale = 1;
/**
* This is a frame border from which we take all elements to draw.
*/
- private Rectangle2D.Double border = null;
+ private Rectangle2D.Double border = null;
/**
* Object that helps to convert {@link ColorSchema} values into colors.
*/
- private ColorExtractor colorExtractor = null;
+ private ColorExtractor colorExtractor = null;
/**
* Util class for simple operations on {@link Element elements}.
*/
- private ElementUtils eu = new ElementUtils();
+ private ElementUtils eu = new ElementUtils();
/**
* This class contains a list of params that are used for drawing.
@@ -675,7 +677,7 @@ public abstract class AbstractImageGenerator {
// draw only elements that don't have parents (aren't included in any
// compartment/complexes)
if (element instanceof Species) {
- if (((Species) element).getComplex() == null && ((Species) element).getCompartment() == null) {
+ if (((Species) element).getComplex() == null && element.getCompartment() == null) {
drawSpecies((Species) element, params.getVisibleLayoutsForElement(element), params);
}
}
@@ -735,7 +737,7 @@ public abstract class AbstractImageGenerator {
// If 'compartment' has not the big enough visibility level then should not
// be visible.
- if (compartment.getVisibilityLevel() > level && params.nested) {
+ if (!(zoomLevelMatcher.isVisible(level, compartment.getVisibilityLevel())) && params.nested) {
return;
}
@@ -746,7 +748,7 @@ public abstract class AbstractImageGenerator {
*/
boolean fill = true;
- if (compartment.getTransparencyLevel() <= level || !params.nested) {
+ if (zoomLevelMatcher.isTransparent(level, compartment.getTransparencyLevel()) || !params.nested) {
fill = false;
}
@@ -817,7 +819,7 @@ public abstract class AbstractImageGenerator {
// VisibilityLevel is big enough, then it is
// displayed.
- if (species.getVisibilityLevel() > level && params.nested) {
+ if (!(zoomLevelMatcher.isVisible(level, species.getVisibilityLevel())) && params.nested) {
return;
}
@@ -832,10 +834,16 @@ public abstract class AbstractImageGenerator {
boolean rescale = false;
if (species instanceof Complex) {
- if (((Complex) species).getElements().size() == 0) {
+ Complex complex = (Complex) species;
+ if (complex.getElements().size() == 0) {
rescale = true;
- } else if (((Complex) species).getElements().get(0).getVisibilityLevel() > level) {
+ } else {
rescale = true;
+ for (Element child : complex.getElements()) {
+ if ((zoomLevelMatcher.isVisible(level, child.getVisibilityLevel())) || !params.nested) {
+ rescale = false;
+ }
+ }
}
}
@@ -862,7 +870,7 @@ public abstract class AbstractImageGenerator {
// mode
if (!complex.getState().equalsIgnoreCase("brief")) {
// depending on current zoom level, children are drawn or not
- if (complex.getTransparencyLevel() <= level) {
+ if (zoomLevelMatcher.isTransparent(level, complex.getTransparencyLevel()) || !params.nested) {
for (Species a : complex.getElements()) {
drawSpecies(a, visibleLayouts, params);
}
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 83ea40c734..fc23fb911c 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
@@ -157,7 +157,7 @@ public abstract class BioEntityConverter<T extends BioEntity> {
*/
protected boolean isVisible(BioEntity bioEntity, ConverterParams params) {
if (params.isSemanticZoomingOn()) {
- boolean result = semanticZoomLevelMatcher.matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
+ boolean result = semanticZoomLevelMatcher.isVisible(params.getLevel(), bioEntity.getVisibilityLevel());
if (bioEntity instanceof Element) {
Compartment compartment = ((Element) bioEntity).getCompartment();
if (compartment != null) {
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java
index 195b6e4916..a5c28959bc 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/SemanticZoomLevelMatcher.java
@@ -12,7 +12,15 @@ public class SemanticZoomLevelMatcher {
* range of levels to be checked
* @return true if level is in the range
*/
- public boolean matchLevel(int level, String semanticZoomLevelVisibility) {
+ public boolean isVisible(int level, String semanticZoomLevelVisibility) {
+ return matchLevel(level, semanticZoomLevelVisibility);
+ }
+
+ public boolean isTransparent(int level, String semanticZoomLevelVisibility) {
+ return matchLevel(level, semanticZoomLevelVisibility);
+ }
+
+ private boolean matchLevel(int level, String semanticZoomLevelVisibility) {
if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
return true;
}
@@ -30,5 +38,6 @@ public class SemanticZoomLevelMatcher {
}
return false;
}
+
}
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 555a06d3d0..842e457046 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
@@ -14,6 +14,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
@@ -33,56 +34,58 @@ 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.
@@ -103,12 +106,13 @@ 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 (params.getLevel() >= alias.getVisibilityLevel() && params.getLevel() < alias.getTransparencyLevel()) {
+ if (zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel())
+ && !zoomLevelMatcher.isTransparent(params.getLevel(), alias.getTransparencyLevel())) {
synchronized (placeFinderSynchronization) {
if (placeFinder == null || placeFinder.getModel() != alias.getModelData()) {
placeFinder = new PlaceFinder(alias.getModelData().getModel());
}
- border = placeFinder.getRetangle(alias);
+ border = placeFinder.getRetangle(alias, params.getLevel());
}
} else if (!params.isTextCentered()) {
border = new Rectangle2D.Double(
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 345fb93944..8c36e5f603 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
@@ -13,6 +13,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
import lcsb.mapviewer.model.graphics.LineType;
@@ -30,20 +31,22 @@ import lcsb.mapviewer.model.map.species.Complex;
*/
public class ComplexConverter extends SpeciesConverter<Complex> {
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
/**
* How big is the triangle trimmed part of the complex.
*/
- private static final int TRIMMED_CORNER_SIZE = 5;
+ private static final int TRIMMED_CORNER_SIZE = 5;
/**
* Describes the distance between border of complex and internal border in
* brief view (without children).
*/
- private static final double INTERNAL_BORDER_DIST = 5.0;
+ private static final double INTERNAL_BORDER_DIST = 5.0;
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ComplexConverter.class.getName());
+ private static Logger logger = Logger.getLogger(ComplexConverter.class.getName());
/**
* Default constructor.
@@ -56,7 +59,6 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
super(colorExtractor);
}
-
@Override
public void draw(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
if (alias.getState().equalsIgnoreCase("complexnoborder")) {
@@ -145,7 +147,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
@Override
public void drawText(final Complex alias, final Graphics2D graphics, final ConverterParams params) {
if (((Complex) alias).getElements().size() > 0) {
- if (alias.getTransparencyLevel() <= params.getLevel()) {
+ if (zoomLevelMatcher.isTransparent(params.getLevel(), alias.getTransparencyLevel())) {
super.drawText(alias, graphics, params);
return;
}
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 73cb492d1e..ce768f1601 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
@@ -21,6 +21,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.EllipseTransformation;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.converter.graphics.ConverterParams;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.layout.ColorSchema;
@@ -39,6 +40,8 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public abstract class SpeciesConverter<T extends Species> extends ElementConverter<T> {
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
/**
* PI value.
*/
@@ -301,7 +304,7 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
Point2D point = alias.getCenter();
if (alias instanceof Complex) {
if (((Complex) alias).getElements().size() > 0) {
- if (alias.getTransparencyLevel() <= params.getLevel()) {
+ if (zoomLevelMatcher.isTransparent(params.getLevel(), alias.getTransparencyLevel())) {
point.setLocation(point.getX(), alias.getY() + alias.getHeight() - graphics.getFontMetrics().getAscent());
}
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
index 36d9e96928..98dc0c33be 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/placefinder/PlaceFinder.java
@@ -8,6 +8,7 @@ import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
@@ -23,6 +24,8 @@ import org.apache.log4j.Logger;
*/
public class PlaceFinder {
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
/**
* Represents small part of the map (enclosed by cuting lines) where something
* can be put. Contains borders (height, weight, location etc). Informatin if
@@ -103,52 +106,52 @@ public class PlaceFinder {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(PlaceFinder.class.getName());
+ private static Logger logger = Logger.getLogger(PlaceFinder.class.getName());
/**
* Whole surface is split into rectangular regions. The lines that cut the
* surface correspond to borders of aliases that overlap current alias. This
* matrix defines which of these regions can be used for description.
*/
- private Field[][] matrix;
+ private Field[][] matrix;
/**
- * List of {@link Compartment compartment aliases} that split surface
- * into regions.
+ * List of {@link Compartment compartment aliases} that split surface into
+ * regions.
*/
- private List<Compartment> aliases;
+ private List<Compartment> aliases;
/**
* Alias for which computation is done.
*/
- private Element mainAlias;
+ private Element mainAlias;
/**
* Left boundary of the rectangle in which we want to fit our description.
*/
- private double leftBound;
+ private double leftBound;
/**
* Right boundary of the rectangle in which we want to fit our description.
*/
- private double rightBound;
+ private double rightBound;
/**
* Top boundary of the rectangle in which we want to fit our description.
*/
- private double upBound;
+ private double upBound;
/**
* Bottom boundary of the rectangle in which we want to fit our description.
*/
- private double bottomBound;
+ private double bottomBound;
/**
* Model for which this {@link PlaceFinder} was created.
*/
- private Model model;
+ private Model model;
/**
* Map with aliases that should be considered when looking for a place to put
* text.
*/
- private Map<Element, List<Compartment>> otherAliases = new HashMap<Element, List<Compartment>>();
+ private Map<Element, Map<Integer, List<Compartment>>> otherAliases = new HashMap<>();
/**
* Default constructor for place finder in a model.
@@ -342,18 +345,23 @@ public class PlaceFinder {
* alias for which we try to determine text position
* @return bounds where text could be put
*/
- public Rectangle2D getRetangle(Compartment alias) {
- List<Compartment> list = otherAliases.get(alias);
+ public Rectangle2D getRetangle(Compartment alias, int level) {
+ Map<Integer, List<Compartment>> lists = otherAliases.get(alias);
+ if (lists == null) {
+ lists = new HashMap<>();
+ otherAliases.put(alias, lists);
+ }
+ List<Compartment> list = lists.get(level);
if (list == null) {
list = new ArrayList<Compartment>();
for (Compartment compAlias : model.getCompartments()) {
- if (compAlias.getVisibilityLevel() <= alias.getVisibilityLevel() && compAlias.getTransparencyLevel() > alias.getVisibilityLevel()) {
+ if (zoomLevelMatcher.isVisible(level, compAlias.getVisibilityLevel()) && !zoomLevelMatcher.isTransparent(level, compAlias.getTransparencyLevel())) {
if (compAlias.cross(alias) && compAlias.getSize() <= alias.getSize()) {
list.add(compAlias);
}
}
}
- otherAliases.put(alias, list);
+ lists.put(level, list);
}
this.mainAlias = alias;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index 36d84707d1..864c939598 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -139,9 +139,9 @@ public class NormalImageGeneratorTest {
layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartments().get(1).setTransparencyLevel(2);
- model.getCompartments().get(0).setTransparencyLevel(2);
- model.getCompartments().get(3).setTransparencyLevel(2);
+ model.getCompartments().get(1).setTransparencyLevel("2");
+ model.getCompartments().get(0).setTransparencyLevel("2");
+ model.getCompartments().get(3).setTransparencyLevel("2");
new PngImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
} catch (Exception e) {
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
index 3d191ad894..6109ab544d 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
@@ -51,9 +51,9 @@ public class PdfImageGeneratorTest {
layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
new CreateHierarchyCommand(model, 1, 8).execute();
- model.getCompartments().get(1).setTransparencyLevel(2);
- model.getCompartments().get(0).setTransparencyLevel(2);
- model.getCompartments().get(3).setTransparencyLevel(2);
+ model.getCompartments().get(1).setTransparencyLevel("2");
+ model.getCompartments().get(0).setTransparencyLevel("2");
+ model.getCompartments().get(3).setTransparencyLevel("2");
PdfImageGenerator pig = new PdfImageGenerator(new Params().level(2).scale(4).width(600).height(600).model(model).nested(true));
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 8ba25ceb5b..9141204ccf 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
@@ -46,7 +46,7 @@ public class BioEntityConverterImplTest {
try {
Graphics2D graphics = Mockito.mock(Graphics2D.class);
Reaction reaction = createReaction(1.0);
- reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
@@ -64,7 +64,7 @@ public class BioEntityConverterImplTest {
Graphics2D graphics = Mockito.mock(Graphics2D.class);
Reaction reaction = createReaction(1.0);
- reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
BioEntityConverterImpl rc = new BioEntityConverterImpl(reaction, false, colorExtractor);
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
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 4623a64019..8d17b603ca 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
@@ -280,7 +280,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(1.0);
- reaction.getModifiers().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(3)).draw(any(GeneralPath.class));
@@ -297,7 +297,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(1.0);
- reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(3)).draw(any(GeneralPath.class));
@@ -314,7 +314,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createReaction(1.0);
- reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(3)).draw(any(GeneralPath.class));
@@ -331,7 +331,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createComplexReaction(1.0);
- reaction.getModifiers().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(12)).draw(any(GeneralPath.class));
@@ -348,8 +348,8 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createComplexReaction(1.0);
- reaction.getModifiers().get(0).getElement().setSemanticZoomLevelVisibility("11");
- reaction.getModifiers().get(1).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getModifiers().get(0).getElement().setVisibilityLevel("11");
+ reaction.getModifiers().get(1).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(9)).draw(any(GeneralPath.class));
@@ -374,7 +374,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createComplexReaction(1.0);
- reaction.getReactants().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getReactants().get(0).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(12)).draw(any(GeneralPath.class));
@@ -391,7 +391,7 @@ public class ReactionConverterTest {
ReactionConverter rc = new ReactionConverter(colorExtractor);
Reaction reaction = createComplexReaction(1.0);
- reaction.getProducts().get(0).getElement().setSemanticZoomLevelVisibility("11");
+ reaction.getProducts().get(0).getElement().setVisibilityLevel("11");
rc.draw(reaction, graphics, new ConverterParams().semanticZoomingOn(true).level(10));
verify(graphics, times(12)).draw(any(GeneralPath.class));
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
index 2ddcd62d38..de5f85db23 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/placefinder/AllPlaceFinderTest.java
@@ -31,7 +31,7 @@ public class AllPlaceFinderTest {
for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
- actual = pf.getRetangle(alias).toString();
+ actual = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel())).toString();
}
String expected = "";
Rectangle2D result = model.getCompartments().get(0).getBorder();
@@ -49,7 +49,7 @@ public class AllPlaceFinderTest {
String expected = "";
for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
- actual = pf.getRetangle(alias).toString();
+ actual = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel())).toString();
Rectangle2D result = alias.getBorder();
expected = result.toString();
assertEquals(expected, actual);
@@ -65,7 +65,7 @@ public class AllPlaceFinderTest {
model.addElement(alias2);
PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias2);
+ Rectangle2D rect = pf.getRetangle(alias2, Integer.valueOf(alias.getVisibilityLevel()));
double actual = rect.getWidth() * rect.getHeight();
double expected = alias2.getWidth() * alias2.getHeight();
assertTrue(actual < expected);
@@ -79,7 +79,7 @@ public class AllPlaceFinderTest {
double actual = 0.0;
for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias);
+ Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
actual = rect.getWidth() * rect.getHeight();
assertTrue(actual > 0);
}
@@ -95,7 +95,7 @@ public class AllPlaceFinderTest {
Rectangle2D result = null;
for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias);
+ Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
actual += rect.getWidth() * rect.getHeight();
}
result = model.getCompartments().get(0).getBorder();
@@ -124,8 +124,8 @@ public class AllPlaceFinderTest {
result.setY(y);
result.setWidth(width);
result.setHeight(height);
- result.setTransparencyLevel(10);
- result.setVisibilityLevel(9);
+ result.setTransparencyLevel("10");
+ result.setVisibilityLevel("9");
return result;
}
@@ -138,7 +138,7 @@ public class AllPlaceFinderTest {
double actual = 0.0;
for (Compartment alias : model.getCompartments()) {
PlaceFinder pf = new PlaceFinder(model);
- Rectangle2D rect = pf.getRetangle(alias);
+ Rectangle2D rect = pf.getRetangle(alias, Integer.valueOf(alias.getVisibilityLevel()));
actual = rect.getWidth() * rect.getHeight();
assertTrue(actual > 0);
}
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 23a0107feb..4ef0375840 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -203,7 +203,7 @@ public class CreateHierarchyCommand extends ModelCommand {
logValue = zoomLevels;
}
}
- alias.setVisibilityLevel(logValue);
+ alias.setVisibilityLevel(logValue + "");
}
}
@@ -218,7 +218,7 @@ public class CreateHierarchyCommand extends ModelCommand {
double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
for (Element child : compartment.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
}
if (maxVisibilityLevel >= zoomLevels) {
maxVisibilityLevel = zoomLevels;
@@ -226,7 +226,7 @@ public class CreateHierarchyCommand extends ModelCommand {
if (maxVisibilityLevel <= 0) {
maxVisibilityLevel = 1;
}
- compartment.setTransparencyLevel(maxVisibilityLevel);
+ compartment.setTransparencyLevel(maxVisibilityLevel + "");
for (Element child : compartment.getElements()) {
child.setVisibilityLevel(compartment.getTransparencyLevel());
}
@@ -243,7 +243,7 @@ public class CreateHierarchyCommand extends ModelCommand {
double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
for (Element child : complex.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, child.getVisibilityLevel());
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(child.getVisibilityLevel()));
}
if (maxVisibilityLevel >= zoomLevels) {
maxVisibilityLevel = zoomLevels;
@@ -251,7 +251,7 @@ public class CreateHierarchyCommand extends ModelCommand {
if (maxVisibilityLevel <= 0) {
maxVisibilityLevel = 1;
}
- complex.setTransparencyLevel(maxVisibilityLevel);
+ complex.setTransparencyLevel(maxVisibilityLevel + "");
for (Element child : complex.getElements()) {
child.setVisibilityLevel(complex.getTransparencyLevel());
}
@@ -270,7 +270,7 @@ public class CreateHierarchyCommand extends ModelCommand {
} else if (alias instanceof Complex) {
settingTransparencyLevelForComplex((Complex) alias);
} else {
- alias.setTransparencyLevel(0);
+ alias.setTransparencyLevel("0");
}
}
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index cc78f07b6e..6ff5608d3c 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -328,8 +328,8 @@ public class CopyCommandTest extends CommandTestFunctions {
Compartment c1 = new SquareCompartment("c1");
Compartment c2 = new SquareCompartment("c2");
- c1.setSemanticZoomLevelVisibility("2");
- c2.setSemanticZoomLevelVisibility("3");
+ c1.setVisibilityLevel("2");
+ c2.setVisibilityLevel("3");
model.addElement(c1);
model.addElement(c2);
@@ -349,7 +349,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Product product = new Product(s2);
product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
reaction.addProduct(product);
- reaction.setSemanticZoomLevelVisibility("4");
+ reaction.setVisibilityLevel("4");
model.addReaction(reaction);
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index 4d733b555e..97eb95a6f9 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -53,7 +53,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
parents.add(alias);
}
- Set<Integer> levels = new HashSet<Integer>();
+ Set<String> levels = new HashSet<>();
for (Element a : model.getElements()) {
levels.add(a.getVisibilityLevel());
}
@@ -150,16 +150,16 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
for (Compartment compartment : model.getCompartments()) {
if (compartment.getCompartment() == null) {
+ int visibilityLevel = Integer.valueOf(compartment.getVisibilityLevel());
assertTrue(
- "Alias " + compartment.getElementId() + " is not visible at levels highers than " + compartment.getVisibilityLevel(),
- compartment.getVisibilityLevel() <= 1);
+ "Alias " + compartment.getElementId() + " is not visible at levels highers than " + compartment.getVisibilityLevel(), visibilityLevel <= 1);
}
}
for (Species species : model.getSpeciesList()) {
if (species.getCompartment() == null) {
- assertTrue(
- "Alias " + species.getElementId() + " is not visible at levels highers than " + species.getVisibilityLevel(), species.getVisibilityLevel() <= 1);
+ int visibilityLevel = Integer.valueOf(species.getVisibilityLevel());
+ assertTrue("Alias " + species.getElementId() + " is not visible at levels highers than " + species.getVisibilityLevel(), visibilityLevel <= 1);
}
}
@@ -179,10 +179,11 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
new CreateHierarchyCommand(model, levels, zoomFactor).execute();
- for (Element alias : model.getElements()) {
+ for (Element element : model.getElements()) {
+ int visibilityLevel = Integer.valueOf(element.getVisibilityLevel());
assertTrue(
- "Alias " + alias.getElementId() + " is not visible even at the bottom level (visibility: " + alias.getVisibilityLevel() + ") ",
- alias.getVisibilityLevel() <= levels);
+ "Alias " + element.getElementId() + " is not visible even at the bottom level (visibility: " + element.getVisibilityLevel() + ") ",
+ visibilityLevel <= levels);
}
} catch (Exception e) {
@@ -262,12 +263,16 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
for (Element alias : model.getElements()) {
Element parentAlias = alias.getCompartment();
if (parentAlias != null) {
- assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
+ int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
+ int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
+ assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
}
if (alias instanceof Species) {
parentAlias = ((Species) alias).getComplex();
if (parentAlias != null) {
- assertTrue(alias.getVisibilityLevel() >= parentAlias.getVisibilityLevel());
+ int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
+ int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
+ assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
}
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index eb2f82d237..b5aa17cc9b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -145,12 +145,20 @@ public interface BioEntity extends Serializable {
* @param zoomLevelVisibility
* semantic zoom level visibility
*/
- void setSemanticZoomLevelVisibility(String zoomLevelVisibility);
+ void setVisibilityLevel(String zoomLevelVisibility);
+
+ /**
+ * Sets semantic zoom level visibility.
+ *
+ * @param zoomLevelVisibility
+ * semantic zoom level visibility
+ */
+ void setVisibilityLevel(Integer zoomLevelVisibility);
/**
* Returns semantic zoom level visibility.
*
* @return semantic zoom level visibility
*/
- String getSemanticZoomLevelVisibility();
+ String getVisibilityLevel();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 6a2fafcf6b..13cd8e3dc2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -183,7 +183,7 @@ public class Reaction implements BioEntity {
/**
* Zoom level visibility for semantic zooming.
*/
- private String zoomLevelVisibility;
+ private String visibilityLevel = "";
/**
* Lists of all synonyms used for describing this element.
@@ -253,7 +253,7 @@ public class Reaction implements BioEntity {
for (String synonym : original.getSynonyms()) {
synonyms.add(synonym);
}
- setSemanticZoomLevelVisibility(original.getSemanticZoomLevelVisibility());
+ setVisibilityLevel(original.getVisibilityLevel());
}
@@ -411,20 +411,14 @@ public class Reaction implements BioEntity {
return "Generic Reaction";
}
- /**
- * Returns visibility level of the reaction in hierarchical view. More
- * information about hierarchical view can be found in
- * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator
- * AbstractImageGenerator}.
- *
- * @return visibility level of the reaction
- */
- public int getVisibilityLevel() {
- int level = 0;
- for (ReactionNode node : getReactionNodes()) {
- level = Math.max(level, node.getElement().getVisibilityLevel());
- }
- return level;
+ @Override
+ public String getVisibilityLevel() {
+ return visibilityLevel;
+ }
+
+ @Override
+ public void setVisibilityLevel(String visibilityLevel) {
+ this.visibilityLevel = visibilityLevel;
}
/**
@@ -874,13 +868,13 @@ public class Reaction implements BioEntity {
}
@Override
- public String getSemanticZoomLevelVisibility() {
- return zoomLevelVisibility;
- }
+ public void setVisibilityLevel(Integer zoomLevelVisibility) {
+ if (zoomLevelVisibility == null) {
+ this.visibilityLevel = null;
+ } else {
+ this.visibilityLevel = zoomLevelVisibility + "";
+ }
- @Override
- public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
- this.zoomLevelVisibility = zoomLevelVisibility;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index 1feda50e2c..a4061e784e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -130,10 +130,9 @@ public class ReactionComparator implements Comparator<Reaction> {
logger.debug("GeneProteinReaction different: " + arg0.getGeneProteinReaction() + ", " + arg1.getGeneProteinReaction());
return stringComparator.compare(arg0.getGeneProteinReaction(), arg1.getGeneProteinReaction());
}
- if (stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility()) != 0) {
- logger.debug(
- "SemanticZoomLevelVisibility different: \"" + arg0.getSemanticZoomLevelVisibility() + "\", \"" + arg1.getSemanticZoomLevelVisibility() + "\"");
- return stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility());
+ if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
+ logger.debug("SemanticZoomLevelVisibility different: \"" + arg0.getVisibilityLevel() + "\", \"" + arg1.getVisibilityLevel() + "\"");
+ return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
}
IntegerComparator integerComparator = new IntegerComparator();
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 01688104f1..0d419f263f 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
@@ -174,7 +174,7 @@ public abstract class Element implements BioEntity, Serializable {
* @see lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params#level
* AbstractImageGenerator.Params#level
*/
- private int visibilityLevel;
+ private String visibilityLevel = "";
/**
* From which level element should be transparent.
@@ -182,7 +182,7 @@ public abstract class Element implements BioEntity, Serializable {
* @see #visibilityLevel
* @see AbstractImageGenerator.Params#level
*/
- private int transparencyLevel;
+ private String transparencyLevel = "";
/**
* List of search indexes that describe this element.
@@ -214,11 +214,6 @@ public abstract class Element implements BioEntity, Serializable {
*/
private String fullName;
- /**
- * Zoom level visibility for semantic zooming.
- */
- private String zoomLevelVisibility;
-
/**
* Abbreviation associated with the element.
*/
@@ -282,7 +277,6 @@ public abstract class Element implements BioEntity, Serializable {
width = original.getWidth();
height = original.getHeight();
fontSize = original.getFontSize();
- visibilityLevel = original.getVisibilityLevel();
color = original.getColor();
for (SearchIndex searchIndex : original.getSearchIndexes()) {
searchIndexes.add(searchIndex.copy());
@@ -301,7 +295,8 @@ public abstract class Element implements BioEntity, Serializable {
addMiriamData(original.getMiriamData());
this.abbreviation = original.getAbbreviation();
this.formula = original.getFormula();
- setSemanticZoomLevelVisibility(original.getSemanticZoomLevelVisibility());
+ setVisibilityLevel(original.getVisibilityLevel());
+ setTransparencyLevel(original.getTransparencyLevel());
}
/**
@@ -325,7 +320,6 @@ public abstract class Element implements BioEntity, Serializable {
width = 0.0;
height = 0.0;
fontSize = DEFAULT_FONT_SIZE;
- visibilityLevel = 0;
color = Color.white;
}
@@ -661,23 +655,25 @@ public abstract class Element implements BioEntity, Serializable {
this.elementId = elementId;
}
- /**
- * @return the visibilityLevel
- * @see #visibilityLevel
- */
- public int getVisibilityLevel() {
+ @Override
+ public String getVisibilityLevel() {
return visibilityLevel;
}
- /**
- * @param visibilityLevel
- * the visibilityLevel to set
- * @see #visibilityLevel
- */
- public void setVisibilityLevel(int visibilityLevel) {
+ @Override
+ public void setVisibilityLevel(String visibilityLevel) {
this.visibilityLevel = visibilityLevel;
}
+ @Override
+ public void setVisibilityLevel(Integer visibilityLevel) {
+ if (visibilityLevel == null) {
+ this.visibilityLevel = null;
+ } else {
+ this.visibilityLevel = visibilityLevel + "";
+ }
+ }
+
/**
* @return the model
* @see #model
@@ -755,7 +751,7 @@ public abstract class Element implements BioEntity, Serializable {
* @return the transparencyLevel
* @see #transparencyLevel
*/
- public int getTransparencyLevel() {
+ public String getTransparencyLevel() {
return transparencyLevel;
}
@@ -764,7 +760,7 @@ public abstract class Element implements BioEntity, Serializable {
* the transparencyLevel to set
* @see #transparencyLevel
*/
- public void setTransparencyLevel(int transparencyLevel) {
+ public void setTransparencyLevel(String transparencyLevel) {
this.transparencyLevel = transparencyLevel;
}
@@ -1092,14 +1088,4 @@ public abstract class Element implements BioEntity, Serializable {
dataMining.setElement(this);
}
- @Override
- public void setSemanticZoomLevelVisibility(String zoomLevelVisibility) {
- this.zoomLevelVisibility = zoomLevelVisibility;
- }
-
- @Override
- public String getSemanticZoomLevelVisibility() {
- return this.zoomLevelVisibility;
- }
-
}
\ 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 4d6d35a87a..a462b0538a 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
@@ -140,9 +140,9 @@ public class ElementComparator implements Comparator<Element> {
return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
}
- if (integerComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
+ if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
logger.debug("Visibility level different: " + arg0.getVisibilityLevel() + ", " + arg1.getVisibilityLevel());
- return integerComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
+ return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
}
if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
@@ -189,12 +189,6 @@ public class ElementComparator implements Comparator<Element> {
return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
}
- if (stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility()) != 0) {
- logger.debug(
- "SemanticZoomLevelVisibility different: \"" + arg0.getSemanticZoomLevelVisibility() + "\", \"" + arg1.getSemanticZoomLevelVisibility() + "\"");
- return stringComparator.compare(arg0.getSemanticZoomLevelVisibility(), arg1.getSemanticZoomLevelVisibility());
- }
-
StringSetComparator stringSetComparator = new StringSetComparator();
StringListComparator stringListComparator = new StringListComparator();
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 7f4a97b6ba..3df3ef0c80 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
@@ -117,7 +117,7 @@ public class CompartmentComparatorTest {
result.setHeight(5);
result.setFontSize(9.0);
result.setColor(Color.BLUE);
- result.setVisibilityLevel(14);
+ result.setVisibilityLevel("14");
result.setThickness(998);
result.setOuterWidth(45);
result.setInnerWidth(65);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index a7d39db9e7..36bbc7596e 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -229,15 +229,10 @@ public class ReactionTest extends ModelTestFunctions {
public void testVisibilityLevel() {
try {
Reaction reaction1 = new Reaction();
- assertEquals(0, reaction1.getVisibilityLevel());
-
- Reactant reactant = new Reactant();
- Element protein = new GenericProtein("id_xyz");
- protein.setVisibilityLevel(2);
- reactant.setElement(protein);
- reaction1.addReactant(reactant);
-
- assertEquals(2, reaction1.getVisibilityLevel());
+ assertEquals(null, reaction1.getVisibilityLevel());
+
+ reaction1.setVisibilityLevel(1);
+ assertEquals("1", reaction1.getVisibilityLevel());
} catch (Exception e) {
e.printStackTrace();
throw e;
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 651379e21f..907dfeeef5 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
@@ -56,7 +56,7 @@ public class ComplexComparatorTest {
result.setHeight(5);
result.setFontSize(9.0);
result.setColor(Color.BLUE);
- result.setVisibilityLevel(14);
+ result.setVisibilityLevel("14");
Species protein = new GenericProtein("S");
protein.setName("a");
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
index 78ee89782a..540521afd2 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
@@ -145,7 +145,7 @@ public class ElementTest extends ModelTestFunctions {
Set<MiriamData> miriamData = new HashSet<>();
Compartment compartment = new Compartment("idd");
int id = 72;
- int transparencyLevel = 2;
+ String transparencyLevel = "2";
Model model = new ModelFullIndexed(modelData);
List<SearchIndex> indexes = new ArrayList<>();
indexes.add(new SearchIndex());
diff --git a/persist/src/db/11/fix_db_20170628.sql b/persist/src/db/11/fix_db_20170628.sql
new file mode 100644
index 0000000000..6f033cadda
--- /dev/null
+++ b/persist/src/db/11/fix_db_20170628.sql
@@ -0,0 +1,8 @@
+-- semantic zooming
+alter table element_table drop column zoomlevelvisibility ;
+alter table reaction_table drop column zoomlevelvisibility ;
+
+ALTER TABLE element_table ALTER COLUMN visibilitylevel TYPE character varying;
+ALTER TABLE element_table ALTER COLUMN transparencylevel TYPE character varying;
+
+alter table reaction_table add column visibilitylevel character varying default null;
\ No newline at end of file
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 ae8fcff5f1..c502dcc853 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -662,10 +662,10 @@ public class ProjectService implements IProjectService {
int level = Integer.valueOf(levelStr);
Model output = new CopyCommand(model).execute();
for (BioEntity bioEntity : output.getAnnotatedObjects()) {
- if (matcher.matchLevel(level, bioEntity.getSemanticZoomLevelVisibility())) {
- bioEntity.setSemanticZoomLevelVisibility(null);
+ if (matcher.isVisible(level, bioEntity.getVisibilityLevel())) {
+ bioEntity.setVisibilityLevel("0");
} else {
- bioEntity.setSemanticZoomLevelVisibility(Integer.MAX_VALUE + "");
+ bioEntity.setVisibilityLevel(Integer.MAX_VALUE + "");
}
}
return output;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 35f74ed3cc..e489843192 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -18,6 +18,7 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.graphics.bioEntity.SemanticZoomLevelMatcher;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -64,6 +65,8 @@ import lcsb.mapviewer.services.utils.SearchIndexer;
@Transactional(value = "txManager")
public class SearchService implements ISearchService {
+ private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+
/**
* Prefix used in search by name interface to limit results only to species.
*/
@@ -447,7 +450,7 @@ public class SearchService implements ISearchService {
if (params.getLevel() == null || params.getLayoutIdentfier() == null) {
return true;
}
- return (!params.isNested()) || alias.getVisibilityLevel() <= params.getLevel();
+ return (!params.isNested()) || zoomLevelMatcher.isVisible(params.getLevel(), alias.getVisibilityLevel());
}
@Override
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
index 10edf3b365..3fdec74966 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullAliasView.java
@@ -147,7 +147,7 @@ public class FullAliasView extends LightAliasView implements IHeavyView {
*/
private Integer initialAmount = null;
- private Integer visibilityLevel = null;
+ private String visibilityLevel = null;
/**
* Initial concentration of species.
@@ -617,15 +617,16 @@ public class FullAliasView extends LightAliasView implements IHeavyView {
* @return the visibilityLevel
* @see #visibilityLevel
*/
- public Integer getVisibilityLevel() {
+ public String getVisibilityLevel() {
return visibilityLevel;
}
/**
- * @param visibilityLevel the visibilityLevel to set
+ * @param visibilityLevel
+ * the visibilityLevel to set
* @see #visibilityLevel
*/
- public void setVisibilityLevel(Integer visibilityLevel) {
+ public void setVisibilityLevel(String visibilityLevel) {
this.visibilityLevel = visibilityLevel;
}
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionView.java b/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionView.java
index 31dbe84374..94ed82542e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionView.java
+++ b/service/src/main/java/lcsb/mapviewer/services/search/data/FullReactionView.java
@@ -126,7 +126,7 @@ public class FullReactionView extends LightReactionView implements IHeavyView {
*/
private Map<String, Object> other = new HashMap<>();
- private Integer visibilityLevel = null;
+ private String visibilityLevel = null;
/**
* Default constructor with localization passed in the argument.
@@ -426,7 +426,7 @@ public class FullReactionView extends LightReactionView implements IHeavyView {
* @return the visibilityLevel
* @see #visibilityLevel
*/
- public Integer getVisibilityLevel() {
+ public String getVisibilityLevel() {
return visibilityLevel;
}
@@ -434,7 +434,7 @@ public class FullReactionView extends LightReactionView implements IHeavyView {
* @param visibilityLevel the visibilityLevel to set
* @see #visibilityLevel
*/
- public void setVisibilityLevel(Integer visibilityLevel) {
+ public void setVisibilityLevel(String visibilityLevel) {
this.visibilityLevel = visibilityLevel;
}
--
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