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 24021c6d339acc1db72e219a2ef94d811c14c5a2..a1ab11fc4ad10cb3e8b74f6fb9e6b0196013f9b4 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
@@ -562,6 +562,14 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ /**
+ * Assigns semanticZoomingLevel to the element from notes string.
+ *
+ * @param element
+ * element to which data should be put to
+ * @param annotationString
+ * notes string
+ */
private void setSemanticZoomLevelVisibility(AnnotatedObject element, String annotationString) {
String zoomLevelVisibility = getParamByPrefix(annotationString, NoteField.SEMANTIC_ZOOM_LEVEL_VISIBILITY.getCommonName() + ":");
if (zoomLevelVisibility == null) {
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 b68a48171a95b851ea030085623717a0388ef1ca..16e997154b53d5419fbf41c379f9d409dd39ac33 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
@@ -172,6 +172,10 @@ public abstract class AbstractImageGenerator {
* Should the visualization include hierarchical view or not.
*/
private boolean nested = false;
+
+ /**
+ * Should the visualization include semantic zoom view or not.
+ */
private boolean semanticZoom = false;
/**
@@ -208,7 +212,13 @@ public abstract class AbstractImageGenerator {
this.scale = scale;
return this;
}
-
+
+ /**
+ * @param semanticZoom
+ * semanticZoom to set
+ * @return object with all parameters
+ * @see #semanticZoom
+ */
public Params semanticZoom(boolean semanticZoom) {
this.semanticZoom = semanticZoom;
return this;
@@ -801,6 +811,7 @@ public abstract class AbstractImageGenerator {
* @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}
*/
@@ -872,6 +883,7 @@ public abstract class AbstractImageGenerator {
* @param visibleLayouts
* list of {@link ColorSchema} used for coloring reaction in layouts
* @param params
+ * list of all params to create apropriate image
*/
protected void drawReaction(final Reaction reaction, List<ColorSchema> visibleLayouts, Params params) {
if (!cross(reaction.getLines())) {
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 56c6e0722c2e4db01ae81a39bd1ce76b475959c8..5e44baf42537fb87f7051a0005efa08c45a86f97 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
@@ -57,22 +57,25 @@ public class MapGenerator {
* Do we want to generate images in hierarchical view or normal.
*
*/
- private boolean nested = false;
- private boolean semanticZoom = false;
+ 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.
*
*/
- private boolean removeEmpty = false;
+ private boolean removeEmpty = false;
/**
* Callback function that update progress information.
*
*/
- private IProgressUpdater updater = new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- };
+ private IProgressUpdater updater = new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ };
/**
* Zoom factor on the lowest level.
@@ -135,7 +138,13 @@ public class MapGenerator {
this.nested = nested;
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;
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 6f9714b2cf08d8227619a279e7295e7f55a69fe3..25fbd300a7cc51d34d57a923dc724d6735c3adc8 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
@@ -34,6 +34,7 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
/**
* Default class logger.
*/
+ @SuppressWarnings("unused")
private final Logger logger = Logger.getLogger(BioEntityConverter.class);
/**
@@ -93,6 +94,16 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
*/
public abstract void drawText(T bioEntity, Graphics2D graphics, ConverterParams params) throws DrawingException;
+ /**
+ * Checks if {@link AbstractNode} is visible according to visualization given
+ * in params.
+ *
+ * @param node
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
protected boolean isVisible(AbstractNode node, ConverterParams params) {
if (node instanceof NodeOperator) {
return isVisible((NodeOperator) node, params);
@@ -103,6 +114,16 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
}
}
+ /**
+ * Checks if {@link NodeOperator} is visible according to visualization given
+ * in params.
+ *
+ * @param operator
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
protected boolean isVisible(NodeOperator operator, ConverterParams params) {
boolean result = false;
if (operator.isModifierOperator() || operator.isReactantOperator()) {
@@ -119,6 +140,16 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
return result;
}
+ /**
+ * Checks if {@link AnnotatedObject} is visible according to visualization
+ * given in params.
+ *
+ * @param bioEntity
+ * visibility of this object will be checked
+ * @param params
+ * visualization params
+ * @return true if object is visible
+ */
protected boolean isVisible(AnnotatedObject bioEntity, ConverterParams params) {
if (params.isSemanticZoomingOn()) {
boolean result = matchLevel(params.getLevel(), bioEntity.getSemanticZoomLevelVisibility());
@@ -139,6 +170,16 @@ public abstract class BioEntityConverter<T extends AnnotatedObject> {
return true;
}
+ /**
+ * Checks if level belongs to the range defined in
+ * semanticZoomLevelVisibility.
+ *
+ * @param level
+ * level to ve checked
+ * @param semanticZoomLevelVisibility
+ * range of levels to be checked
+ * @return true if level is in the range
+ */
protected boolean matchLevel(int level, String semanticZoomLevelVisibility) {
if (semanticZoomLevelVisibility == null || semanticZoomLevelVisibility.isEmpty()) {
return true;
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
index 2fb83e5d857d08503c4d1c7840c238107400c650..bb5eba0424d844789420b16d4b88a0c4c8962213 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/package-info.java
@@ -1,7 +1,6 @@
/**
- * Provides classes that draws aliases of
+ * Provides classes that draws
* {@link lcsb.mapviewer.db.model.map.species.Species Species} on the Graphics2D
* object.
*/
package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
-
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
index b50c7ef53d1d4e382dc07264e9351a2c26ff2e9a..1881210ae7ea63ec35a9382d0950bafea12cfc9d 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java
@@ -222,19 +222,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
graphics.setColor(color);
}
- /**
- * Draw reaction on the graphics2D.
- *
- * @param reaction
- * object to be drawn
- * @param graphics
- * where we want to draw the object
- * @param sbgnFormat
- * true if reaction is to be drawn in SBGN format
- * @param visualizedLayoutsColorSchemas
- * list of {@link ColorSchema} that were used for visualizing this
- * alias in different layouts that should be overlayed on the alias
- */
+ @Override
public void draw(final Reaction reaction, final Graphics2D graphics, final ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) {
if (visualizedLayoutsColorSchemas.size() == 0) {
draw(reaction, graphics, params);