package name must be lowercase

checkstyle.xml

@@ -127,7 +127,7 @@
                     STATIC_INIT, INSTANCE_INIT, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>
             <property name="allowNoEmptyLineBetweenFields" value="true"/>
         </module>
-<!--        <module name="SeparatorWrap">
+        <module name="SeparatorWrap">
             <property name="id" value="SeparatorWrapDot"/>
             <property name="tokens" value="DOT"/>
             <property name="option" value="nl"/>
@@ -157,7 +157,7 @@
             <message key="name.invalidPattern"
                      value="Package name ''{0}'' must match pattern ''{1}''."/>
         </module>
-        <module name="TypeName">
+<!--        <module name="TypeName">
             <property name="tokens" value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF"/>
             <message key="name.invalidPattern"
                      value="Type name ''{0}'' must match pattern ''{1}''."/>

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -46,8 +46,8 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.SpeciesConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.reaction.ReactionConverter;
 import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
 import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -48,7 +48,7 @@ import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.SpeciesConverter;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java

@@ -17,7 +17,7 @@ import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
 import lcsb.mapviewer.common.MimeType;
 import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverterImpl;
+import lcsb.mapviewer.converter.graphics.bioentity.BioEntityConverterImpl;
 import lcsb.mapviewer.converter.graphics.layer.LayerLineConverter;
 import lcsb.mapviewer.converter.graphics.layer.LayerOvalConverter;
 import lcsb.mapviewer.converter.graphics.layer.LayerRectConverter;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/BioEntityConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity;
+package lcsb.mapviewer.converter.graphics.bioentity;
 
 import java.awt.Graphics2D;
 import java.util.ArrayList;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImpl.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/BioEntityConverterImpl.java

-package lcsb.mapviewer.converter.graphics.bioEntity;
+package lcsb.mapviewer.converter.graphics.bioentity;
 
 import java.awt.Graphics2D;
 import java.util.List;
@@ -11,29 +11,29 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.BottomSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.LeftSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.OvalCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.PathwayCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.RightSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.SquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.compartment.TopSquareCompartmentConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.AntisenseRnaConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ComplexSbgnConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DegradedConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.DrugConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.GeneConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.IonConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.PhenotypeConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.ProteinSbgnConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.RnaConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SBGNNucleicAcidFeatureConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SimpleMoleculeSbgnConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.species.UnknownConverter;
-import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.BottomSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.LeftSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.OvalCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.PathwayCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.RightSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.SquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.compartment.TopSquareCompartmentConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.AntisenseRnaConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.ComplexConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.ComplexSbgnConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.DegradedConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.DrugConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.GeneConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.IonConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.PhenotypeConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.ProteinConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.ProteinSbgnConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.RnaConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.SBGNNucleicAcidFeatureConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.SimpleMoleculeConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.SimpleMoleculeSbgnConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.species.UnknownConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.reaction.ReactionConverter;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
 import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/ElementConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element;
+package lcsb.mapviewer.converter.graphics.bioentity.element;
 
 import java.awt.Color;
 import java.awt.Graphics2D;
@@ -12,7 +12,7 @@ import javax.imageio.ImageIO;
 import lcsb.mapviewer.commands.ColorExtractor;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.BioEntityConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.BioEntityConverter;
 import lcsb.mapviewer.model.map.layout.graphics.Glyph;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.overlay.DataOverlayEntry;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/BottomSquareCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/BottomSquareCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Shape;
 import java.awt.geom.Area;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/CompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -17,7 +17,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.common.geometry.LineTransformation;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.converter.graphics.DrawingException;
-import lcsb.mapviewer.converter.graphics.bioEntity.element.ElementConverter;
+import lcsb.mapviewer.converter.graphics.bioentity.element.ElementConverter;
 import lcsb.mapviewer.converter.graphics.geometry.FontFinder;
 import lcsb.mapviewer.converter.graphics.geometry.RectangleTooSmallException;
 import lcsb.mapviewer.converter.graphics.placefinder.PlaceFinder;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/LeftSquareCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/LeftSquareCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Shape;
 import java.awt.geom.Area;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/OvalCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/OvalCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Shape;
 import java.awt.geom.Ellipse2D;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/PathwayCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/PathwayCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Color;
 import java.awt.Graphics2D;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/RightSquareCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/RightSquareCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Shape;
 import java.awt.geom.Area;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/SquareCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/SquareCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Graphics2D;
 import java.awt.Shape;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/TopSquareCompartmentConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/TopSquareCompartmentConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;
 
 import java.awt.Graphics2D;
 import java.awt.Shape;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/package-info.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/compartment/package-info.java

@@ -2,4 +2,4 @@
  * Provides classes that draws different implemention of {@link Compartment} on
  * the {@link Graphics2D}.
  */
-package lcsb.mapviewer.converter.graphics.bioEntity.element.compartment;
+package lcsb.mapviewer.converter.graphics.bioentity.element.compartment;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/package-info.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/package-info.java

@@ -2,4 +2,4 @@
  * Provides classes that draws {@link lcsb.mapviewer.model.map.species.Element
  * Elements} on the Graphics2D object.
  */
-package lcsb.mapviewer.converter.graphics.bioEntity.element;
+package lcsb.mapviewer.converter.graphics.bioentity.element;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/AntisenseRnaConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+package lcsb.mapviewer.converter.graphics.bioentity.element.species;
 
 import java.awt.Color;
 import java.awt.Graphics2D;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ComplexConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+package lcsb.mapviewer.converter.graphics.bioentity.element.species;
 
 import java.awt.Color;
 import java.awt.Font;

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexSbgnConverter.java → converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ComplexSbgnConverter.java

-package lcsb.mapviewer.converter.graphics.bioEntity.element.species;
+package lcsb.mapviewer.converter.graphics.bioentity.element.species;
 
 import java.awt.Color;
 import java.awt.Graphics2D;