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minerva
core
Commits
27648099
Commit
27648099
authored
Sep 13, 2021
by
Piotr Gawron
Browse files
package name must be lowercase
parent
bb5073e8
Changes
108
Hide whitespace changes
Inline
Side-by-side
checkstyle.xml
View file @
27648099
...
...
@@ -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
View file @
27648099
...
...
@@ -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.bio
E
ntity.element.species.SpeciesConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.reaction.ReactionConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.SpeciesConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.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
View file @
27648099
...
...
@@ -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.bio
E
ntity.element.species.SpeciesConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.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
View file @
27648099
...
...
@@ -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.bio
E
ntity.BioEntityConverterImpl
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.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/bio
E
ntity/BioEntityConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/BioEntityConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity
;
import
java.awt.Graphics2D
;
import
java.util.ArrayList
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/BioEntityConverterImpl.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/BioEntityConverterImpl.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity
;
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.bio
E
ntity.element.compartment.BottomSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment.LeftSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment.OvalCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment.PathwayCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment.RightSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment.SquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment.TopSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.AntisenseRnaConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.ComplexConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.ComplexSbgnConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.DegradedConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.DrugConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.GeneConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.IonConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.PhenotypeConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.ProteinConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.ProteinSbgnConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.RnaConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.SBGNNucleicAcidFeatureConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.SimpleMoleculeConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.SimpleMoleculeSbgnConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species.UnknownConverter
;
import
lcsb.mapviewer.converter.graphics.bio
E
ntity.reaction.ReactionConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.BottomSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.LeftSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.OvalCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.PathwayCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.RightSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.SquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment.TopSquareCompartmentConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.AntisenseRnaConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.ComplexConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.ComplexSbgnConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.DegradedConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.DrugConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.GeneConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.IonConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.PhenotypeConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.ProteinConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.ProteinSbgnConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.RnaConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.SBGNNucleicAcidFeatureConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.SimpleMoleculeConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.SimpleMoleculeSbgnConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species.UnknownConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.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/bio
E
ntity/element/ElementConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/ElementConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.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.bio
E
ntity.BioEntityConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.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/bio
E
ntity/element/compartment/BottomSquareCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/BottomSquareCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Shape
;
import
java.awt.geom.Area
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/CompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/CompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.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.bio
E
ntity.element.ElementConverter
;
import
lcsb.mapviewer.converter.graphics.bio
e
ntity.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/bio
E
ntity/element/compartment/LeftSquareCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/LeftSquareCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Shape
;
import
java.awt.geom.Area
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/OvalCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/OvalCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Shape
;
import
java.awt.geom.Ellipse2D
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/PathwayCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/PathwayCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Color
;
import
java.awt.Graphics2D
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/RightSquareCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/RightSquareCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Shape
;
import
java.awt.geom.Area
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/SquareCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/SquareCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Graphics2D
;
import
java.awt.Shape
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/TopSquareCompartmentConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/TopSquareCompartmentConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
import
java.awt.Graphics2D
;
import
java.awt.Shape
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/compartment/package-info.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/compartment/package-info.java
View file @
27648099
...
...
@@ -2,4 +2,4 @@
* Provides classes that draws different implemention of {@link Compartment} on
* the {@link Graphics2D}.
*/
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.compartment
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.compartment
;
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/package-info.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/package-info.java
View file @
27648099
...
...
@@ -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.bio
E
ntity.element
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element
;
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/species/AntisenseRnaConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/species/AntisenseRnaConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species
;
import
java.awt.Color
;
import
java.awt.Graphics2D
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/species/ComplexConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/species/ComplexConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species
;
import
java.awt.Color
;
import
java.awt.Font
;
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
E
ntity/element/species/ComplexSbgnConverter.java
→
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bio
e
ntity/element/species/ComplexSbgnConverter.java
View file @
27648099
package
lcsb.mapviewer.converter.graphics.bio
E
ntity.element.species
;
package
lcsb.mapviewer.converter.graphics.bio
e
ntity.element.species
;
import
java.awt.Color
;
import
java.awt.Graphics2D
;
...
...
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