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minerva
core
Commits
ca2b405f
Commit
ca2b405f
authored
Apr 20, 2021
by
Piotr Gawron
Browse files
method names unified
parent
4b7bd7d5
Changes
15
Hide whitespace changes
Inline
Side-by-side
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/AntisenseRnaConverter.java
View file @
ca2b405f
...
...
@@ -42,7 +42,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
@Override
protected
void
drawImpl
(
final
AntisenseRna
antisenseRna
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
Color
oldColor
=
graphics
.
getColor
();
GeneralPath
path
=
get
AntisenseRnaPath
(
antisenseRna
);
GeneralPath
path
=
get
Shape
(
antisenseRna
);
graphics
.
setColor
(
antisenseRna
.
getFillColor
());
graphics
.
fill
(
path
);
Stroke
stroke
=
graphics
.
getStroke
();
...
...
@@ -66,7 +66,8 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
* {@link AntisenseRna} for which we want to get border
* @return border of the {@link AntisenseRna}
*/
private
GeneralPath
getAntisenseRnaPath
(
final
AntisenseRna
antisenseRna
)
{
@Override
protected
GeneralPath
getShape
(
final
AntisenseRna
antisenseRna
)
{
// CHECKSTYLE:OFF
GeneralPath
path
=
new
GeneralPath
(
Path2D
.
WIND_EVEN_ODD
,
4
);
path
.
moveTo
(
antisenseRna
.
getX
(),
antisenseRna
.
getY
());
...
...
@@ -80,7 +81,7 @@ public class AntisenseRnaConverter extends SpeciesConverter<AntisenseRna> {
@Override
public
PathIterator
getBoundPathIterator
(
final
AntisenseRna
alias
)
{
return
get
AntisenseRnaPath
(
alias
).
getPathIterator
(
new
AffineTransform
());
return
get
Shape
(
alias
).
getPathIterator
(
new
AffineTransform
());
}
}
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ComplexConverter.java
View file @
ca2b405f
...
...
@@ -68,7 +68,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
complex
.
setX
(
complex
.
getX
()
-
SpeciesConverter
.
HOMODIMER_OFFSET
);
complex
.
setY
(
complex
.
getY
()
-
SpeciesConverter
.
HOMODIMER_OFFSET
);
GeneralPath
path
=
get
AliasPath
(
complex
);
GeneralPath
path
=
get
Shape
(
complex
);
Stroke
stroke
=
graphics
.
getStroke
();
graphics
.
setColor
(
complex
.
getFillColor
());
...
...
@@ -79,14 +79,14 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
if
(
complex
.
getState
().
equals
(
"brief"
))
{
complex
.
increaseBorder
(-
INTERNAL_BORDER_DIST
);
path
=
get
AliasPath
(
complex
);
path
=
get
Shape
(
complex
);
complex
.
increaseBorder
(
INTERNAL_BORDER_DIST
);
graphics
.
setStroke
(
LineType
.
DOTTED
.
getStroke
());
graphics
.
draw
(
path
);
}
if
(
complex
.
getActivity
()
&&
!
params
.
isSbgnFormat
())
{
complex
.
increaseBorder
(
INTERNAL_BORDER_DIST
);
path
=
get
AliasPath
(
complex
);
path
=
get
Shape
(
complex
);
complex
.
increaseBorder
(-
INTERNAL_BORDER_DIST
);
graphics
.
setStroke
(
LineType
.
DOTTED
.
getStroke
());
graphics
.
draw
(
path
);
...
...
@@ -128,7 +128,7 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
@Override
public
PathIterator
getBoundPathIterator
(
final
Complex
complex
)
{
return
get
AliasPath
(
complex
).
getPathIterator
(
new
AffineTransform
());
return
get
Shape
(
complex
).
getPathIterator
(
new
AffineTransform
());
}
/**
...
...
@@ -138,7 +138,8 @@ public class ComplexConverter extends SpeciesConverter<Complex> {
* exact object for which we want to get a border
* @return border of the {@link Complex}
*/
private
GeneralPath
getAliasPath
(
final
Complex
complex
)
{
@Override
protected
GeneralPath
getShape
(
final
Complex
complex
)
{
GeneralPath
path
=
new
GeneralPath
(
Path2D
.
WIND_EVEN_ODD
);
path
.
moveTo
(
complex
.
getX
()
+
TRIMMED_CORNER_SIZE
,
complex
.
getY
());
path
.
lineTo
(
complex
.
getX
()
+
complex
.
getWidth
()
-
TRIMMED_CORNER_SIZE
,
complex
.
getY
());
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DegradedConverter.java
View file @
ca2b405f
...
...
@@ -45,6 +45,21 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
@Override
protected
void
drawImpl
(
final
Degraded
degraded
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
Area
a1
=
getShape
(
degraded
);
Color
oldColor
=
graphics
.
getColor
();
graphics
.
setColor
(
degraded
.
getFillColor
());
graphics
.
fill
(
a1
);
graphics
.
setColor
(
degraded
.
getBorderColor
());
Stroke
stroke
=
graphics
.
getStroke
();
graphics
.
setStroke
(
getBorderLine
(
degraded
));
graphics
.
draw
(
a1
);
graphics
.
setStroke
(
stroke
);
drawText
(
degraded
,
graphics
,
params
);
graphics
.
setColor
(
oldColor
);
}
@Override
protected
Area
getShape
(
final
Degraded
degraded
)
{
double
diameter
=
getDiameter
(
degraded
);
double
x
=
getXCoord
(
degraded
,
diameter
);
double
y
=
getYCoord
(
degraded
);
...
...
@@ -64,16 +79,7 @@ public class DegradedConverter extends SpeciesConverter<Degraded> {
path
.
closePath
();
a1
.
exclusiveOr
(
new
Area
(
path
));
Color
oldColor
=
graphics
.
getColor
();
graphics
.
setColor
(
degraded
.
getFillColor
());
graphics
.
fill
(
a1
);
graphics
.
setColor
(
degraded
.
getBorderColor
());
Stroke
stroke
=
graphics
.
getStroke
();
graphics
.
setStroke
(
getBorderLine
(
degraded
));
graphics
.
draw
(
a1
);
graphics
.
setStroke
(
stroke
);
drawText
(
degraded
,
graphics
,
params
);
graphics
.
setColor
(
oldColor
);
return
a1
;
}
/**
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/DrugConverter.java
View file @
ca2b405f
...
...
@@ -56,14 +56,15 @@ public class DrugConverter extends SpeciesConverter<Drug> {
* {@link Drug} for which we are looking for a border
* @return Shape object defining given alias
*/
private
Shape
getDrugShape
(
final
Drug
drug
)
{
@Override
protected
Shape
getShape
(
final
Drug
drug
)
{
return
new
RoundRectangle2D
.
Double
(
drug
.
getX
(),
drug
.
getY
(),
drug
.
getWidth
(),
drug
.
getHeight
(),
RECTANGLE_CORNER_ARC_SIZE
,
RECTANGLE_CORNER_ARC_SIZE
);
}
@Override
protected
void
drawImpl
(
Drug
drug
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
Shape
a1
=
get
Drug
Shape
(
drug
);
Shape
a1
=
getShape
(
drug
);
double
offset
=
OFFSET_BETWEEN_BORDERS
;
Shape
a2
=
new
RoundRectangle2D
.
Double
(
drug
.
getX
()
+
offset
,
drug
.
getY
()
+
offset
,
drug
.
getWidth
()
-
2
*
offset
,
drug
.
getHeight
()
-
2
*
offset
,
...
...
@@ -113,7 +114,7 @@ public class DrugConverter extends SpeciesConverter<Drug> {
@Override
public
PathIterator
getBoundPathIterator
(
Drug
drug
)
{
return
get
Drug
Shape
(
drug
).
getPathIterator
(
new
AffineTransform
());
return
getShape
(
drug
).
getPathIterator
(
new
AffineTransform
());
}
}
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/GeneConverter.java
View file @
ca2b405f
...
...
@@ -41,7 +41,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
@Override
protected
void
drawImpl
(
final
Gene
gene
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
Shape
shape
=
get
Gene
Shape
(
gene
);
Shape
shape
=
getShape
(
gene
);
Color
c
=
graphics
.
getColor
();
graphics
.
setColor
(
gene
.
getFillColor
());
graphics
.
fill
(
shape
);
...
...
@@ -66,7 +66,8 @@ public class GeneConverter extends SpeciesConverter<Gene> {
* {@link Gene} for which we are looking for a {@link Shape}
* @return {@link Shape} that represents {@link Gene}
*/
private
Shape
getGeneShape
(
final
Gene
gene
)
{
@Override
protected
Shape
getShape
(
final
Gene
gene
)
{
Shape
shape
;
shape
=
new
Rectangle
(
gene
.
getX
().
intValue
(),
gene
.
getY
().
intValue
(),
gene
.
getWidth
().
intValue
(),
gene
.
getHeight
().
intValue
());
...
...
@@ -75,7 +76,7 @@ public class GeneConverter extends SpeciesConverter<Gene> {
@Override
public
PathIterator
getBoundPathIterator
(
final
Gene
gene
)
{
return
get
Gene
Shape
(
gene
).
getPathIterator
(
new
AffineTransform
());
return
getShape
(
gene
).
getPathIterator
(
new
AffineTransform
());
}
}
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/IonConverter.java
View file @
ca2b405f
...
...
@@ -40,10 +40,7 @@ public class IonConverter extends SpeciesConverter<Ion> {
@Override
protected
void
drawImpl
(
Ion
ion
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
double
diameter
=
getDiameter
(
ion
);
double
x
=
getXCoord
(
ion
,
diameter
);
double
y
=
getYCoord
(
ion
);
Shape
shape
=
new
Ellipse2D
.
Double
(
x
,
y
,
diameter
,
diameter
);
Shape
shape
=
getShape
(
ion
);
Color
oldColor
=
graphics
.
getColor
();
graphics
.
setColor
(
ion
.
getFillColor
());
graphics
.
fill
(
shape
);
...
...
@@ -56,6 +53,15 @@ public class IonConverter extends SpeciesConverter<Ion> {
graphics
.
setColor
(
oldColor
);
}
@Override
protected
Shape
getShape
(
Ion
ion
)
{
double
diameter
=
getDiameter
(
ion
);
double
x
=
getXCoord
(
ion
,
diameter
);
double
y
=
getYCoord
(
ion
);
Shape
shape
=
new
Ellipse2D
.
Double
(
x
,
y
,
diameter
,
diameter
);
return
shape
;
}
/**
* Returns transformed y coordinate for the {@link Ion}.
*
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/PhenotypeConverter.java
View file @
ca2b405f
...
...
@@ -38,7 +38,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
@Override
protected
void
drawImpl
(
Phenotype
phenotype
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
GeneralPath
path
=
get
PhenotypePath
(
phenotype
);
GeneralPath
path
=
get
Shape
(
phenotype
);
Color
oldColor
=
graphics
.
getColor
();
graphics
.
setColor
(
phenotype
.
getFillColor
());
...
...
@@ -60,7 +60,8 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
* @return {@link GeneralPath} object defining border of the given
* {@link Phenotype}
*/
private
GeneralPath
getPhenotypePath
(
final
Phenotype
phenotype
)
{
@Override
protected
GeneralPath
getShape
(
final
Phenotype
phenotype
)
{
// CHECKSTYLE:OFF
GeneralPath
path
=
new
GeneralPath
(
Path2D
.
WIND_EVEN_ODD
,
6
);
path
.
moveTo
(
phenotype
.
getX
()
+
phenotype
.
getWidth
()
/
6
,
phenotype
.
getY
());
...
...
@@ -76,7 +77,7 @@ public class PhenotypeConverter extends SpeciesConverter<Phenotype> {
@Override
public
PathIterator
getBoundPathIterator
(
Phenotype
phenotype
)
{
return
get
PhenotypePath
(
phenotype
).
getPathIterator
(
new
AffineTransform
());
return
get
Shape
(
phenotype
).
getPathIterator
(
new
AffineTransform
());
}
}
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinConverter.java
View file @
ca2b405f
...
...
@@ -50,8 +50,8 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
* Default constructor.
*
* @param colorExtractor
* Object that helps to convert {@link DataOverlayEntry} values into
colors
* when drawing {@link Species}
* Object that helps to convert {@link DataOverlayEntry} values into
*
colors
when drawing {@link Species}
*/
public
ProteinConverter
(
ColorExtractor
colorExtractor
)
{
super
(
colorExtractor
);
...
...
@@ -93,7 +93,8 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
protein
.
setX
(
protein
.
getX
()
-
SpeciesConverter
.
HOMODIMER_OFFSET
);
protein
.
setY
(
protein
.
getY
()
-
SpeciesConverter
.
HOMODIMER_OFFSET
);
Shape
shape
=
getShape
(
protein
,
graphics
);
drawActivityShape
(
protein
,
graphics
);
Shape
shape
=
getShape
(
protein
);
Color
oldColor
=
graphics
.
getColor
();
graphics
.
setColor
(
protein
.
getFillColor
());
graphics
.
fill
(
shape
);
...
...
@@ -119,25 +120,27 @@ public class ProteinConverter extends SpeciesConverter<Protein> {
protein
.
setHeight
(
protein
.
getHeight
()
+
SpeciesConverter
.
HOMODIMER_OFFSET
*
(
protein
.
getHomodimer
()
-
1
));
}
Shape
getShape
(
final
Protein
protein
,
final
Graphics2D
graphics
)
{
void
drawActivityShape
(
final
Protein
protein
,
final
Graphics2D
graphics
)
{
if
(
protein
instanceof
GenericProtein
&&
protein
.
getActivity
())
{
drawActivityGenericProtein
(
protein
,
graphics
);
}
else
if
(
protein
instanceof
TruncatedProtein
&&
protein
.
getActivity
())
{
drawActivityTruncatedShape
(
protein
,
graphics
);
}
else
if
(
protein
instanceof
ReceptorProtein
&&
protein
.
getActivity
())
{
drawActivityReceptorProtein
(
protein
,
graphics
);
}
}
@Override
protected
Shape
getShape
(
final
Protein
protein
)
{
Shape
shape
=
null
;
if
(
protein
instanceof
GenericProtein
)
{
shape
=
getGenericShape
(
protein
);
if
(
protein
.
getActivity
())
{
drawActivityGenericProtein
(
protein
,
graphics
);
}
}
else
if
(
protein
instanceof
IonChannelProtein
)
{
shape
=
getIonChannelShape
(
protein
);
}
else
if
(
protein
instanceof
TruncatedProtein
)
{
shape
=
getTruncatedShape
(
protein
);
if
(
protein
.
getActivity
())
{
drawActivityTruncatedShape
(
protein
,
graphics
);
}
}
else
if
(
protein
instanceof
ReceptorProtein
)
{
shape
=
getReceptorShape
(
protein
);
if
(
protein
.
getActivity
())
{
drawActivityReceptorProtein
(
protein
,
graphics
);
}
}
else
{
logger
.
warn
(
new
LogMarker
(
ProjectLogEntryType
.
DRAWING_ISSUE
,
protein
)
+
"Unknown shape for protein"
);
shape
=
getDefaultAliasShape
(
protein
);
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/ProteinSbgnConverter.java
View file @
ca2b405f
...
...
@@ -78,9 +78,13 @@ public class ProteinSbgnConverter extends ProteinConverter {
}
@Override
Shape
getShape
(
final
Protein
protein
,
final
Graphics2D
graphics
)
{
protected
Shape
getShape
(
final
Protein
protein
)
{
return
getGenericShape
(
protein
);
}
@Override
void
drawActivityShape
(
final
Protein
protein
,
final
Graphics2D
graphics
)
{
}
@Override
Shape
getStructuralStateShape
(
StructuralState
state
)
{
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/RnaConverter.java
View file @
ca2b405f
...
...
@@ -46,7 +46,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
@Override
protected
void
drawImpl
(
final
Rna
rna
,
final
Graphics2D
graphics
,
final
ConverterParams
params
)
{
GeneralPath
path
=
get
RnaPath
(
rna
);
GeneralPath
path
=
get
Shape
(
rna
);
Color
oldColor
=
graphics
.
getColor
();
graphics
.
setColor
(
rna
.
getFillColor
());
graphics
.
fill
(
path
);
...
...
@@ -71,7 +71,8 @@ public class RnaConverter extends SpeciesConverter<Rna> {
* {@link Rna} for which we are looking for a border
* @return {@link GeneralPath} object defining border of the given {@link Rna}
*/
private
GeneralPath
getRnaPath
(
final
Rna
rna
)
{
@Override
protected
GeneralPath
getShape
(
final
Rna
rna
)
{
// CHECKSTYLE:OFF
GeneralPath
path
=
new
GeneralPath
(
Path2D
.
WIND_EVEN_ODD
,
4
);
path
.
moveTo
(
rna
.
getX
()
+
rna
.
getWidth
()
/
4
,
rna
.
getY
());
...
...
@@ -85,7 +86,7 @@ public class RnaConverter extends SpeciesConverter<Rna> {
@Override
public
PathIterator
getBoundPathIterator
(
final
Rna
rna
)
{
return
get
RnaPath
(
rna
).
getPathIterator
(
new
AffineTransform
());
return
get
Shape
(
rna
).
getPathIterator
(
new
AffineTransform
());
}
}
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SBGNNucleicAcidFeatureConverter.java
View file @
ca2b405f
...
...
@@ -42,7 +42,8 @@ public class SBGNNucleicAcidFeatureConverter extends SpeciesConverter<Species> {
* {@link Species} for which the shape should be returned
* @return shape of the SBGN Nucleic acid feature for given alias
*/
private
Shape
getShape
(
final
Species
species
)
{
@Override
protected
Shape
getShape
(
final
Species
species
)
{
GeneralPath
bottomRoundedRectangle
=
new
GeneralPath
(
GeneralPath
.
WIND_EVEN_ODD
);
double
x
=
species
.
getX
(),
y
=
species
.
getY
(),
width
=
species
.
getWidth
(),
height
=
species
.
getHeight
();
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeConverter.java
View file @
ca2b405f
...
...
@@ -66,7 +66,8 @@ public class SimpleMoleculeConverter extends SpeciesConverter<SimpleMolecule> {
drawText
(
simpleMolecule
,
graphics
,
params
);
}
Shape
getShape
(
final
SimpleMolecule
simpleMolecule
)
{
@Override
protected
Shape
getShape
(
final
SimpleMolecule
simpleMolecule
)
{
return
new
Ellipse2D
.
Double
(
simpleMolecule
.
getX
(),
simpleMolecule
.
getY
(),
simpleMolecule
.
getWidth
(),
simpleMolecule
.
getHeight
());
}
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SimpleMoleculeSbgnConverter.java
View file @
ca2b405f
...
...
@@ -65,7 +65,8 @@ public class SimpleMoleculeSbgnConverter extends SimpleMoleculeConverter {
graphics
.
setColor
(
oldColor
);
}
Shape
getShape
(
final
SimpleMolecule
simpleMolecule
)
{
@Override
protected
Shape
getShape
(
final
SimpleMolecule
simpleMolecule
)
{
int
arc
=
(
int
)
Math
.
min
(
simpleMolecule
.
getWidth
(),
simpleMolecule
.
getHeight
());
return
new
RoundRectangle2D
.
Double
(
simpleMolecule
.
getX
(),
simpleMolecule
.
getY
(),
simpleMolecule
.
getWidth
(),
simpleMolecule
.
getHeight
(),
arc
,
arc
);
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java
View file @
ca2b405f
...
...
@@ -626,4 +626,6 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
this
.
arrowTransformation
=
arrowTransformation
;
}
protected
abstract
Shape
getShape
(
T
species
);
}
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/UnknownConverter.java
View file @
ca2b405f
...
...
@@ -45,7 +45,7 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
if
(
unknown
.
getActivity
())
{
int
border
=
ACTIVITY_BORDER_DISTANCE
;
unknown
.
increaseBorder
(
border
);
Shape
shape2
=
new
Ellipse2D
.
Double
(
unknown
.
getX
(),
unknown
.
getY
(),
unknown
.
getWidth
(),
unknown
.
getHeight
()
);
Shape
shape2
=
getShape
(
unknown
);
Stroke
stroke
=
graphics
.
getStroke
();
graphics
.
setStroke
(
LineType
.
DOTTED
.
getStroke
());
graphics
.
draw
(
shape2
);
...
...
@@ -53,7 +53,7 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
unknown
.
increaseBorder
(-
border
);
}
Shape
shape
=
new
Ellipse2D
.
Double
(
unknown
.
getX
(),
unknown
.
getY
(),
unknown
.
getWidth
(),
unknown
.
getHeight
()
);
Shape
shape
=
getShape
(
unknown
);
Color
c
=
graphics
.
getColor
();
graphics
.
setColor
(
unknown
.
getFillColor
());
graphics
.
fill
(
shape
);
...
...
@@ -61,6 +61,12 @@ public class UnknownConverter extends SpeciesConverter<Unknown> {
drawText
(
unknown
,
graphics
,
params
);
}
@Override
protected
Shape
getShape
(
Unknown
unknown
)
{
Shape
shape
=
new
Ellipse2D
.
Double
(
unknown
.
getX
(),
unknown
.
getY
(),
unknown
.
getWidth
(),
unknown
.
getHeight
());
return
shape
;
}
@Override
public
PathIterator
getBoundPathIterator
(
Unknown
unknown
)
{
throw
new
InvalidStateException
(
"This class doesn't provide boundPath"
);
...
...
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