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minerva
core
Commits
ee3ebaf0
Commit
ee3ebaf0
authored
Sep 15, 2021
by
Piotr Gawron
Browse files
formatting issues
parent
11837633
Changes
7
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checkstyle.xml
View file @
ee3ebaf0
...
...
@@ -224,13 +224,6 @@
</module>
<module
name=
"OverloadMethodsDeclarationOrder"
/>
<!-- <module name="VariableDeclarationUsageDistance"/>
<module name="CustomImportOrder">
<property name="sortImportsInGroupAlphabetically" value="true"/>
<property name="separateLineBetweenGroups" value="true"/>
<property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
<property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/>
</module>
<module
name=
"MethodParamPad"
>
<property
name=
"tokens"
value=
"CTOR_DEF, LITERAL_NEW, METHOD_CALL, METHOD_DEF,
...
...
@@ -241,7 +234,7 @@
value=
"COMMA, SEMI, POST_INC, POST_DEC, DOT, ELLIPSIS, METHOD_REF"
/>
<property
name=
"allowLineBreaks"
value=
"true"
/>
</module>
<module name="ParenPad">
<!--
<module name="ParenPad">
<property name="tokens"
value="ANNOTATION, ANNOTATION_FIELD_DEF, CTOR_CALL, CTOR_DEF, DOT, ENUM_CONSTANT_DEF,
EXPR, LITERAL_CATCH, LITERAL_DO, LITERAL_FOR, LITERAL_IF, LITERAL_NEW,
...
...
@@ -308,6 +301,13 @@
<property name="tokens"
value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF, ANNOTATION_FIELD_DEF,
PARAMETER_DEF, VARIABLE_DEF, METHOD_DEF"/>
</module>
<module name="VariableDeclarationUsageDistance"/>
<module name="CustomImportOrder">
<property name="sortImportsInGroupAlphabetically" value="true"/>
<property name="separateLineBetweenGroups" value="true"/>
<property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
<property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/>
</module>
-->
</module>
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/ComplexSbgnConverter.java
View file @
ee3ebaf0
...
...
@@ -32,8 +32,8 @@ public class ComplexSbgnConverter extends ComplexConverter {
* 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
ComplexSbgnConverter
(
final
ColorExtractor
colorExtractor
)
{
super
(
colorExtractor
);
...
...
@@ -73,7 +73,7 @@ public class ComplexSbgnConverter extends ComplexConverter {
@Override
Shape
getStructuralStateShape
(
final
StructuralState
state
)
{
double
arcSize
=
Math
.
min
(
state
.
getWidth
(),
state
.
getHeight
())
;
double
arcSize
=
Math
.
min
(
state
.
getWidth
(),
state
.
getHeight
());
return
new
RoundRectangle2D
.
Double
(
state
.
getPosition
().
getX
(),
state
.
getPosition
().
getY
(),
state
.
getWidth
(),
state
.
getHeight
(),
arcSize
,
arcSize
);
}
...
...
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParserTest.java
View file @
ee3ebaf0
...
...
@@ -16,8 +16,8 @@ import lcsb.mapviewer.model.map.species.Protein;
public
class
SbmlElementParserTest
extends
SbmlTestFunctions
{
SbmlElementParser
<?>
parser
;
SbmlElementParser
<?>
parser
;
@Before
public
void
setUp
()
{
Model
sbmlModel
=
new
Model
();
...
...
@@ -27,9 +27,9 @@ public class SbmlElementParserTest extends SbmlTestFunctions {
layoutPlugin
.
add
(
layout
);
sbmlModel
.
addExtension
(
"layout"
,
layoutPlugin
);
parser
=
new
SbmlSpeciesParser
(
sbmlModel
,
null
);
parser
=
new
SbmlSpeciesParser
(
sbmlModel
,
null
);
}
@Test
public
void
testCreateElementWithLayoutWithoutBox
()
throws
Exception
{
Protein
protein
=
super
.
createProtein
();
...
...
@@ -37,7 +37,7 @@ public class SbmlElementParserTest extends SbmlTestFunctions {
Element
result
=
parser
.
createElementWithLayout
(
protein
,
glyph
);
assertNotNull
(
result
);
}
@Test
public
void
testCreateElementWithLayoutWithoutPosition
()
throws
Exception
{
Protein
protein
=
super
.
createProtein
();
...
...
model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
View file @
ee3ebaf0
...
...
@@ -54,7 +54,7 @@ public class ModelComparator extends Comparator<Model> {
private
SetComparator
<
Reaction
>
reactionSetComparator
;
private
ElementComparator
elementComparator
;
private
ElementComparator
elementComparator
;
private
ElementUtils
eu
=
new
ElementUtils
();
...
...
@@ -205,8 +205,8 @@ public class ModelComparator extends Comparator<Model> {
* first set of layers
* @param layers2
* second set of layers
* @return if sets are equal then returns 0. If they are different then -1/1
is
* returned.
* @return if sets are equal then returns 0. If they are different then -1/1
*
is
returned.
*/
private
int
compareLayers
(
final
Set
<
Layer
>
layers
,
final
Set
<
Layer
>
layers2
)
{
LayerComparator
layerComparator
=
new
LayerComparator
(
epsilon
);
...
...
@@ -242,8 +242,8 @@ public class ModelComparator extends Comparator<Model> {
* first set of elements
* @param elements2
* second set of elements
* @return if sets are equal then returns 0. If they are different then -1/1
is
* returned.
* @return if sets are equal then returns 0. If they are different then -1/1
*
is
returned.
*/
private
int
compareElements
(
final
Set
<
Element
>
elements
,
final
Set
<
Element
>
elements2
)
{
...
...
pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/BiopaxParserTest.java
View file @
ee3ebaf0
...
...
@@ -16,7 +16,7 @@ import lcsb.mapviewer.wikipathway.xml.BiopaxParser;
public
class
BiopaxParserTest
extends
WikipathwaysTestFunctions
{
BiopaxParser
parser
;
BiopaxParser
parser
;
@Before
public
void
setUp
()
throws
Exception
{
...
...
pathvisio/src/test/java/lcsb/mapviewer/wikipathway/xml/EdgeParserTest.java
View file @
ee3ebaf0
...
...
@@ -22,13 +22,13 @@ public class EdgeParserTest {
Logger
logger
=
LogManager
.
getLogger
();
EdgeParser
parser
;
EdgeParser
parser
;
@Before
public
void
setUp
()
{
parser
=
new
EdgeParser
(
"mapName"
);
}
@Test
public
void
testGetPointsWithoutTargetDirection
()
throws
Exception
{
List
<
PointData
>
gpmlPoints
=
new
ArrayList
<>();
...
...
service/src/test/java/lcsb/mapviewer/services/search/chemical/ChemicalServiceTest.java
View file @
ee3ebaf0
...
...
@@ -100,9 +100,9 @@ public class ChemicalServiceTest extends ServiceTestFunctions {
public
void
testCacheDataForModelWithAnyIdentifierType
()
throws
Exception
{
Model
model
=
new
ModelFullIndexed
(
null
);
model
.
setProject
(
new
Project
());
model
.
getProject
().
setDisease
(
new
MiriamData
(
MiriamType
.
MESH_2012
,
"X111111"
));
model
.
getProject
().
setDisease
(
new
MiriamData
(
MiriamType
.
MESH_2012
,
"X111111"
));
GenericProtein
protein
=
new
GenericProtein
(
"x"
);
for
(
final
MiriamType
type:
MiriamType
.
values
())
{
for
(
final
MiriamType
type
:
MiriamType
.
values
())
{
protein
.
addMiriamData
(
new
MiriamData
(
type
,
type
.
getExampleIdentifier
()));
}
model
.
addElement
(
protein
);
...
...
@@ -110,7 +110,7 @@ public class ChemicalServiceTest extends ServiceTestFunctions {
chemicalService
.
cacheDataForModel
(
model
,
new
IProgressUpdater
()
{
@Override
public
void
setProgress
(
final
double
progress
)
{
called
.
setValue
(
true
);
;
called
.
setValue
(
true
);
}
});
assertTrue
(
called
.
booleanValue
());
...
...
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