Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
minerva
core
Commits
a065c619
Commit
a065c619
authored
Sep 14, 2021
by
Piotr Gawron
Browse files
indentation issues
parent
b5f1c021
Changes
25
Expand all
Hide whitespace changes
Inline
Side-by-side
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
View file @
a065c619
...
...
@@ -74,22 +74,22 @@ public class CopyPastePlugin extends CellDesignerPlugin {
return
new
KeyEventDispatcher
()
{
public
boolean
dispatchKeyEvent
(
final
KeyEvent
e
)
{
switch
(
e
.
getID
())
{
case
KeyEvent
.
KEY_PRESSED
:
if
(
e
.
getKeyCode
()
==
java
.
awt
.
event
.
KeyEvent
.
VK_V
&&
e
.
isControlDown
()
&&
e
.
isAltDown
())
{
getPastePluginAction
().
myActionPerformed
(
null
);
return
true
;
}
else
if
(
e
.
getKeyCode
()
==
java
.
awt
.
event
.
KeyEvent
.
VK_C
&&
e
.
isControlDown
()
&&
e
.
isAltDown
())
{
getCopyPluginAction
().
myActionPerformed
(
null
);
return
true
;
}
else
{
case
KeyEvent
.
KEY_PRESSED
:
if
(
e
.
getKeyCode
()
==
java
.
awt
.
event
.
KeyEvent
.
VK_V
&&
e
.
isControlDown
()
&&
e
.
isAltDown
())
{
getPastePluginAction
().
myActionPerformed
(
null
);
return
true
;
}
else
if
(
e
.
getKeyCode
()
==
java
.
awt
.
event
.
KeyEvent
.
VK_C
&&
e
.
isControlDown
()
&&
e
.
isAltDown
())
{
getCopyPluginAction
().
myActionPerformed
(
null
);
return
true
;
}
else
{
return
false
;
}
default
:
return
false
;
}
default
:
return
false
;
}
}
};
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
View file @
a065c619
...
...
@@ -92,7 +92,8 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param element
* object to be annotated
* @throws AnnotatorException
* thrown when there is a problem with annotating not related to data
* thrown when there is a problem with annotating not related to
* data
*/
public
void
annotateElement
(
final
BioEntity
element
)
throws
AnnotatorException
{
annotateElement
(
element
,
createAnnotatorData
());
...
...
@@ -107,7 +108,8 @@ public abstract class ElementAnnotator extends CachableInterface {
* list of parameters passed to the annotator which is expected to be
* in the same order as its {@link this#parameterDefs}
* @throws AnnotatorException
* thrown when there is a problem with annotating not related to data
* thrown when there is a problem with annotating not related to
* data
*/
public
final
void
annotateElement
(
final
BioEntity
bioEntity
,
final
AnnotatorData
parameters
)
throws
AnnotatorException
{
if
(
isAnnotatable
(
bioEntity
))
{
...
...
@@ -161,8 +163,8 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
* Returns <code>true</code> if this annotator can annotate the object given
in
* the parameter.
* Returns <code>true</code> if this annotator can annotate the object given
*
in
the parameter.
*
* @param object
* object to be tested if can be annotated
...
...
@@ -214,7 +216,8 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
* Returns list with definitions of the parameters available for this annotator.
* Returns list with definitions of the parameters available for this
* annotator.
*
* @return the parameters {@link AnnotatorParamDefinition} list
*/
...
...
@@ -233,8 +236,8 @@ public abstract class ElementAnnotator extends CachableInterface {
}
/**
* Returns <code>true</code> if this annotator can annotate the object of
given
* class type.
* Returns <code>true</code> if this annotator can annotate the object of
*
given
class type.
*
* @param clazz
* class to be tested if can be annotated
...
...
@@ -688,68 +691,68 @@ public abstract class ElementAnnotator extends CachableInterface {
return
collection
;
}
else
{
switch
(
output
.
getField
())
{
case
ABBREVIATION:
return
originalBioEntity
.
getAbbreviation
();
case
CHARGE:
if
(
originalBioEntity
instanceof
Species
)
{
return
((
Species
)
originalBioEntity
).
getCharge
();
}
else
{
return
null
;
}
case
DESCRIPTION:
return
originalBioEntity
.
getNotes
();
case
FORMULA:
return
originalBioEntity
.
getFormula
();
case
FULL_NAME:
if
(
originalBioEntity
instanceof
Element
)
{
return
((
Element
)
originalBioEntity
).
getFullName
();
}
else
{
return
null
;
}
case
INCHI:
if
(
originalBioEntity
instanceof
Chemical
)
{
return
((
Chemical
)
originalBioEntity
).
getInChI
();
}
else
{
return
null
;
}
case
INCHI_KEY:
if
(
originalBioEntity
instanceof
Chemical
)
{
return
((
Chemical
)
originalBioEntity
).
getInChIKey
();
}
else
{
return
null
;
}
case
NAME:
return
originalBioEntity
.
getName
();
case
MCS:
if
(
originalBioEntity
instanceof
Reaction
)
{
return
((
Reaction
)
originalBioEntity
).
getMechanicalConfidenceScore
();
}
else
{
return
null
;
}
case
PREVIOUS_SYMBOLS:
if
(
originalBioEntity
instanceof
Element
)
{
return
((
Element
)
originalBioEntity
).
getFormerSymbols
();
}
else
{
return
null
;
}
case
SMILE:
if
(
originalBioEntity
instanceof
Chemical
)
{
return
((
Chemical
)
originalBioEntity
).
getSmiles
();
}
else
{
return
null
;
}
case
SUBSYSTEM:
if
(
originalBioEntity
instanceof
Reaction
)
{
return
((
Reaction
)
originalBioEntity
).
getSubsystem
();
}
else
{
return
null
;
}
case
SYMBOL:
return
originalBioEntity
.
getSymbol
();
case
SYNONYMS:
return
originalBioEntity
.
getSynonyms
();
default
:
throw
new
NotImplementedException
(
output
.
getField
()
+
""
);
case
ABBREVIATION:
return
originalBioEntity
.
getAbbreviation
();
case
CHARGE:
if
(
originalBioEntity
instanceof
Species
)
{
return
((
Species
)
originalBioEntity
).
getCharge
();
}
else
{
return
null
;
}
case
DESCRIPTION:
return
originalBioEntity
.
getNotes
();
case
FORMULA:
return
originalBioEntity
.
getFormula
();
case
FULL_NAME:
if
(
originalBioEntity
instanceof
Element
)
{
return
((
Element
)
originalBioEntity
).
getFullName
();
}
else
{
return
null
;
}
case
INCHI:
if
(
originalBioEntity
instanceof
Chemical
)
{
return
((
Chemical
)
originalBioEntity
).
getInChI
();
}
else
{
return
null
;
}
case
INCHI_KEY:
if
(
originalBioEntity
instanceof
Chemical
)
{
return
((
Chemical
)
originalBioEntity
).
getInChIKey
();
}
else
{
return
null
;
}
case
NAME:
return
originalBioEntity
.
getName
();
case
MCS:
if
(
originalBioEntity
instanceof
Reaction
)
{
return
((
Reaction
)
originalBioEntity
).
getMechanicalConfidenceScore
();
}
else
{
return
null
;
}
case
PREVIOUS_SYMBOLS:
if
(
originalBioEntity
instanceof
Element
)
{
return
((
Element
)
originalBioEntity
).
getFormerSymbols
();
}
else
{
return
null
;
}
case
SMILE:
if
(
originalBioEntity
instanceof
Chemical
)
{
return
((
Chemical
)
originalBioEntity
).
getSmiles
();
}
else
{
return
null
;
}
case
SUBSYSTEM:
if
(
originalBioEntity
instanceof
Reaction
)
{
return
((
Reaction
)
originalBioEntity
).
getSubsystem
();
}
else
{
return
null
;
}
case
SYMBOL:
return
originalBioEntity
.
getSymbol
();
case
SYNONYMS:
return
originalBioEntity
.
getSynonyms
();
default
:
throw
new
NotImplementedException
(
output
.
getField
()
+
""
);
}
}
}
...
...
checkstyle.xml
View file @
a065c619
...
...
@@ -204,7 +204,7 @@
</module>
<module
name=
"NoFinalizer"
/>
<module
name=
"FinalParameters"
/>
<!--
<module name="GenericWhitespace">
<module
name=
"GenericWhitespace"
>
<message
key=
"ws.followed"
value=
"GenericWhitespace ''{0}'' is followed by whitespace."
/>
<message
key=
"ws.preceded"
...
...
@@ -222,7 +222,7 @@
<property
name=
"lineWrappingIndentation"
value=
"4"
/>
<property
name=
"arrayInitIndent"
value=
"2"
/>
</module>
<module name="AbbreviationAsWordInName">
<!--
<module name="AbbreviationAsWordInName">
<property name="ignoreFinal" value="false"/>
<property name="allowedAbbreviationLength" value="1"/>
<property name="tokens"
...
...
commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java
View file @
a065c619
...
...
@@ -63,24 +63,24 @@ public class LineTransformation {
last
=
actual
;
actual
=
new
Point2D
.
Double
(
coordinates
[
0
],
coordinates
[
1
]);
switch
(
type
)
{
case
PathIterator
.
SEG_MOVETO
:
break
;
case
PathIterator
.
SEG_LINETO
:
break
;
case
PathIterator
.
SEG_QUADTO
:
break
;
case
PathIterator
.
SEG_CUBICTO
:
// in case when there is an arc we define only end points of the arc
// as a border
actual
=
new
Point2D
.
Double
(
coordinates
[
SEG_CUBICTO_END_X_COORDINATE_INDEX
],
coordinates
[
SEG_CUBICTO_END_Y_COORDINATE_INDEX
]);
break
;
case
PathIterator
.
SEG_CLOSE
:
actual
=
first
;
break
;
default
:
break
;
case
PathIterator
.
SEG_MOVETO
:
break
;
case
PathIterator
.
SEG_LINETO
:
break
;
case
PathIterator
.
SEG_QUADTO
:
break
;
case
PathIterator
.
SEG_CUBICTO
:
// in case when there is an arc we define only end points of the arc
// as a border
actual
=
new
Point2D
.
Double
(
coordinates
[
SEG_CUBICTO_END_X_COORDINATE_INDEX
],
coordinates
[
SEG_CUBICTO_END_Y_COORDINATE_INDEX
]);
break
;
case
PathIterator
.
SEG_CLOSE
:
actual
=
first
;
break
;
default
:
break
;
}
if
(
first
==
null
)
{
first
=
actual
;
...
...
@@ -155,13 +155,15 @@ public class LineTransformation {
}
/**
* Returns a point that is on the line and is as close as possible to the point.
* Returns a point that is on the line and is as close as possible to the
* point.
*
* @param line
* line on which the point should be found
* @param point
* point to which the result should be as close as possible
* @return point on the line that is as close as possible to the parameter point
* @return point on the line that is as close as possible to the parameter
* point
*/
public
Point2D
closestPointOnSegmentLineToPoint
(
final
Line2D
line
,
final
Point2D
point
)
{
Point2D
result
=
closestPointOnSegmentLineToPoint
(
line
.
getP1
(),
line
.
getP2
(),
point
);
...
...
@@ -169,8 +171,8 @@ public class LineTransformation {
}
/**
* Returns a point that is on the line (v-w) and is as close as possible to
the
* point.
* Returns a point that is on the line (v-w) and is as close as possible to
*
the
point.
*
* @param v
* start of the line segment
...
...
@@ -178,8 +180,8 @@ public class LineTransformation {
* end of the line segment
* @param p
* point to which the result should be as close as possible
* @return point on the line (v-w) that is as close as possible to the
parameter
* point
* @return point on the line (v-w) that is as close as possible to the
*
parameter
point
*/
public
Point2D
closestPointOnSegmentLineToPoint
(
final
Point2D
v
,
final
Point2D
w
,
final
Point2D
p
)
{
// Return minimum distance between line segment vw and point p
...
...
commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
View file @
a065c619
...
...
@@ -50,9 +50,9 @@ public class PointTransformation {
}
/**
* Checks if a point given in the parameter is valid (can be used for
drawing).
* The point is considered as valid if coordinates are finite (final
NaN and Infinity
* are invalid - they cannot be drawn).
* Checks if a point given in the parameter is valid (can be used for
*
drawing).
The point is considered as valid if coordinates are finite (final
*
NaN and Infinity
are invalid - they cannot be drawn).
*
* @param point
* point to check
...
...
@@ -105,24 +105,24 @@ public class PointTransformation {
last
=
actual
;
actual
=
new
Point2D
.
Double
(
coordinates
[
0
],
coordinates
[
1
]);
switch
(
type
)
{
case
PathIterator
.
SEG_MOVETO
:
break
;
case
PathIterator
.
SEG_LINETO
:
break
;
case
PathIterator
.
SEG_QUADTO
:
break
;
case
PathIterator
.
SEG_CUBICTO
:
// in case when there is an arc we define only end points of the arc
// as a border
actual
=
new
Point2D
.
Double
(
coordinates
[
LineTransformation
.
SEG_CUBICTO_END_X_COORDINATE_INDEX
],
coordinates
[
LineTransformation
.
SEG_CUBICTO_END_Y_COORDINATE_INDEX
]);
break
;
case
PathIterator
.
SEG_CLOSE
:
actual
=
first
;
break
;
default
:
break
;
case
PathIterator
.
SEG_MOVETO
:
break
;
case
PathIterator
.
SEG_LINETO
:
break
;
case
PathIterator
.
SEG_QUADTO
:
break
;
case
PathIterator
.
SEG_CUBICTO
:
// in case when there is an arc we define only end points of the arc
// as a border
actual
=
new
Point2D
.
Double
(
coordinates
[
LineTransformation
.
SEG_CUBICTO_END_X_COORDINATE_INDEX
],
coordinates
[
LineTransformation
.
SEG_CUBICTO_END_Y_COORDINATE_INDEX
]);
break
;
case
PathIterator
.
SEG_CLOSE
:
actual
=
first
;
break
;
default
:
break
;
}
if
(
first
==
null
)
{
first
=
actual
;
...
...
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
View file @
a065c619
...
...
@@ -616,13 +616,13 @@ public class SbgnmlXmlExporter {
}
/**
* Returns glyph with unit of information extracted from the alias or null if
no
* unit of information was found.
* Returns glyph with unit of information extracted from the alias or null if
*
no
unit of information was found.
*
* @param species
* input species
* @return glyph with unit of information extracted from the alias or null if
no
* unit of information was found
* @return glyph with unit of information extracted from the alias or null if
*
no
unit of information was found
*/
private
Glyph
getUnitOfInformationGlyph
(
final
Species
species
)
{
Glyph
uoiGlyph
=
null
;
...
...
@@ -865,12 +865,12 @@ public class SbgnmlXmlExporter {
List
<
Point2D
>
pointList
=
new
ArrayList
<>();
pointList
.
add
(
reaction
.
getReactants
().
get
(
0
).
getLine
().
getStartPoint
());
for
(
final
Line2D
line:
reaction
.
getReactants
().
get
(
0
).
getLine
().
getLines
())
{
for
(
final
Line2D
line
:
reaction
.
getReactants
().
get
(
0
).
getLine
().
getLines
())
{
pointList
.
add
(
line
.
getP2
());
}
pointList
.
add
(
reaction
.
getProducts
().
get
(
0
).
getLine
().
getStartPoint
());
for
(
final
Line2D
line:
reaction
.
getProducts
().
get
(
0
).
getLine
().
getLines
())
{
for
(
final
Line2D
line
:
reaction
.
getProducts
().
get
(
0
).
getLine
().
getLines
())
{
pointList
.
add
(
line
.
getP2
());
}
...
...
@@ -1110,7 +1110,7 @@ public class SbgnmlXmlExporter {
List
<
Point2D
>
arcPoints
=
new
ArrayList
<>();
arcPoints
.
add
(
node
.
getLine
().
getStartPoint
());
for
(
final
Line2D
line:
node
.
getLine
().
getLines
())
{
for
(
final
Line2D
line
:
node
.
getLine
().
getLines
())
{
arcPoints
.
add
(
line
.
getP2
());
}
Start
start
=
new
Start
();
...
...
@@ -1206,20 +1206,20 @@ public class SbgnmlXmlExporter {
if
(
node
instanceof
NodeOperator
)
{
ArrowType
arrowType
=
node
.
getLine
().
getEndAtd
().
getArrowType
();
switch
(
arrowType
)
{
case
BLANK:
return
ArcClazz
.
STIMULATION
;
case
BLANK_CROSSBAR:
return
ArcClazz
.
NECESSARY_STIMULATION
;
case
CIRCLE:
return
ArcClazz
.
CATALYSIS
;
case
CROSSBAR:
return
ArcClazz
.
INHIBITION
;
case
DIAMOND:
return
ArcClazz
.
MODULATION
;
case
NONE:
return
ArcClazz
.
LOGIC_ARC
;
default
:
throw
new
InvalidArgumentException
();
case
BLANK:
return
ArcClazz
.
STIMULATION
;
case
BLANK_CROSSBAR:
return
ArcClazz
.
NECESSARY_STIMULATION
;
case
CIRCLE:
return
ArcClazz
.
CATALYSIS
;
case
CROSSBAR:
return
ArcClazz
.
INHIBITION
;
case
DIAMOND:
return
ArcClazz
.
MODULATION
;
case
NONE:
return
ArcClazz
.
LOGIC_ARC
;
default
:
throw
new
InvalidArgumentException
();
}
}
throw
new
InvalidArgumentException
();
...
...
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
View file @
a065c619
This diff is collapsed.
Click to expand it.
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/SpeciesConverter.java
View file @
a065c619
...
...
@@ -221,8 +221,8 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
/**
* This method draws a string on graphics using current font. The coordinates
of
* the text is given as a point. Both parameters centered described if text
* This method draws a string on graphics using current font. The coordinates
*
of
the text is given as a point. Both parameters centered described if text
* should be automatically centered horizontally and vertically.
*
* @param border
...
...
@@ -244,35 +244,35 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
double
lineHeight
=
graphics
.
getFontMetrics
().
getHeight
();
switch
(
verticalAlign
)
{
case
TOP:
y
=
border
.
getMinY
()
+
graphics
.
getFontMetrics
().
getAscent
();
break
;
case
MIDDLE:
y
=
border
.
getCenterY
()
-
(
textHeight
/
2
-
graphics
.
getFontMetrics
().
getAscent
());
break
;
case
BOTTOM:
y
=
border
.
getMaxY
()
-
(
textHeight
-
graphics
.
getFontMetrics
().
getAscent
());
break
;
default
:
throw
new
InvalidArgumentException
(
"Don't know how to align text with: "
+
verticalAlign
);
case
TOP:
y
=
border
.
getMinY
()
+
graphics
.
getFontMetrics
().
getAscent
();
break
;
case
MIDDLE:
y
=
border
.
getCenterY
()
-
(
textHeight
/
2
-
graphics
.
getFontMetrics
().
getAscent
());
break
;
case
BOTTOM:
y
=
border
.
getMaxY
()
-
(
textHeight
-
graphics
.
getFontMetrics
().
getAscent
());
break
;
default
:
throw
new
InvalidArgumentException
(
"Don't know how to align text with: "
+
verticalAlign
);
}
for
(
final
String
string
:
lines
)
{
double
currX
;
switch
(
horizontalAlign
)
{
case
LEFT:
currX
=
border
.
getX
();
break
;
case
CENTER:
currX
=
border
.
getCenterX
()
-
getTextWidth
(
string
,
graphics
)
/
2
;
break
;
case
RIGTH:
currX
=
border
.
getMaxX
()
-
getTextWidth
(
string
,
graphics
);
break
;
default
:
throw
new
InvalidArgumentException
(
"Don't know how to align text with: "
+
horizontalAlign
);
case
LEFT:
currX
=
border
.
getX
();
break
;
case
CENTER:
currX
=
border
.
getCenterX
()
-
getTextWidth
(
string
,
graphics
)
/
2
;
break
;
case
RIGTH:
currX
=
border
.
getMaxX
()
-
getTextWidth
(
string
,
graphics
);
break
;
default
:
throw
new
InvalidArgumentException
(
"Don't know how to align text with: "
+
horizontalAlign
);
}
graphics
.
drawString
(
string
,
(
int
)
currX
,
(
int
)
y
);
y
+=
lineHeight
;
}
...
...
@@ -388,8 +388,8 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
/**
* Draws unit of information for the {@link Species} (rectangle in the top
part
* of the alias).
* Draws unit of information for the {@link Species} (rectangle in the top
*
part
of the alias).
*
* @param text
* unit of information text
...
...
@@ -453,9 +453,10 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
}
/**
* This method draws modification of the alias. If drawEmptyModification is set
* to false then modification is not drawn if empty. If drawDescription is set
* then also description (position) of the modification is drawn on the canvas.
* This method draws modification of the alias. If drawEmptyModification is
* set to false then modification is not drawn if empty. If drawDescription is
* set then also description (position) of the modification is drawn on the
* canvas.
*
* @param protein
* object that is 'parent' of the residue
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/FontFinder.java
View file @
a065c619
...
...
@@ -215,34 +215,34 @@ public final class FontFinder {
double
lineHeight
=
graphics
.
getFontMetrics
().
getHeight
();
double
y
;
switch
(
verticalAlign
)
{
case
TOP:
y
=
border
.
getY
()
+
lineHeight
/
2
;
break
;
case
MIDDLE:
y
=
(
int
)
(
border
.
getCenterY
()
-
lineHeight
*
lines
.
size
()
/
2.0
+
graphics
.
getFontMetrics
().
getAscent
());
break
;
case
BOTTOM:
y
=
border
.
getMaxY
()
-
lineHeight
/
2
-
lineHeight
*
lines
.
size
();
break
;
default
:
throw
new
InvalidArgumentException
(
"Don't know how to align text with: "
+
verticalAlign
);