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minerva
core
Commits
09221ef7
Commit
09221ef7
authored
Sep 15, 2021
by
Piotr Gawron
Browse files
operators should not be the last token in line
parent
ee3ebaf0
Changes
38
Hide whitespace changes
Inline
Side-by-side
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java
View file @
09221ef7
...
...
@@ -21,15 +21,14 @@ public class CdPluginFunctions {
public
UnitTestFailedWatcher
unitTestFailedWatcher
=
new
UnitTestFailedWatcher
();
String
rdfString
=
"<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+
"<rdf:Description rdf:about=\"#s3\">\n"
+
"<bqmodel:is>\n"
+
"<rdf:Bag>\n"
+
"<rdf:li rdf:resource=\"urn:miriam:wikipedia.en:1\"/>\n"
+
"</rdf:Bag>\n"
+
"</bqmodel:is>\n"
+
"</rdf:Description>\n"
+
"</rdf:RDF>\n"
;
+
"<rdf:Description rdf:about=\"#s3\">\n"
+
"<bqmodel:is>\n"
+
"<rdf:Bag>\n"
+
"<rdf:li rdf:resource=\"urn:miriam:wikipedia.en:1\"/>\n"
+
"</rdf:Bag>\n"
+
"</bqmodel:is>\n"
+
"</rdf:Description>\n"
+
"</rdf:RDF>\n"
;
private
MinervaLoggerAppender
appender
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/ChemicalSerializer.java
View file @
09221ef7
...
...
@@ -93,8 +93,8 @@ public class ChemicalSerializer extends JsonSerializer<Chemical> {
}
private
void
writeField
(
final
JsonGenerator
gen
,
final
String
field
,
final
Object
value
,
final
PropertyFilter
filter
)
throws
IOException
{
if
(
filter
==
null
||
(
filter
instanceof
CustomExceptFilter
&&
((
CustomExceptFilter
)
filter
).
includeField
(
field
)))
{
if
(
filter
==
null
||
(
filter
instanceof
CustomExceptFilter
&&
((
CustomExceptFilter
)
filter
).
includeField
(
field
)))
{
gen
.
writeObjectField
(
field
,
value
);
}
}
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/DrugSerializer.java
View file @
09221ef7
...
...
@@ -56,8 +56,8 @@ public class DrugSerializer extends JsonSerializer<Drug> {
}
private
void
writeField
(
final
JsonGenerator
gen
,
final
String
field
,
final
Object
value
,
final
PropertyFilter
filter
)
throws
IOException
{
if
(
filter
==
null
||
(
filter
instanceof
CustomExceptFilter
&&
((
CustomExceptFilter
)
filter
).
includeField
(
field
)))
{
if
(
filter
==
null
||
(
filter
instanceof
CustomExceptFilter
&&
((
CustomExceptFilter
)
filter
).
includeField
(
field
)))
{
gen
.
writeObjectField
(
field
,
value
);
}
}
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/data/serializer/MiRNASerializer.java
View file @
09221ef7
...
...
@@ -50,8 +50,8 @@ public class MiRNASerializer extends JsonSerializer<MiRNA> {
}
private
void
writeField
(
final
JsonGenerator
gen
,
final
String
field
,
final
Object
value
,
final
PropertyFilter
filter
)
throws
IOException
{
if
(
filter
==
null
||
(
filter
instanceof
CustomExceptFilter
&&
((
CustomExceptFilter
)
filter
).
includeField
(
field
)))
{
if
(
filter
==
null
||
(
filter
instanceof
CustomExceptFilter
&&
((
CustomExceptFilter
)
filter
).
includeField
(
field
)))
{
gen
.
writeObjectField
(
field
,
value
);
}
}
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
View file @
09221ef7
...
...
@@ -478,8 +478,8 @@ public abstract class ElementAnnotator extends CachableInterface {
if
(
oldValue
==
null
||
oldValue
.
trim
().
equals
(
""
)
||
oldValue
.
equals
(
newValue
))
{
return
true
;
}
else
{
logger
.
warn
(
getLogMarker
(
ProjectLogEntryType
.
ANNOTATION_CONFLICT
),
field
.
getCommonName
()
+
" doesn't match: \""
+
newValue
+
"\", \""
+
oldValue
+
"\""
);
logger
.
warn
(
getLogMarker
(
ProjectLogEntryType
.
ANNOTATION_CONFLICT
),
field
.
getCommonName
()
+
" doesn't match: \""
+
newValue
+
"\", \""
+
oldValue
+
"\""
);
return
false
;
}
}
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/ChemicalParser.java
View file @
09221ef7
...
...
@@ -143,8 +143,8 @@ public class ChemicalParser {
String
content
=
dapiConnector
.
getAuthenticatedContent
(
url
+
"/drugs/?size=1000&columns=sourceIdentifier&target_identifier="
+
URLEncoder
.
encode
(
t
.
getPrefixedIdentifier
(),
"UTF-8"
)
+
"&target_disease_identifier="
+
URLEncoder
.
encode
(
disease
.
getPrefixedIdentifier
(),
"UTF-8"
));
+
URLEncoder
.
encode
(
t
.
getPrefixedIdentifier
(),
"UTF-8"
)
+
"&target_disease_identifier="
+
URLEncoder
.
encode
(
disease
.
getPrefixedIdentifier
(),
"UTF-8"
));
ListChemicalEntityDto
dto
=
objectMapper
.
readValue
(
content
,
ListChemicalEntityDto
.
class
);
...
...
checkstyle.xml
View file @
09221ef7
...
...
@@ -234,7 +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,
...
...
@@ -247,7 +247,7 @@
value=
"BAND, BOR, BSR, BXOR, DIV, EQUAL, GE, GT, LAND, LE, LITERAL_INSTANCEOF, LOR,
LT, MINUS, MOD, NOT_EQUAL, PLUS, QUESTION, SL, SR, STAR, METHOD_REF "
/>
</module>
<module name="AnnotationLocation">
<!--
<module name="AnnotationLocation">
<property name="id" value="AnnotationLocationMostCases"/>
<property name="tokens"
value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF"/>
...
...
commons/src/test/java/lcsb/mapviewer/common/TextFileUtilsTest.java
View file @
09221ef7
...
...
@@ -28,11 +28,11 @@ public class TextFileUtilsTest extends CommonTestFunctions {
@Test
public
void
testGetHeaderParametersFromFile
()
throws
Exception
{
String
fileContent
=
"#header\n"
+
"#param1=value1\n"
+
"#\n"
+
"no header\n"
+
"#param2=value\n"
;
String
fileContent
=
"#header\n"
+
"#param1=value1\n"
+
"#\n"
+
"no header\n"
+
"#param2=value\n"
;
Map
<
String
,
String
>
params
=
TextFileUtils
.
getHeaderParametersFromFile
(
new
ByteArrayInputStream
(
fileContent
.
getBytes
(
StandardCharsets
.
UTF_8
)));
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
View file @
09221ef7
...
...
@@ -130,8 +130,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
}
/**
* This method computes coordinates that should be associated with the angle
on
* the border of the alias.
* This method computes coordinates that should be associated with the angle
*
on
the border of the alias.
*
* @param alias
* alias to be investigated
...
...
@@ -230,8 +230,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
double
minDist
=
Math
.
min
(
Math
.
min
(
distanceLeft
,
distanceRight
),
Math
.
min
(
distanceTop
,
distanceBottom
));
if
(
distanceRight
==
minDist
&&
pointOnBorder
.
getY
()
-
element
.
getY
()
-
element
.
getHeight
()
/
2
<
epsilon
)
{
if
(
distanceRight
==
minDist
&&
pointOnBorder
.
getY
()
-
element
.
getY
()
-
element
.
getHeight
()
/
2
<
epsilon
)
{
double
ratio
=
1
-
(
pointOnBorder
.
getY
()
-
element
.
getY
())
/
element
.
getHeight
();
result
=
(
ratio
-
0.5
)
*
(
PI
/
2
);
}
else
if
(
distanceTop
==
minDist
)
{
...
...
@@ -243,8 +243,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
}
else
if
(
distanceBottom
==
minDist
)
{
double
ratio
=
(
pointOnBorder
.
getX
()
-
element
.
getX
())
/
element
.
getWidth
();
result
=
ratio
*
(
PI
/
2
)
+
LEFT_RESIDUE_MAX_ANGLE
;
}
else
if
(
distanceRight
==
minDist
&&
pointOnBorder
.
getY
()
-
element
.
getY
()
-
element
.
getHeight
()
<
epsilon
)
{
}
else
if
(
distanceRight
==
minDist
&&
pointOnBorder
.
getY
()
-
element
.
getY
()
-
element
.
getHeight
()
<
epsilon
)
{
double
ratio
=
1
-
(
pointOnBorder
.
getY
()
-
element
.
getY
())
/
element
.
getHeight
();
result
=
ratio
*
(
PI
/
2
)
+
BOTTOM_RESIDUE_MAX_ANGLE
;
}
else
{
...
...
@@ -280,7 +280,6 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
throw
new
NotImplementedException
(
"Not implemented for: "
+
this
.
getClass
());
}
/**
* This method returns border of the alias as a PathIterator.
*
...
...
@@ -385,8 +384,8 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
* @param elemnt
* {@link Element} on border which the point is looked for
* @param angle
* angle between X axis center point of {@link Species} and point
that
* we are looking for
* angle between X axis center point of {@link Species} and point
*
that
we are looking for
* @return coordinates on the {@link Species} border that correspond to the
* angle
*/
...
...
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
View file @
09221ef7
...
...
@@ -67,7 +67,7 @@ public abstract class CellDesignerTestFunctions {
private
static
int
BLOCK_SIZE
=
65536
;
protected
static
double
EPSILON
=
Configuration
.
EPSILON
;
@Rule
public
UnitTestFailedWatcher
unitTestFailedWatcher
=
new
UnitTestFailedWatcher
();
private
Logger
logger
=
LogManager
.
getLogger
();
...
...
@@ -261,10 +261,10 @@ public abstract class CellDesignerTestFunctions {
// import of unbounded compartments is problematic
for
(
final
Compartment
compartment
:
model
.
getCompartments
())
{
if
(
compartment
instanceof
BottomSquareCompartment
||
compartment
instanceof
TopSquareCompartment
||
compartment
instanceof
LeftSquareCompartment
||
compartment
instanceof
RightSquareCompartment
)
{
if
(
compartment
instanceof
BottomSquareCompartment
||
compartment
instanceof
TopSquareCompartment
||
compartment
instanceof
LeftSquareCompartment
||
compartment
instanceof
RightSquareCompartment
)
{
model2
.
getElementByElementId
(
compartment
.
getElementId
()).
setWidth
(
compartment
.
getWidth
());
model2
.
getElementByElementId
(
compartment
.
getElementId
()).
setHeight
(
compartment
.
getHeight
());
}
...
...
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
View file @
09221ef7
...
...
@@ -283,13 +283,13 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
public
void
testGetNotesWithMissingBody
()
throws
Exception
{
RestAnnotationParser
rap
=
new
RestAnnotationParser
();
Node
node
=
super
.
getNodeFromXmlString
(
"<celldesigner:notes>\n"
+
" <html xmlns=\"http://www.w3.org/1999/xhtml\">\n"
+
" <head>\n"
+
" <title/>\n"
+
" </head>\n"
+
" </html>\n"
+
" </celldesigner:notes>"
);
Node
node
=
super
.
getNodeFromXmlString
(
"<celldesigner:notes>\n"
+
" <html xmlns=\"http://www.w3.org/1999/xhtml\">\n"
+
" <head>\n"
+
" <title/>\n"
+
" </head>\n"
+
" </html>\n"
+
" </celldesigner:notes>"
);
String
notes
=
rap
.
getNotes
(
node
);
assertNotNull
(
notes
);
}
...
...
@@ -298,18 +298,18 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
public
void
testGetNotesWithLinkInside
()
throws
Exception
{
RestAnnotationParser
rap
=
new
RestAnnotationParser
();
Node
node
=
super
.
getNodeFromXmlString
(
"<notes>\n"
+
"Name: L-cystine\n"
+
"Synonyms: (R,R)-3,3'-dithiobis(2-aminopropanoic acid), "
Node
node
=
super
.
getNodeFromXmlString
(
"<notes>\n"
+
"Name: L-cystine\n"
+
"Synonyms: (R,R)-3,3'-dithiobis(2-aminopropanoic acid), "
+
"(R-(R*,R*))-3,3'-Dithiobis(2-aminopropanoic acid), "
+
"3,3'-Dithiobis-L-alanine, beta,beta'-diamino-beta,beta'-dicarboxydiethyl disulfide, "
+
"beta,beta'-dithiodialanine, bis(beta-amino-beta-carboxyethyl) disulfide, E921, "
+
"L-alpha-Diamino-beta-dithiolactic acid, L-Cystine, L-Dicysteine, oxidized L-cysteine, final Recon metabolite: mma\n"
+
"Description: VMH database: <a xmlns=\"http://www.w3.org/1999/xhtml\" href=\"http://vmh.uni.lu/#metabolite/mma\">mma</a>\n"
+
"SemanticZoomLevelVisibility: 5\n"
+
"Charge: 0\n"
+
"</notes>\n"
+
""
);
+
"SemanticZoomLevelVisibility: 5\n"
+
"Charge: 0\n"
+
"</notes>\n"
+
""
);
String
notes
=
rap
.
getNotes
(
node
);
assertFalse
(
notes
.
contains
(
"http://www.w3.org/1999/xhtml"
));
}
...
...
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
View file @
09221ef7
...
...
@@ -1003,8 +1003,8 @@ public class SbgnmlXmlExporter {
arcList
.
add
(
getArcFromNode
(
node
,
glyphList
));
}
catch
(
final
InvalidArgumentException
ex
)
{
logger
.
warn
(
new
LogMarker
(
ProjectLogEntryType
.
EXPORT_ISSUE
,
node
),
new
ElementUtils
().
getElementTag
(
node
.
getElement
())
+
"Node skipped in export process, since it is not compliant with SBGN-ML format."
);
new
ElementUtils
().
getElementTag
(
node
.
getElement
())
+
"Node skipped in export process, since it is not compliant with SBGN-ML format."
);
continue
;
}
}
...
...
converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
View file @
09221ef7
...
...
@@ -1722,8 +1722,8 @@ public class SbgnmlXmlParser {
Product
firstProduct
=
reaction
.
getProducts
().
get
(
0
);
boolean
shouldReverse
=
reaction
.
getProducts
().
size
()
>
1
;
for
(
final
Product
product
:
reaction
.
getProducts
())
{
if
(
product
.
getLine
().
getStartPoint
().
distance
(
firstProduct
.
getLine
().
getStartPoint
())
<
Configuration
.
EPSILON
&&
product
.
getLine
().
getEndPoint
().
distance
(
firstProduct
.
getLine
().
getEndPoint
())
>
Configuration
.
EPSILON
)
{
if
(
product
.
getLine
().
getStartPoint
().
distance
(
firstProduct
.
getLine
().
getStartPoint
())
<
Configuration
.
EPSILON
&&
product
.
getLine
().
getEndPoint
().
distance
(
firstProduct
.
getLine
().
getEndPoint
())
>
Configuration
.
EPSILON
)
{
shouldReverse
=
false
;
}
}
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/ConverterParams.java
View file @
09221ef7
...
...
@@ -107,11 +107,11 @@ public class ConverterParams {
@Override
public
String
toString
()
{
String
result
=
"["
+
this
.
getClass
().
getSimpleName
()
+
"] "
+
"level:"
+
level
+
","
+
"scale:"
+
scale
+
","
+
"nested:"
+
nested
+
","
+
"sbgnFormat:"
+
sbgnFormat
;
String
result
=
"["
+
this
.
getClass
().
getSimpleName
()
+
"] "
+
"level:"
+
level
+
","
+
"scale:"
+
scale
+
","
+
"nested:"
+
nested
+
","
+
"sbgnFormat:"
+
sbgnFormat
;
return
result
;
}
...
...
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
View file @
09221ef7
...
...
@@ -95,8 +95,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
sbmlElementByElementId
.
put
(
getElementId
(
bioEntity
),
sbmlElement
);
}
catch
(
final
Exception
e
)
{
throw
new
InconsistentModelException
(
new
ElementUtils
().
getElementTag
(
bioEntity
)
+
"Problem with exporting bioEntity"
,
e
);
throw
new
InconsistentModelException
(
new
ElementUtils
().
getElementTag
(
bioEntity
)
+
"Problem with exporting bioEntity"
,
e
);
}
}
if
(
isExtensionEnabled
(
SbmlExtension
.
LAYOUT
))
{
...
...
@@ -106,8 +106,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
AbstractReferenceGlyph
elementGlyph
=
createGlyph
(
bioEntity
);
sbmlGlyphByElementId
.
put
(
getElementId
(
bioEntity
),
elementGlyph
);
}
catch
(
final
Exception
e
)
{
throw
new
InconsistentModelException
(
new
ElementUtils
().
getElementTag
(
bioEntity
)
+
"Problem with exporting bioEntity"
,
e
);
throw
new
InconsistentModelException
(
new
ElementUtils
().
getElementTag
(
bioEntity
)
+
"Problem with exporting bioEntity"
,
e
);
}
}
}
...
...
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
View file @
09221ef7
...
...
@@ -288,8 +288,8 @@ public class SbmlParser extends Converter {
private
void
checkAvailableExtensions
(
final
org
.
sbml
.
jsbml
.
Model
sbmlModel
)
{
if
(
sbmlModel
.
getExtensionCount
()
>
0
)
{
for
(
final
SBasePlugin
plugin
:
sbmlModel
.
getExtensionPackages
().
values
())
{
if
(!
plugin
.
getClass
().
equals
(
LayoutModelPlugin
.
class
)
&&
!
plugin
.
getClass
().
equals
(
MultiModelPlugin
.
class
))
{
if
(!
plugin
.
getClass
().
equals
(
LayoutModelPlugin
.
class
)
&&
!
plugin
.
getClass
().
equals
(
MultiModelPlugin
.
class
))
{
logger
.
warn
(
"Unknown sbml plugin: "
+
plugin
);
}
}
...
...
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
View file @
09221ef7
...
...
@@ -126,7 +126,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
try
{
Map
<
ReactionNode
,
SpeciesReferenceGlyph
>
glyphByNode
=
new
HashMap
<>();
Reaction
reactionWithLayout
=
source
.
copy
();
// getId doesn't have to be unique, therefore we concatenate with reaction
// getId doesn't have to be unique, therefore we concatenate with
// reaction
reactionWithLayout
.
setIdReaction
(
glyph
.
getReaction
()
+
"__"
+
glyph
.
getId
());
// z index
...
...
@@ -280,7 +281,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
for
(
final
Reaction
reaction
:
reactions
)
{
if
(!
used
.
contains
(
reaction
))
{
for
(
final
ReactionNode
node
:
reaction
.
getReactionNodes
())
{
// we might have different elements here, the reason is that single SBML species
// we might have different elements here, the reason is that single
// SBML species
// can be split into two or more (due to layout)
node
.
setElement
(
speciesParser
.
getAnyElementBySbmlElementId
(
node
.
getElement
().
getElementId
()));
}
...
...
@@ -330,8 +332,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
PolylineData
line
=
new
PolylineData
();
reaction
.
setLine
(
line
);
// if there is no layout don't create center line
if
(
startNode
.
getLine
()
!=
null
&&
startNode
.
getLine
().
length
()
>
Configuration
.
EPSILON
&&
endNode
.
getLine
()
!=
null
&&
endNode
.
getLine
().
length
()
>
Configuration
.
EPSILON
)
{
if
(
startNode
.
getLine
()
!=
null
&&
startNode
.
getLine
().
length
()
>
Configuration
.
EPSILON
&&
endNode
.
getLine
()
!=
null
&&
endNode
.
getLine
().
length
()
>
Configuration
.
EPSILON
)
{
startNode
.
getLine
().
trimEnd
(
ReactionCellDesignerConverter
.
RECT_SIZE
);
endNode
.
getLine
().
trimBegin
(
ReactionCellDesignerConverter
.
RECT_SIZE
);
...
...
@@ -409,9 +411,10 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
/**
* Extracts {@link Curve} associated to {@link ReactionGlyph}. If curve doesn't
* exist then method will try to create it from {@link BoundingBox} (due to SBML
* specification). This {@link Curve} is split into parts belonging to:
* Extracts {@link Curve} associated to {@link ReactionGlyph}. If curve
* doesn't exist then method will try to create it from {@link BoundingBox}
* (due to SBML specification). This {@link Curve} is split into parts
* belonging to:
* <ul>
* <li>input operator</li>
* <li>center line</li>
...
...
@@ -421,9 +424,9 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
*
* @param reactionGlyph
* @param operator
* class of {@link NodeOperator} that requires the line (this line
can
* be separated into 3 different segments - reactant, center,
product
* parts)
* class of {@link NodeOperator} that requires the line (this line
*
can
be separated into 3 different segments - reactant, center,
*
product
parts)
* @return
*/
PolylineData
extractCurve
(
final
ReactionGlyph
reactionGlyph
,
final
Reaction
reaction
,
...
...
@@ -517,20 +520,20 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
PolylineData
result
=
new
PolylineData
();
if
(
operator
==
TruncationOperator
.
class
||
operator
==
DissociationOperator
.
class
||
operator
==
SplitOperator
.
class
)
{
if
(
operator
==
TruncationOperator
.
class
||
operator
==
DissociationOperator
.
class
||
operator
==
SplitOperator
.
class
)
{
// Product operator
for
(
int
i
=
productLineStarts
;
i
<
curve
.
getCurveSegmentCount
();
i
++)
{
CurveSegment
segment
=
curve
.
getCurveSegment
(
i
);
CurveSegment
segment
=
curve
.
getCurveSegment
(
i
);
result
.
addLine
(
segment
.
getStart
().
getX
(),
segment
.
getStart
().
getY
(),
segment
.
getEnd
().
getX
(),
segment
.
getEnd
().
getY
());
}
}
else
if
(
operator
==
AssociationOperator
.
class
||
operator
==
AndOperator
.
class
)
{
// Reactant operator
for
(
int
i
=
0
;
i
<
reactantLineEnds
;
i
++)
{
CurveSegment
segment
=
curve
.
getCurveSegment
(
i
);
CurveSegment
segment
=
curve
.
getCurveSegment
(
i
);
result
.
addLine
(
segment
.
getStart
().
getX
(),
segment
.
getStart
().
getY
(),
segment
.
getEnd
().
getX
(),
segment
.
getEnd
().
getY
());
}
}
else
if
(
operator
==
null
)
{
...
...
converter/src/test/java/lcsb/mapviewer/converter/ColorSchemaReaderTest.java
View file @
09221ef7
...
...
@@ -205,9 +205,9 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
Map
<
String
,
String
>
params
=
new
HashMap
<>();
params
.
put
(
TextFileUtils
.
COLUMN_COUNT_PARAM
,
"3"
);
String
input
=
"name\tcolor\tvalue\n"
+
"s1\t#ff0000\t\n"
+
"s2\t\t1.0\n"
;
String
input
=
"name\tcolor\tvalue\n"
+
"s1\t#ff0000\t\n"
+
"s2\t\t1.0\n"
;
Collection
<
DataOverlayEntry
>
schemas
=
reader
.
readColorSchema
(
new
ByteArrayInputStream
(
input
.
getBytes
(
StandardCharsets
.
UTF_8
)),
params
);
assertEquals
(
2
,
schemas
.
size
());
...
...
@@ -218,8 +218,8 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
Map
<
String
,
String
>
params
=
new
HashMap
<>();
params
.
put
(
TextFileUtils
.
COLUMN_COUNT_PARAM
,
"3"
);
String
input
=
"type\tname\tvalue\n"
+
"protein\t\t1.0\n"
;
String
input
=
"type\tname\tvalue\n"
+
"protein\t\t1.0\n"
;
Collection
<
DataOverlayEntry
>
schemas
=
reader
.
readColorSchema
(
new
ByteArrayInputStream
(
input
.
getBytes
(
StandardCharsets
.
UTF_8
)),
params
);
assertEquals
(
1
,
schemas
.
size
());
...
...
@@ -320,8 +320,8 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
@Test
public
void
testColoringWithModelName
()
throws
Exception
{
String
input
=
"name\tcolor\tmap_name\n"
+
"s1\t#ff0000\txxx\n"
;
String
input
=
"name\tcolor\tmap_name\n"
+
"s1\t#ff0000\txxx\n"
;
Map
<
String
,
String
>
params
=
new
HashMap
<>();
params
.
put
(
TextFileUtils
.
COLUMN_COUNT_PARAM
,
"3"
);
...
...
@@ -333,8 +333,8 @@ public class ColorSchemaReaderTest extends ConverterTestFunctions {
@Test
public
void
testColoringWithMapName
()
throws
Exception
{
String
input
=
"name\tcolor\tmap_name\n"
+
"s1\t#ff0000\txxx\n"
;
String
input
=
"name\tcolor\tmap_name\n"
+
"s1\t#ff0000\txxx\n"
;
Map
<
String
,
String
>
params
=
new
HashMap
<>();
params
.
put
(
TextFileUtils
.
COLUMN_COUNT_PARAM
,
"3"
);
...
...
converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
View file @
09221ef7
...
...
@@ -183,8 +183,8 @@ public class OverviewParserTest extends ConverterTestFunctions {
*/
@Test
(
expected
=
InvalidOverviewFile
.
class
)
public
void
testParseInvalidCoordinates
()
throws
Exception
{
String
invalidCoordinates
=
"test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\n"
+
"test.png\t10,10 10,400 400,400 400,10\tmain.xml\t10,10\t4"
;
String
invalidCoordinates
=
"test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\n"
+
"test.png\t10,10 10,400 400,400 400,10\tmain.xml\t10,10\t4"
;
Set
<
Model
>
models
=
createValidTestMapModel
();
List
<
OverviewImage
>
images
=
new
ArrayList
<
OverviewImage
>();
...
...
@@ -199,9 +199,9 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public
void
testParseValidCoordinates
()
throws
Exception
{
String
invalidCoordinates
=
"FILE\tPOLYGON\tLINK_TARGET\tMODEL_COORDINATES\tMODEL_ZOOM_LEVEL\tLINK_TYPE\n"
+
"test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\tMODEL\n"
+
"test.png\t200,200 200,400 400,400 400,200\tmain.xml\t10,10\t4\tMODEL"
;
String
invalidCoordinates
=
"FILE\tPOLYGON\tLINK_TARGET\tMODEL_COORDINATES\tMODEL_ZOOM_LEVEL\tLINK_TYPE\n"
+
"test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\tMODEL\n"
+
"test.png\t200,200 200,400 400,400 400,200\tmain.xml\t10,10\t4\tMODEL"
;
Set
<
Model
>
models
=
createValidTestMapModel
();
List
<
OverviewImage
>
images
=
new
ArrayList
<
OverviewImage
>();
...
...
model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
View file @
09221ef7
...
...
@@ -365,11 +365,11 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
Layer
layer
=
new
Layer
();
LayerText
layerText
=
new
LayerText
();
layerText
.
setNotes
(
"colors check\n"
+
"SemanticZoomLevelVisibility: 3\n"
+
"SemanticZoomLevelTransparency: 4\n"
+
"BackgroundColor:#0000ee\n"
+
"BorderColor:#00ee00"
);
layerText
.
setNotes
(
"colors check\n"
+
"SemanticZoomLevelVisibility: 3\n"
+
"SemanticZoomLevelTransparency: 4\n"
+
"BackgroundColor:#0000ee\n"
+
"BorderColor:#00ee00"
);
layer
.
addLayerText
(
layerText
);
model
.
addLayer
(
layer
);
...
...
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