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minerva
core
Commits
7db011fc
Commit
7db011fc
authored
Sep 17, 2021
by
Piotr Gawron
Browse files
StringListComparator removed
parent
a3c43f90
Changes
7
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Inline
Side-by-side
commons/src/main/java/lcsb/mapviewer/common/comparator/StringListComparator.java
deleted
100644 → 0
View file @
a3c43f90
package
lcsb.mapviewer.common.comparator
;
import
java.util.Comparator
;
import
java.util.List
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
/**
* Comparator used for list of strings.
*
* @author Piotr Gawron
*
*/
public
class
StringListComparator
implements
Comparator
<
List
<
String
>>
{
/**
* Default class logger.
*/
private
static
Logger
logger
=
LogManager
.
getLogger
();
/**
* String comparator used for comparing strings.
*/
private
StringComparator
stringComparator
=
new
StringComparator
();
/**
* Integer comparator used for comparing integers.
*/
private
IntegerComparator
integerComparator
=
new
IntegerComparator
();
@Override
public
int
compare
(
final
List
<
String
>
arg0
,
final
List
<
String
>
arg1
)
{
if
(
arg0
==
null
)
{
if
(
arg1
==
null
)
{
return
0
;
}
else
{
return
1
;
}
}
else
if
(
arg1
==
null
)
{
return
-
1
;
}
if
(
arg0
.
size
()
!=
arg1
.
size
())
{
logger
.
debug
(
"String lists have different size: "
+
arg0
.
size
()
+
", "
+
arg1
.
size
());
return
integerComparator
.
compare
(
arg0
.
size
(),
arg1
.
size
());
}
for
(
int
i
=
0
;
i
<
arg0
.
size
();
i
++)
{
if
(
stringComparator
.
compare
(
arg0
.
get
(
i
),
arg1
.
get
(
i
))
!=
0
)
{
logger
.
debug
(
"Strings in list different: \""
+
arg0
.
get
(
i
)
+
"\", \""
+
arg1
.
get
(
i
)
+
"\""
);
return
stringComparator
.
compare
(
arg0
.
get
(
i
),
arg1
.
get
(
i
));
}
}
return
0
;
}
}
commons/src/test/java/lcsb/mapviewer/common/comparator/StringListComparatorTest.java
deleted
100644 → 0
View file @
a3c43f90
package
lcsb.mapviewer.common.comparator
;
import
static
org
.
junit
.
Assert
.
assertFalse
;
import
static
org
.
junit
.
Assert
.
assertTrue
;
import
java.util.ArrayList
;
import
java.util.List
;
import
org.junit.After
;
import
org.junit.Before
;
import
org.junit.Test
;
public
class
StringListComparatorTest
{
@Before
public
void
setUp
()
throws
Exception
{
}
@After
public
void
tearDown
()
throws
Exception
{
}
@Test
public
void
testNotNullComparisonEqualLength
()
{
List
<
String
>
list1
=
new
ArrayList
<>();
List
<
String
>
list2
=
new
ArrayList
<>();
List
<
String
>
list3
=
new
ArrayList
<>();
list1
.
add
(
"str1"
);
list2
.
add
(
"str2"
);
list3
.
add
(
"str1"
);
StringListComparator
comp
=
new
StringListComparator
();
assertTrue
(
comp
.
compare
(
list1
,
list3
)
==
0
);
assertFalse
(
comp
.
compare
(
list1
,
list2
)
==
0
);
assertFalse
(
comp
.
compare
(
list2
,
list3
)
==
0
);
}
@Test
public
void
testNotNullComparisonDiffLength
()
{
List
<
String
>
list1
=
new
ArrayList
<>();
List
<
String
>
list2
=
new
ArrayList
<>();
list1
.
add
(
"str1"
);
list2
.
add
(
"str2"
);
list2
.
add
(
"str1"
);
StringListComparator
comp
=
new
StringListComparator
();
assertFalse
(
comp
.
compare
(
list1
,
list2
)
==
0
);
}
@Test
public
void
testNullComparison
()
{
StringListComparator
comp
=
new
StringListComparator
();
assertTrue
(
comp
.
compare
(
null
,
null
)
==
0
);
assertFalse
(
comp
.
compare
(
new
ArrayList
<>(),
null
)
==
0
);
assertFalse
(
comp
.
compare
(
null
,
new
ArrayList
<>())
==
0
);
}
}
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
View file @
7db011fc
...
...
@@ -20,6 +20,7 @@ import org.xml.sax.SAXParseException;
import
lcsb.mapviewer.common.XmlParser
;
import
lcsb.mapviewer.common.exception.InvalidStateException
;
import
lcsb.mapviewer.common.geometry.DoubleDimension
;
import
lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine
;
import
lcsb.mapviewer.converter.model.celldesigner.structure.fields.View
;
import
lcsb.mapviewer.model.map.MiriamRelationType
;
...
...
@@ -32,31 +33,8 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
*/
public
class
CommonXmlParser
{
private
static
class
DimensionDouble
extends
Dimension2D
{
private
double
width
;
private
double
height
;
@Override
public
double
getWidth
()
{
return
width
;
}
@Override
public
double
getHeight
()
{
return
height
;
}
@Override
public
void
setSize
(
final
double
width
,
final
double
height
)
{
this
.
width
=
width
;
this
.
height
=
height
;
}
}
public
static
final
Set
<
MiriamRelationType
>
RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER
=
new
HashSet
<>();
{
RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER
.
addAll
(
Arrays
.
asList
(
MiriamRelationType
.
values
()));
RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER
.
remove
(
MiriamRelationType
.
BQ_MODEL_IS_DERIVED_FROM
);
...
...
@@ -120,8 +98,7 @@ public class CommonXmlParser {
public
Dimension2D
getDimension
(
final
Node
node
)
{
double
width
=
Double
.
parseDouble
(
XmlParser
.
getNodeAttr
(
"width"
,
node
));
double
height
=
Double
.
parseDouble
(
XmlParser
.
getNodeAttr
(
"height"
,
node
));
DimensionDouble
result
=
new
DimensionDouble
();
result
.
setSize
(
width
,
height
);
DoubleDimension
result
=
new
DoubleDimension
(
width
,
height
);
return
result
;
}
...
...
@@ -147,7 +124,8 @@ public class CommonXmlParser {
*/
public
Color
getColor
(
final
Node
node
)
{
String
color
=
XmlParser
.
getNodeAttr
(
"color"
,
node
);
// cellDesigner has a bug that removes info about alpha when alpha is 0 (#1103)
// cellDesigner has a bug that removes info about alpha when alpha is 0
// (#1103)
color
=
StringUtils
.
leftPad
(
color
,
8
,
"0"
);
return
XmlParser
.
stringToColor
(
color
);
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
View file @
7db011fc
...
...
@@ -19,8 +19,8 @@ import org.w3c.dom.Node;
import
lcsb.mapviewer.common.XmlParser
;
import
lcsb.mapviewer.common.comparator.DoubleComparator
;
import
lcsb.mapviewer.common.comparator.IntegerComparator
;
import
lcsb.mapviewer.common.comparator.ListComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.common.comparator.StringListComparator
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
import
lcsb.mapviewer.common.exception.InvalidXmlSchemaException
;
...
...
@@ -506,7 +506,7 @@ public class RestAnnotationParser {
if
(
element
.
getFormerSymbols
()
==
null
||
element
.
getFormerSymbols
().
size
()
==
0
)
{
element
.
setFormerSymbols
(
formerSymbols
);
}
else
{
String
ListComparator
stringListComparator
=
new
String
List
Comparator
();
ListComparator
<
String
>
stringListComparator
=
new
ListComparator
<>(
new
StringComparator
()
)
;
if
(
stringListComparator
.
compare
(
element
.
getFormerSymbols
(),
formerSymbols
)
!=
0
)
{
logger
.
warn
(
elementUtils
.
getElementTag
(
element
)
+
" Former symbols list different than default ["
+
formerSymbols
+
"]["
+
element
.
getFormerSymbols
()
+
"]. Ignoring."
);
...
...
model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
View file @
7db011fc
...
...
@@ -4,8 +4,8 @@ import org.apache.logging.log4j.LogManager;
import
org.apache.logging.log4j.Logger
;
import
lcsb.mapviewer.common.Comparator
;
import
lcsb.mapviewer.common.comparator.ListComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.common.comparator.StringListComparator
;
public
class
SbmlFunctionComparator
extends
Comparator
<
SbmlFunction
>
{
private
static
Logger
logger
=
LogManager
.
getLogger
();
...
...
@@ -17,7 +17,7 @@ public class SbmlFunctionComparator extends Comparator<SbmlFunction> {
@Override
protected
int
internalCompare
(
final
SbmlFunction
arg0
,
final
SbmlFunction
arg1
)
{
StringComparator
stringComparator
=
new
StringComparator
();
String
ListComparator
stringListComparator
=
new
String
ListComparator
(
);
ListComparator
<
String
>
stringListComparator
=
new
ListComparator
<>(
stringComparator
);
if
(
stringComparator
.
compare
(
arg0
.
getFunctionId
(),
arg1
.
getFunctionId
())
!=
0
)
{
logger
.
debug
(
"functionId different"
);
return
stringComparator
.
compare
(
arg0
.
getFunctionId
(),
arg1
.
getFunctionId
());
...
...
model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
View file @
7db011fc
...
...
@@ -8,10 +8,10 @@ import lcsb.mapviewer.common.Configuration;
import
lcsb.mapviewer.common.comparator.BooleanComparator
;
import
lcsb.mapviewer.common.comparator.DoubleComparator
;
import
lcsb.mapviewer.common.comparator.IntegerComparator
;
import
lcsb.mapviewer.common.comparator.ListComparator
;
import
lcsb.mapviewer.common.comparator.PointComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.common.comparator.StringListComparator
;
import
lcsb.mapviewer.model.graphics.PolylineDataComparator
;
import
lcsb.mapviewer.model.map.MiriamData
;
import
lcsb.mapviewer.model.map.MiriamDataComparator
;
...
...
@@ -130,7 +130,7 @@ public class ReactionComparator extends Comparator<Reaction> {
return
doubleComparator
.
compare
(
arg0
.
getUpperBound
(),
arg1
.
getUpperBound
());
}
String
ListComparator
stringListComparator
=
new
String
ListComparator
(
);
ListComparator
<
String
>
stringListComparator
=
new
ListComparator
<>(
stringComparator
);
if
(
stringListComparator
.
compare
(
arg0
.
getSynonyms
(),
arg1
.
getSynonyms
())
!=
0
)
{
logger
.
debug
(
"Synonyms dataset different"
);
...
...
model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
View file @
7db011fc
...
...
@@ -9,9 +9,9 @@ import lcsb.mapviewer.common.comparator.ColorComparator;
import
lcsb.mapviewer.common.comparator.DoubleComparator
;
import
lcsb.mapviewer.common.comparator.EnumComparator
;
import
lcsb.mapviewer.common.comparator.IntegerComparator
;
import
lcsb.mapviewer.common.comparator.ListComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.common.comparator.StringListComparator
;
import
lcsb.mapviewer.model.graphics.HorizontalAlign
;
import
lcsb.mapviewer.model.graphics.VerticalAlign
;
import
lcsb.mapviewer.model.map.MiriamData
;
...
...
@@ -168,7 +168,7 @@ public class ElementComparator extends Comparator<Element> {
return
stringComparator
.
compare
(
arg0
.
getFormula
(),
arg1
.
getFormula
());
}
String
ListComparator
stringListComparator
=
new
String
ListComparator
(
);
ListComparator
<
String
>
stringListComparator
=
new
ListComparator
<>(
stringComparator
);
if
(
stringListComparator
.
compare
(
arg0
.
getSynonyms
(),
arg1
.
getSynonyms
())
!=
0
)
{
logger
.
debug
(
"List of synonyms different"
);
...
...
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