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minerva
core
Commits
1c9d80be
Commit
1c9d80be
authored
Sep 17, 2021
by
Piotr Gawron
Browse files
StringSetComparator removed
parent
7db011fc
Changes
9
Hide whitespace changes
Inline
Side-by-side
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
View file @
1c9d80be
...
...
@@ -11,7 +11,8 @@ import org.apache.logging.log4j.LogManager;
import
org.apache.logging.log4j.Logger
;
import
lcsb.mapviewer.annotation.cache.CachableInterface
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
import
lcsb.mapviewer.common.exception.NotImplementedException
;
import
lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical
;
...
...
@@ -437,7 +438,7 @@ public abstract class ElementAnnotator extends CachableInterface {
}
else
if
(
newCollection
==
null
||
newCollection
.
size
()
==
0
)
{
return
false
;
}
else
{
String
SetComparator
stringSetComparator
=
new
String
Set
Comparator
();
SetComparator
<
String
>
stringSetComparator
=
new
SetComparator
<>(
new
StringComparator
()
)
;
Set
<
String
>
set1
=
new
HashSet
<>();
Set
<
String
>
set2
=
new
HashSet
<>();
...
...
commons/src/main/java/lcsb/mapviewer/common/comparator/StringSetComparator.java
deleted
100644 → 0
View file @
7db011fc
package
lcsb.mapviewer.common.comparator
;
import
java.util.Comparator
;
import
java.util.Set
;
import
org.apache.logging.log4j.LogManager
;
import
org.apache.logging.log4j.Logger
;
/**
* Comparator used for comparing sets of strings.
*
* @author Piotr Gawron
*
*/
public
class
StringSetComparator
implements
Comparator
<
Set
<
String
>>
{
/**
* Default class logger.
*/
private
Logger
logger
=
LogManager
.
getLogger
();
@Override
public
int
compare
(
final
Set
<
String
>
arg0
,
final
Set
<
String
>
arg1
)
{
if
(
arg0
==
null
)
{
if
(
arg1
==
null
)
{
return
0
;
}
else
{
return
1
;
}
}
else
if
(
arg1
==
null
)
{
return
-
1
;
}
for
(
final
String
string
:
arg1
)
{
if
(!
arg0
.
contains
(
string
))
{
logger
.
debug
(
string
+
" couldn't be found in "
+
arg0
);
return
1
;
}
}
for
(
final
String
string
:
arg0
)
{
if
(!
arg1
.
contains
(
string
))
{
logger
.
debug
(
string
+
" couldn't be found in "
+
arg1
);
return
-
1
;
}
}
return
0
;
}
}
commons/src/test/java/lcsb/mapviewer/common/comparator/AllComparatorTests.java
View file @
1c9d80be
...
...
@@ -14,8 +14,6 @@ import org.junit.runners.Suite.SuiteClasses;
ListComparatorTest
.
class
,
PointComparatorTest
.
class
,
StringComparatorTest
.
class
,
StringListComparatorTest
.
class
,
StringSetComparatorTest
.
class
,
SetComparatorTest
.
class
,
})
public
class
AllComparatorTests
{
...
...
commons/src/test/java/lcsb/mapviewer/common/comparator/StringSetComparatorTest.java
deleted
100644 → 0
View file @
7db011fc
package
lcsb.mapviewer.common.comparator
;
import
static
org
.
junit
.
Assert
.
assertFalse
;
import
static
org
.
junit
.
Assert
.
assertTrue
;
import
java.util.HashSet
;
import
java.util.Set
;
import
org.junit.After
;
import
org.junit.Before
;
import
org.junit.Test
;
public
class
StringSetComparatorTest
{
@Before
public
void
setUp
()
throws
Exception
{
}
@After
public
void
tearDown
()
throws
Exception
{
}
@Test
public
void
testNotNullComparisonEqualLength
()
{
Set
<
String
>
list1
=
new
HashSet
<>();
Set
<
String
>
list2
=
new
HashSet
<>();
Set
<
String
>
list3
=
new
HashSet
<>();
list1
.
add
(
"str1"
);
list1
.
add
(
"x"
);
list2
.
add
(
"str2"
);
list2
.
add
(
"x"
);
list3
.
add
(
"x"
);
list3
.
add
(
"str1"
);
StringSetComparator
comp
=
new
StringSetComparator
();
assertTrue
(
comp
.
compare
(
list1
,
list3
)
==
0
);
assertFalse
(
comp
.
compare
(
list1
,
list2
)
==
0
);
assertFalse
(
comp
.
compare
(
list2
,
list3
)
==
0
);
}
@Test
public
void
testNotNullComparisonDiffLength
()
{
Set
<
String
>
list1
=
new
HashSet
<>();
Set
<
String
>
list2
=
new
HashSet
<>();
list1
.
add
(
"str1"
);
list2
.
add
(
"str2"
);
list2
.
add
(
"str1"
);
StringSetComparator
comp
=
new
StringSetComparator
();
assertFalse
(
comp
.
compare
(
list1
,
list2
)
==
0
);
assertFalse
(
comp
.
compare
(
list2
,
list1
)
==
0
);
}
@Test
public
void
testNullComparison
()
{
StringSetComparator
comp
=
new
StringSetComparator
();
assertTrue
(
comp
.
compare
(
null
,
null
)
==
0
);
assertFalse
(
comp
.
compare
(
new
HashSet
<>(),
null
)
==
0
);
assertFalse
(
comp
.
compare
(
null
,
new
HashSet
<>())
==
0
);
}
}
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
View file @
1c9d80be
...
...
@@ -20,8 +20,8 @@ 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.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.exception.InvalidArgumentException
;
import
lcsb.mapviewer.common.exception.InvalidXmlSchemaException
;
import
lcsb.mapviewer.common.exception.NotImplementedException
;
...
...
@@ -478,7 +478,7 @@ public class RestAnnotationParser {
if
(
element
.
getSynonyms
()
==
null
||
element
.
getSynonyms
().
size
()
==
0
)
{
element
.
setSynonyms
(
synonyms
);
}
else
{
String
SetComparator
stringSetComparator
=
new
String
Set
Comparator
();
SetComparator
<
String
>
stringSetComparator
=
new
SetComparator
<>(
new
StringComparator
()
)
;
Set
<
String
>
set1
=
new
HashSet
<
String
>();
Set
<
String
>
set2
=
new
HashSet
<
String
>();
set1
.
addAll
(
element
.
getSynonyms
());
...
...
model/src/main/java/lcsb/mapviewer/model/map/species/AntisenseRnaComparator.java
View file @
1c9d80be
...
...
@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
import
lcsb.mapviewer.common.Comparator
;
import
lcsb.mapviewer.common.Configuration
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.model.map.species.field.ModificationResidue
;
/**
...
...
@@ -54,7 +55,7 @@ public class AntisenseRnaComparator extends Comparator<AntisenseRna> {
@Override
protected
int
internalCompare
(
final
AntisenseRna
arg0
,
final
AntisenseRna
arg1
)
{
String
SetComparator
stringSetComparator
=
new
String
Set
Comparator
();
SetComparator
<
String
>
stringSetComparator
=
new
SetComparator
<>(
new
StringComparator
()
)
;
Set
<
String
>
set1
=
new
HashSet
<>();
Set
<
String
>
set2
=
new
HashSet
<>();
...
...
model/src/main/java/lcsb/mapviewer/model/map/species/GeneComparator.java
View file @
1c9d80be
...
...
@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
import
lcsb.mapviewer.common.Comparator
;
import
lcsb.mapviewer.common.Configuration
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.model.map.species.field.ModificationResidue
;
import
lcsb.mapviewer.modelutils.map.ElementUtils
;
...
...
@@ -55,7 +56,7 @@ public class GeneComparator extends Comparator<Gene> {
@Override
protected
int
internalCompare
(
final
Gene
arg0
,
final
Gene
arg1
)
{
String
SetComparator
stringSetComparator
=
new
String
Set
Comparator
();
SetComparator
<
String
>
stringSetComparator
=
new
SetComparator
<>(
new
StringComparator
()
)
;
Set
<
String
>
set1
=
new
HashSet
<>();
Set
<
String
>
set2
=
new
HashSet
<>();
...
...
model/src/main/java/lcsb/mapviewer/model/map/species/ProteinComparator.java
View file @
1c9d80be
...
...
@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
import
lcsb.mapviewer.common.Comparator
;
import
lcsb.mapviewer.common.Configuration
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.model.map.species.field.ModificationResidue
;
import
lcsb.mapviewer.model.map.species.field.StructuralStateComparator
;
...
...
@@ -60,7 +61,7 @@ public class ProteinComparator extends Comparator<Protein> {
@Override
protected
int
internalCompare
(
final
Protein
arg0
,
final
Protein
arg1
)
{
StructuralStateComparator
structuralStateComparator
=
new
StructuralStateComparator
(
epsilon
);
String
SetComparator
stringSetComparator
=
new
String
Set
Comparator
();
SetComparator
<
String
>
stringSetComparator
=
new
SetComparator
<>(
new
StringComparator
()
)
;
if
(
structuralStateComparator
.
compare
(
arg0
.
getStructuralState
(),
arg1
.
getStructuralState
())
!=
0
)
{
logger
.
debug
(
"structural state different: "
+
arg0
.
getStructuralState
()
+
", "
+
arg1
.
getStructuralState
());
...
...
model/src/main/java/lcsb/mapviewer/model/map/species/RnaComparator.java
View file @
1c9d80be
...
...
@@ -8,7 +8,8 @@ import org.apache.logging.log4j.Logger;
import
lcsb.mapviewer.common.Comparator
;
import
lcsb.mapviewer.common.Configuration
;
import
lcsb.mapviewer.common.comparator.StringSetComparator
;
import
lcsb.mapviewer.common.comparator.SetComparator
;
import
lcsb.mapviewer.common.comparator.StringComparator
;
import
lcsb.mapviewer.model.map.species.field.ModificationResidue
;
/**
...
...
@@ -54,7 +55,7 @@ public class RnaComparator extends Comparator<Rna> {
@Override
protected
int
internalCompare
(
final
Rna
arg0
,
final
Rna
arg1
)
{
String
SetComparator
stringSetComparator
=
new
String
Set
Comparator
();
SetComparator
<
String
>
stringSetComparator
=
new
SetComparator
<>(
new
StringComparator
()
)
;
Set
<
String
>
set1
=
new
HashSet
<>();
Set
<
String
>
set2
=
new
HashSet
<>();
...
...
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