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minerva
core
Commits
859dcef4
Commit
859dcef4
authored
Sep 15, 2021
by
Piotr Gawron
Browse files
remove empty javadoc tags
parent
09221ef7
Changes
43
Hide whitespace changes
Inline
Side-by-side
annotation/src/main/java/lcsb/mapviewer/annotation/cache/BigFileCache.java
View file @
859dcef4
...
...
@@ -230,7 +230,6 @@ public class BigFileCache {
* @return new {@link BigFileEntry} for given url
* @throws URISyntaxException
* thrown when url is invalid
* @throws IOException
*/
private
BigFileEntry
createEntryForBigFile
(
final
String
url
)
throws
URISyntaxException
,
IOException
{
String
localPath
=
configurationDao
.
getValueByType
(
ConfigurationElementType
.
BIG_FILE_STORAGE_DIR
);
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCache.java
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859dcef4
...
...
@@ -89,9 +89,7 @@ public class PermanentDatabaseLevelCache implements PermanentDatabaseLevelCacheI
/**
* http://forum.spring.io/forum/spring-projects/aop/52011-need-to-unwrap-a-proxy-to-get-the-object-being-proxied
*
* @param bean
* @return
* @throws Exception
*/
private
final
Object
unwrapProxy
(
final
Object
bean
)
throws
Exception
{
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheInterface.java
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859dcef4
...
...
@@ -24,8 +24,6 @@ public interface PermanentDatabaseLevelCacheInterface extends QueryCacheInterfac
/**
* Waits for all tasks in the cache to finish (refresh/get/etc).
*
* @throws ExecutionException
* @throws InterruptedException
*/
void
waitToFinishTasks
()
throws
InterruptedException
,
ExecutionException
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
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859dcef4
...
...
@@ -224,7 +224,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
* organisms names. If the value has not been set by the user, null
* will be passed.
* @return {@link MiriamType#PUBMED}s found on the page
* @throws UniprotSearchException
*/
private
Collection
<
MiriamData
>
parseKegg
(
final
String
pageContent
,
final
AnnotatorData
params
)
throws
UniprotSearchException
{
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java
View file @
859dcef4
...
...
@@ -331,7 +331,6 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
* {@link #referenceGenome}
* @param name
* {@link #name}
* @throws ReferenceGenomeConnectorException
*/
private
DownloadGeneMappingGenomeVersionTask
(
final
ReferenceGenome
referenceGenome
,
final
String
name
,
final
String
url
,
final
IProgressUpdater
updater
)
throws
ReferenceGenomeConnectorException
{
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
View file @
859dcef4
...
...
@@ -126,9 +126,6 @@ public class MeSHParserTest extends AnnotationTestFunctions {
parserUnderTest
.
getMeSH
(
meshID
);
}
/**
* @throws Exception
*/
@Test
public
void
testExternalDBStatus
()
throws
Exception
{
ExternalServiceStatus
status
=
meshParser
.
getServiceStatus
();
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/services/PubmedParserTest.java
View file @
859dcef4
...
...
@@ -104,8 +104,6 @@ public class PubmedParserTest extends AnnotationTestFunctions {
/**
* This case was problematic with old API used to retrieve data from pubmed
*
* @throws PubmedSearchException
*/
@Test
public
void
testProblematicCase
()
throws
PubmedSearchException
{
...
...
checkstyle.xml
View file @
859dcef4
...
...
@@ -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"
/>
...
...
@@ -258,7 +258,7 @@
<property
name=
"allowSamelineMultipleAnnotations"
value=
"true"
/>
</module>
<module
name=
"NonEmptyAtclauseDescription"
/>
<module name="InvalidJavadocPosition"/>
<!--
<module name="InvalidJavadocPosition"/>
<module name="JavadocTagContinuationIndentation"/>
<module name="SummaryJavadoc">
<property name="forbiddenSummaryFragments"
...
...
commons/src/main/java/lcsb/mapviewer/common/MinervaLoggerAppender.java
View file @
859dcef4
...
...
@@ -67,11 +67,6 @@ public class MinervaLoggerAppender extends AbstractAppender {
* Private constructor preventing instantiation. Appender should be created
* using factory method: {@link MinervaLoggerAppender#createAppender()}.
*
* @param name
* @param filter
* @param layout
* @param ignoreExceptions
* @param currentThreadLogOnly
*/
private
MinervaLoggerAppender
(
final
String
name
,
final
Filter
filter
,
final
Layout
<?
extends
Serializable
>
layout
,
final
boolean
ignoreExceptions
,
final
boolean
currentThreadLogOnly
)
{
...
...
commons/src/main/java/lcsb/mapviewer/common/geometry/ColorParser.java
View file @
859dcef4
...
...
@@ -135,8 +135,6 @@ public class ColorParser {
/**
* Transforms {@link Color} into html RGB representation: #RRGGBB
*
* @param color
* @return
*/
public
String
colorToHtml
(
final
Color
color
)
{
...
...
commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java
View file @
859dcef4
...
...
@@ -15,6 +15,7 @@ import lcsb.mapviewer.common.Configuration;
*
*/
public
class
PointTransformation
{
/**
* Default class logger.
*/
...
...
@@ -77,9 +78,6 @@ public class PointTransformation {
/**
* Returns a point on line.
*
* @param start
* @param end
* @param coef
* @return {@link Point2D} on line defined by input points
*/
public
Point2D
getPointOnLine
(
final
Point2D
start
,
final
Point2D
end
,
final
double
coef
)
{
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
View file @
859dcef4
...
...
@@ -631,7 +631,6 @@ public class CellDesignerXmlParser extends Converter {
* @return CellDesigner xml string for the model
* @throws InconsistentModelException
* thrown when then model is invalid
* @throws InconsistentModelException
*/
public
String
model2Xml
(
final
Model
model
,
final
boolean
appendWarnings
)
throws
InconsistentModelException
{
MinervaLoggerAppender
appender
=
MinervaLoggerAppender
.
createAppender
();
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java
View file @
859dcef4
...
...
@@ -27,8 +27,6 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
* from CellDesigner specific format into standard layout.
*
* @author Piotr Gawron
*
* @param <T>
*/
public
abstract
class
AbstractCellDesignerAliasConverter
<
T
extends
Element
>
implements
ICellDesignerAliasConverter
<
T
>
{
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ICellDesignerAliasConverter.java
View file @
859dcef4
...
...
@@ -12,10 +12,9 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
* from objects retrieved from CellDesigner xml into absolute values.
*
* @author Piotr Gawron
*
* @param <T>
*/
public
interface
ICellDesignerAliasConverter
<
T
extends
Element
>
{
/**
* This method computes which anchor is the most probable for describing the
* point on the border of alias. There are 16 possible anchors on the border of
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
View file @
859dcef4
...
...
@@ -565,7 +565,6 @@ public class ReactionFromXml {
* @param result
* initial data
* @return reaction with a new type
* @throws ReactionParserException
*/
Reaction
createProperTypeReaction
(
final
String
type
,
final
Reaction
result
)
throws
ReactionParserException
{
ReactionLineData
rdl
=
ReactionLineData
.
getByCellDesignerString
(
type
);
...
...
@@ -585,7 +584,6 @@ public class ReactionFromXml {
* @throws InvalidXmlSchemaException
* thrown when xml node contains data that is not supported by xml
* schema
* @throws ReactionParserException
*/
private
EditPoints
gateMembersToPoints
(
final
Reaction
reaction
,
final
Node
gateMembers
)
throws
InvalidXmlSchemaException
,
ReactionParserException
{
...
...
@@ -643,7 +641,6 @@ public class ReactionFromXml {
*
* @param modifier
* modifier to update
* @throws ReactionParserException
*/
private
void
createLineForModifier
(
final
Modifier
modifier
)
throws
ReactionParserException
{
try
{
...
...
@@ -1125,7 +1122,6 @@ public class ReactionFromXml {
* information about points
* @param hasGateMemebers
* does the reaction has gate members
* @param rld
* @throws ReactionParserException
* thrown when data for reaction is invalid
*/
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
View file @
859dcef4
...
...
@@ -387,7 +387,6 @@ public enum ReactionLineData {
* original data
* @return instance of {@link Reaction} represented by this enum and copies the
* data from result parameter
* @throws ReactionParserException
*/
public
Reaction
createReaction
(
final
Reaction
result
)
throws
ReactionParserException
{
try
{
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
View file @
859dcef4
...
...
@@ -115,7 +115,6 @@ public class ReactionToXml {
* @param reaction
* reaction to transform
* @return xml representation of reaction
* @throws ConverterException
*/
public
String
toXml
(
final
Reaction
reaction
)
throws
InconsistentModelException
{
if
(
reaction
.
getReactants
().
get
(
0
).
getElement
().
equals
(
reaction
.
getProducts
().
get
(
0
).
getElement
()))
{
...
...
@@ -167,7 +166,6 @@ public class ReactionToXml {
* @param reaction
* reaction for which list is generated
* @return xml node with list of modification
* @throws InconsistentModelException
*/
private
String
getListOfModificationsXmlStringForReaction
(
final
Reaction
reaction
)
throws
InconsistentModelException
{
StringBuilder
sb
=
new
StringBuilder
();
...
...
@@ -327,7 +325,6 @@ public class ReactionToXml {
* @param gate
* operator to which modifier is connected (if any)
* @return xml node for given modifier
* @throws InconsistentModelException
*/
private
String
getModifierXmlString
(
final
Modifier
modifier
,
final
NodeOperator
gate
)
throws
InconsistentModelException
{
StringBuilder
sb
=
new
StringBuilder
();
...
...
@@ -499,7 +496,6 @@ public class ReactionToXml {
* @param reaction
* reaction to be processed
* @return xml node representing annotation part
* @throws InconsistentModelException
*/
private
String
getAnnotationXmlStringForReaction
(
final
Reaction
reaction
)
throws
InconsistentModelException
{
String
reactionClassString
=
getCellDesignerReactionTypeString
(
reaction
);
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
View file @
859dcef4
...
...
@@ -67,7 +67,6 @@ public class ReactionXmlParser {
* @param reaction
* reaction to transform
* @return xml representation of reaction
* @throws ConverterException
*/
public
String
toXml
(
final
Reaction
reaction
)
throws
InconsistentModelException
{
return
reactionToXml
.
toXml
(
reaction
);
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
View file @
859dcef4
...
...
@@ -122,7 +122,6 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* {@link Pair#getRight()}.
* @throws InvalidXmlSchemaException
* thrown when xml is invalid
* @throws CompartmentParserException
*/
public
abstract
Pair
<
String
,
T
>
parseXmlElement
(
final
Node
node
)
throws
InvalidXmlSchemaException
,
CellDesignerParserException
;
...
...
@@ -139,7 +138,6 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* {@link Pair#getRight()}.
* @throws InvalidXmlSchemaException
* thrown when xmlString is invalid
* @throws CellDesignerParserException
*/
public
Pair
<
String
,
T
>
parseXmlElement
(
final
String
xmlString
)
throws
InvalidXmlSchemaException
,
CellDesignerParserException
{
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/fields/LineProperties.java
View file @
859dcef4
...
...
@@ -40,8 +40,6 @@ public class LineProperties {
/**
* Create properties from {@link PolylineData}.
*
* @param line
*/
public
LineProperties
(
final
PolylineData
line
)
{
width
=
line
.
getWidth
();
...
...
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