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minerva
core
Commits
0cc66184
Commit
0cc66184
authored
Sep 15, 2021
by
Piotr Gawron
Browse files
javadoc formattng issues
parent
7af9e4ce
Changes
17
Hide whitespace changes
Inline
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CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java
View file @
0cc66184
...
...
@@ -14,7 +14,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
/**
* This class represent a plugin to cell designer with copy past functionality
* that allows to copy and paste notes and annotations of species.
*
*
<p>
* It overrides:
* <ul>
* <li>ALT + CTRL + C shortcut - copy annotations from selected element into
...
...
@@ -24,6 +24,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
* element(s), if many elements are selected then all elements will be modified,
* </li>
* </ul>
* </p>
*
* @author Piotr Gawron
*
...
...
CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java
View file @
0cc66184
...
...
@@ -22,8 +22,9 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
* This class represent a plugin to CellDesigner that add info text box with
* informations about species. Plugin run in pooling mode (there is no other way
* in CellDesigner...).
*
*
<p>
* It overrides <i>CTRL + T shortcut</i> - shows/hide info text window.
* </p>
*
* @author Piotr Gawron
*
...
...
@@ -87,9 +88,9 @@ public class InfoPlugin extends CellDesignerPlugin {
onChangeSelectListener
=
new
ActionListener
()
{
/**
* This string contains a simple hash of all species shown in the last
run of
* this listener. Due to this information we don't have to
refresh this
* information at every run.
* This string contains a simple hash of all species shown in the last
*
run of
this listener. Due to this information we don't have to
*
refresh this
information at every run.
*/
private
String
selectedElementsId
=
""
;
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
View file @
0cc66184
...
...
@@ -147,9 +147,10 @@ public class ModelAnnotator {
* <li>notes,</li>
* <li>other elements with the same name and type.</li>
* </ul>
*
*
<p>
* This method copies data to elements without annotations from other elements
* with the same name and type.
* </p>
*
* @param model
* model in which element annotations are updated
...
...
@@ -184,8 +185,9 @@ public class ModelAnnotator {
* this map contains lists of {@link ElementAnnotator} objects that
* should be used for a given classes
* @param annotatorsParams
* this map contains lists of {@link AnnotatorConfigParameter} objects
* that should be used for a given {@link ElementAnnotator} class
* this map contains lists of {@link AnnotatorConfigParameter}
* objects that should be used for a given {@link ElementAnnotator}
* class
* @param model
* model where annotation should be updated
* @param progressUpdater
...
...
@@ -238,8 +240,8 @@ public class ModelAnnotator {
}
/**
* Returns list of default {@link ElementAnnotator} names that are available
for
* class given in the parameter.
* Returns list of default {@link ElementAnnotator} names that are available
*
for
class given in the parameter.
*
* @param clazz
* class for which list of default annotators will be returned
...
...
@@ -261,11 +263,11 @@ public class ModelAnnotator {
* @param m
* model
* @param updater
* updater call back function that update information about progress
of
* the function
* updater call back function that update information about progress
*
of
the function
* @param validAnnotations
* map that contains information which {@link MiriamType miriam
types}
* are valid for which class
* map that contains information which {@link MiriamType miriam
*
types}
are valid for which class
* @return list of improper annotations
*/
public
Collection
<
ImproperAnnotations
>
findImproperAnnotations
(
final
Model
m
,
final
IProgressUpdater
updater
,
...
...
@@ -337,8 +339,8 @@ public class ModelAnnotator {
* @param m
* model where the search is performed
* @param requestedAnnotations
* map that contains information which {@link MiriamType miriam
types}
* are obligatory for which class
* map that contains information which {@link MiriamType miriam
*
types}
are obligatory for which class
*
* @return list of all elements that miss annotation
*/
...
...
@@ -372,9 +374,10 @@ public class ModelAnnotator {
* @param element
* object to be checked
* @param requestedAnnotations
* at list one of this annotations should appear in the element, if the
* list is null then check is skipped, if the list is empty (size()==0)
* then method checks if element contains at least one miriam
* at list one of this annotations should appear in the element, if
* the list is null then check is skipped, if the list is empty
* (size()==0) then method checks if element contains at least one
* miriam
* @return list of containing improper annotations about element
*/
private
List
<
ProblematicAnnotation
>
findMissing
(
final
BioEntity
element
,
final
Collection
<
MiriamType
>
requestedAnnotations
)
{
...
...
@@ -446,8 +449,8 @@ public class ModelAnnotator {
}
/**
* Converts list of strings into list of {@link ElementAnnotator}. Strings
must
* be valid {@link ElementAnnotator} common names.
* Converts list of strings into list of {@link ElementAnnotator}. Strings
*
must
be valid {@link ElementAnnotator} common names.
*
* @param list
* list of {@link ElementAnnotator#getCommonName()}.
...
...
@@ -505,11 +508,11 @@ public class ModelAnnotator {
}
/**
* Returns map with informations about default required {@link MiriamType
miriam
* types } for {@link BioEntity} class type.
* Returns map with informations about default required {@link MiriamType
*
miriam
types } for {@link BioEntity} class type.
*
* @return map with informations about required {@link MiriamType miriam types
}
* for {@link BioEntity} class type
* @return map with informations about required {@link MiriamType miriam types
*
}
for {@link BioEntity} class type
*/
@SuppressWarnings
(
"unchecked"
)
public
Map
<
Class
<?
extends
BioEntity
>,
Set
<
MiriamType
>>
getDefaultRequiredClasses
()
{
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
View file @
0cc66184
...
...
@@ -37,7 +37,6 @@ import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
* UniProt IDs would be indistinguishable from the UniProt IDs describing the
* molecule.
*
*
* @author David Hoksza
*
*/
...
...
@@ -95,9 +94,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
return
false
;
}
if
(
identifier
.
getDataType
().
equals
(
MiriamType
.
TAIR_LOCUS
))
{
// UniProt are only obained from TAIR's which were provided by the annotator
// UniProt are only obained from TAIR's which were provided by the
// annotator
// (otherwise we would get
// also UniProt IDs for, e.g., homologous genes' TAIR IDs obtained from KEGG
// also UniProt IDs for, e.g., homologous genes' TAIR IDs obtained from
// KEGG
Collection
<
MiriamData
>
collection
=
tairToUniprot
(
identifier
);
if
(
collection
.
size
()
>
0
)
{
object
.
addMiriamData
(
collection
);
...
...
@@ -137,8 +138,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
/**
* Returns URL to UniProt result containing mapped UniProtIds for submitted
TAIR
* entry.
* Returns URL to UniProt result containing mapped UniProtIds for submitted
*
TAIR
entry.
*
* @param tairId
* TAIR identifier
...
...
@@ -153,8 +154,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
/**
* Parse UniProt result page which contains list of Uniprot ids mapped to
* submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT}
and
* returns it.
* submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT}
*
and
returns it.
*
* @param pageContent
* uniprot REST API result page
...
...
@@ -174,10 +175,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
/**
* Transform TAIR identifier into uniprot identifier.
*
* Used to use the TAIR record page, but that tends to change and moreover TAIR
* limits number of accesses from an address. So now the transformation queries
* directly UniProt from which the mapping can be obtained as well.
* <p>
* Used to use the TAIR record page, but that tends to change and moreover
* TAIR limits number of accesses from an address. So now the transformation
* queries directly UniProt from which the mapping can be obtained as well.
* </p>
*
* @param tair
* {@link MiriamData} with TAIR identifier
...
...
checkstyle.xml
View file @
0cc66184
...
...
@@ -259,13 +259,9 @@
</module>
<module
name=
"NonEmptyAtclauseDescription"
/>
<module
name=
"InvalidJavadocPosition"
/>
<!-- <module name="JavadocTagContinuationIndentation"/>
<module name="SummaryJavadoc">
<property name="forbiddenSummaryFragments"
value="^@return the *|^This method returns |^A [{]@code [a-zA-Z0-9]+[}]( is a )"/>
</module>
<module
name=
"JavadocTagContinuationIndentation"
/>
<module
name=
"JavadocParagraph"
/>
<module name="AtclauseOrder">
<!--
<module name="AtclauseOrder">
<property name="tagOrder" value="@param, @return, @throws, @deprecated"/>
<property name="target"
value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>
...
...
@@ -308,6 +304,10 @@
<property name="separateLineBetweenGroups" value="true"/>
<property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
<property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/>
</module>
<module name="SummaryJavadoc">
<property name="forbiddenSummaryFragments"
value="^@return the *|^This method returns |^A [{]@code [a-zA-Z0-9]+[}]( is a )"/>
</module>
-->
</module>
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerLineTransformation.java
View file @
0cc66184
...
...
@@ -36,13 +36,13 @@ public class CellDesignerLineTransformation extends LineTransformation {
/**
* Transform data in CellDesigner format into typical x,y coordinates for all
* points.
*
* CellDesigner format stores coordinates of a line in a different base. In
this
* base we have two points that define a base: vector between these
points is 1
* unit in first coordinate, and orthogonal vector to the one
mentioned before
* is 1 unit in the second coordinate. Moreover, these two
points defining base
* belong to this line.
*
*
<p>
* CellDesigner format stores coordinates of a line in a different base. In
*
this
base we have two points that define a base: vector between these
*
points is 1
unit in first coordinate, and orthogonal vector to the one
*
mentioned before
is 1 unit in the second coordinate. Moreover, these two
*
points defining base
belong to this line.
*
</p>
*
* @param startPoint
* first point defining CellDesigner base
...
...
@@ -70,7 +70,8 @@ public class CellDesignerLineTransformation extends LineTransformation {
double
distDx
=
dx1
*
dx1
+
dy1
*
dy1
;
// this is special case if end and start point are equal then CellDesigner uses
// this is special case if end and start point are equal then CellDesigner
// uses
// relative coordinates
if
(
distDx
<=
Configuration
.
EPSILON
)
{
dx1
=
1
;
...
...
@@ -99,17 +100,18 @@ public class CellDesignerLineTransformation extends LineTransformation {
/**
* Transform line of typical x,y coordinates into coordinates used by
* CellDesigner.
*
* CellDesigner format stores coordinates of a line in a different base. In this
* base we have two points that define a base: vector between these points is 1
* unit in first coordinate, and orthogonal vector to the one mentioned before
* is 1 unit in the second coordinate. These two points are the first and the
* last.
* <p>
* CellDesigner format stores coordinates of a line in a different base. In
* this base we have two points that define a base: vector between these
* points is 1 unit in first coordinate, and orthogonal vector to the one
* mentioned before is 1 unit in the second coordinate. These two points are
* the first and the last.
* </p>
*
* @param line
* line to be transformed into CellDesigner format
* @return points of the line in CellDesigner format (without the first and
the
* last)
* @return points of the line in CellDesigner format (without the first and
*
the
last)
*/
public
List
<
Point2D
>
getPointsFromLine
(
final
PolylineData
line
)
{
if
(
line
==
null
)
{
...
...
@@ -131,7 +133,8 @@ public class CellDesignerLineTransformation extends LineTransformation {
List
<
Point2D
>
result
=
new
ArrayList
<
Point2D
>();
if
(
dy
*
dy
+
dx
*
dx
==
0
)
{
// this is special case - if start and end point are equals then cell designer
// this is special case - if start and end point are equals then cell
// designer
// requires relative coordinates
for
(
int
i
=
1
;
i
<
line
.
getLines
().
size
();
i
++)
{
double
ox
=
line
.
getLines
().
get
(
i
).
getX1
();
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/helper/CellDesignerPointTransformation.java
View file @
0cc66184
...
...
@@ -23,10 +23,12 @@ public class CellDesignerPointTransformation extends PointTransformation {
/**
* This method transform coordinates of pointP in CellDesginer format (base:
* pointA, pointB, pointC) into normal x,y coordinates.
*
*
<p>
* In CellDesigner some points are in different base consisted from three
* points. In this base vector between pointA and pointC is 1 unit on X axis (in
* normal world); and vector between pointB and pointC is 1 unit on Y axis.
* points. In this base vector between pointA and pointC is 1 unit on X axis
* (in normal world); and vector between pointB and pointC is 1 unit on Y
* axis.
* </p>
*
* @param pointA
* central point of CellDesigner base
...
...
@@ -57,10 +59,12 @@ public class CellDesignerPointTransformation extends PointTransformation {
/**
* This method transform coordinates of pointP in x,y coordinates into
* celldesginer format (base: pointA, pointB, pointC)
*
*
<p>
* In CellDesigner some points are in different base consisted from three
* points. In this base vector between pointA and pointC is 1 unit on X axis (in
* normal world); and vector between pointB and pointC is 1 unit on Y axis.
* points. In this base vector between pointA and pointC is 1 unit on X axis
* (in normal world); and vector between pointB and pointC is 1 unit on Y
* axis.
* </p>
*
* @param pointA
* central point of CellDesigner base
...
...
converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
View file @
0cc66184
...
...
@@ -58,7 +58,6 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry;
* that we want to see as little elements as possible, whereas level=infinity
* means that we want to see everything</li>
* </ul>
*
* <p>
* All draw operations are performed in default constructor. Therefore if we
* want to create image of a different part of the map we have to create new
...
...
@@ -69,8 +68,7 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry;
* <li>when we have everything drawn we can extract different parts of the image
* from graphics2D and save it into separate files</li>
* </ul>
*
*
* </p>
*
* @author Piotr Gawron
*
...
...
@@ -80,12 +78,13 @@ public abstract class AbstractImageGenerator {
/**
* Model is drawn as a partial image (x,y,width,height parameters of
* {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
* Params} class. This partial image sometimes contains some object that
doesn't
* intersect with this border (usually text descriptions). This margin
defines
* how far extend drawing.
*
* Params} class. This partial image sometimes contains some object that
*
doesn't
intersect with this border (usually text descriptions). This margin
*
defines
how far extend drawing.
*
<p>
* TODO maybe more efficient (and safe) solution would be to include text
* Description as parts of the object border
* </p>
*/
private
static
final
int
SINGLE_FRAME_MARGIN
=
100
;
/**
...
...
@@ -156,8 +155,8 @@ public abstract class AbstractImageGenerator {
}
/**
* This method creates a graphics object for different implementations of
canvas
* with fixed width and height.
* This method creates a graphics object for different implementations of
*
canvas
with fixed width and height.
*
* @param width
* width of the canvas (graphics2d) to be created
...
...
@@ -440,7 +439,8 @@ public abstract class AbstractImageGenerator {
}
/**
* Saves generated image from {@link #getGraphics()} into {@link OutputStream} .
* Saves generated image from {@link #getGraphics()} into {@link OutputStream}
* .
*
* @param os
* stream where the images should be saved
...
...
@@ -636,29 +636,29 @@ public abstract class AbstractImageGenerator {
private
double
scale
=
1
;
/**
* x coordinate from which we start to draw a map. This is absolute value on
the
* map (scale doesn't influence it).
* x coordinate from which we start to draw a map. This is absolute value on
*
the
map (scale doesn't influence it).
*/
private
double
x
=
0
;
/**
* y coordinate from which we start to draw a map. This is absolute value on
the
* map (scale doesn't influence it).
* y coordinate from which we start to draw a map. This is absolute value on
*
the
map (scale doesn't influence it).
*/
private
double
y
=
0
;
/**
* width of the generated image. It's an absolute value in pixels, therefore
* when scale is set to value different than 1.0 the width on the map will
also
* be modified to fit into width pixels.
* when scale is set to value different than 1.0 the width on the map will
*
also
be modified to fit into width pixels.
*/
private
Double
width
=
null
;
/**
* height of the generated image. It's an absolute value in pixels,
therefore
* when scale is set to value different than 1.0 the height on the
map will also
* be modified to fit into height pixels.
* height of the generated image. It's an absolute value in pixels,
*
therefore
when scale is set to value different than 1.0 the height on the
*
map will also
be modified to fit into height pixels.
*/
private
Double
height
=
null
;
...
...
@@ -673,9 +673,9 @@ public abstract class AbstractImageGenerator {
private
boolean
background
=
true
;
/**
* At which hierarchy level we visualize map. Level=0 means that we want to
see
* as little elements as possible, whereas level=infinity means that we
want to
* see everything.
* At which hierarchy level we visualize map. Level=0 means that we want to
*
see
as little elements as possible, whereas level=infinity means that we
*
want to
see everything.
*/
private
int
level
=
Integer
.
MAX_VALUE
;
...
...
@@ -691,9 +691,10 @@ public abstract class AbstractImageGenerator {
/**
* List of objects containing information about layouts visualized in the
* JavaScript (on client side). Every object (map) represents data for single
* layout. In this map we have pairs between {@link Element}/ {@link Reaction}
* and {@link DataOverlayEntry} used to visualize the element.
* JavaScript (on client side). Every object (map) represents data for
* single layout. In this map we have pairs between {@link Element}/
* {@link Reaction} and {@link DataOverlayEntry} used to visualize the
* element.
*
*/
private
List
<
List
<
Pair
<?
extends
BioEntity
,
DataOverlayEntry
>>>
visibleDataOverlays
=
new
ArrayList
<>();
...
...
@@ -983,9 +984,9 @@ public abstract class AbstractImageGenerator {
}
/**
* Adds layout data that is visualized on the client side. Data overlay
contains
* mapping between {@link Element}/{@link Reaction} and
{@link DataOverlayEntry}
* used for coloring specific element.
* Adds layout data that is visualized on the client side. Data overlay
*
contains
mapping between {@link Element}/{@link Reaction} and
*
{@link DataOverlayEntry}
used for coloring specific element.
*
* @param map
* layout data containing mapping between {@link Element}/
...
...
@@ -1026,11 +1027,11 @@ public abstract class AbstractImageGenerator {
}
/**
* Returns {@link Color} that should be used for drawing overlays with
maximum
* value.
* Returns {@link Color} that should be used for drawing overlays with
*
maximum
value.
*
* @return {@link Color} that should be used for drawing overlays with
maximum
* value
* @return {@link Color} that should be used for drawing overlays with
*
maximum
value
*/
public
Color
getMaxColor
()
{
return
maxColor
;
...
...
@@ -1041,11 +1042,11 @@ public abstract class AbstractImageGenerator {
}
/**
* Returns {@link Color} that should be used for drawing overlays with
minimum
* value.
* Returns {@link Color} that should be used for drawing overlays with
*
minimum
value.
*
* @return {@link Color} that should be used for drawing overlays with
minimum
* value
* @return {@link Color} that should be used for drawing overlays with
*
minimum
value
*/
public
Color
getMinColor
()
{
return
minColor
;
...
...
@@ -1111,7 +1112,7 @@ public abstract class AbstractImageGenerator {
}
public
Params
neutralColor
(
final
Color
neutralColor
)
{
this
.
neutralColor
=
neutralColor
;
this
.
neutralColor
=
neutralColor
;
return
this
;
}
...
...
@@ -1119,6 +1120,5 @@ public abstract class AbstractImageGenerator {
return
this
.
neutralColor
;
}
}
}
\ No newline at end of file
converter/src/main/java/lcsb/mapviewer/converter/ConverterParams.java
View file @
0cc66184
...
...
@@ -46,7 +46,6 @@ public class ConverterParams {
}
/**
*
* Set input stream as input source.
*
* @param is
...
...
model/src/main/java/lcsb/mapviewer/model/graphics/LineType.java
View file @
0cc66184
...
...
@@ -49,7 +49,6 @@ public enum LineType {
* - - - - - - -
* </pre>
*
* .
*/
DASHED
(
1
,
new
float
[]
{
8.0f
,
8.0f
}),
...
...
@@ -60,7 +59,6 @@ public enum LineType {
* . . . . . . . .
* </pre>
*
* .
*/
DOTTED
(
1
,
new
float
[]
{
2.0f
,
5.0f
}),
...
...
@@ -71,7 +69,6 @@ public enum LineType {
* - - - - - - -
* </pre>
*
* .
*/
DASHED_BOLD
(
3
,
new
float
[]
{
8.0f
,
8.0f
}),
...
...
model/src/main/java/lcsb/mapviewer/model/map/reaction/package-info.java
View file @
0cc66184
...
...
@@ -3,9 +3,10 @@
* reaction is {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction}. It
* is extended by several different types of reactions that were put in the
* {@link lcsb.mapviewer.model.map.reaction.type type} sub-package.
*
*
<p>
* Every reaction contains set of nodes that extend
* {@link lcsb.mapviewer.model.map.reaction.AbstractNode AbstractNode} class.
* </p>
*
*/
package
lcsb.mapviewer.model.map.reaction
;
model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
View file @
0cc66184
package
lcsb.mapviewer.model.map.reaction.type
;
/**
*
* Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
* Reaction} extensions that implements reduced notation in CellDesigner. These
* classes should have no more than one reactant and product and cannot have any
...
...
pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java
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0cc66184
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@@ -49,7 +49,6 @@ public abstract class PathwayElement implements Serializable {
private
String
groupRef
;
/**
*
* Reference to BioPax node with references about this element.
*/
private
List
<
String
>
biopaxReferences
=
new
ArrayList
<>();
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rest-api/src/main/java/lcsb/mapviewer/api/ContentNegotiationConfig.java
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0cc66184
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@@ -9,7 +9,7 @@ import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
* This class is a configuration for spring that disables content type
* recognition based on the "extension" (last part after dot in url). It allows
* API to return json for urls like: http://localhost:8080/minerva/api/users/t.t
*
*
<p>
* More info can be found here:
* <ul>
* <li>https://spring.io/blog/2013/05/11/content-negotiation-using-spring-mvc
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@@ -17,6 +17,7 @@ import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
* <li>https://stackoverflow.com/questions/30793717/spring-throwing-
* httpmediatypenotacceptableexception-could-not-find-acceptable-r</li>
* </ul>
* </p>
*
* @author Piotr Gawron
*
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service/src/main/java/lcsb/mapviewer/services/interfaces/IDataOverlayService.java
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0cc66184
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@@ -35,7 +35,6 @@ public interface IDataOverlayService {
private
User
user
;