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Commit 0cc66184 authored by Piotr Gawron's avatar Piotr Gawron
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javadoc formattng issues

parent 7af9e4ce
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Showing with 127 additions and 115 deletions
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
View file @ 0cc66184
......@@ -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<>();
......
rest-api/src/main/java/lcsb/mapviewer/api/ContentNegotiationConfig.java
View file @ 0cc66184
......@@ -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
......@@ -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
*
......
service/src/main/java/lcsb/mapviewer/services/interfaces/IDataOverlayService.java
View file @ 0cc66184
......@@ -35,7 +35,6 @@ public interface IDataOverlayService {
private User user;
/**