Commit 0cc66184 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

javadoc formattng issues

parent 7af9e4ce
...@@ -14,7 +14,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase; ...@@ -14,7 +14,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
/** /**
* This class represent a plugin to cell designer with copy past functionality * This class represent a plugin to cell designer with copy past functionality
* that allows to copy and paste notes and annotations of species. * that allows to copy and paste notes and annotations of species.
* * <p>
* It overrides: * It overrides:
* <ul> * <ul>
* <li>ALT + CTRL + C shortcut - copy annotations from selected element into * <li>ALT + CTRL + C shortcut - copy annotations from selected element into
...@@ -24,6 +24,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase; ...@@ -24,6 +24,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
* element(s), if many elements are selected then all elements will be modified, * element(s), if many elements are selected then all elements will be modified,
* </li> * </li>
* </ul> * </ul>
* </p>
* *
* @author Piotr Gawron * @author Piotr Gawron
* *
......
...@@ -22,8 +22,9 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias; ...@@ -22,8 +22,9 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
* This class represent a plugin to CellDesigner that add info text box with * 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 * informations about species. Plugin run in pooling mode (there is no other way
* in CellDesigner...). * in CellDesigner...).
* * <p>
* It overrides <i>CTRL + T shortcut</i> - shows/hide info text window. * It overrides <i>CTRL + T shortcut</i> - shows/hide info text window.
* </p>
* *
* @author Piotr Gawron * @author Piotr Gawron
* *
...@@ -87,9 +88,9 @@ public class InfoPlugin extends CellDesignerPlugin { ...@@ -87,9 +88,9 @@ public class InfoPlugin extends CellDesignerPlugin {
onChangeSelectListener = new ActionListener() { onChangeSelectListener = new ActionListener() {
/** /**
* This string contains a simple hash of all species shown in the last run of * This string contains a simple hash of all species shown in the last
* this listener. Due to this information we don't have to refresh this * run of this listener. Due to this information we don't have to
* information at every run. * refresh this information at every run.
*/ */
private String selectedElementsId = ""; private String selectedElementsId = "";
......
...@@ -147,9 +147,10 @@ public class ModelAnnotator { ...@@ -147,9 +147,10 @@ public class ModelAnnotator {
* <li>notes,</li> * <li>notes,</li>
* <li>other elements with the same name and type.</li> * <li>other elements with the same name and type.</li>
* </ul> * </ul>
* * <p>
* This method copies data to elements without annotations from other elements * This method copies data to elements without annotations from other elements
* with the same name and type. * with the same name and type.
* </p>
* *
* @param model * @param model
* model in which element annotations are updated * model in which element annotations are updated
...@@ -184,8 +185,9 @@ public class ModelAnnotator { ...@@ -184,8 +185,9 @@ public class ModelAnnotator {
* this map contains lists of {@link ElementAnnotator} objects that * this map contains lists of {@link ElementAnnotator} objects that
* should be used for a given classes * should be used for a given classes
* @param annotatorsParams * @param annotatorsParams
* this map contains lists of {@link AnnotatorConfigParameter} objects * this map contains lists of {@link AnnotatorConfigParameter}
* that should be used for a given {@link ElementAnnotator} class * objects that should be used for a given {@link ElementAnnotator}
* class
* @param model * @param model
* model where annotation should be updated * model where annotation should be updated
* @param progressUpdater * @param progressUpdater
...@@ -238,8 +240,8 @@ public class ModelAnnotator { ...@@ -238,8 +240,8 @@ public class ModelAnnotator {
} }
/** /**
* Returns list of default {@link ElementAnnotator} names that are available for * Returns list of default {@link ElementAnnotator} names that are available
* class given in the parameter. * for class given in the parameter.
* *
* @param clazz * @param clazz
* class for which list of default annotators will be returned * class for which list of default annotators will be returned
...@@ -261,11 +263,11 @@ public class ModelAnnotator { ...@@ -261,11 +263,11 @@ public class ModelAnnotator {
* @param m * @param m
* model * model
* @param updater * @param updater
* updater call back function that update information about progress of * updater call back function that update information about progress
* the function * of the function
* @param validAnnotations * @param validAnnotations
* map that contains information which {@link MiriamType miriam types} * map that contains information which {@link MiriamType miriam
* are valid for which class * types} are valid for which class
* @return list of improper annotations * @return list of improper annotations
*/ */
public Collection<ImproperAnnotations> findImproperAnnotations(final Model m, final IProgressUpdater updater, public Collection<ImproperAnnotations> findImproperAnnotations(final Model m, final IProgressUpdater updater,
...@@ -337,8 +339,8 @@ public class ModelAnnotator { ...@@ -337,8 +339,8 @@ public class ModelAnnotator {
* @param m * @param m
* model where the search is performed * model where the search is performed
* @param requestedAnnotations * @param requestedAnnotations
* map that contains information which {@link MiriamType miriam types} * map that contains information which {@link MiriamType miriam
* are obligatory for which class * types} are obligatory for which class
* *
* @return list of all elements that miss annotation * @return list of all elements that miss annotation
*/ */
...@@ -372,9 +374,10 @@ public class ModelAnnotator { ...@@ -372,9 +374,10 @@ public class ModelAnnotator {
* @param element * @param element
* object to be checked * object to be checked
* @param requestedAnnotations * @param requestedAnnotations
* at list one of this annotations should appear in the element, if the * at list one of this annotations should appear in the element, if
* list is null then check is skipped, if the list is empty (size()==0) * the list is null then check is skipped, if the list is empty
* then method checks if element contains at least one miriam * (size()==0) then method checks if element contains at least one
* miriam
* @return list of containing improper annotations about element * @return list of containing improper annotations about element
*/ */
private List<ProblematicAnnotation> findMissing(final BioEntity element, final Collection<MiriamType> requestedAnnotations) { private List<ProblematicAnnotation> findMissing(final BioEntity element, final Collection<MiriamType> requestedAnnotations) {
...@@ -446,8 +449,8 @@ public class ModelAnnotator { ...@@ -446,8 +449,8 @@ public class ModelAnnotator {
} }
/** /**
* Converts list of strings into list of {@link ElementAnnotator}. Strings must * Converts list of strings into list of {@link ElementAnnotator}. Strings
* be valid {@link ElementAnnotator} common names. * must be valid {@link ElementAnnotator} common names.
* *
* @param list * @param list
* list of {@link ElementAnnotator#getCommonName()}. * list of {@link ElementAnnotator#getCommonName()}.
...@@ -505,11 +508,11 @@ public class ModelAnnotator { ...@@ -505,11 +508,11 @@ public class ModelAnnotator {
} }
/** /**
* Returns map with informations about default required {@link MiriamType miriam * Returns map with informations about default required {@link MiriamType
* types } for {@link BioEntity} class type. * miriam types } for {@link BioEntity} class type.
* *
* @return map with informations about required {@link MiriamType miriam types } * @return map with informations about required {@link MiriamType miriam types
* for {@link BioEntity} class type * } for {@link BioEntity} class type
*/ */
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultRequiredClasses() { public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultRequiredClasses() {
......
...@@ -37,7 +37,6 @@ import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter; ...@@ -37,7 +37,6 @@ import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
* UniProt IDs would be indistinguishable from the UniProt IDs describing the * UniProt IDs would be indistinguishable from the UniProt IDs describing the
* molecule. * molecule.
* *
*
* @author David Hoksza * @author David Hoksza
* *
*/ */
...@@ -95,9 +94,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService ...@@ -95,9 +94,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
return false; return false;
} }
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) { 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 // (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); Collection<MiriamData> collection = tairToUniprot(identifier);
if (collection.size() > 0) { if (collection.size() > 0) {
object.addMiriamData(collection); object.addMiriamData(collection);
...@@ -137,8 +138,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService ...@@ -137,8 +138,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
} }
/** /**
* Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR * Returns URL to UniProt result containing mapped UniProtIds for submitted
* entry. * TAIR entry.
* *
* @param tairId * @param tairId
* TAIR identifier * TAIR identifier
...@@ -153,8 +154,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService ...@@ -153,8 +154,8 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
/** /**
* Parse UniProt result page which contains list of Uniprot ids mapped to * Parse UniProt result page which contains list of Uniprot ids mapped to
* submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT} and * submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT}
* returns it. * and returns it.
* *
* @param pageContent * @param pageContent
* uniprot REST API result page * uniprot REST API result page
...@@ -174,10 +175,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService ...@@ -174,10 +175,11 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
/** /**
* Transform TAIR identifier into uniprot identifier. * Transform TAIR identifier into uniprot identifier.
* * <p>
* Used to use the TAIR record page, but that tends to change and moreover TAIR * Used to use the TAIR record page, but that tends to change and moreover
* limits number of accesses from an address. So now the transformation queries * TAIR limits number of accesses from an address. So now the transformation
* directly UniProt from which the mapping can be obtained as well. * queries directly UniProt from which the mapping can be obtained as well.
* </p>
* *
* @param tair * @param tair
* {@link MiriamData} with TAIR identifier * {@link MiriamData} with TAIR identifier
......
...@@ -259,13 +259,9 @@ ...@@ -259,13 +259,9 @@
</module> </module>
<module name="NonEmptyAtclauseDescription"/> <module name="NonEmptyAtclauseDescription"/>
<module name="InvalidJavadocPosition"/> <module name="InvalidJavadocPosition"/>
<!-- <module name="JavadocTagContinuationIndentation"/> <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="JavadocParagraph"/> <module name="JavadocParagraph"/>
<module name="AtclauseOrder"> <!-- <module name="AtclauseOrder">
<property name="tagOrder" value="@param, @return, @throws, @deprecated"/> <property name="tagOrder" value="@param, @return, @throws, @deprecated"/>
<property name="target" <property name="target"
value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/> value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>
...@@ -308,6 +304,10 @@ ...@@ -308,6 +304,10 @@
<property name="separateLineBetweenGroups" value="true"/> <property name="separateLineBetweenGroups" value="true"/>
<property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/> <property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE###STANDARD_JAVA_PACKAGE"/>
<property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/> <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>
--> -->
</module> </module>
......
...@@ -36,13 +36,13 @@ public class CellDesignerLineTransformation extends LineTransformation { ...@@ -36,13 +36,13 @@ public class CellDesignerLineTransformation extends LineTransformation {
/** /**
* Transform data in CellDesigner format into typical x,y coordinates for all * Transform data in CellDesigner format into typical x,y coordinates for all
* points. * points.
* * <p>
* CellDesigner format stores coordinates of a line in a different base. In this * CellDesigner format stores coordinates of a line in a different base. In
* base we have two points that define a base: vector between these points is 1 * this base we have two points that define a base: vector between these
* unit in first coordinate, and orthogonal vector to the one mentioned before * points is 1 unit in first coordinate, and orthogonal vector to the one
* is 1 unit in the second coordinate. Moreover, these two points defining base * mentioned before is 1 unit in the second coordinate. Moreover, these two
* belong to this line. * points defining base belong to this line.
* * </p>
* *
* @param startPoint * @param startPoint
* first point defining CellDesigner base * first point defining CellDesigner base
...@@ -70,7 +70,8 @@ public class CellDesignerLineTransformation extends LineTransformation { ...@@ -70,7 +70,8 @@ public class CellDesignerLineTransformation extends LineTransformation {
double distDx = dx1 * dx1 + dy1 * dy1; 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 // relative coordinates
if (distDx <= Configuration.EPSILON) { if (distDx <= Configuration.EPSILON) {
dx1 = 1; dx1 = 1;
...@@ -99,17 +100,18 @@ public class CellDesignerLineTransformation extends LineTransformation { ...@@ -99,17 +100,18 @@ public class CellDesignerLineTransformation extends LineTransformation {
/** /**
* Transform line of typical x,y coordinates into coordinates used by * Transform line of typical x,y coordinates into coordinates used by
* CellDesigner. * CellDesigner.
* * <p>
* CellDesigner format stores coordinates of a line in a different base. In this * CellDesigner format stores coordinates of a line in a different base. In
* base we have two points that define a base: vector between these points is 1 * this base we have two points that define a base: vector between these
* unit in first coordinate, and orthogonal vector to the one mentioned before * points is 1 unit in first coordinate, and orthogonal vector to the one
* is 1 unit in the second coordinate. These two points are the first and the * mentioned before is 1 unit in the second coordinate. These two points are
* last. * the first and the last.
* </p>
* *
* @param line * @param line
* line to be transformed into CellDesigner format * line to be transformed into CellDesigner format
* @return points of the line in CellDesigner format (without the first and the * @return points of the line in CellDesigner format (without the first and
* last) * the last)
*/ */
public List<Point2D> getPointsFromLine(final PolylineData line) { public List<Point2D> getPointsFromLine(final PolylineData line) {
if (line == null) { if (line == null) {
...@@ -131,7 +133,8 @@ public class CellDesignerLineTransformation extends LineTransformation { ...@@ -131,7 +133,8 @@ public class CellDesignerLineTransformation extends LineTransformation {
List<Point2D> result = new ArrayList<Point2D>(); List<Point2D> result = new ArrayList<Point2D>();
if (dy * dy + dx * dx == 0) { 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 // requires relative coordinates
for (int i = 1; i < line.getLines().size(); i++) { for (int i = 1; i < line.getLines().size(); i++) {
double ox = line.getLines().get(i).getX1(); double ox = line.getLines().get(i).getX1();
......
...@@ -23,10 +23,12 @@ public class CellDesignerPointTransformation extends PointTransformation { ...@@ -23,10 +23,12 @@ public class CellDesignerPointTransformation extends PointTransformation {
/** /**
* This method transform coordinates of pointP in CellDesginer format (base: * This method transform coordinates of pointP in CellDesginer format (base:
* pointA, pointB, pointC) into normal x,y coordinates. * pointA, pointB, pointC) into normal x,y coordinates.
* * <p>
* In CellDesigner some points are in different base consisted from three * 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 * points. In this base vector between pointA and pointC is 1 unit on X axis
* normal world); and vector between pointB and pointC is 1 unit on Y axis. * (in normal world); and vector between pointB and pointC is 1 unit on Y
* axis.
* </p>
* *
* @param pointA * @param pointA
* central point of CellDesigner base * central point of CellDesigner base
...@@ -57,10 +59,12 @@ public class CellDesignerPointTransformation extends PointTransformation { ...@@ -57,10 +59,12 @@ public class CellDesignerPointTransformation extends PointTransformation {
/** /**
* This method transform coordinates of pointP in x,y coordinates into * This method transform coordinates of pointP in x,y coordinates into
* celldesginer format (base: pointA, pointB, pointC) * celldesginer format (base: pointA, pointB, pointC)
* * <p>
* In CellDesigner some points are in different base consisted from three * 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 * points. In this base vector between pointA and pointC is 1 unit on X axis
* normal world); and vector between pointB and pointC is 1 unit on Y axis. * (in normal world); and vector between pointB and pointC is 1 unit on Y
* axis.
* </p>
* *
* @param pointA * @param pointA
* central point of CellDesigner base * central point of CellDesigner base
......
...@@ -58,7 +58,6 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry; ...@@ -58,7 +58,6 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry;
* that we want to see as little elements as possible, whereas level=infinity * that we want to see as little elements as possible, whereas level=infinity
* means that we want to see everything</li> * means that we want to see everything</li>
* </ul> * </ul>
*
* <p> * <p>
* All draw operations are performed in default constructor. Therefore if we * 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 * 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; ...@@ -69,8 +68,7 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry;
* <li>when we have everything drawn we can extract different parts of the image * <li>when we have everything drawn we can extract different parts of the image
* from graphics2D and save it into separate files</li> * from graphics2D and save it into separate files</li>
* </ul> * </ul>
* * </p>
*
* *
* @author Piotr Gawron * @author Piotr Gawron
* *
...@@ -80,12 +78,13 @@ public abstract class AbstractImageGenerator { ...@@ -80,12 +78,13 @@ public abstract class AbstractImageGenerator {
/** /**
* Model is drawn as a partial image (x,y,width,height parameters of * Model is drawn as a partial image (x,y,width,height parameters of
* {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params * {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
* Params} class. This partial image sometimes contains some object that doesn't * Params} class. This partial image sometimes contains some object that
* intersect with this border (usually text descriptions). This margin defines * doesn't intersect with this border (usually text descriptions). This margin
* how far extend drawing. * defines how far extend drawing.
* * <p>
* TODO maybe more efficient (and safe) solution would be to include text * TODO maybe more efficient (and safe) solution would be to include text
* Description as parts of the object border * Description as parts of the object border
* </p>
*/ */
private static final int SINGLE_FRAME_MARGIN = 100; private static final int SINGLE_FRAME_MARGIN = 100;
/** /**
...@@ -156,8 +155,8 @@ public abstract class AbstractImageGenerator { ...@@ -156,8 +155,8 @@ public abstract class AbstractImageGenerator {
} }
/** /**
* This method creates a graphics object for different implementations of canvas * This method creates a graphics object for different implementations of
* with fixed width and height. * canvas with fixed width and height.
* *
* @param width * @param width
* width of the canvas (graphics2d) to be created * width of the canvas (graphics2d) to be created
...@@ -440,7 +439,8 @@ public abstract class AbstractImageGenerator { ...@@ -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 * @param os
* stream where the images should be saved * stream where the images should be saved
...@@ -636,29 +636,29 @@ public abstract class AbstractImageGenerator { ...@@ -636,29 +636,29 @@ public abstract class AbstractImageGenerator {
private double scale = 1; private double scale = 1;
/** /**
* x coordinate from which we start to draw a map. This is absolute value on the * x coordinate from which we start to draw a map. This is absolute value on
* map (scale doesn't influence it). * the map (scale doesn't influence it).
*/ */
private double x = 0; private double x = 0;
/** /**
* y coordinate from which we start to draw a map. This is absolute value on the * y coordinate from which we start to draw a map. This is absolute value on
* map (scale doesn't influence it). * the map (scale doesn't influence it).
*/ */
private double y = 0; private double y = 0;
/** /**
* width of the generated image. It's an absolute value in pixels, therefore * 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 * when scale is set to value different than 1.0 the width on the map will
* be modified to fit into width pixels. * also be modified to fit into width pixels.
*/ */
private Double width = null; private Double width = null;
/** /**
* height of the generated image. It's an absolute value in pixels, therefore * height of the generated image. It's an absolute value in pixels,
* when scale is set to value different than 1.0 the height on the map will also * therefore when scale is set to value different than 1.0 the height on the
* be modified to fit into height pixels. * map will also be modified to fit into height pixels.
*/ */
private Double height = null; private Double height = null;