javadoc formattng issues

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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;