overriden methods should be grouped together

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

@@ -237,6 +237,22 @@ public class ModelAnnotator {
     return defaultAnnotators;
   }
 
+  /**
+   * 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
+   * @return annotators names for a given class
+   */
+  public List<AnnotatorData> getDefaultAnnotators(final Class<?> clazz) {
+    List<AnnotatorData> result = new ArrayList<>();
+    for (final ElementAnnotator annotator : getAvailableDefaultAnnotators(clazz)) {
+      result.add(annotator.createAnnotatorData());
+    }
+    return result;
+  }
+
   /**
    * This method returns list of improper annotations for the model. Improper
    * annotation is the annotation of the wrong type for given type of element.
@@ -411,22 +427,6 @@ public class ModelAnnotator {
     return result;
   }
 
-  /**
-   * 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
-   * @return annotators names for a given class
-   */
-  public List<AnnotatorData> getDefaultAnnotators(final Class<?> clazz) {
-    List<AnnotatorData> result = new ArrayList<>();
-    for (final ElementAnnotator annotator : getAvailableDefaultAnnotators(clazz)) {
-      result.add(annotator.createAnnotatorData());
-    }
-    return result;
-  }
-
   /**
    * Returns list of default {@link ElementAnnotator annotators} that are
    * available for class given in the parameter.

annotation/src/main/java/lcsb/mapviewer/annotation/services/PubmedParser.java

@@ -284,6 +284,20 @@ public class PubmedParser extends CachableInterface implements IExternalService
     return result;
   }
 
+  /**
+   * Get the summary of the article.
+   *
+   * @param id
+   *          pubmed identifier
+   * @return summary of the article.
+   * @throws PubmedSearchException
+   *           thrown when there is a problem with accessing information about
+   *           pubmed
+   */
+  public String getSummary(final String id) throws PubmedSearchException {
+    return getSummary(Integer.valueOf(id));
+  }
+
   @Override
   public ExternalServiceStatus getServiceStatus() {
     ExternalServiceStatus status = new ExternalServiceStatus("Europe PubMed Central",
@@ -339,20 +353,6 @@ public class PubmedParser extends CachableInterface implements IExternalService
     }
   }
 
-  /**
-   * Get the summary of the article.
-   *
-   * @param id
-   *          pubmed identifier
-   * @return summary of the article.
-   * @throws PubmedSearchException
-   *           thrown when there is a problem with accessing information about
-   *           pubmed
-   */
-  public String getSummary(final String id) throws PubmedSearchException {
-    return getSummary(Integer.valueOf(id));
-  }
-
   /**
    * @return the miriamConnector
    * @see #miriamConnector

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java

@@ -181,6 +181,24 @@ public abstract class ElementAnnotator extends CachableInterface {
     return false;
   }
 
+  /**
+   * Returns <code>true</code> if this annotator can annotate the object of
+   * given class type.
+   * 
+   * @param clazz
+   *          class to be tested if can be annotated
+   * @return <code>true</code> if class can be annotated by this annotator,
+   *         <code>false</code> otherwise
+   */
+  public boolean isAnnotatable(final Class<?> clazz) {
+    for (final Class<?> clazz2 : validClasses) {
+      if (clazz2.isAssignableFrom(clazz)) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   /**
    * Adds a class to list of classes that can be annotated by the annotator.
    *
@@ -235,24 +253,6 @@ public abstract class ElementAnnotator extends CachableInterface {
     this.paramsDefs = paramDefs;
   }
 
-  /**
-   * Returns <code>true</code> if this annotator can annotate the object of
-   * given class type.
-   * 
-   * @param clazz
-   *          class to be tested if can be annotated
-   * @return <code>true</code> if class can be annotated by this annotator,
-   *         <code>false</code> otherwise
-   */
-  public boolean isAnnotatable(final Class<?> clazz) {
-    for (final Class<?> clazz2 : validClasses) {
-      if (clazz2.isAssignableFrom(clazz)) {
-        return true;
-      }
-    }
-    return false;
-  }
-
   /**
    * 
    * @return {@link #isDefault}
@@ -362,6 +362,24 @@ public abstract class ElementAnnotator extends CachableInterface {
       }
     }
 
+    public void addMiriamData(final MiriamType miriamType, final String resource) {
+      addMiriamData(new MiriamData(miriamType, resource));
+    }
+
+    public void addMiriamData(final String generalIdentifier) {
+      MiriamData md = null;
+      try {
+        md = MiriamType.getMiriamByUri(generalIdentifier);
+      } catch (final InvalidArgumentException e) {
+        try {
+          md = MiriamType.getMiriamByUri("urn:miriam:" + generalIdentifier);
+        } catch (final InvalidArgumentException e1) {
+          logger.warn(getLogMarker(ProjectLogEntryType.INVALID_IDENTIFIER), "Unknown miriam uri: " + generalIdentifier);
+        }
+      }
+      addMiriamData(md);
+    }
+
     public boolean contains(final MiriamData identifier) {
       MiriamData copy = new MiriamData(identifier);
       copy.setAnnotator(null);
@@ -531,20 +549,6 @@ public abstract class ElementAnnotator extends CachableInterface {
       }
     }
 
-    public void addMiriamData(final String generalIdentifier) {
-      MiriamData md = null;
-      try {
-        md = MiriamType.getMiriamByUri(generalIdentifier);
-      } catch (final InvalidArgumentException e) {
-        try {
-          md = MiriamType.getMiriamByUri("urn:miriam:" + generalIdentifier);
-        } catch (final InvalidArgumentException e1) {
-          logger.warn(getLogMarker(ProjectLogEntryType.INVALID_IDENTIFIER), "Unknown miriam uri: " + generalIdentifier);
-        }
-      }
-      addMiriamData(md);
-    }
-
     /**
      * Sets {@link CellDesignerChemical#inChI}.
      *
@@ -598,10 +602,6 @@ public abstract class ElementAnnotator extends CachableInterface {
       }
     }
 
-    public void addMiriamData(final MiriamType miriamType, final String resource) {
-      addMiriamData(new MiriamData(miriamType, resource));
-    }
-
     /**
      * Sets {@link Species#charge}.
      *

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/DapiConnectorImpl.java

@@ -129,6 +129,11 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
     }
   }
 
+  @Override
+  public String getAuthenticatedContent(final String string) throws DapiConnectionException {
+    return getAuthenticatedContent(string, true);
+  }
+
   @Override
   public String getLatestReleaseUrl(final String databaseName) throws DapiConnectionException {
     String release = getLatestReleaseAvailable(databaseName);
@@ -138,11 +143,6 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
     return DAPI_BASE_URL + "database/" + databaseName + "/releases/" + getLatestReleaseAvailable(databaseName) + "/";
   }
 
-  @Override
-  public String getAuthenticatedContent(final String string) throws DapiConnectionException {
-    return getAuthenticatedContent(string, true);
-  }
-
   @Override
   public boolean isAuthenticated() {
     Calendar nowMinus10Minutes = Calendar.getInstance();
@@ -171,10 +171,6 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
     }
   }
 
-  public String getDapiPassword() {
-    return configurationDao.getValueByType(ConfigurationElementType.DAPI_PASSWORD);
-  }
-
   void login(final String login, final String password)
       throws MalformedURLException, IOException, ProtocolException, DapiConnectionException {
     if (login == null || password == null) {
@@ -203,6 +199,10 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
     }
   }
 
+  public String getDapiPassword() {
+    return configurationDao.getValueByType(ConfigurationElementType.DAPI_PASSWORD);
+  }
+
   @Override
   public boolean isValidConnection() {
     if (getDapiLogin() == null || getDapiLogin().isEmpty() || getDapiPassword() == null

checkstyle.xml

@@ -222,15 +222,9 @@
             <property name="lineWrappingIndentation" value="4"/>
             <property name="arrayInitIndent" value="2"/>
         </module>
-<!--        <module name="AbbreviationAsWordInName">
-            <property name="ignoreFinal" value="false"/>
-            <property name="allowedAbbreviationLength" value="1"/>
-            <property name="tokens"
-                      value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF, ANNOTATION_FIELD_DEF,
-                    PARAMETER_DEF, VARIABLE_DEF, METHOD_DEF"/>
-        </module>
+    
         <module name="OverloadMethodsDeclarationOrder"/>
-        <module name="VariableDeclarationUsageDistance"/>
+<!--        <module name="VariableDeclarationUsageDistance"/>
         <module name="CustomImportOrder">
             <property name="sortImportsInGroupAlphabetically" value="true"/>
             <property name="separateLineBetweenGroups" value="true"/>
@@ -304,9 +298,17 @@
         <module name="CommentsIndentation">
             <property name="tokens" value="SINGLE_LINE_COMMENT, BLOCK_COMMENT_BEGIN"/>
         </module>
-
         <module name="VisibilityModifier">
             <property name="protectedAllowed" value="true"/>
-        </module> -->
+        </module>
+
+        <module name="AbbreviationAsWordInName">
+            <property name="ignoreFinal" value="false"/>
+            <property name="allowedAbbreviationLength" value="1"/>
+            <property name="tokens"
+                      value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF, ANNOTATION_FIELD_DEF,
+                    PARAMETER_DEF, VARIABLE_DEF, METHOD_DEF"/>
+        </module>
+         -->
     </module> 
 </module>

commons/src/main/java/lcsb/mapviewer/common/Configuration.java

@@ -168,18 +168,6 @@ public final class Configuration {
     return systemBuildVersion;
   }
 
-  /**
-   * @param baseDir
-   *          directory where the system is placed
-   * @return {@link #systemVersion}
-   */
-  public static String getSystemVersion(final String baseDir) {
-    if (systemVersion == null) {
-      loadSystemVersion(baseDir);
-    }
-    return systemVersion;
-  }
-
   /**
    * @param baseDir
    *          directory where the system is placed
@@ -194,6 +182,18 @@ public final class Configuration {
     return getSystemBuildVersion(baseDir);
   }
 
+  /**
+   * @param baseDir
+   *          directory where the system is placed
+   * @return {@link #systemVersion}
+   */
+  public static String getSystemVersion(final String baseDir) {
+    if (systemVersion == null) {
+      loadSystemVersion(baseDir);
+    }
+    return systemVersion;
+  }
+
   /**
    * @param baseDir
    *          directory where the system is placed

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -346,6 +346,91 @@ public class RestAnnotationParser {
     processNotes(notes, element);
   }
 
+  /**
+   * Process notes and assign structural information from it.
+   *
+   * @param element
+   *          object with notes to be processed
+   */
+  public void processNotes(final Element element) {
+    processNotes(element.getNotes(), element);
+  }
+
+  /**
+   * Process notes and assign structural information from it.
+   *
+   * @param notes
+   *          notes about element
+   * @param object
+   *          where the structural data should be put
+   */
+  public void processNotes(final String notes, final Drawable object) {
+    StringBuilder annotations = new StringBuilder();
+
+    String[] string = notes.split("\n");
+    StringBuilder newNotes = new StringBuilder("");
+    for (final String string2 : string) {
+      boolean remove = false;
+      for (final NoteField field : NoteField.values()) {
+        if (string2.startsWith(field.getCommonName() + ":") && field.getClazz().isAssignableFrom(object.getClass())) {
+          remove = true;
+        } else if (string2.startsWith(field.getCommonName() + "=")
+            && field.getClazz().isAssignableFrom(object.getClass())) {
+          remove = true;
+        }
+
+      }
+      if (remove) {
+        annotations.append(string2 + "\n");
+      } else {
+        newNotes.append(string2 + "\n");
+      }
+    }
+    String ann = annotations.toString();
+    setZIndex(object, ann);
+    if (object instanceof LayerText) {
+      LayerText layerText = (LayerText) object;
+      setBackgroundColor(layerText, ann);
+      setBorderColor(layerText, ann);
+      layerText.setNotes(newNotes.toString().trim());
+    }
+    if (object instanceof BioEntity) {
+      BioEntity bioEntity = (BioEntity) object;
+      bioEntity.setNotes(newNotes.toString().trim());
+
+      setNotes(bioEntity, ann);
+      setSymbol(bioEntity, ann);
+      setSynonyms(bioEntity, ann);
+      setSemanticZoomLevelVisibility(bioEntity, ann);
+      setAbbreviation(bioEntity, ann);
+      setFormula(bioEntity, ann);
+      if (object instanceof Reaction) {
+        Reaction reaction = (Reaction) object;
+        setMechanicalConfidenceScoreToReaction(reaction, ann);
+        setLowerBoundToReaction(reaction, ann);
+        setUpperBoundToReaction(reaction, ann);
+        setSubsystemToReaction(reaction, ann);
+        setGeneProteinReactionToReaction(reaction, ann);
+      } else if (object instanceof Element) {
+        setTransparencyZoomLevelVisibility((Element) object, ann);
+        setFullNameToSpecies((Element) object, ann);
+        setFormerSymbolsToSpecies((Element) object, ann);
+        if (object instanceof Species) {
+          setCharge((Species) object, ann);
+        }
+      } else {
+        throw new NotImplementedException("Don't know how to process class: " + object.getClass());
+      }
+
+      try {
+        processRdfDescription(bioEntity);
+      } catch (final InvalidXmlSchemaException e) {
+        String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
+        logger.warn(warning);
+      }
+    }
+  }
+
   /**
    * Transforms xml node into notes.
    *
@@ -767,81 +852,6 @@ public class RestAnnotationParser {
     return getParamByPrefix(annotationString, NoteField.DESCRIPTION.getCommonName() + ":");
   }
 
-  /**
-   * Process notes and assign structural information from it.
-   *
-   * @param notes
-   *          notes about element
-   * @param object
-   *          where the structural data should be put
-   */
-  public void processNotes(final String notes, final Drawable object) {
-    StringBuilder annotations = new StringBuilder();
-
-    String[] string = notes.split("\n");
-    StringBuilder newNotes = new StringBuilder("");
-    for (final String string2 : string) {
-      boolean remove = false;
-      for (final NoteField field : NoteField.values()) {
-        if (string2.startsWith(field.getCommonName() + ":") && field.getClazz().isAssignableFrom(object.getClass())) {
-          remove = true;
-        } else if (string2.startsWith(field.getCommonName() + "=")
-            && field.getClazz().isAssignableFrom(object.getClass())) {
-          remove = true;
-        }
-
-      }
-      if (remove) {
-        annotations.append(string2 + "\n");
-      } else {
-        newNotes.append(string2 + "\n");
-      }
-    }
-    String ann = annotations.toString();
-    setZIndex(object, ann);
-    if (object instanceof LayerText) {
-      LayerText layerText = (LayerText) object;
-      setBackgroundColor(layerText, ann);
-      setBorderColor(layerText, ann);
-      layerText.setNotes(newNotes.toString().trim());
-    }
-    if (object instanceof BioEntity) {
-      BioEntity bioEntity = (BioEntity) object;
-      bioEntity.setNotes(newNotes.toString().trim());
-
-      setNotes(bioEntity, ann);
-      setSymbol(bioEntity, ann);
-      setSynonyms(bioEntity, ann);
-      setSemanticZoomLevelVisibility(bioEntity, ann);
-      setAbbreviation(bioEntity, ann);
-      setFormula(bioEntity, ann);
-      if (object instanceof Reaction) {
-        Reaction reaction = (Reaction) object;
-        setMechanicalConfidenceScoreToReaction(reaction, ann);
-        setLowerBoundToReaction(reaction, ann);
-        setUpperBoundToReaction(reaction, ann);
-        setSubsystemToReaction(reaction, ann);
-        setGeneProteinReactionToReaction(reaction, ann);
-      } else if (object instanceof Element) {
-        setTransparencyZoomLevelVisibility((Element) object, ann);
-        setFullNameToSpecies((Element) object, ann);
-        setFormerSymbolsToSpecies((Element) object, ann);
-        if (object instanceof Species) {
-          setCharge((Species) object, ann);
-        }
-      } else {
-        throw new NotImplementedException("Don't know how to process class: " + object.getClass());
-      }
-
-      try {
-        processRdfDescription(bioEntity);
-      } catch (final InvalidXmlSchemaException e) {
-        String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
-        logger.warn(warning);
-      }
-    }
-  }
-
   private void setBackgroundColor(final LayerText layerText, final String ann) {
     Color color = getColor(ann, NoteField.BACKGROUND_COLOR.getCommonName());
     if (color == null) {
@@ -907,16 +917,6 @@ public class RestAnnotationParser {
     }
   }
 
-  /**
-   * Process notes and assign structural information from it.
-   *
-   * @param element
-   *          object with notes to be processed
-   */
-  public void processNotes(final Element element) {
-    processNotes(element.getNotes(), element);
-  }
-
   boolean isFieldAnnotated(final NoteField field, final Class<? extends Annotation> annotationClass) {
     try {
       Field f = field.getClass().getField(field.name());

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/AbstractCellDesignerAliasConverter.java

@@ -129,6 +129,36 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
     }
   }
 
+  /**
+   * This method computes coordinates that should be associated with the angle on
+   * the border of the alias.
+   *
+   * @param alias
+   *          alias to be investigated
+   * @param angle
+   *          angle on the border of the alias
+   * @return coordinates on the border of the alias described by the angle
+   */
+  protected Point2D getAnchorPointCoordinates(final T alias, final double angle) {
+    Point2D result = null;
+    if (alias.getWidth() == 0 && alias.getHeight() == 0) {
+      result = alias.getCenter();
+    } else {
+      double dist = Math.max(alias.getWidth(), alias.getHeight()) * 2;
+      Point2D startPoint = alias.getCenter();
+      double x = startPoint.getX() - Math.cos(angle) * dist;
+      double y = startPoint.getY() - Math.sin(angle) * dist;
+      Point2D endPoint = new Point2D.Double(x, y);
+      Line2D line = new Line2D.Double(startPoint, endPoint);
+      result = lineTransformation.getIntersectionWithPathIterator(line, getBoundPathIterator(alias));
+      if (result == null) {
+        logger.warn("Unknown crossing point: " + line.getP1() + "; " + line.getP2());
+        result = alias.getCenter();
+      }
+    }
+    return result;
+  }
+
   /**
    * Returns coordinates on the {@link Species} border for given angle for
    * residues.
@@ -250,35 +280,6 @@ public abstract class AbstractCellDesignerAliasConverter<T extends Element> impl
     throw new NotImplementedException("Not implemented for: " + this.getClass());
   }
 
-  /**
-   * This method computes coordinates that should be associated with the angle on
-   * the border of the alias.
-   *
-   * @param alias
-   *          alias to be investigated
-   * @param angle
-   *          angle on the border of the alias
-   * @return coordinates on the border of the alias described by the angle
-   */
-  protected Point2D getAnchorPointCoordinates(final T alias, final double angle) {
-    Point2D result = null;
-    if (alias.getWidth() == 0 && alias.getHeight() == 0) {
-      result = alias.getCenter();
-    } else {
-      double dist = Math.max(alias.getWidth(), alias.getHeight()) * 2;
-      Point2D startPoint = alias.getCenter();
-      double x = startPoint.getX() - Math.cos(angle) *