indentation issues

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

@@ -74,22 +74,22 @@ public class CopyPastePlugin extends CellDesignerPlugin {
     return new KeyEventDispatcher() {
       public boolean dispatchKeyEvent(final KeyEvent e) {
         switch (e.getID()) {
-        case KeyEvent.KEY_PRESSED:
-          if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
-              && e.isControlDown()
-              && e.isAltDown()) {
-            getPastePluginAction().myActionPerformed(null);
-            return true;
-          } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
-              && e.isControlDown()
-              && e.isAltDown()) {
-            getCopyPluginAction().myActionPerformed(null);
-            return true;
-          } else {
+          case KeyEvent.KEY_PRESSED:
+            if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
+                && e.isControlDown()
+                && e.isAltDown()) {
+              getPastePluginAction().myActionPerformed(null);
+              return true;
+            } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
+                && e.isControlDown()
+                && e.isAltDown()) {
+              getCopyPluginAction().myActionPerformed(null);
+              return true;
+            } else {
+              return false;
+            }
+          default:
             return false;
-          }
-        default:
-          return false;
         }
       }
     };

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

@@ -92,7 +92,8 @@ public abstract class ElementAnnotator extends CachableInterface {
    * @param element
    *          object to be annotated
    * @throws AnnotatorException
-   *           thrown when there is a problem with annotating not related to data
+   *           thrown when there is a problem with annotating not related to
+   *           data
    */
   public void annotateElement(final BioEntity element) throws AnnotatorException {
     annotateElement(element, createAnnotatorData());
@@ -107,7 +108,8 @@ public abstract class ElementAnnotator extends CachableInterface {
    *          list of parameters passed to the annotator which is expected to be
    *          in the same order as its {@link this#parameterDefs}
    * @throws AnnotatorException
-   *           thrown when there is a problem with annotating not related to data
+   *           thrown when there is a problem with annotating not related to
+   *           data
    */
   public final void annotateElement(final BioEntity bioEntity, final AnnotatorData parameters) throws AnnotatorException {
     if (isAnnotatable(bioEntity)) {
@@ -161,8 +163,8 @@ public abstract class ElementAnnotator extends CachableInterface {
   }
 
   /**
-   * Returns <code>true</code> if this annotator can annotate the object given in
-   * the parameter.
+   * Returns <code>true</code> if this annotator can annotate the object given
+   * in the parameter.
    *
    * @param object
    *          object to be tested if can be annotated
@@ -214,7 +216,8 @@ public abstract class ElementAnnotator extends CachableInterface {
   }
 
   /**
-   * Returns list with definitions of the parameters available for this annotator.
+   * Returns list with definitions of the parameters available for this
+   * annotator.
    *
    * @return the parameters {@link AnnotatorParamDefinition} list
    */
@@ -233,8 +236,8 @@ public abstract class ElementAnnotator extends CachableInterface {
   }
 
   /**
-   * Returns <code>true</code> if this annotator can annotate the object of given
-   * class type.
+   * 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
@@ -688,68 +691,68 @@ public abstract class ElementAnnotator extends CachableInterface {
         return collection;
       } else {
         switch (output.getField()) {
-        case ABBREVIATION:
-          return originalBioEntity.getAbbreviation();
-        case CHARGE:
-          if (originalBioEntity instanceof Species) {
-            return ((Species) originalBioEntity).getCharge();
-          } else {
-            return null;
-          }
-        case DESCRIPTION:
-          return originalBioEntity.getNotes();
-        case FORMULA:
-          return originalBioEntity.getFormula();
-        case FULL_NAME:
-          if (originalBioEntity instanceof Element) {
-            return ((Element) originalBioEntity).getFullName();
-          } else {
-            return null;
-          }
-        case INCHI:
-          if (originalBioEntity instanceof Chemical) {
-            return ((Chemical) originalBioEntity).getInChI();
-          } else {
-            return null;
-          }
-        case INCHI_KEY:
-          if (originalBioEntity instanceof Chemical) {
-            return ((Chemical) originalBioEntity).getInChIKey();
-          } else {
-            return null;
-          }
-        case NAME:
-          return originalBioEntity.getName();
-        case MCS:
-          if (originalBioEntity instanceof Reaction) {
-            return ((Reaction) originalBioEntity).getMechanicalConfidenceScore();
-          } else {
-            return null;
-          }
-        case PREVIOUS_SYMBOLS:
-          if (originalBioEntity instanceof Element) {
-            return ((Element) originalBioEntity).getFormerSymbols();
-          } else {
-            return null;
-          }
-        case SMILE:
-          if (originalBioEntity instanceof Chemical) {
-            return ((Chemical) originalBioEntity).getSmiles();
-          } else {
-            return null;
-          }
-        case SUBSYSTEM:
-          if (originalBioEntity instanceof Reaction) {
-            return ((Reaction) originalBioEntity).getSubsystem();
-          } else {
-            return null;
-          }
-        case SYMBOL:
-          return originalBioEntity.getSymbol();
-        case SYNONYMS:
-          return originalBioEntity.getSynonyms();
-        default:
-          throw new NotImplementedException(output.getField() + "");
+          case ABBREVIATION:
+            return originalBioEntity.getAbbreviation();
+          case CHARGE:
+            if (originalBioEntity instanceof Species) {
+              return ((Species) originalBioEntity).getCharge();
+            } else {
+              return null;
+            }
+          case DESCRIPTION:
+            return originalBioEntity.getNotes();
+          case FORMULA:
+            return originalBioEntity.getFormula();
+          case FULL_NAME:
+            if (originalBioEntity instanceof Element) {
+              return ((Element) originalBioEntity).getFullName();
+            } else {
+              return null;
+            }
+          case INCHI:
+            if (originalBioEntity instanceof Chemical) {
+              return ((Chemical) originalBioEntity).getInChI();
+            } else {
+              return null;
+            }
+          case INCHI_KEY:
+            if (originalBioEntity instanceof Chemical) {
+              return ((Chemical) originalBioEntity).getInChIKey();
+            } else {
+              return null;
+            }
+          case NAME:
+            return originalBioEntity.getName();
+          case MCS:
+            if (originalBioEntity instanceof Reaction) {
+              return ((Reaction) originalBioEntity).getMechanicalConfidenceScore();
+            } else {
+              return null;
+            }
+          case PREVIOUS_SYMBOLS:
+            if (originalBioEntity instanceof Element) {
+              return ((Element) originalBioEntity).getFormerSymbols();
+            } else {
+              return null;
+            }
+          case SMILE:
+            if (originalBioEntity instanceof Chemical) {
+              return ((Chemical) originalBioEntity).getSmiles();
+            } else {
+              return null;
+            }
+          case SUBSYSTEM:
+            if (originalBioEntity instanceof Reaction) {
+              return ((Reaction) originalBioEntity).getSubsystem();
+            } else {
+              return null;
+            }
+          case SYMBOL:
+            return originalBioEntity.getSymbol();
+          case SYNONYMS:
+            return originalBioEntity.getSynonyms();
+          default:
+            throw new NotImplementedException(output.getField() + "");
         }
       }
     }

checkstyle.xml

@@ -204,7 +204,7 @@
         </module>
         <module name="NoFinalizer"/>
         <module name="FinalParameters"/>
-<!--        <module name="GenericWhitespace">
+        <module name="GenericWhitespace">
             <message key="ws.followed"
                      value="GenericWhitespace ''{0}'' is followed by whitespace."/>
             <message key="ws.preceded"
@@ -222,7 +222,7 @@
             <property name="lineWrappingIndentation" value="4"/>
             <property name="arrayInitIndent" value="2"/>
         </module>
-        <module name="AbbreviationAsWordInName">
+<!--        <module name="AbbreviationAsWordInName">
             <property name="ignoreFinal" value="false"/>
             <property name="allowedAbbreviationLength" value="1"/>
             <property name="tokens"

commons/src/main/java/lcsb/mapviewer/common/geometry/LineTransformation.java

@@ -63,24 +63,24 @@ public class LineTransformation {
       last = actual;
       actual = new Point2D.Double(coordinates[0], coordinates[1]);
       switch (type) {
-      case PathIterator.SEG_MOVETO:
-        break;
-      case PathIterator.SEG_LINETO:
-        break;
-      case PathIterator.SEG_QUADTO:
-        break;
-      case PathIterator.SEG_CUBICTO:
-
-        // in case when there is an arc we define only end points of the arc
-        // as a border
-        actual = new Point2D.Double(coordinates[SEG_CUBICTO_END_X_COORDINATE_INDEX],
-            coordinates[SEG_CUBICTO_END_Y_COORDINATE_INDEX]);
-        break;
-      case PathIterator.SEG_CLOSE:
-        actual = first;
-        break;
-      default:
-        break;
+        case PathIterator.SEG_MOVETO:
+          break;
+        case PathIterator.SEG_LINETO:
+          break;
+        case PathIterator.SEG_QUADTO:
+          break;
+        case PathIterator.SEG_CUBICTO:
+
+          // in case when there is an arc we define only end points of the arc
+          // as a border
+          actual = new Point2D.Double(coordinates[SEG_CUBICTO_END_X_COORDINATE_INDEX],
+              coordinates[SEG_CUBICTO_END_Y_COORDINATE_INDEX]);
+          break;
+        case PathIterator.SEG_CLOSE:
+          actual = first;
+          break;
+        default:
+          break;
       }
       if (first == null) {
         first = actual;
@@ -155,13 +155,15 @@ public class LineTransformation {
   }
 
   /**
-   * Returns a point that is on the line and is as close as possible to the point.
+   * Returns a point that is on the line and is as close as possible to the
+   * point.
    * 
    * @param line
    *          line on which the point should be found
    * @param point
    *          point to which the result should be as close as possible
-   * @return point on the line that is as close as possible to the parameter point
+   * @return point on the line that is as close as possible to the parameter
+   *         point
    */
   public Point2D closestPointOnSegmentLineToPoint(final Line2D line, final Point2D point) {
     Point2D result = closestPointOnSegmentLineToPoint(line.getP1(), line.getP2(), point);
@@ -169,8 +171,8 @@ public class LineTransformation {
   }
 
   /**
-   * Returns a point that is on the line (v-w) and is as close as possible to the
-   * point.
+   * Returns a point that is on the line (v-w) and is as close as possible to
+   * the point.
    * 
    * @param v
    *          start of the line segment
@@ -178,8 +180,8 @@ public class LineTransformation {
    *          end of the line segment
    * @param p
    *          point to which the result should be as close as possible
-   * @return point on the line (v-w) that is as close as possible to the parameter
-   *         point
+   * @return point on the line (v-w) that is as close as possible to the
+   *         parameter point
    */
   public Point2D closestPointOnSegmentLineToPoint(final Point2D v, final Point2D w, final Point2D p) {
     // Return minimum distance between line segment vw and point p

commons/src/main/java/lcsb/mapviewer/common/geometry/PointTransformation.java

@@ -50,9 +50,9 @@ public class PointTransformation {
   }
 
   /**
-   * Checks if a point given in the parameter is valid (can be used for drawing).
-   * The point is considered as valid if coordinates are finite (final NaN and Infinity
-   * are invalid - they cannot be drawn).
+   * Checks if a point given in the parameter is valid (can be used for
+   * drawing). The point is considered as valid if coordinates are finite (final
+   * NaN and Infinity are invalid - they cannot be drawn).
    * 
    * @param point
    *          point to check
@@ -105,24 +105,24 @@ public class PointTransformation {
       last = actual;
       actual = new Point2D.Double(coordinates[0], coordinates[1]);
       switch (type) {
-      case PathIterator.SEG_MOVETO:
-        break;
-      case PathIterator.SEG_LINETO:
-        break;
-      case PathIterator.SEG_QUADTO:
-        break;
-      case PathIterator.SEG_CUBICTO:
-
-        // in case when there is an arc we define only end points of the arc
-        // as a border
-        actual = new Point2D.Double(coordinates[LineTransformation.SEG_CUBICTO_END_X_COORDINATE_INDEX],
-            coordinates[LineTransformation.SEG_CUBICTO_END_Y_COORDINATE_INDEX]);
-        break;
-      case PathIterator.SEG_CLOSE:
-        actual = first;
-        break;
-      default:
-        break;
+        case PathIterator.SEG_MOVETO:
+          break;
+        case PathIterator.SEG_LINETO:
+          break;
+        case PathIterator.SEG_QUADTO:
+          break;
+        case PathIterator.SEG_CUBICTO:
+
+          // in case when there is an arc we define only end points of the arc
+          // as a border
+          actual = new Point2D.Double(coordinates[LineTransformation.SEG_CUBICTO_END_X_COORDINATE_INDEX],
+              coordinates[LineTransformation.SEG_CUBICTO_END_Y_COORDINATE_INDEX]);
+          break;
+        case PathIterator.SEG_CLOSE:
+          actual = first;
+          break;
+        default:
+          break;
       }
       if (first == null) {
         first = actual;

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -616,13 +616,13 @@ public class SbgnmlXmlExporter {
   }
 
   /**
-   * Returns glyph with unit of information extracted from the alias or null if no
-   * unit of information was found.
+   * Returns glyph with unit of information extracted from the alias or null if
+   * no unit of information was found.
    * 
    * @param species
    *          input species
-   * @return glyph with unit of information extracted from the alias or null if no
-   *         unit of information was found
+   * @return glyph with unit of information extracted from the alias or null if
+   *         no unit of information was found
    */
   private Glyph getUnitOfInformationGlyph(final Species species) {
     Glyph uoiGlyph = null;
@@ -865,12 +865,12 @@ public class SbgnmlXmlExporter {
 
     List<Point2D> pointList = new ArrayList<>();
     pointList.add(reaction.getReactants().get(0).getLine().getStartPoint());
-    for (final Line2D line: reaction.getReactants().get(0).getLine().getLines()) {
+    for (final Line2D line : reaction.getReactants().get(0).getLine().getLines()) {
       pointList.add(line.getP2());
     }
-    
+
     pointList.add(reaction.getProducts().get(0).getLine().getStartPoint());
-    for (final Line2D line: reaction.getProducts().get(0).getLine().getLines()) {
+    for (final Line2D line : reaction.getProducts().get(0).getLine().getLines()) {
       pointList.add(line.getP2());
     }
 
@@ -1110,7 +1110,7 @@ public class SbgnmlXmlExporter {
 
     List<Point2D> arcPoints = new ArrayList<>();
     arcPoints.add(node.getLine().getStartPoint());
-    for (final Line2D line: node.getLine().getLines()) {
+    for (final Line2D line : node.getLine().getLines()) {
       arcPoints.add(line.getP2());
     }
     Start start = new Start();
@@ -1206,20 +1206,20 @@ public class SbgnmlXmlExporter {
     if (node instanceof NodeOperator) {
       ArrowType arrowType = node.getLine().getEndAtd().getArrowType();
       switch (arrowType) {
-      case BLANK:
-        return ArcClazz.STIMULATION;
-      case BLANK_CROSSBAR:
-        return ArcClazz.NECESSARY_STIMULATION;
-      case CIRCLE:
-        return ArcClazz.CATALYSIS;
-      case CROSSBAR:
-        return ArcClazz.INHIBITION;
-      case DIAMOND:
-        return ArcClazz.MODULATION;
-      case NONE:
-        return ArcClazz.LOGIC_ARC;
-      default:
-        throw new InvalidArgumentException();
+        case BLANK:
+          return ArcClazz.STIMULATION;
+        case BLANK_CROSSBAR:
+          return ArcClazz.NECESSARY_STIMULATION;
+        case CIRCLE:
+          return ArcClazz.CATALYSIS;
+        case CROSSBAR:
+          return ArcClazz.INHIBITION;
+        case DIAMOND:
+          return ArcClazz.MODULATION;
+        case NONE:
+          return ArcClazz.LOGIC_ARC;
+        default:
+          throw new InvalidArgumentException();
       }
     }
     throw new InvalidArgumentException();

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioentity/element/species/SpeciesConverter.java

@@ -221,8 +221,8 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
   }
 
   /**
-   * This method draws a string on graphics using current font. The coordinates of
-   * the text is given as a point. Both parameters centered described if text
+   * This method draws a string on graphics using current font. The coordinates
+   * of the text is given as a point. Both parameters centered described if text
    * should be automatically centered horizontally and vertically.
    *
    * @param border
@@ -244,35 +244,35 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
     double lineHeight = graphics.getFontMetrics().getHeight();
 
     switch (verticalAlign) {
-    case TOP:
-      y = border.getMinY() + graphics.getFontMetrics().getAscent();
-      break;
-    case MIDDLE:
-      y = border.getCenterY() - (textHeight / 2 - graphics.getFontMetrics().getAscent());
-      break;
-    case BOTTOM:
-      y = border.getMaxY() - (textHeight - graphics.getFontMetrics().getAscent());
-      break;
-    default:
-      throw new InvalidArgumentException("Don't know how to align text with: " + verticalAlign);
+      case TOP:
+        y = border.getMinY() + graphics.getFontMetrics().getAscent();
+        break;
+      case MIDDLE:
+        y = border.getCenterY() - (textHeight / 2 - graphics.getFontMetrics().getAscent());
+        break;
+      case BOTTOM:
+        y = border.getMaxY() - (textHeight - graphics.getFontMetrics().getAscent());
+        break;
+      default:
+        throw new InvalidArgumentException("Don't know how to align text with: " + verticalAlign);
     }
 
     for (final String string : lines) {
       double currX;
       switch (horizontalAlign) {
-      case LEFT:
-        currX = border.getX();
-        break;
-      case CENTER:
-        currX = border.getCenterX() - getTextWidth(string, graphics) / 2;
-        break;
-      case RIGTH:
-        currX = border.getMaxX() - getTextWidth(string, graphics);
-        break;
-      default:
-        throw new InvalidArgumentException("Don't know how to align text with: " + horizontalAlign);
+        case LEFT:
+          currX = border.getX();
+          break;
+        case CENTER:
+          currX = border.getCenterX() - getTextWidth(string, graphics) / 2;
+          break;
+        case RIGTH:
+          currX = border.getMaxX() - getTextWidth(string, graphics);
+          break;
+        default:
+          throw new InvalidArgumentException("Don't know how to align text with: " + horizontalAlign);
       }
-      
+
       graphics.drawString(string, (int) currX, (int) y);
       y += lineHeight;
     }
@@ -388,8 +388,8 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
   }
 
   /**
-   * Draws unit of information for the {@link Species} (rectangle in the top part
-   * of the alias).
+   * Draws unit of information for the {@link Species} (rectangle in the top
+   * part of the alias).
    *
    * @param text
    *          unit of information text
@@ -453,9 +453,10 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
   }
 
   /**
-   * This method draws modification of the alias. If drawEmptyModification is set
-   * to false then modification is not drawn if empty. If drawDescription is set
-   * then also description (position) of the modification is drawn on the canvas.
+   * This method draws modification of the alias. If drawEmptyModification is
+   * set to false then modification is not drawn if empty. If drawDescription is
+   * set then also description (position) of the modification is drawn on the
+   * canvas.
    * 
    * @param protein
    *          object that is 'parent' of the residue

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/geometry/FontFinder.java

@@ -215,34 +215,34 @@ public final class FontFinder {
     double lineHeight = graphics.getFontMetrics().getHeight();
     double y;
     switch (verticalAlign) {
-    case TOP:
-      y = border.getY() + lineHeight / 2;
-      break;
-    case MIDDLE:
-      y = (int) (border.getCenterY() - lineHeight * lines.size() / 2.0 + graphics.getFontMetrics().getAscent());
-      break;
-    case BOTTOM:
-      y = border.getMaxY() - lineHeight / 2 - lineHeight * lines.size();