parameter name standard enforced

checkstyle.xml

@@ -167,12 +167,12 @@
             <message key="name.invalidPattern"
                      value="Member name ''{0}'' must match pattern ''{1}''."/>
         </module>
-<!--        <module name="ParameterName">
+        <module name="ParameterName">
             <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
             <message key="name.invalidPattern"
                      value="Parameter name ''{0}'' must match pattern ''{1}''."/>
         </module>
-        <module name="LambdaParameterName">
+<!--        <module name="LambdaParameterName">
             <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
             <message key="name.invalidPattern"
                      value="Lambda parameter name ''{0}'' must match pattern ''{1}''."/>

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

@@ -303,12 +303,12 @@ public final class Configuration {
   }
 
   /**
-   * @param xFrametDomains
+   * @param domains
    *          the xFrametDomain to set
    * @see #xFrametDomain
    */
-  public static void setxFrameDomain(List<String> xFrametDomains) {
-    Configuration.xFrametDomain = xFrametDomains;
+  public static void setxFrameDomain(List<String> domains) {
+    Configuration.xFrametDomain = domains;
   }
 
   /**

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

@@ -52,11 +52,11 @@ public class SystemClipboard implements ClipboardOwner {
    * Place a String on the clipboard, and make this class the owner of the
    * Clipboard's contents.
    *
-   * @param aString
+   * @param string
    *          what we want to put into clipboard
    */
-  public void setClipboardContents(String aString) {
-    StringSelection stringSelection = new StringSelection(aString);
+  public void setClipboardContents(String string) {
+    StringSelection stringSelection = new StringSelection(string);
     Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
     clipboard.setContents(stringSelection, this);
   }

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

@@ -318,16 +318,16 @@ public class RestAnnotationParser {
    *
    * @param type
    *          - relationtype of the annotaion ids
-   * @param mType
+   * @param miriamType
    *          {@link MiriamType type} of the reference resource
    * @param ids
    *          - list of ids
    * @return set of miriam data
    */
-  private Set<MiriamData> idsToData(MiriamRelationType type, MiriamType mType, ArrayList<String> ids) {
+  private Set<MiriamData> idsToData(MiriamRelationType type, MiriamType miriamType, ArrayList<String> ids) {
     Set<MiriamData> result = new HashSet<MiriamData>();
     for (String id : ids) {
-      MiriamData md = new MiriamData(type, mType, id);
+      MiriamData md = new MiriamData(type, miriamType, id);
       result.add(md);
     }
     return result;

model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java

@@ -31,12 +31,12 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
    *
    */
   private static final long serialVersionUID = 1L;
-  
+
   /**
    * Default class logger.
    */
   private static Logger logger = LogManager.getLogger();
-  
+
   /**
    * Unique database identifier.
    */
@@ -199,27 +199,17 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
   }
 
   @Override
-  public boolean equals(Object aThat) {
-    // check for self-comparison
-    if (this == aThat) {
+  public boolean equals(Object o) {
+    if (this == o) {
       return true;
     }
 
-    // use instanceof instead of getClass here for two reasons
-    // 1. if need be, it can match any supertype, and not just one class;
-    // 2. it renders an explict check for "that == null" redundant, since
-    // it does the check for null already - "null instanceof [type]" always
-    // returns false. (See Effective Java by Joshua Bloch.)
-    if (!(aThat instanceof MiriamData)) {
+    if (!(o instanceof MiriamData)) {
       return false;
     }
-    // Alternative to the above line :
-    // if ( aThat == null || aThat.getClass() != this.getClass() ) return false;
 
-    // cast to native object is now safe
-    MiriamData that = (MiriamData) aThat;
+    MiriamData that = (MiriamData) o;
 
-    // now a proper field-by-field evaluation can be made
     return this.compareTo(that) == 0;
   }
 

model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java

@@ -131,12 +131,12 @@ public class OverviewModelLink extends OverviewLink {
   }
 
   /**
-   * @param xCoord
+   * @param x
    *          the xCoord to set
    * @see #xCoord
    */
-  public void setxCoord(Integer xCoord) {
-    this.xCoord = xCoord;
+  public void setxCoord(Integer x) {
+    this.xCoord = x;
   }
 
   /**
@@ -163,12 +163,12 @@ public class OverviewModelLink extends OverviewLink {
   }
 
   /**
-   * @param yCoord
+   * @param y
    *          the yCoord to set
    * @see #yCoord
    */
-  public void setyCoord(Integer yCoord) {
-    this.yCoord = yCoord;
+  public void setyCoord(Integer y) {
+    this.yCoord = y;
   }
 
   /**

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/DataNode.java

@@ -132,17 +132,17 @@ public class DataNode extends GraphicalPathwayElement {
    * @return the vAlign
    * @see #verticalAlign
    */
-  public String getvAlign() {
+  public String getVerticalAlign() {
     return verticalAlign;
   }
 
   /**
-   * @param vAlign
+   * @param verticalAlign
    *          the vAlign to set
    * @see #verticalAlign
    */
-  public void setvAlign(String vAlign) {
-    this.verticalAlign = vAlign;
+  public void setVerticalAlign(String verticalAlign) {
+    this.verticalAlign = verticalAlign;
   }
 
   /**

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Edge.java

@@ -454,12 +454,12 @@ public class Edge implements Serializable {
   }
 
   /**
-   * @param zOrder
+   * @param z
    *          the zOrder to set
    * @see #zOrder
    */
-  public void setzOrder(Integer zOrder) {
-    this.zOrder = zOrder;
+  public void setzOrder(Integer z) {
+    this.zOrder = z;
   }
 
   /**

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Label.java

@@ -112,17 +112,17 @@ public class Label extends GraphicalPathwayElement {
    * @return the vAlign
    * @see #verticalAlign
    */
-  public String getvAlign() {
+  public String getVerticalAlign() {
     return verticalAlign;
   }
 
   /**
-   * @param vAlign
+   * @param verticalAlign
    *          the vAlign to set
    * @see #verticalAlign
    */
-  public void setvAlign(String vAlign) {
-    this.verticalAlign = vAlign;
+  public void setVerticalAlign(String verticalAlign) {
+    this.verticalAlign = verticalAlign;
   }
 
   /**

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/PathwayElement.java

@@ -127,12 +127,12 @@ public abstract class PathwayElement implements Serializable {
   }
 
   /**
-   * @param zOrder
+   * @param z
    *          the zOrder to set
    * @see #zOrder
    */
-  public void setzOrder(Integer zOrder) {
-    this.zOrder = zOrder;
+  public void setzOrder(Integer z) {
+    this.zOrder = z;
   }
 
   /**

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/Shape.java

@@ -163,17 +163,17 @@ public class Shape extends GraphicalPathwayElement {
    * @return the vAlign
    * @see #verticalAlign
    */
-  public String getvAlign() {
+  public String getVerticalAlign() {
     return verticalAlign;
   }
 
   /**
-   * @param vAlign
+   * @param verticalAlign
    *          the vAlign to set
    * @see #verticalAlign
    */
-  public void setvAlign(String vAlign) {
-    this.verticalAlign = vAlign;
+  public void setVerticalAlign(String verticalAlign) {
+    this.verticalAlign = verticalAlign;
   }
 
   /**

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/DataNodeParser.java

@@ -47,12 +47,12 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
   }
 
   @Override
-  public DataNode parse(Element eElement) throws UnknownTypeException {
-    if (!eElement.getNodeName().equals("DataNode")) {
+  public DataNode parse(Element element) throws UnknownTypeException {
+    if (!element.getNodeName().equals("DataNode")) {
       throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only DataNode xml nodes");
     }
 
-    String id = eElement.getAttribute("GraphId");
+    String id = element.getAttribute("GraphId");
     if (id == null || id.isEmpty()) {
       id = "gen_dn_" + counter++;
       logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "DataNode", null, getMapName()),
@@ -60,7 +60,7 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
     }
     DataNode node = new DataNode(id, getMapName());
 
-    for (Pair<String, String> entry : getAttributes(eElement)) {
+    for (Pair<String, String> entry : getAttributes(element)) {
       switch (entry.getLeft()) {
       case ("GraphId"):
         break;
@@ -79,7 +79,7 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
       }
     }
 
-    NodeList tmpList = eElement.getChildNodes();
+    NodeList tmpList = element.getChildNodes();
     for (int j = 0; j < tmpList.getLength(); j++) {
       Node tmpNode = tmpList.item(j);
       if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
@@ -105,7 +105,7 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
           break;
         default:
           logger.warn(node.getLogMarker(),
-              "Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+              "Unknown sub-node of " + element.getNodeName() + " node: " + eTmp.getNodeName());
           break;
         }
       }
@@ -127,19 +127,19 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
   /**
    * Parse graphics xml node in the shape node.
    *
-   * @param eTmp
+   * @param element
    *          xml node with graphics
    * @param shape
    *          shape where data should be added
    * @throws UnknownTypeException
    *           thrown when node contains unknown types
    */
-  private void parseGraphics(Element eTmp, DataNode shape) throws UnknownTypeException {
+  private void parseGraphics(Element element, DataNode shape) throws UnknownTypeException {
     Double centerX = null;
     Double centerY = null;
     Double width = null;
     Double height = null;
-    for (Pair<String, String> entry : getAttributes(eTmp)) {
+    for (Pair<String, String> entry : getAttributes(element)) {
       if (!parseCommonGraphicAttributes(shape, entry)) {
         switch (entry.getLeft()) {
         case ("CenterX"):
@@ -178,10 +178,10 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
           shape.setFontWeight(entry.getRight());
           break;
         case ("Valign"):
-          shape.setvAlign(entry.getRight());
+          shape.setVerticalAlign(entry.getRight());
           break;
         default:
-          logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft());
+          logger.warn("Unknown attribute of " + element.getNodeName() + " node: " + entry.getLeft());
           break;
         }
       }
@@ -192,14 +192,14 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
   /**
    * Method that parses {@link DataNode} xml attribute.
    *
-   * @param eTmp
+   * @param element
    *          xml node with attribute
    * @param shape
    *          shape where data should be added
    */
-  private void parseAttribute(Element eTmp, DataNode shape) {
-    String key = eTmp.getAttribute("Key");
-    String value = eTmp.getAttribute("Value");
+  private void parseAttribute(Element element, DataNode shape) {
+    String key = element.getAttribute("Key");
+    String value = element.getAttribute("Value");
     switch (key) {
     case ("org.pathvisio.model.BackpageHead"):
       // it's deprecated in PathVisio so we can skip it

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/EdgeLineParser.java

@@ -46,14 +46,14 @@ public class EdgeLineParser extends ElementGpmlParser<Edge> {
    * @throws ConverterException
    */
   @Override
-  public Edge parse(Element eElement) throws ConverterException {
-    if (!eElement.getNodeName().equals("GraphicalLine")) {
+  public Edge parse(Element element) throws ConverterException {
+    if (!element.getNodeName().equals("GraphicalLine")) {
       throw new InvalidArgumentException(
-          ShapeParser.class.getSimpleName() + " can parse only GraphicalLine xml nodes. But " + eElement.getNodeName());
+          ShapeParser.class.getSimpleName() + " can parse only GraphicalLine xml nodes. But " + element.getNodeName());
     }
     Edge line = edgeParser.createEmpty();
-    NodeList nodes = eElement.getChildNodes();
-    for (Pair<String, String> entry : getAttributes(eElement)) {
+    NodeList nodes = element.getChildNodes();
+    for (Pair<String, String> entry : getAttributes(element)) {
       switch (entry.getLeft()) {
       case ("GraphId"):
         line.setGraphId(entry.getRight());
@@ -62,7 +62,7 @@ public class EdgeLineParser extends ElementGpmlParser<Edge> {
         line.setGroupRef(entry.getRight());
         break;
       default:
-        logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+        logger.warn("Unknown attribute of " + element.getNodeName() + " node: " + entry.getLeft());
       }
     }
 

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/EdgeParser.java

@@ -87,15 +87,15 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
    *           thrown when there is a problem with parsing edge
    */
   @Override
-  public Edge parse(Element eElement) throws ConverterException {
+  public Edge parse(Element parentElement) throws ConverterException {
 
-    String graphId = eElement.getAttribute("GraphId");
+    String graphId = parentElement.getAttribute("GraphId");
     if (graphId == null || graphId.equals("")) {
       graphId = getNewId();
     }
     Edge edge = new Edge(graphId, getMapName());
 
-    for (Pair<String, String> entry : getAttributes(eElement)) {
+    for (Pair<String, String> entry : getAttributes(parentElement)) {
       switch (entry.getLeft()) {
       case ("GraphId"):
         break;
@@ -103,12 +103,12 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
         edge.setGroupRef(entry.getRight());
         break;
       default:
-        logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+        logger.warn("Unknown attribute of " + parentElement.getNodeName() + " node: " + entry.getLeft());
         break;
       }
     }
 
-    NodeList nodes = eElement.getChildNodes();
+    NodeList nodes = parentElement.getChildNodes();
     boolean graphicsParsed = false;
     for (int i = 0; i < nodes.getLength(); i++) {
       Node node = nodes.item(i);
@@ -581,14 +581,14 @@ public class EdgeParser extends ElementGpmlParser<Edge> {
   /**
    * Method that parses {@link Edge} xml attribute.
    *
-   * @param eTmp
+   * @param element
    *          xml node with attribute
    * @param edge
    *          edge where data should be added
    */
-  private void parseAttribute(Element eTmp, Edge edge) {
-    String key = eTmp.getAttribute("Key");
-    String value = eTmp.getAttribute("Value");
+  private void parseAttribute(Element element, Edge edge) {
+    String key = element.getAttribute("Key");
+    String value = element.getAttribute("Value");
     switch (key) {
     case ("org.pathvisio.core.ds"):
       // skip for now (no idea what does it mean)

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/GpmlParser.java

@@ -698,11 +698,11 @@ public class GpmlParser {
     return result;
   }
 
-  private PolylineData parseLine(Node lNode) throws UnknownTypeException {
+  private PolylineData parseLine(Node parentNode) throws UnknownTypeException {
     int refs = 0;
     PolylineData line = new PolylineData();
     List<Point2D> points = new ArrayList<>();
-    NodeList nodes = lNode.getChildNodes();
+    NodeList nodes = parentNode.getChildNodes();
     for (int i = 0; i < nodes.getLength(); i++) {
       Node node = nodes.item(i);
       if (node.getNodeType() == Node.ELEMENT_NODE) {

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/LabelParser.java

@@ -41,13 +41,13 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
   }
 
   @Override
-  public Label parse(Element eElement) throws UnknownTypeException {
-    if (!eElement.getNodeName().equals("Label")) {
+  public Label parse(Element element) throws UnknownTypeException {
+    if (!element.getNodeName().equals("Label")) {
       throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Label xml nodes");
     }
-    Label label = new Label(eElement.getAttribute("GraphId"), getMapName());
+    Label label = new Label(element.getAttribute("GraphId"), getMapName());
 
-    for (Pair<String, String> entry : getAttributes(eElement)) {
+    for (Pair<String, String> entry : getAttributes(element)) {
       switch (entry.getLeft()) {
       case ("GraphId"):
         break;
@@ -70,12 +70,12 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
         label.setGroupRef(entry.getRight());
         break;
       default:
-        logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+        logger.warn("Unknown attribute of " + element.getNodeName() + " node: " + entry.getLeft());
         break;
       }
     }
 
-    NodeList tmpList = eElement.getChildNodes();
+    NodeList tmpList = element.getChildNodes();
     for (int j = 0; j < tmpList.getLength(); j++) {
       Node tmpNode = tmpList.item(j);
       if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
@@ -94,7 +94,7 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
           parseAttribute(eTmp, label);
           break;
         default:
-          logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+          logger.warn("Unknown sub-node of " + element.getNodeName() + " node: " + eTmp.getNodeName());
           break;
         }
       }
@@ -116,19 +116,19 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
   /**
    * Parse graphics xml node in the shape node.
    *
-   * @param eTmp
+   * @param element
    *          xml node with graphics
    * @param shape
    *          shape where data should be added
    * @throws UnknownTypeException
    *           thrown when some elements contain unknown typevalues
    */
-  protected void parseGraphics(Element eTmp, Label shape) throws UnknownTypeException {
+  protected void parseGraphics(Element element, Label shape) throws UnknownTypeException {
     Double centerX = null;
     Double centerY = null;
     Double width = null;
     Double height = null;
-    for (Pair<String, String> entry : getAttributes(eTmp)) {
+    for (Pair<String, String> entry : getAttributes(element)) {
       if (!parseCommonGraphicAttributes(shape, entry)) {
         switch (entry.getLeft()) {
         case ("CenterX"):
@@ -159,13 +159,13 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
           shape.setFontWeight(entry.getRight());
           break;
         case ("Valign"):
-          shape.setvAlign(entry.getRight());
+          shape.setVerticalAlign(entry.getRight());
           break;
         case ("ShapeType"):
           shape.setShape(entry.getRight());
           break;
         default:
-          logger.warn("Unknown attribute of " + eTmp.getNodeName() + " node: " + entry.getLeft() + "; value: "
+          logger.warn("Unknown attribute of " + element.getNodeName() + " node: " + entry.getLeft() + "; value: "
               + entry.getRight());
           break;
         }
@@ -177,14 +177,14 @@ public class LabelParser extends GraphicalPathwayElementParser<Label> {
   /**
    * Method that parses {@link Label} xml attribute.
    *
-   * @param eTmp
+   * @param element
    *          xml node with attribute
    * @param shape
    *          shape where data should be added
    */
-  private void parseAttribute(Element eTmp, Label shape) {
-    String key = eTmp.getAttribute("Key");
-    String value = eTmp.getAttribute("Value");
+  private void parseAttribute(Element element, Label shape) {
+    String key = element.getAttribute("Key");
+    String value = element.getAttribute("Value");
     switch (key) {
     case ("org.pathvisio.model.GenMAPP-Xref"):
       // skip it when it's empty

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ShapeParser.java

@@ -39,12 +39,12 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
   }
 
   @Override
-  public Shape parse(Element eElement) throws ConverterException {
-    if (!eElement.getNodeName().equals("Shape")) {
+  public Shape parse(Element element) throws ConverterException {
+    if (!element.getNodeName().equals("Shape")) {
       throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only Shape xml nodes");
     }
-    Shape shape = new Shape(eElement.getAttribute("GraphId"), getMapName());
-    for (Pair<String, String> entry : getAttributes(eElement)) {
+    Shape shape = new Shape(element.getAttribute("GraphId"), getMapName());
+    for (Pair<String, String> entry : getAttributes(element)) {
       switch (entry.getLeft()) {
       case ("GraphId"):
         break;
@@ -55,12 +55,12 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
         shape.setGroupRef(entry.getRight());
         break;
       default:
-        logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+        logger.warn("Unknown attribute of " + element.getNodeName() + " node: " + entry.getLeft());
         break;
       }
     }
 
-    NodeList tmpList = eElement.getChildNodes();
+    NodeList tmpList = element.getChildNodes();
     for (int j = 0; j < tmpList.getLength(); j++) {
       Node tmpNode = tmpList.item(j);
       if (tmpNode.getNodeType() == Node.ELEMENT_NODE) {
@@ -79,7 +79,7 @@ public class ShapeParser extends GraphicalPathwayElementParser<Shape> {
           shape.addBiopaxReference(eTmp.getTextContent());
           break;