comments formatting issues

checkstyle.xml

@@ -273,21 +273,13 @@
             <property name="allowedAnnotations" value="Override, Test"/>
             <property name="tokens" value="METHOD_DEF, CTOR_DEF, ANNOTATION_FIELD_DEF"/>
         </module>
-<!--        <module name="MethodName">
-            <property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9_]*$"/>
-            <message key="name.invalidPattern"
-                     value="Method name ''{0}'' must match pattern ''{1}''."/>
-        </module>
         <module name="SingleLineJavadoc">
             <property name="ignoreInlineTags" value="false"/>
         </module>
-        <module name="EmptyCatchBlock">
-            <property name="exceptionVariableName" value="expected"/>
-        </module>
         <module name="CommentsIndentation">
             <property name="tokens" value="SINGLE_LINE_COMMENT, BLOCK_COMMENT_BEGIN"/>
         </module>
-        <module name="VisibilityModifier">
+<!--        <module name="VisibilityModifier">
             <property name="protectedAllowed" value="true"/>
         </module>
 
@@ -308,6 +300,14 @@
         <module name="SummaryJavadoc">
             <property name="forbiddenSummaryFragments"
                       value="^@return the *|^This method returns |^A [{]@code [a-zA-Z0-9]+[}]( is a )"/>
+        </module>
+        <module name="MethodName">
+            <property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9_]*$"/>
+            <message key="name.invalidPattern"
+                     value="Method name ''{0}'' must match pattern ''{1}''."/>
+        </module>
+        <module name="EmptyCatchBlock">
+            <property name="exceptionVariableName" value="expected"/>
         </module>
          -->
     </module> 

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioentity/reaction/ReactionConverterTest.java

@@ -175,11 +175,11 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
     ImageIO.write(bi, "PNG", outputStream);
     byte[] output2 = outputStream.toByteArray();
 
-//     FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
-//     FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
+    // FileUtils.writeByteArrayToFile(new File("tmp.png"), output1);
+    // FileUtils.writeByteArrayToFile(new File("tmp2.png"), output2);
 
-//     Desktop.getDesktop().open(new File("tmp.png"));
-//     Desktop.getDesktop().open(new File("tmp2.png"));
+    // Desktop.getDesktop().open(new File("tmp.png"));
+    // Desktop.getDesktop().open(new File("tmp2.png"));
 
     assertTrue(Arrays.equals(output1, output2));
 

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

@@ -236,8 +236,9 @@ class ReactionLayoutFinder {
           int currentScore = countedReactants + (productPoints - countedProducts);
           if (point == null || score < currentScore) {
             score = currentScore;
-            if (reactantPoints == 0) { // shift to most right possible line when
-                                       // there are no other reactants
+            if (reactantPoints == 0) { 
+              // shift to most right possible line when
+              // there are no other reactants
               point = getRightCenterPoint(interaction.getLine(), previousPoint, pair.getRight());
             } else if (productPoints == 0) {
               point = getLeftCenterPoint(interaction.getLine(), previousPoint, pair.getRight());

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java

@@ -270,12 +270,9 @@ public class ModelController extends BaseController {
     }
 
     Params params = new Params().x(minX).y(minY).height((maxY - minY) / scale).width((maxX - minX) / scale)
-        .level(level - Configuration.MIN_ZOOM_LEVEL).nested(false). // automatically
-                                                                    // set
-                                                                    // nested
-                                                                    // view as
-                                                                    // invalid
-        scale(scale).colorExtractor(colorExtractor).sbgn(originalModel.getProject().isSbgnFormat()).model(part);
+        .level(level - Configuration.MIN_ZOOM_LEVEL)
+        // automatically set nested view as disabled
+        .nested(false).scale(scale).colorExtractor(colorExtractor).sbgn(originalModel.getProject().isSbgnFormat()).model(part);
     if (background != null) {
       params.nested(background.isHierarchicalView());
     }