Fixed all the documentation issues found by generating the javadoc

src/main/java/com/insightfullogic/honest_profiler/core/ThreadedAgent.java

@@ -30,7 +30,7 @@ public interface Block
     {
         /**
          * @return false iff you're ready to stop, true otherwise
-         * @throws Exception
+         * @throws Exception when things go bump
          */
         boolean run() throws Exception;
     }

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/AggregationProfile.java

@@ -112,6 +112,8 @@ public Tree getTree(CombinedGrouping grouping)
      *
      * The {@link LeanThreadNode}s, which are the root {@link Node}s in the {@link LeanProfile}, are themselves already
      * aggregations of all their descendant Frame {@link LeanNode}s, so we don't need to descend any further.
+     *
+     * @return the {@link NumericInfo} containing the aggregated data
      */
     private NumericInfo aggregateGlobal()
     {

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/ReferenceUtil.java

@@ -21,7 +21,7 @@ public final class ReferenceUtil
      * @param tree the {@link Tree} whose references are to be changed
      * @param mode the strategy for setting the references
      */
-    public static <K> void switchReference(Tree tree, ReferenceMode mode)
+    public static void switchReference(Tree tree, ReferenceMode mode)
     {
         switch (mode)
         {
@@ -52,7 +52,7 @@ public static <K> void switchReference(Tree tree, ReferenceMode mode)
      * @param treeDiff the {@link TreeDiff} whose references are to be changed
      * @param mode the strategy for setting the references
      */
-    public static <K> void switchReference(TreeDiff treeDiff, ReferenceMode mode)
+    public static void switchReference(TreeDiff treeDiff, ReferenceMode mode)
     {
         switchReference(treeDiff.getBaseAggregation(), mode);
         switchReference(treeDiff.getNewAggregation(), mode);
@@ -68,7 +68,7 @@ public static <K> void switchReference(TreeDiff treeDiff, ReferenceMode mode)
      * @param parent the parent {@link Node}
      * @param child the child {@link Node}
      */
-    private static <K> void setReferenceToParent(Node parent, Node child)
+    private static void setReferenceToParent(Node parent, Node child)
     {
 
         if (parent == null)

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/aggregator/DescendantFlatAggregator.java

@@ -11,7 +11,6 @@
 import com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat;
 import com.insightfullogic.honest_profiler.core.aggregation.result.straight.Node;
 import com.insightfullogic.honest_profiler.core.aggregation.result.straight.Tree;
-import com.insightfullogic.honest_profiler.core.profiles.lean.LeanNode;
 
 /**
  * Aggregator which takes a {@link Node}, and aggregates the values of the {@link Node} and its descendants into a
@@ -23,7 +22,7 @@ public class DescendantFlatAggregator implements SubAggregator<Node, Entry>
      * This method aggregates all descendants of a {@link Node} into a {@link Flat}, using the original
      * {@link CombinedGrouping} from the {@link Tree} the {@link Node} belongs to.
      *
-     * @see SubAggregator#aggregate(Object, LeanNode)
+     * @see SubAggregator#aggregate(Object)
      */
     @Override
     public Flat aggregate(Node parent)

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/aggregator/ProfileAggregator.java

@@ -7,7 +7,7 @@
 
 /**
  * Generic interface for aggregation functions which operate on the entire {@link AggregationProfile}. An Aggregator
- * aggregates an input {@link AggregationProfile} into an {@link Aggregation} containing results of type <T>, which are
+ * aggregates an input {@link AggregationProfile} into an {@link Aggregation} containing results of type T, which are
  * keyed by a String.
  *
  * @param <T> the type of the content items in the resulting {@link Aggregation}
@@ -18,6 +18,7 @@ public interface ProfileAggregator<T extends Keyed<String>>
      * Aggregate the provided {@link AggregationProfile}.
      *
      * @param input the {@link AggregationProfile} to be aggregated
+     * @param grouping the {@link CombinedGrouping} to be used when aggregating
      * @return the resulting {@link Aggregation}
      */
     Aggregation<T> aggregate(AggregationProfile input, CombinedGrouping grouping);

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/aggregator/SubAggregator.java

@@ -5,10 +5,10 @@
 
 /**
  * Generic interface for aggregation functions which operate on already aggregated items. An Aggregator aggregates input
- * of type <I> into an {@link Aggregation} containing results of type <T>, which are keyed by a key of type String.
+ * of type I into an {@link Aggregation} containing results of type T, which are keyed by a key of type String.
  *
- * @param <I> the type of the input being aggregated
- * @param <T> the type of the content items in the resulting {@link Aggregation}
+ * @param I the type of the input being aggregated
+ * @param T the type of the content items in the resulting {@link Aggregation}
  */
 public interface SubAggregator<I, T extends Keyed<String>>
 {

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/filter/Comparison.java

@@ -12,7 +12,7 @@
  * whether the item fulfills the condition.
  *
  * It would have been nice to be able to parametrize the Enum, it might have been possible to make the internal factory
- * methods lighter. May be revisited if {@link http://openjdk.java.net/jeps/301} gets implemented.
+ * methods lighter. May be revisited if <a href="http://openjdk.java.net/jeps/301">JEP 301</a> gets implemented.
  */
 public enum Comparison
 {
@@ -194,6 +194,7 @@ private Comparison(String name)
     /**
      * Returns a {@link Predicate} which will evaluate this comparison against the provided value.
      *
+     * @param <T> the type of the {@link Object} tested by the {@link Predicate}
      * @param value the value the {@link Predicate} will compare against
      * @return a {@link Predicate} which compares input to the provided value
      */

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/filter/FilterItem.java

@@ -74,8 +74,8 @@ public U getValue()
     // Filter Creation
 
     /**
-     * Creates the {@link FilterPredicate} which can filter items of type <T> by extracting the value specified by
-     * {@link Target} from them. The {@link ItemType} explicity describes the type <T>, and is needed for implementation
+     * Creates the {@link FilterPredicate} which can filter items of type T by extracting the value specified by
+     * {@link Target} from them. The {@link ItemType} explicity describes the type T, and is needed for implementation
      * reasons.
      *
      * @param type the type of the item the {@link FilterPredicate} can be used on

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/filter/FilterSpecification.java

@@ -52,6 +52,8 @@ public FilterSpecification(ItemType type)
      * specified {@link ItemType}.
      *
      * @param type the type of items the filter can filter
+     * @param hideErrors a boolean specifying if error frames should be filtered out
+     * @param filters a {@link List} of the contained {@link FilterItem}s
      */
     public FilterSpecification(ItemType type, boolean hideErrors, List<FilterItem<T, ?>> filters)
     {
@@ -91,7 +93,7 @@ public boolean isFiltering()
     /**
      * Sets the quickfilter String, which when not empty will generate an extra {@link Predicate} for filtering the key.
      *
-     * @param value
+     * @param value the value used for filtering
      */
     public void setQuickFilter(String value)
     {
@@ -101,7 +103,7 @@ public void setQuickFilter(String value)
     // Filter Construction Methods
 
     /**
-     * Generates a {@link Predicate} which accepts items of type <T> if they are accepted by all of the filters from all
+     * Generates a {@link Predicate} which accepts items of type T if they are accepted by all of the filters from all
      * contained {@link FilterItem}s, and optionally if they do not contain errors and/or if the key contains the String
      * specified by the quickfilter String.
      *

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/filter/Target.java

@@ -150,6 +150,8 @@ public ValueType getType()
      * Returns the extractor {@link Function} which can extract the Target value from the aggregation items with the
      * specified {@link ValueType}.
      *
+     * @param <T> the type of the input of the extractor {@link Function}
+     * @param <U> the type of the result of the extractor {@link Function}
      * @param type the {@link ValueType} of the aggregation items the extractor will accept
      * @return the extractor {@link Function} for extracting the Target value
      */

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/filter/ValueType.java

@@ -38,7 +38,8 @@ public enum ValueType
      * Returns a validator {@link Predicate} which tests the String by trying to apply corresponding the convertor. If
      * that operation throws an Exception, the String cannot be converted.
      *
-     * @param convertor the convertor {@link Function} which converts a String to a value of the specified type <T>
+     * @param <T> the type of the result of the convertor {@link Function}
+     * @param convertor the convertor {@link Function} which converts a String to a value of the specified type T
      * @return a validator {@link Predicate}
      */
     private static final <T> Predicate<String> validatorFor(Function<String, T> convertor)
@@ -133,6 +134,7 @@ public Predicate<String> getValidator()
     /**
      * Returns a {@link Function} for converting a String to a value of this type.
      *
+     * @param <T> the type of the result of the conversion {@link Function}
      * @return a {@link Function} for converting a String to a value of this type
      */
     @SuppressWarnings("unchecked")

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/grouping/CombinedGrouping.java

@@ -48,7 +48,7 @@ private CombinedGrouping(ThreadGrouping threadGrouping, FrameGrouping frameGroup
      *
      * @param profile the input {@link AggregationProfile}
      * @param node the {@link LeanNode} for which the key will be calculated
-     * @return
+     * @return the calculated key
      */
     @Override
     public String apply(AggregationProfile profile, LeanNode node)

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/grouping/FrameGrouping.java

@@ -18,17 +18,17 @@
 public enum FrameGrouping implements BiFunction<AggregationProfile, LeanNode, String>
 {
     /**
-     * Group frames by Fully Qualified Method Name. The constructed key is "<Fully Qualified ClassName>.<Method Name>".
+     * Group frames by Fully Qualified Method Name. The constructed key is "[Fully Qualified ClassName].[Method Name]".
      */
     BY_FQMN("By FQMN", (profile, node) -> profile.getSource().getMethodInfoMap().get(node.getFrame().getMethodId()).getFqmn()),
     /**
-     * Group frames by Fully Qualified Method Name and line number. The constructed key is "<Fully Qualified
-     * ClassName>.<Method Name>:<Line Number>".
+     * Group frames by Fully Qualified Method Name and line number. The constructed key is "[Fully Qualified
+     * ClassName].[Method Name]:[Line Number]".
      */
     BY_FQMN_LINENR("By FQMN + Line Nr", (profile, node) -> profile.getSource().getFqmnPlusLineNr(node)),
     /**
-     * Group frames by Fully Qualified Method Name and BCI (byte code index). The constructed key is "<Fully Qualified
-     * ClassName>.<Method Name>:<BCI>".
+     * Group frames by Fully Qualified Method Name and BCI (byte code index). The constructed key is "[Fully Qualified
+     * ClassName].[Method Name]:[BCI]".
      */
     BY_BCI("By FQMN + BCI", (profile, node) -> profile.getSource().getBciKey(node));
 

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/result/diff/AbstractDiff.java

@@ -32,6 +32,7 @@ public abstract class AbstractDiff<T extends Keyed<String>, U extends Keyed<Stri
      * Sets the {@link Aggregation}s which will be compared.
      *
      * @param baseAggregation the Base Aggregation
+     * @param newAggregation the New Aggregation
      */
     protected void setAggregations(V baseAggregation, V newAggregation)
     {

src/main/java/com/insightfullogic/honest_profiler/core/aggregation/result/diff/DiffEntry.java

@@ -33,7 +33,7 @@ public DiffEntry(Entry baseEntry, Entry newEntry)
      * Sets the Base {@link Entry}.
      *
      * The return value is provided as a convenience for
-     * {@link FlatDiff#setBase(com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat)}.
+     * {@link FlatDiff#set(com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat, com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat)}.
      *
      * @param entry the Base {@link Entry}
      * @return this {@link DiffEntry}
@@ -48,7 +48,7 @@ public DiffEntry setBase(Entry entry)
      * Sets the New {@link Entry}.
      *
      * The return value is provided as a convenience for
-     * {@link FlatDiff#setNew(com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat)}.
+     * {@link FlatDiff#set(com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat, com.insightfullogic.honest_profiler.core.aggregation.result.straight.Flat)}.
      *
      * @param entry the New {@link Entry}
      * @return this {@link DiffEntry}
@@ -87,6 +87,8 @@ public String getKey()
 
     /**
      * @see Entry#getSelfTime()
+     *
+     * @return the Base aggregated self time in nanoseconds
      */
     public long getBaseSelfTime()
     {
@@ -95,6 +97,8 @@ public long getBaseSelfTime()
 
     /**
      * @see Entry#getTotalTime()
+     *
+     * @return the Base aggregated total time in nanoseconds
      */
     public long getBaseTotalTime()
     {
@@ -103,6 +107,8 @@ public long getBaseTotalTime()
 
     /**
      * @see Entry#getSelfCnt()
+     *
+     * @return the Base aggregated self sample count
      */
     public int getBaseSelfCnt()
     {
@@ -111,6 +117,8 @@ public int getBaseSelfCnt()
 
     /**
      * @see Entry#getTotalCnt()
+     *
+     * @return the Base aggregated total sample count
      */
     public int getBaseTotalCnt()
     {
@@ -119,6 +127,8 @@ public int getBaseTotalCnt()
 
     /**
      * @see Entry#getSelfTimePct()
+     *
+     * @return the Base self time divided by the Base reference total time
      */
     public double getBaseSelfTimePct()
     {
@@ -127,6 +137,8 @@ public double getBaseSelfTimePct()
 
     /**
      * @see Entry#getTotalTimePct()
+     *
+     * @return the Base total time divided by the Base reference total time
      */
     public double getBaseTotalTimePct()
     {
@@ -135,6 +147,8 @@ public double getBaseTotalTimePct()
 
     /**
      * @see Entry#getSelfCntPct()
+     *
+     * @return the Base self sample count divided by the Base reference total sample count
      */
     public double getBaseSelfCntPct()
     {
@@ -143,14 +157,18 @@ public double getBaseSelfCntPct()
 
     /**
      * @see Entry#getTotalCntPct()
+     *
+     * @return the Base total sample count divided by the Base reference total sample count
      */
     public double getBaseTotalCntPct()
     {
         return baseEntry.getTotalCntPct();
     }
 
     /**
-     * @see Entry#getSelfTime()()
+     * @see Entry#getSelfTime()
+     *
+     * @return the New aggregated self time in nanoseconds
      */
     public long getNewSelfTime()
     {
@@ -159,6 +177,8 @@ public long getNewSelfTime()
 
     /**
      * @see Entry#getTotalTime()
+     *
+     * @return the New aggregated total time in nanoseconds
      */
     public long getNewTotalTime()
     {
@@ -167,6 +187,8 @@ public long getNewTotalTime()
 
     /**
      * @see Entry#getSelfCnt()
+     *
+     * @return the New aggregated self sample count
      */
     public int getNewSelfCnt()
     {
@@ -175,6 +197,8 @@ public int getNewSelfCnt()
 
     /**
      * @see Entry#getTotalCnt()
+     *
+     * @return the New aggregated total sample count
      */
     public int getNewTotalCnt()
     {
@@ -183,6 +207,8 @@ public int getNewTotalCnt()
 
     /**
      * @see Entry#getSelfTimePct()
+     *
+     * @return the New self time divided by the New reference total time
      */
     public double getNewSelfTimePct()
     {
@@ -191,6 +217,8 @@ public double getNewSelfTimePct()
 
     /**
      * @see Entry#getTotalTimePct()
+     *
+     * @return the New total time divided by the New reference total time
      */
     public double getNewTotalTimePct()
     {
@@ -199,6 +227,8 @@ public double getNewTotalTimePct()
 
     /**
      * @see Entry#getSelfCntPct()
+     *
+     * @return the New self sample count divided by the New reference total sample count
      */
     public double getNewSelfCntPct()
     {
@@ -207,6 +237,8 @@ public double getNewSelfCntPct()
 
     /**
      * @see Entry#getTotalCntPct()
+     *
+     * @return the New total sample count divided by the New reference total sample count
      */
     public double getNewTotalCntPct()
     {
@@ -215,6 +247,8 @@ public double getNewTotalCntPct()
 
     /**
      * @see Entry#getRefCnt()
+     *
+     * @return the Base reference total sample count
      */
     public int getBaseRefCnt()
     {
@@ -223,6 +257,8 @@ public int getBaseRefCnt()
 
     /**
      * @see Entry#getRefCnt()
+     *
+     * @return the New reference total sample count
      */
     public int getNewRefCnt()
     {