2016.04.30_stellar

Lefteris Paraskevas

[ADD]: Generated JavaDoc.
[REF]: Various name changes.
[REA]: Various JavaDoc fixes.
--------------------------------------------------
#All comments must be removed prior to commit except from the 'Committing two milestones' info

nbproject/project.properties

@@ -1,8 +1,7 @@
-file.reference.commons-cli-1.3.1-javadoc.jar=lib/commons-cli-1.3.1-javadoc.jar
-file.reference.commons-cli-1.3.1.jar=lib/commons-cli-1.3.1.jar
-#Fri Apr 29 13:47:44 EEST 2016
+#Sat Apr 30 17:10:14 EEST 2016
 jnlp.offline-allowed=false
 javadoc.splitindex=true
+file.reference.commons-cli-1.3.1-javadoc.jar=lib/commons-cli-1.3.1-javadoc.jar
 file.reference.twitter4j-examples-4.0.4.jar=lib/twitter4j-examples-4.0.4.jar
 file.reference.bson-3.0.4.jar=lib/bson-3.0.4.jar
 build.classes.excludes=**/*.java,**/*.form
@@ -11,9 +10,7 @@ build.sysclasspath=ignore
 file.reference.twitter4j-media-support-4.0.4.jar=lib/twitter4j-media-support-4.0.4.jar
 javac.target=1.8
 build.generated.dir=${build.dir}/generated
-run.classpath=\
-    ${javac.classpath}:\
-    ${build.classes.dir}
+run.classpath=${javac.classpath}\:${build.classes.dir}
 file.reference.mongodb-driver-3.0.4.jar=lib/mongodb-driver-3.0.4.jar
 file.reference.reflections-0.9.9-RC1.jar=lib/reflections-0.9.9-RC1.jar
 debug.test.classpath=${run.test.classpath}
@@ -48,9 +45,7 @@ run.jvmargs=
 manifest.custom.permissions=
 javac.test.processorpath=${javac.test.classpath}
 dist.archive.excludes=
-run.test.classpath=\
-    ${javac.test.classpath}:\
-    ${build.test.classes.dir}
+run.test.classpath=${javac.test.classpath}\:${build.test.classes.dir}
 build.generated.sources.dir=${build.dir}/generated-sources
 jnlp.signing=
 javadoc.notree=false
@@ -67,77 +62,42 @@ dist.javadoc.dir=${dist.dir}/javadoc
 file.reference.xom.jar=lib/xom.jar
 file.reference.commons-math3-3.4.jar=lib/commons-math3-3.4.jar
 javadoc.additionalparam=
-javac.classpath=\
-    ${file.reference.HAC.jar}:\
-    ${file.reference.twitter4j-async-4.0.4.jar}:\
-    ${file.reference.twitter4j-core-4.0.4.jar}:\
-    ${file.reference.twitter4j-examples-4.0.4.jar}:\
-    ${file.reference.twitter4j-media-support-4.0.4.jar}:\
-    ${file.reference.twitter4j-stream-4.0.4.jar}:\
-    ${file.reference.bson-3.0.4.jar}:\
-    ${file.reference.commons-io-2.4.jar}:\
-    ${file.reference.commons-lang3-3.1.jar}:\
-    ${file.reference.commons-math3-3.4.jar}:\
-    ${file.reference.controlsfx-8.40.10-20150826.135843-344.jar}:\
-    ${file.reference.gs-algo-1.2.jar}:\
-    ${file.reference.gs-core-1.2.jar}:\
-    ${file.reference.gs-ui-1.2.jar}:\
-    ${file.reference.guava-18.0.jar}:\
-    ${file.reference.javassist.jar}:\
-    ${file.reference.jmod-1.2b.jar}:\
-    ${file.reference.jtransforms-2.4.jar}:\
-    ${file.reference.lucene-analyzers-common-4.10.2.jar}:\
-    ${file.reference.lucene-core-4.10.2.jar}:\
-    ${file.reference.mongodb-driver-3.0.4.jar}:\
-    ${file.reference.mongodb-driver-async-3.0.4.jar}:\
-    ${file.reference.mongodb-driver-core-3.0.4.jar}:\
-    ${file.reference.reflections-0.9.9-RC1.jar}:\
-    ${file.reference.xom.jar}:\
-    ${file.reference.ejml-0.23.jar}:\
-    ${file.reference.stanford-corenlp-3.5.2.jar}:\
-    ${file.reference.stanford-corenlp-3.5.2-models.jar}:\
-    ${file.reference.jWave_java_groovy.jar}:\
-    ${file.reference.commons-cli-1.3.1-javadoc.jar}:\
-    ${file.reference.commons-cli-1.3.1.jar}
+javac.classpath=${file.reference.HAC.jar}\:${file.reference.twitter4j-async-4.0.4.jar}\:${file.reference.twitter4j-core-4.0.4.jar}\:${file.reference.twitter4j-examples-4.0.4.jar}\:${file.reference.twitter4j-media-support-4.0.4.jar}\:${file.reference.twitter4j-stream-4.0.4.jar}\:${file.reference.bson-3.0.4.jar}\:${file.reference.commons-io-2.4.jar}\:${file.reference.commons-lang3-3.1.jar}\:${file.reference.commons-math3-3.4.jar}\:${file.reference.controlsfx-8.40.10-20150826.135843-344.jar}\:${file.reference.gs-algo-1.2.jar}\:${file.reference.gs-core-1.2.jar}\:${file.reference.gs-ui-1.2.jar}\:${file.reference.guava-18.0.jar}\:${file.reference.javassist.jar}\:${file.reference.jmod-1.2b.jar}\:${file.reference.jtransforms-2.4.jar}\:${file.reference.lucene-analyzers-common-4.10.2.jar}\:${file.reference.lucene-core-4.10.2.jar}\:${file.reference.mongodb-driver-3.0.4.jar}\:${file.reference.mongodb-driver-async-3.0.4.jar}\:${file.reference.mongodb-driver-core-3.0.4.jar}\:${file.reference.reflections-0.9.9-RC1.jar}\:${file.reference.xom.jar}\:${file.reference.ejml-0.23.jar}\:${file.reference.stanford-corenlp-3.5.2.jar}\:${file.reference.stanford-corenlp-3.5.2-models.jar}\:${file.reference.jWave_java_groovy.jar}\:${file.reference.commons-cli-1.3.1-javadoc.jar}\:${file.reference.commons-cli-1.3.1.jar}
 javadoc.noindex=false
 manifest.custom.codebase=
 file.reference.jtransforms-2.4.jar=lib/jtransforms-2.4.jar
+file.reference.commons-cli-1.3.1.jar=lib/commons-cli-1.3.1.jar
 annotation.processing.enabled.in.editor=false
 file.reference.controlsfx-8.40.10-20150826.135843-344.jar=lib/controlsfx-8.40.10-20150826.135843-344.jar
-javadoc.private=false
 file.reference.commons-io-2.4.jar=lib/commons-io-2.4.jar
-build.test.classes.dir=${build.dir}/test/classes
+javadoc.private=false
 javadoc.encoding=${source.encoding}
+build.test.classes.dir=${build.dir}/test/classes
 jar.index=${jnlp.enabled}
 javac.compilerargs=
 file.reference.lucene-analyzers-common-4.10.2.jar=lib/lucene-analyzers-common-4.10.2.jar
-project.license=gpl30
 source.encoding=UTF-8
+project.license=gpl30
 file.reference.gs-algo-1.2.jar=lib/gs-algo-1.2.jar
 jnlp.signing.keystore=
 meta.inf.dir=${src.dir}/META-INF
-excludes=
 annotation.processing.run.all.processors=true
+excludes=
 application.title=MSc
 jnlp.codebase.type=no.codebase
 file.reference.stanford-corenlp-3.5.2-models.jar=lib/stanford-corenlp-3.5.2-models.jar
-javac.processorpath=\
-    ${javac.classpath}
+javac.processorpath=${javac.classpath}
 build.test.results.dir=${build.dir}/test/results
 file.reference.commons-lang3-3.1.jar=lib/commons-lang3-3.1.jar
-endorsed.classpath=
 javadoc.use=true
+endorsed.classpath=
 javadoc.nonavbar=false
 jnlp.signing.alias=
 javadoc.windowtitle=
-javac.test.classpath=\
-    ${javac.classpath}:\
-    ${build.classes.dir}:\
-    ${libs.junit_4.classpath}:\
-    ${libs.hamcrest.classpath}
+javac.test.classpath=${javac.classpath}\:${build.classes.dir}\:${libs.junit_4.classpath}\:${libs.hamcrest.classpath}
 file.reference.mongodb-driver-core-3.0.4.jar=lib/mongodb-driver-core-3.0.4.jar
 src.dir=src
-annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
 file.reference.HAC.jar=lib/HAC.jar
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
 debug.classpath=${run.classpath}
 jnlp.enabled=false

src/edmodule/AbstractEDMethod.java

@@ -22,7 +22,7 @@
  * but every separate ED technique has to implement these 6 methods.
  * 
  * @author  Lefteris Paraskevas
- * @version 2016.04.09_1945
+ * @version 2016.04.30_1825
  */
 public interface AbstractEDMethod {
 
@@ -35,7 +35,7 @@ public interface AbstractEDMethod {
     /**
      * Get the citation of the paper that introduced the used Event Detection algorithm.
      * @return A String containing the citation. The String must start and end
-     * with '<li>' tags.
+     * with '&lt;li&gt;' tags.
      */
     public abstract String getCitation();
 
@@ -55,6 +55,7 @@ public interface AbstractEDMethod {
 
     /**
      * Main method that starts the execution of the Event Detection algorithm.
+     * @throws java.lang.Exception General Exception
      */
     public abstract void apply() throws Exception;
 

src/edmodule/EDMethodPicker.java

@@ -92,7 +92,7 @@ public static void selectEDMethod(Config config, boolean showInlineInfo,
                 List<BinPair<String, Integer>> bins = BinsCreator.createBins(corpus, config, window);
 
                 PeakFindingExperimenter exper = new PeakFindingExperimenter(corpus, 
-                        bins, alpha, taph, pi, window, config);
+                        bins, alpha, taph, pi, config);
 
                 //Experiment with Taph
                 List<String> lines = exper.experimentUsingTaph(1, 10, 1, showInlineInfo);

src/edmodule/data/EDCoWCorpus.java

@@ -40,7 +40,7 @@
 /**
  *
  * @author  Lefteris Paraskevas
- * @version 2016.04.09_1959
+ * @version 2016.04.30_1826
  */
 public class EDCoWCorpus {
 
@@ -175,6 +175,7 @@ public final void createCorpus() {
      * into that time period.
      * @param cal A Calendar instance, already set.
      * @param date The date to be checked.
+     * @return A String key with date information.
      */
     public final String updateMessageDistribution(Calendar cal, Date date) {
         String key = StringDateUtils.getDateKey(cal, date, refreshWindow);
@@ -202,7 +203,7 @@ public List<String> getTerms() {
 
     /**
      * Initializes and stores a list containing objects of DocumentTermFrequencyItem
-     * class. <br/>
+     * class. <br>
      * More formally, each listing in this list contains a triplet with the ID of
      * a document, the ID of a term that the document contains and the term's
      * frequency.

src/edmodule/data/PeakFindingCorpus.java

@@ -29,7 +29,7 @@
 /**
  *
  * @author  Lefteris Paraskevas
- * @version 2016.04.09_2000
+ * @version 2016.04.30_1826
  */
 public class PeakFindingCorpus {
 
@@ -64,13 +64,13 @@ public PeakFindingCorpus(Config config, List<Tweet> tweets, StopWordsHandlers sw
      * earliest and the latest date of corpus if needed (assuming that the corpus
      * has some extend of sparseness).
      * @param window An integer indicating the time interval in which the tweets
-     * should be counted. All values in minutes. <br/>
-     * E.g. For 1 minute interval --> 1. <br/>
-     * For half an hour interval --> 30. <br/>
-     * For 5 hours interval --> 300.
+     * should be counted. All values in minutes. <br>
+     * E.g. For 1 minute interval, 1. <br>
+     * For half an hour interval, 30. <br>
+     * For 5 hours interval, 300.
      * @return A HashMap containing the bins.
-     * @see BinsCreator BinsCreator class.
-     * @see OfflinePeakFinding OfflinePeakFinding class.
+     * @see edmodule.peakfinding.BinsCreator BinsCreator class.
+     * @see edmodule.peakfinding.OfflinePeakFinding OfflinePeakFinding class.
      */
     public final HashMap<String, Integer> createCorpus(int window) {   
         //Initialize variables

src/edmodule/edcow/EDCoW.java

@@ -30,10 +30,10 @@
 /**
  *
  * @author  Adrien GUILLE, ERIC Lab, University of Lyon 2
- * @email   adrien.guille@univ-lyon2.fr
+ * email    adrien.guille@univ-lyon2.fr
  * 
  * @author  Lefteris Paraskevas (configurations in EDCoW to omit missing components)
- * @version 2016.04.09_2001 (For EvS project version alignment) 
+ * @version 2016.04.30_1826 (For EvS project version alignment) 
  */
 public class EDCoW implements AbstractEDMethod {
     private final int delta; //6
@@ -51,12 +51,12 @@ public class EDCoW implements AbstractEDMethod {
     private long executionTime;
 
     /**
-     * Default constructor with minimum parameters. <br/>
+     * Default constructor with minimum parameters. <br>
      * Delta is set to 6, gamma is set to 5, minimum term support is set to
      * 0.0001 and maximum term support is set to 0.01. If you wish to change the
      * aforementioned values use the {@link #EDCoW(int, int, int, double, double,
      * int, int, EDCoWCorpus) second constructor}.
-     * @param delta2 Delta2 value. <br/>
+     * @param delta2 Delta2 value. <br>
      * Prime divisors of the number of documents are required as values. It must
      * be cross-referenced with the number of documents. More specifically, the
      * outcome of the division between the number of documents and this metric
@@ -78,21 +78,21 @@ public EDCoW(int delta2, int timeSliceA, int timeSliceB, EDCoWCorpus corpus) {
 
     /**
      * Default constructor with the full set of parameters.
-     * @param delta1 Delta value (suggested 6). <br/>
+     * @param delta1 Delta value (suggested 6). <br>
      * It directly affects the number of events. Increasing this value, reduces
      * the number of them and vice versa.
-     * @param delta2 Delta2 value. <br/>
+     * @param delta2 Delta2 value. <br>
      * Prime divisors of the number of documents are required as values. It must
      * be cross-referenced with the number of documents. More specifically, the
      * outcome of the division between the number of documents and this metric
      * should result the number of total windows.
-     * @param gamma Gamma value (suggested 5). <br/>
+     * @param gamma Gamma value (suggested 5). <br>
      * It affects the quality of the uncovered events. Values greater than 15,
      * seem to increase the number of the uncovered events.
-     * @param minTermSupport Minimum term support value (suggested 0.0001). <br/>
+     * @param minTermSupport Minimum term support value (suggested 0.0001). <br>
      * Changing this value would result in altering the lower bound below which
      * a term should not be included in the keywords list of an event.
-     * @param maxTermSupport Maximum term support value (suggested 0.01). <br/>
+     * @param maxTermSupport Maximum term support value (suggested 0.01). <br>
      * Changing this value would result in altering the upper bound above which
      * a term should not be included in the keywords list of an event.
      * @param timeSliceA Starting timeslice.
@@ -199,6 +199,7 @@ public void apply() {
      * Method to run the algorithm and analyze terms and frequencies in a
      * specific window.
      * @param window The window index (0, 1, 2 etc).
+     * @throws java.lang.Exception General Exception.
      */
     public void processWindow(int window) throws Exception {
         LinkedList<EDCoWKeyword> keyWords = new LinkedList<>();

src/edmodule/peakfinding/BinsCreator.java

@@ -29,20 +29,21 @@
 /**
  *
  * @author  Lefteris Paraskevas
- * @version 2016.02.19_1711
+ * @version 2016.04.30_1826
  */
 public class BinsCreator {
 
     /**
      * Method to create and return the bins needed for OfflinePeakFinding algorithm to operate.
      * More formally, it creates an List of BinPair objects, containing the count
      * of tweets in pre-specified time intervals (windows).
+     * @param corpus A PeakFindingCorpus object.
      * @param config A Configuration object.
      * @param refreshWindow An integer indicating the time interval in which the tweets
-     * should be counted.All values in minutes. <br/>
-     * E.g. For 1 minute interval --> 1. <br/>
-     * For half an hour interval --> 30. <br/>
-     * For 5 hours interval --> 300.
+     * should be counted.All values in minutes. <br>
+     * E.g. For 1 minute interval --&gt; 1. <br>
+     * For half an hour interval --&gt; 30. <br>
+     * For 5 hours interval --&gt; 300.
      * @return An List of BinPair objects containing the bins.
      * @see StringDateUtils StringDateUtils class.
      * @see BinPair BinPair class.

src/edmodule/peakfinding/OfflinePeakFinding.java

@@ -29,7 +29,7 @@
 /**
  *
  * @author  Lefteris Paraskevas
- * @version 2016.04.09_2003
+ * @version 2016.04.30_1826
  * 
  * Based on [1] Marcus A. et al., "TwitInfo: Aggregating and Visualizing Microblogs 
  * for PeakFindingEvent Exploration", CHI 2011.
@@ -55,7 +55,6 @@ public class OfflinePeakFinding implements AbstractEDMethod {
      * @param a Alpha parameter to capture historical information. Values lower than 1 are recommended.
      * @param t Threshold parameter. 
      * @param p Primary parameter indicates the first bins to be considered in calculating initial mean deviance.
-     * @param refreshWindow An integer representing the refresh window of every bin.
      * @param corpus A PeakFindingCorpus object.
      */
     public OfflinePeakFinding(List<BinPair<String, Integer>> bins, double a, int t, int p, PeakFindingCorpus corpus) {

src/edmodule/peakfinding/event/PeakFindingEvent.java

@@ -33,7 +33,7 @@
 /**
  *
  * @author  Lefteris Paraskevas
- * @version 2016.04.09_2004
+ * @version 2016.04.30_1827
  */
 public class PeakFindingEvent {
 
@@ -83,7 +83,7 @@ public PeakFindingEvent(int id, Window<Integer, Integer> window, List<Tweet> twe
 
     /**
      * Generates a List with the most common terms of the tweetsOfEvent that belong
-     * to the specific event. <br/>
+     * to the specific event. <br>
      * More formally, it parses every single tweet of the event, tokenizes it
      * and stores the terms in a HashMap with their respective occurencies as
      * values.
@@ -148,7 +148,7 @@ public final List<String> getTweetIDs() {
     /**
      * Returns the five most common terms as a single String.
      * @return A String containing the five most common terms.
-     * @see getCommonTerms() getCommonTerms() method.
+     * @see #getCommonTerms() getCommonTerms() method.
      */
     public final String getCommonTermsAsString() {
         if(commonTerms.isEmpty()) {
@@ -167,7 +167,7 @@ public final String getCommonTermsAsString() {
     /**
      * Auxiliary method to sort a Map by value.
      * @param unsortedMap The Map to be sorted.
-     * @return A sorted List of the String keys.
+     * @param stemHandler A StemUtils object.
      */
     public final void sortMapByValue(HashMap<String, Integer> unsortedMap, StemUtils stemHandler) {
         //Initialize variables

src/edmodule/peakfinding/event/PeakFindingEvents.java

@@ -28,7 +28,7 @@
 /**
  *
  * @author  Lefteris Paraskevas
- * @version 2016.04.09_2005
+ * @version 2016.04.30_1827
  */
 public class PeakFindingEvents {
 
@@ -46,6 +46,7 @@ public class PeakFindingEvents {
      * @param bins A List of BinPair objects, containing all bins.
      * @param eventWindows A List of Window objects, containing the generated eventsTweets.
      * @param corpus A PeakFindingCorpus object.
+     * @param stemsHandler A StemUtils object.
      */
     public PeakFindingEvents(HashMap<String, ArrayList<Tweet>> tweetsByWindow, 
             List<BinPair<String, Integer>> bins, 
@@ -59,7 +60,7 @@ public PeakFindingEvents(HashMap<String, ArrayList<Tweet>> tweetsByWindow,
     }
 
     /**
-     * Returns the tweets that belong to a certain event. <br/>
+     * Returns the tweets that belong to a certain event. <br>
      * More formally, it parses the auxiliary tweetsByWindow HashMap and appends
      * the relevant tweets into a String list.
      * @param window A Window object, the actual event.