From a885fd23fad04607c919826804268231bb0dbab7 Mon Sep 17 00:00:00 2001
From: Nicolai Erbs <nico@erbs.eu>
Date: Tue, 19 Jan 2016 12:56:35 +0100
Subject: [PATCH 1/6] Making it a maven project

---
 pom.xml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 pom.xml

diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..7b98d72
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,15 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.wcohen</groupId>
+  <artifactId>com.wcohen.ss</artifactId>
+  <version>0.0.1-SNAPSHOT</version>
+  <name>SecondString</name>
+  <description>A bunch of fancy soft string matching routines, with some accompanying datasets</description>
+  <dependencies>
+  	<dependency>
+  		<groupId>log4j</groupId>
+  		<artifactId>log4j</artifactId>
+  		<version>1.2.8</version>
+  	</dependency>
+  </dependencies>
+</project>
\ No newline at end of file

From 66369449bad59d376c7a1c074d3556bbd479a7a8 Mon Sep 17 00:00:00 2001
From: Nicolai Erbs <nico@erbs.eu>
Date: Tue, 19 Jan 2016 14:17:41 +0100
Subject: [PATCH 2/6] Moving java classes to source folder

---
 src/{ => main/java}/com/wcohen/ss/AbbreviationAlignment.java   | 0
 .../com/wcohen/ss/AbstractSourcedStatisticalTokenDistance.java | 0
 .../com/wcohen/ss/AbstractSourcedTokenizedStringDistance.java  | 0
 .../java}/com/wcohen/ss/AbstractStatisticalTokenDistance.java  | 0
 src/{ => main/java}/com/wcohen/ss/AbstractStringDistance.java  | 0
 .../java}/com/wcohen/ss/AbstractTokenizedStringDistance.java   | 0
 src/{ => main/java}/com/wcohen/ss/AffineGap.java               | 0
 src/{ => main/java}/com/wcohen/ss/ApproxMemoMatrix.java        | 0
 src/{ => main/java}/com/wcohen/ss/ApproxNeedlemanWunsch.java   | 0
 .../java}/com/wcohen/ss/AveragedStringDistanceLearner.java     | 0
 src/{ => main/java}/com/wcohen/ss/BagOfSourcedTokens.java      | 0
 src/{ => main/java}/com/wcohen/ss/BagOfTokens.java             | 0
 .../java}/com/wcohen/ss/BasicDistanceInstanceIterator.java     | 0
 .../java}/com/wcohen/ss/BasicSourcedStringWrapperIterator.java | 0
 src/{ => main/java}/com/wcohen/ss/BasicStringWrapper.java      | 0
 .../java}/com/wcohen/ss/BasicStringWrapperIterator.java        | 0
 src/{ => main/java}/com/wcohen/ss/CharMatchScore.java          | 0
 .../java}/com/wcohen/ss/CombinedStringDistanceLearner.java     | 0
 src/{ => main/java}/com/wcohen/ss/DirichletJS.java             | 0
 src/{ => main/java}/com/wcohen/ss/DistanceLearnerFactory.java  | 0
 src/{ => main/java}/com/wcohen/ss/Jaccard.java                 | 0
 src/{ => main/java}/com/wcohen/ss/Jaro.java                    | 0
 src/{ => main/java}/com/wcohen/ss/JaroTFIDF.java               | 0
 src/{ => main/java}/com/wcohen/ss/JaroWinkler.java             | 0
 src/{ => main/java}/com/wcohen/ss/JaroWinklerTFIDF.java        | 0
 src/{ => main/java}/com/wcohen/ss/JelinekMercerJS.java         | 0
 src/{ => main/java}/com/wcohen/ss/JensenShannonDistance.java   | 0
 src/{ => main/java}/com/wcohen/ss/Level2.java                  | 0
 src/{ => main/java}/com/wcohen/ss/Level2Jaro.java              | 0
 src/{ => main/java}/com/wcohen/ss/Level2JaroWinkler.java       | 0
 src/{ => main/java}/com/wcohen/ss/Level2Levenstein.java        | 0
 src/{ => main/java}/com/wcohen/ss/Level2MongeElkan.java        | 0
 src/{ => main/java}/com/wcohen/ss/Levenstein.java              | 0
 src/{ => main/java}/com/wcohen/ss/MemoMatrix.java              | 0
 src/{ => main/java}/com/wcohen/ss/Mixture.java                 | 0
 src/{ => main/java}/com/wcohen/ss/MongeElkan.java              | 0
 src/{ => main/java}/com/wcohen/ss/MongeElkanTFIDF.java         | 0
 src/{ => main/java}/com/wcohen/ss/MultiStringAvgDistance.java  | 0
 src/{ => main/java}/com/wcohen/ss/MultiStringDistance.java     | 0
 src/{ => main/java}/com/wcohen/ss/MultiStringWrapper.java      | 0
 src/{ => main/java}/com/wcohen/ss/NeedlemanWunsch.java         | 0
 src/{ => main/java}/com/wcohen/ss/PrintfFormat.java            | 0
 src/{ => main/java}/com/wcohen/ss/ScaledLevenstein.java        | 0
 src/{ => main/java}/com/wcohen/ss/SmithWaterman.java           | 0
 src/{ => main/java}/com/wcohen/ss/SoftTFIDF.java               | 0
 src/{ => main/java}/com/wcohen/ss/SoftTokenFelligiSunter.java  | 0
 src/{ => main/java}/com/wcohen/ss/SourcedSoftTFIDF.java        | 0
 src/{ => main/java}/com/wcohen/ss/SourcedTFIDF.java            | 0
 src/{ => main/java}/com/wcohen/ss/TFIDF.java                   | 0
 src/{ => main/java}/com/wcohen/ss/TagLink.java                 | 0
 src/{ => main/java}/com/wcohen/ss/TokenFelligiSunter.java      | 0
 src/{ => main/java}/com/wcohen/ss/UnsmoothedJS.java            | 0
 src/{ => main/java}/com/wcohen/ss/WinklerRescorer.java         | 0
 .../wcohen/ss/abbvGapsHmm/AbbreviationAlignmentContainer.java  | 0
 src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java | 0
 .../java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java  | 0
 .../wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsEvaluator.java   | 0
 .../ss/abbvGapsHmm/AbbvGapsHmmBackwardsViterbiEvaluator.java   | 0
 .../wcohen/ss/abbvGapsHmm/AbbvGapsHmmExpectationEvaluator.java | 0
 .../com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmForwardEvaluator.java | 0
 src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/Acronym.java     | 3 ---
 .../com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java    | 0
 src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/Matrix3D.java    | 0
 src/{ => main/java}/com/wcohen/ss/api/DistanceInstance.java    | 0
 .../java}/com/wcohen/ss/api/DistanceInstanceIterator.java      | 0
 .../java}/com/wcohen/ss/api/IdentifiedStringWrapper.java       | 0
 .../java}/com/wcohen/ss/api/SourcedStringWrapper.java          | 0
 .../java}/com/wcohen/ss/api/SourcedStringWrapperIterator.java  | 0
 src/{ => main/java}/com/wcohen/ss/api/SourcedToken.java        | 0
 src/{ => main/java}/com/wcohen/ss/api/SourcedTokenizer.java    | 0
 src/{ => main/java}/com/wcohen/ss/api/StringDistance.java      | 0
 .../java}/com/wcohen/ss/api/StringDistanceLearner.java         | 0
 .../java}/com/wcohen/ss/api/StringDistanceTeacher.java         | 0
 src/{ => main/java}/com/wcohen/ss/api/StringWrapper.java       | 0
 .../java}/com/wcohen/ss/api/StringWrapperIterator.java         | 0
 src/{ => main/java}/com/wcohen/ss/api/Token.java               | 0
 src/{ => main/java}/com/wcohen/ss/api/Tokenizer.java           | 0
 .../java}/com/wcohen/ss/expt/AbbreviationsBlocker.java         | 0
 src/{ => main/java}/com/wcohen/ss/expt/BasicTeacher.java       | 0
 src/{ => main/java}/com/wcohen/ss/expt/Blocker.java            | 0
 .../java}/com/wcohen/ss/expt/ClusterNGramBlocker.java          | 0
 .../java}/com/wcohen/ss/expt/ClusterTokenBlocker.java          | 0
 .../java}/com/wcohen/ss/expt/ExtractAbbreviations.java         | 0
 src/{ => main/java}/com/wcohen/ss/expt/MatchData.java          | 0
 src/{ => main/java}/com/wcohen/ss/expt/MatchDataTeacher.java   | 0
 src/{ => main/java}/com/wcohen/ss/expt/MatchExpt.java          | 0
 src/{ => main/java}/com/wcohen/ss/expt/MatchExptScript.java    | 0
 src/{ => main/java}/com/wcohen/ss/expt/NGramBlocker.java       | 0
 src/{ => main/java}/com/wcohen/ss/expt/NullBlocker.java        | 0
 src/{ => main/java}/com/wcohen/ss/expt/SourcedMatchData.java   | 0
 src/{ => main/java}/com/wcohen/ss/expt/SpecialMatchExpt.java   | 0
 src/{ => main/java}/com/wcohen/ss/expt/TokenBlocker.java       | 0
 src/{ => main/java}/com/wcohen/ss/lookup/FastLookup.java       | 0
 src/{ => main/java}/com/wcohen/ss/lookup/LookupResult.java     | 0
 .../com/wcohen/ss/lookup/RescoringSoftTFIDFDictionary.java     | 0
 src/{ => main/java}/com/wcohen/ss/lookup/SoftDictionary.java   | 0
 .../java}/com/wcohen/ss/lookup/SoftTFIDFDictionary.java        | 0
 src/{ => main/java}/com/wcohen/ss/package.html                 | 0
 .../java}/com/wcohen/ss/tokens/BasicSourcedToken.java          | 0
 src/{ => main/java}/com/wcohen/ss/tokens/BasicToken.java       | 0
 .../java}/com/wcohen/ss/tokens/CharacterTokenizer.java         | 0
 src/{ => main/java}/com/wcohen/ss/tokens/NGramTokenizer.java   | 0
 .../java}/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java     | 0
 src/{ => main/java}/com/wcohen/ss/tokens/SimpleTokenizer.java  | 0
 src/{ => main/java}/com/wcohen/ss/tokens/TagLinkToken.java     | 0
 105 files changed, 3 deletions(-)
 rename src/{ => main/java}/com/wcohen/ss/AbbreviationAlignment.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AbstractSourcedStatisticalTokenDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AbstractSourcedTokenizedStringDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AbstractStatisticalTokenDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AbstractStringDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AbstractTokenizedStringDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AffineGap.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/ApproxMemoMatrix.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/ApproxNeedlemanWunsch.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/AveragedStringDistanceLearner.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/BagOfSourcedTokens.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/BagOfTokens.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/BasicDistanceInstanceIterator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/BasicSourcedStringWrapperIterator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/BasicStringWrapper.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/BasicStringWrapperIterator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/CharMatchScore.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/CombinedStringDistanceLearner.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/DirichletJS.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/DistanceLearnerFactory.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Jaccard.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Jaro.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/JaroTFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/JaroWinkler.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/JaroWinklerTFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/JelinekMercerJS.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/JensenShannonDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Level2.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Level2Jaro.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Level2JaroWinkler.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Level2Levenstein.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Level2MongeElkan.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Levenstein.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/MemoMatrix.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/Mixture.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/MongeElkan.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/MongeElkanTFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/MultiStringAvgDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/MultiStringDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/MultiStringWrapper.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/NeedlemanWunsch.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/PrintfFormat.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/ScaledLevenstein.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/SmithWaterman.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/SoftTFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/SoftTokenFelligiSunter.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/SourcedSoftTFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/SourcedTFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/TFIDF.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/TagLink.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/TokenFelligiSunter.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/UnsmoothedJS.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/WinklerRescorer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbreviationAlignmentContainer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsEvaluator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsViterbiEvaluator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmExpectationEvaluator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmForwardEvaluator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/Acronym.java (97%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/abbvGapsHmm/Matrix3D.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/DistanceInstance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/DistanceInstanceIterator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/IdentifiedStringWrapper.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/SourcedStringWrapper.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/SourcedStringWrapperIterator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/SourcedToken.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/SourcedTokenizer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/StringDistance.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/StringDistanceLearner.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/StringDistanceTeacher.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/StringWrapper.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/StringWrapperIterator.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/Token.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/api/Tokenizer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/AbbreviationsBlocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/BasicTeacher.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/Blocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/ClusterNGramBlocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/ClusterTokenBlocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/ExtractAbbreviations.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/MatchData.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/MatchDataTeacher.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/MatchExpt.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/MatchExptScript.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/NGramBlocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/NullBlocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/SourcedMatchData.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/SpecialMatchExpt.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/expt/TokenBlocker.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/lookup/FastLookup.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/lookup/LookupResult.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/lookup/RescoringSoftTFIDFDictionary.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/lookup/SoftDictionary.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/lookup/SoftTFIDFDictionary.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/package.html (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/BasicSourcedToken.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/BasicToken.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/CharacterTokenizer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/NGramTokenizer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/SimpleTokenizer.java (100%)
 rename src/{ => main/java}/com/wcohen/ss/tokens/TagLinkToken.java (100%)

diff --git a/src/com/wcohen/ss/AbbreviationAlignment.java b/src/main/java/com/wcohen/ss/AbbreviationAlignment.java
similarity index 100%
rename from src/com/wcohen/ss/AbbreviationAlignment.java
rename to src/main/java/com/wcohen/ss/AbbreviationAlignment.java
diff --git a/src/com/wcohen/ss/AbstractSourcedStatisticalTokenDistance.java b/src/main/java/com/wcohen/ss/AbstractSourcedStatisticalTokenDistance.java
similarity index 100%
rename from src/com/wcohen/ss/AbstractSourcedStatisticalTokenDistance.java
rename to src/main/java/com/wcohen/ss/AbstractSourcedStatisticalTokenDistance.java
diff --git a/src/com/wcohen/ss/AbstractSourcedTokenizedStringDistance.java b/src/main/java/com/wcohen/ss/AbstractSourcedTokenizedStringDistance.java
similarity index 100%
rename from src/com/wcohen/ss/AbstractSourcedTokenizedStringDistance.java
rename to src/main/java/com/wcohen/ss/AbstractSourcedTokenizedStringDistance.java
diff --git a/src/com/wcohen/ss/AbstractStatisticalTokenDistance.java b/src/main/java/com/wcohen/ss/AbstractStatisticalTokenDistance.java
similarity index 100%
rename from src/com/wcohen/ss/AbstractStatisticalTokenDistance.java
rename to src/main/java/com/wcohen/ss/AbstractStatisticalTokenDistance.java
diff --git a/src/com/wcohen/ss/AbstractStringDistance.java b/src/main/java/com/wcohen/ss/AbstractStringDistance.java
similarity index 100%
rename from src/com/wcohen/ss/AbstractStringDistance.java
rename to src/main/java/com/wcohen/ss/AbstractStringDistance.java
diff --git a/src/com/wcohen/ss/AbstractTokenizedStringDistance.java b/src/main/java/com/wcohen/ss/AbstractTokenizedStringDistance.java
similarity index 100%
rename from src/com/wcohen/ss/AbstractTokenizedStringDistance.java
rename to src/main/java/com/wcohen/ss/AbstractTokenizedStringDistance.java
diff --git a/src/com/wcohen/ss/AffineGap.java b/src/main/java/com/wcohen/ss/AffineGap.java
similarity index 100%
rename from src/com/wcohen/ss/AffineGap.java
rename to src/main/java/com/wcohen/ss/AffineGap.java
diff --git a/src/com/wcohen/ss/ApproxMemoMatrix.java b/src/main/java/com/wcohen/ss/ApproxMemoMatrix.java
similarity index 100%
rename from src/com/wcohen/ss/ApproxMemoMatrix.java
rename to src/main/java/com/wcohen/ss/ApproxMemoMatrix.java
diff --git a/src/com/wcohen/ss/ApproxNeedlemanWunsch.java b/src/main/java/com/wcohen/ss/ApproxNeedlemanWunsch.java
similarity index 100%
rename from src/com/wcohen/ss/ApproxNeedlemanWunsch.java
rename to src/main/java/com/wcohen/ss/ApproxNeedlemanWunsch.java
diff --git a/src/com/wcohen/ss/AveragedStringDistanceLearner.java b/src/main/java/com/wcohen/ss/AveragedStringDistanceLearner.java
similarity index 100%
rename from src/com/wcohen/ss/AveragedStringDistanceLearner.java
rename to src/main/java/com/wcohen/ss/AveragedStringDistanceLearner.java
diff --git a/src/com/wcohen/ss/BagOfSourcedTokens.java b/src/main/java/com/wcohen/ss/BagOfSourcedTokens.java
similarity index 100%
rename from src/com/wcohen/ss/BagOfSourcedTokens.java
rename to src/main/java/com/wcohen/ss/BagOfSourcedTokens.java
diff --git a/src/com/wcohen/ss/BagOfTokens.java b/src/main/java/com/wcohen/ss/BagOfTokens.java
similarity index 100%
rename from src/com/wcohen/ss/BagOfTokens.java
rename to src/main/java/com/wcohen/ss/BagOfTokens.java
diff --git a/src/com/wcohen/ss/BasicDistanceInstanceIterator.java b/src/main/java/com/wcohen/ss/BasicDistanceInstanceIterator.java
similarity index 100%
rename from src/com/wcohen/ss/BasicDistanceInstanceIterator.java
rename to src/main/java/com/wcohen/ss/BasicDistanceInstanceIterator.java
diff --git a/src/com/wcohen/ss/BasicSourcedStringWrapperIterator.java b/src/main/java/com/wcohen/ss/BasicSourcedStringWrapperIterator.java
similarity index 100%
rename from src/com/wcohen/ss/BasicSourcedStringWrapperIterator.java
rename to src/main/java/com/wcohen/ss/BasicSourcedStringWrapperIterator.java
diff --git a/src/com/wcohen/ss/BasicStringWrapper.java b/src/main/java/com/wcohen/ss/BasicStringWrapper.java
similarity index 100%
rename from src/com/wcohen/ss/BasicStringWrapper.java
rename to src/main/java/com/wcohen/ss/BasicStringWrapper.java
diff --git a/src/com/wcohen/ss/BasicStringWrapperIterator.java b/src/main/java/com/wcohen/ss/BasicStringWrapperIterator.java
similarity index 100%
rename from src/com/wcohen/ss/BasicStringWrapperIterator.java
rename to src/main/java/com/wcohen/ss/BasicStringWrapperIterator.java
diff --git a/src/com/wcohen/ss/CharMatchScore.java b/src/main/java/com/wcohen/ss/CharMatchScore.java
similarity index 100%
rename from src/com/wcohen/ss/CharMatchScore.java
rename to src/main/java/com/wcohen/ss/CharMatchScore.java
diff --git a/src/com/wcohen/ss/CombinedStringDistanceLearner.java b/src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java
similarity index 100%
rename from src/com/wcohen/ss/CombinedStringDistanceLearner.java
rename to src/main/java/com/wcohen/ss/CombinedStringDistanceLearner.java
diff --git a/src/com/wcohen/ss/DirichletJS.java b/src/main/java/com/wcohen/ss/DirichletJS.java
similarity index 100%
rename from src/com/wcohen/ss/DirichletJS.java
rename to src/main/java/com/wcohen/ss/DirichletJS.java
diff --git a/src/com/wcohen/ss/DistanceLearnerFactory.java b/src/main/java/com/wcohen/ss/DistanceLearnerFactory.java
similarity index 100%
rename from src/com/wcohen/ss/DistanceLearnerFactory.java
rename to src/main/java/com/wcohen/ss/DistanceLearnerFactory.java
diff --git a/src/com/wcohen/ss/Jaccard.java b/src/main/java/com/wcohen/ss/Jaccard.java
similarity index 100%
rename from src/com/wcohen/ss/Jaccard.java
rename to src/main/java/com/wcohen/ss/Jaccard.java
diff --git a/src/com/wcohen/ss/Jaro.java b/src/main/java/com/wcohen/ss/Jaro.java
similarity index 100%
rename from src/com/wcohen/ss/Jaro.java
rename to src/main/java/com/wcohen/ss/Jaro.java
diff --git a/src/com/wcohen/ss/JaroTFIDF.java b/src/main/java/com/wcohen/ss/JaroTFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/JaroTFIDF.java
rename to src/main/java/com/wcohen/ss/JaroTFIDF.java
diff --git a/src/com/wcohen/ss/JaroWinkler.java b/src/main/java/com/wcohen/ss/JaroWinkler.java
similarity index 100%
rename from src/com/wcohen/ss/JaroWinkler.java
rename to src/main/java/com/wcohen/ss/JaroWinkler.java
diff --git a/src/com/wcohen/ss/JaroWinklerTFIDF.java b/src/main/java/com/wcohen/ss/JaroWinklerTFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/JaroWinklerTFIDF.java
rename to src/main/java/com/wcohen/ss/JaroWinklerTFIDF.java
diff --git a/src/com/wcohen/ss/JelinekMercerJS.java b/src/main/java/com/wcohen/ss/JelinekMercerJS.java
similarity index 100%
rename from src/com/wcohen/ss/JelinekMercerJS.java
rename to src/main/java/com/wcohen/ss/JelinekMercerJS.java
diff --git a/src/com/wcohen/ss/JensenShannonDistance.java b/src/main/java/com/wcohen/ss/JensenShannonDistance.java
similarity index 100%
rename from src/com/wcohen/ss/JensenShannonDistance.java
rename to src/main/java/com/wcohen/ss/JensenShannonDistance.java
diff --git a/src/com/wcohen/ss/Level2.java b/src/main/java/com/wcohen/ss/Level2.java
similarity index 100%
rename from src/com/wcohen/ss/Level2.java
rename to src/main/java/com/wcohen/ss/Level2.java
diff --git a/src/com/wcohen/ss/Level2Jaro.java b/src/main/java/com/wcohen/ss/Level2Jaro.java
similarity index 100%
rename from src/com/wcohen/ss/Level2Jaro.java
rename to src/main/java/com/wcohen/ss/Level2Jaro.java
diff --git a/src/com/wcohen/ss/Level2JaroWinkler.java b/src/main/java/com/wcohen/ss/Level2JaroWinkler.java
similarity index 100%
rename from src/com/wcohen/ss/Level2JaroWinkler.java
rename to src/main/java/com/wcohen/ss/Level2JaroWinkler.java
diff --git a/src/com/wcohen/ss/Level2Levenstein.java b/src/main/java/com/wcohen/ss/Level2Levenstein.java
similarity index 100%
rename from src/com/wcohen/ss/Level2Levenstein.java
rename to src/main/java/com/wcohen/ss/Level2Levenstein.java
diff --git a/src/com/wcohen/ss/Level2MongeElkan.java b/src/main/java/com/wcohen/ss/Level2MongeElkan.java
similarity index 100%
rename from src/com/wcohen/ss/Level2MongeElkan.java
rename to src/main/java/com/wcohen/ss/Level2MongeElkan.java
diff --git a/src/com/wcohen/ss/Levenstein.java b/src/main/java/com/wcohen/ss/Levenstein.java
similarity index 100%
rename from src/com/wcohen/ss/Levenstein.java
rename to src/main/java/com/wcohen/ss/Levenstein.java
diff --git a/src/com/wcohen/ss/MemoMatrix.java b/src/main/java/com/wcohen/ss/MemoMatrix.java
similarity index 100%
rename from src/com/wcohen/ss/MemoMatrix.java
rename to src/main/java/com/wcohen/ss/MemoMatrix.java
diff --git a/src/com/wcohen/ss/Mixture.java b/src/main/java/com/wcohen/ss/Mixture.java
similarity index 100%
rename from src/com/wcohen/ss/Mixture.java
rename to src/main/java/com/wcohen/ss/Mixture.java
diff --git a/src/com/wcohen/ss/MongeElkan.java b/src/main/java/com/wcohen/ss/MongeElkan.java
similarity index 100%
rename from src/com/wcohen/ss/MongeElkan.java
rename to src/main/java/com/wcohen/ss/MongeElkan.java
diff --git a/src/com/wcohen/ss/MongeElkanTFIDF.java b/src/main/java/com/wcohen/ss/MongeElkanTFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/MongeElkanTFIDF.java
rename to src/main/java/com/wcohen/ss/MongeElkanTFIDF.java
diff --git a/src/com/wcohen/ss/MultiStringAvgDistance.java b/src/main/java/com/wcohen/ss/MultiStringAvgDistance.java
similarity index 100%
rename from src/com/wcohen/ss/MultiStringAvgDistance.java
rename to src/main/java/com/wcohen/ss/MultiStringAvgDistance.java
diff --git a/src/com/wcohen/ss/MultiStringDistance.java b/src/main/java/com/wcohen/ss/MultiStringDistance.java
similarity index 100%
rename from src/com/wcohen/ss/MultiStringDistance.java
rename to src/main/java/com/wcohen/ss/MultiStringDistance.java
diff --git a/src/com/wcohen/ss/MultiStringWrapper.java b/src/main/java/com/wcohen/ss/MultiStringWrapper.java
similarity index 100%
rename from src/com/wcohen/ss/MultiStringWrapper.java
rename to src/main/java/com/wcohen/ss/MultiStringWrapper.java
diff --git a/src/com/wcohen/ss/NeedlemanWunsch.java b/src/main/java/com/wcohen/ss/NeedlemanWunsch.java
similarity index 100%
rename from src/com/wcohen/ss/NeedlemanWunsch.java
rename to src/main/java/com/wcohen/ss/NeedlemanWunsch.java
diff --git a/src/com/wcohen/ss/PrintfFormat.java b/src/main/java/com/wcohen/ss/PrintfFormat.java
similarity index 100%
rename from src/com/wcohen/ss/PrintfFormat.java
rename to src/main/java/com/wcohen/ss/PrintfFormat.java
diff --git a/src/com/wcohen/ss/ScaledLevenstein.java b/src/main/java/com/wcohen/ss/ScaledLevenstein.java
similarity index 100%
rename from src/com/wcohen/ss/ScaledLevenstein.java
rename to src/main/java/com/wcohen/ss/ScaledLevenstein.java
diff --git a/src/com/wcohen/ss/SmithWaterman.java b/src/main/java/com/wcohen/ss/SmithWaterman.java
similarity index 100%
rename from src/com/wcohen/ss/SmithWaterman.java
rename to src/main/java/com/wcohen/ss/SmithWaterman.java
diff --git a/src/com/wcohen/ss/SoftTFIDF.java b/src/main/java/com/wcohen/ss/SoftTFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/SoftTFIDF.java
rename to src/main/java/com/wcohen/ss/SoftTFIDF.java
diff --git a/src/com/wcohen/ss/SoftTokenFelligiSunter.java b/src/main/java/com/wcohen/ss/SoftTokenFelligiSunter.java
similarity index 100%
rename from src/com/wcohen/ss/SoftTokenFelligiSunter.java
rename to src/main/java/com/wcohen/ss/SoftTokenFelligiSunter.java
diff --git a/src/com/wcohen/ss/SourcedSoftTFIDF.java b/src/main/java/com/wcohen/ss/SourcedSoftTFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/SourcedSoftTFIDF.java
rename to src/main/java/com/wcohen/ss/SourcedSoftTFIDF.java
diff --git a/src/com/wcohen/ss/SourcedTFIDF.java b/src/main/java/com/wcohen/ss/SourcedTFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/SourcedTFIDF.java
rename to src/main/java/com/wcohen/ss/SourcedTFIDF.java
diff --git a/src/com/wcohen/ss/TFIDF.java b/src/main/java/com/wcohen/ss/TFIDF.java
similarity index 100%
rename from src/com/wcohen/ss/TFIDF.java
rename to src/main/java/com/wcohen/ss/TFIDF.java
diff --git a/src/com/wcohen/ss/TagLink.java b/src/main/java/com/wcohen/ss/TagLink.java
similarity index 100%
rename from src/com/wcohen/ss/TagLink.java
rename to src/main/java/com/wcohen/ss/TagLink.java
diff --git a/src/com/wcohen/ss/TokenFelligiSunter.java b/src/main/java/com/wcohen/ss/TokenFelligiSunter.java
similarity index 100%
rename from src/com/wcohen/ss/TokenFelligiSunter.java
rename to src/main/java/com/wcohen/ss/TokenFelligiSunter.java
diff --git a/src/com/wcohen/ss/UnsmoothedJS.java b/src/main/java/com/wcohen/ss/UnsmoothedJS.java
similarity index 100%
rename from src/com/wcohen/ss/UnsmoothedJS.java
rename to src/main/java/com/wcohen/ss/UnsmoothedJS.java
diff --git a/src/com/wcohen/ss/WinklerRescorer.java b/src/main/java/com/wcohen/ss/WinklerRescorer.java
similarity index 100%
rename from src/com/wcohen/ss/WinklerRescorer.java
rename to src/main/java/com/wcohen/ss/WinklerRescorer.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbreviationAlignmentContainer.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbreviationAlignmentContainer.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbreviationAlignmentContainer.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbreviationAlignmentContainer.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMM.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHMMEvaluator.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsEvaluator.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsEvaluator.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsEvaluator.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsEvaluator.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsViterbiEvaluator.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsViterbiEvaluator.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsViterbiEvaluator.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmBackwardsViterbiEvaluator.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmExpectationEvaluator.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmExpectationEvaluator.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmExpectationEvaluator.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmExpectationEvaluator.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmForwardEvaluator.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmForwardEvaluator.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmForwardEvaluator.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AbbvGapsHmmForwardEvaluator.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/Acronym.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/Acronym.java
similarity index 97%
rename from src/com/wcohen/ss/abbvGapsHmm/Acronym.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/Acronym.java
index ea616eb..9c8d248 100644
--- a/src/com/wcohen/ss/abbvGapsHmm/Acronym.java
+++ b/src/main/java/com/wcohen/ss/abbvGapsHmm/Acronym.java
@@ -31,7 +31,6 @@ public Acronym(String shortForm, String longForm, Integer frequency){
 	/* (non-Javadoc)
 	 * @see java.lang.Comparable#compareTo(java.lang.Object)
 	 */
-	@Override
 	public int compareTo(Acronym o) {
 		int compScore = _shortForm.compareTo(o._shortForm);
 		if(compScore == 0){
@@ -54,14 +53,12 @@ public int hashCode(){
 	
 	
 	public static class AcronymShortFormComparator implements Comparator<Acronym>{
-	    @Override
 	    public int compare(Acronym t1, Acronym t2) {
 	        return t1._shortForm.compareTo(t2._shortForm); 
 	    }
 	}
 
 	public static class AcronymFrequencyComparator implements Comparator<Acronym>{
-	    @Override
 	    public int compare(Acronym t1, Acronym t2) {
 	        return new Integer(t1._frequency).compareTo(t2._frequency); 
 	    }
diff --git a/src/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/AlignmentPredictionModel.java
diff --git a/src/com/wcohen/ss/abbvGapsHmm/Matrix3D.java b/src/main/java/com/wcohen/ss/abbvGapsHmm/Matrix3D.java
similarity index 100%
rename from src/com/wcohen/ss/abbvGapsHmm/Matrix3D.java
rename to src/main/java/com/wcohen/ss/abbvGapsHmm/Matrix3D.java
diff --git a/src/com/wcohen/ss/api/DistanceInstance.java b/src/main/java/com/wcohen/ss/api/DistanceInstance.java
similarity index 100%
rename from src/com/wcohen/ss/api/DistanceInstance.java
rename to src/main/java/com/wcohen/ss/api/DistanceInstance.java
diff --git a/src/com/wcohen/ss/api/DistanceInstanceIterator.java b/src/main/java/com/wcohen/ss/api/DistanceInstanceIterator.java
similarity index 100%
rename from src/com/wcohen/ss/api/DistanceInstanceIterator.java
rename to src/main/java/com/wcohen/ss/api/DistanceInstanceIterator.java
diff --git a/src/com/wcohen/ss/api/IdentifiedStringWrapper.java b/src/main/java/com/wcohen/ss/api/IdentifiedStringWrapper.java
similarity index 100%
rename from src/com/wcohen/ss/api/IdentifiedStringWrapper.java
rename to src/main/java/com/wcohen/ss/api/IdentifiedStringWrapper.java
diff --git a/src/com/wcohen/ss/api/SourcedStringWrapper.java b/src/main/java/com/wcohen/ss/api/SourcedStringWrapper.java
similarity index 100%
rename from src/com/wcohen/ss/api/SourcedStringWrapper.java
rename to src/main/java/com/wcohen/ss/api/SourcedStringWrapper.java
diff --git a/src/com/wcohen/ss/api/SourcedStringWrapperIterator.java b/src/main/java/com/wcohen/ss/api/SourcedStringWrapperIterator.java
similarity index 100%
rename from src/com/wcohen/ss/api/SourcedStringWrapperIterator.java
rename to src/main/java/com/wcohen/ss/api/SourcedStringWrapperIterator.java
diff --git a/src/com/wcohen/ss/api/SourcedToken.java b/src/main/java/com/wcohen/ss/api/SourcedToken.java
similarity index 100%
rename from src/com/wcohen/ss/api/SourcedToken.java
rename to src/main/java/com/wcohen/ss/api/SourcedToken.java
diff --git a/src/com/wcohen/ss/api/SourcedTokenizer.java b/src/main/java/com/wcohen/ss/api/SourcedTokenizer.java
similarity index 100%
rename from src/com/wcohen/ss/api/SourcedTokenizer.java
rename to src/main/java/com/wcohen/ss/api/SourcedTokenizer.java
diff --git a/src/com/wcohen/ss/api/StringDistance.java b/src/main/java/com/wcohen/ss/api/StringDistance.java
similarity index 100%
rename from src/com/wcohen/ss/api/StringDistance.java
rename to src/main/java/com/wcohen/ss/api/StringDistance.java
diff --git a/src/com/wcohen/ss/api/StringDistanceLearner.java b/src/main/java/com/wcohen/ss/api/StringDistanceLearner.java
similarity index 100%
rename from src/com/wcohen/ss/api/StringDistanceLearner.java
rename to src/main/java/com/wcohen/ss/api/StringDistanceLearner.java
diff --git a/src/com/wcohen/ss/api/StringDistanceTeacher.java b/src/main/java/com/wcohen/ss/api/StringDistanceTeacher.java
similarity index 100%
rename from src/com/wcohen/ss/api/StringDistanceTeacher.java
rename to src/main/java/com/wcohen/ss/api/StringDistanceTeacher.java
diff --git a/src/com/wcohen/ss/api/StringWrapper.java b/src/main/java/com/wcohen/ss/api/StringWrapper.java
similarity index 100%
rename from src/com/wcohen/ss/api/StringWrapper.java
rename to src/main/java/com/wcohen/ss/api/StringWrapper.java
diff --git a/src/com/wcohen/ss/api/StringWrapperIterator.java b/src/main/java/com/wcohen/ss/api/StringWrapperIterator.java
similarity index 100%
rename from src/com/wcohen/ss/api/StringWrapperIterator.java
rename to src/main/java/com/wcohen/ss/api/StringWrapperIterator.java
diff --git a/src/com/wcohen/ss/api/Token.java b/src/main/java/com/wcohen/ss/api/Token.java
similarity index 100%
rename from src/com/wcohen/ss/api/Token.java
rename to src/main/java/com/wcohen/ss/api/Token.java
diff --git a/src/com/wcohen/ss/api/Tokenizer.java b/src/main/java/com/wcohen/ss/api/Tokenizer.java
similarity index 100%
rename from src/com/wcohen/ss/api/Tokenizer.java
rename to src/main/java/com/wcohen/ss/api/Tokenizer.java
diff --git a/src/com/wcohen/ss/expt/AbbreviationsBlocker.java b/src/main/java/com/wcohen/ss/expt/AbbreviationsBlocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/AbbreviationsBlocker.java
rename to src/main/java/com/wcohen/ss/expt/AbbreviationsBlocker.java
diff --git a/src/com/wcohen/ss/expt/BasicTeacher.java b/src/main/java/com/wcohen/ss/expt/BasicTeacher.java
similarity index 100%
rename from src/com/wcohen/ss/expt/BasicTeacher.java
rename to src/main/java/com/wcohen/ss/expt/BasicTeacher.java
diff --git a/src/com/wcohen/ss/expt/Blocker.java b/src/main/java/com/wcohen/ss/expt/Blocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/Blocker.java
rename to src/main/java/com/wcohen/ss/expt/Blocker.java
diff --git a/src/com/wcohen/ss/expt/ClusterNGramBlocker.java b/src/main/java/com/wcohen/ss/expt/ClusterNGramBlocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/ClusterNGramBlocker.java
rename to src/main/java/com/wcohen/ss/expt/ClusterNGramBlocker.java
diff --git a/src/com/wcohen/ss/expt/ClusterTokenBlocker.java b/src/main/java/com/wcohen/ss/expt/ClusterTokenBlocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/ClusterTokenBlocker.java
rename to src/main/java/com/wcohen/ss/expt/ClusterTokenBlocker.java
diff --git a/src/com/wcohen/ss/expt/ExtractAbbreviations.java b/src/main/java/com/wcohen/ss/expt/ExtractAbbreviations.java
similarity index 100%
rename from src/com/wcohen/ss/expt/ExtractAbbreviations.java
rename to src/main/java/com/wcohen/ss/expt/ExtractAbbreviations.java
diff --git a/src/com/wcohen/ss/expt/MatchData.java b/src/main/java/com/wcohen/ss/expt/MatchData.java
similarity index 100%
rename from src/com/wcohen/ss/expt/MatchData.java
rename to src/main/java/com/wcohen/ss/expt/MatchData.java
diff --git a/src/com/wcohen/ss/expt/MatchDataTeacher.java b/src/main/java/com/wcohen/ss/expt/MatchDataTeacher.java
similarity index 100%
rename from src/com/wcohen/ss/expt/MatchDataTeacher.java
rename to src/main/java/com/wcohen/ss/expt/MatchDataTeacher.java
diff --git a/src/com/wcohen/ss/expt/MatchExpt.java b/src/main/java/com/wcohen/ss/expt/MatchExpt.java
similarity index 100%
rename from src/com/wcohen/ss/expt/MatchExpt.java
rename to src/main/java/com/wcohen/ss/expt/MatchExpt.java
diff --git a/src/com/wcohen/ss/expt/MatchExptScript.java b/src/main/java/com/wcohen/ss/expt/MatchExptScript.java
similarity index 100%
rename from src/com/wcohen/ss/expt/MatchExptScript.java
rename to src/main/java/com/wcohen/ss/expt/MatchExptScript.java
diff --git a/src/com/wcohen/ss/expt/NGramBlocker.java b/src/main/java/com/wcohen/ss/expt/NGramBlocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/NGramBlocker.java
rename to src/main/java/com/wcohen/ss/expt/NGramBlocker.java
diff --git a/src/com/wcohen/ss/expt/NullBlocker.java b/src/main/java/com/wcohen/ss/expt/NullBlocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/NullBlocker.java
rename to src/main/java/com/wcohen/ss/expt/NullBlocker.java
diff --git a/src/com/wcohen/ss/expt/SourcedMatchData.java b/src/main/java/com/wcohen/ss/expt/SourcedMatchData.java
similarity index 100%
rename from src/com/wcohen/ss/expt/SourcedMatchData.java
rename to src/main/java/com/wcohen/ss/expt/SourcedMatchData.java
diff --git a/src/com/wcohen/ss/expt/SpecialMatchExpt.java b/src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java
similarity index 100%
rename from src/com/wcohen/ss/expt/SpecialMatchExpt.java
rename to src/main/java/com/wcohen/ss/expt/SpecialMatchExpt.java
diff --git a/src/com/wcohen/ss/expt/TokenBlocker.java b/src/main/java/com/wcohen/ss/expt/TokenBlocker.java
similarity index 100%
rename from src/com/wcohen/ss/expt/TokenBlocker.java
rename to src/main/java/com/wcohen/ss/expt/TokenBlocker.java
diff --git a/src/com/wcohen/ss/lookup/FastLookup.java b/src/main/java/com/wcohen/ss/lookup/FastLookup.java
similarity index 100%
rename from src/com/wcohen/ss/lookup/FastLookup.java
rename to src/main/java/com/wcohen/ss/lookup/FastLookup.java
diff --git a/src/com/wcohen/ss/lookup/LookupResult.java b/src/main/java/com/wcohen/ss/lookup/LookupResult.java
similarity index 100%
rename from src/com/wcohen/ss/lookup/LookupResult.java
rename to src/main/java/com/wcohen/ss/lookup/LookupResult.java
diff --git a/src/com/wcohen/ss/lookup/RescoringSoftTFIDFDictionary.java b/src/main/java/com/wcohen/ss/lookup/RescoringSoftTFIDFDictionary.java
similarity index 100%
rename from src/com/wcohen/ss/lookup/RescoringSoftTFIDFDictionary.java
rename to src/main/java/com/wcohen/ss/lookup/RescoringSoftTFIDFDictionary.java
diff --git a/src/com/wcohen/ss/lookup/SoftDictionary.java b/src/main/java/com/wcohen/ss/lookup/SoftDictionary.java
similarity index 100%
rename from src/com/wcohen/ss/lookup/SoftDictionary.java
rename to src/main/java/com/wcohen/ss/lookup/SoftDictionary.java
diff --git a/src/com/wcohen/ss/lookup/SoftTFIDFDictionary.java b/src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java
similarity index 100%
rename from src/com/wcohen/ss/lookup/SoftTFIDFDictionary.java
rename to src/main/java/com/wcohen/ss/lookup/SoftTFIDFDictionary.java
diff --git a/src/com/wcohen/ss/package.html b/src/main/java/com/wcohen/ss/package.html
similarity index 100%
rename from src/com/wcohen/ss/package.html
rename to src/main/java/com/wcohen/ss/package.html
diff --git a/src/com/wcohen/ss/tokens/BasicSourcedToken.java b/src/main/java/com/wcohen/ss/tokens/BasicSourcedToken.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/BasicSourcedToken.java
rename to src/main/java/com/wcohen/ss/tokens/BasicSourcedToken.java
diff --git a/src/com/wcohen/ss/tokens/BasicToken.java b/src/main/java/com/wcohen/ss/tokens/BasicToken.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/BasicToken.java
rename to src/main/java/com/wcohen/ss/tokens/BasicToken.java
diff --git a/src/com/wcohen/ss/tokens/CharacterTokenizer.java b/src/main/java/com/wcohen/ss/tokens/CharacterTokenizer.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/CharacterTokenizer.java
rename to src/main/java/com/wcohen/ss/tokens/CharacterTokenizer.java
diff --git a/src/com/wcohen/ss/tokens/NGramTokenizer.java b/src/main/java/com/wcohen/ss/tokens/NGramTokenizer.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/NGramTokenizer.java
rename to src/main/java/com/wcohen/ss/tokens/NGramTokenizer.java
diff --git a/src/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java b/src/main/java/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java
rename to src/main/java/com/wcohen/ss/tokens/SimpleSourcedTokenizer.java
diff --git a/src/com/wcohen/ss/tokens/SimpleTokenizer.java b/src/main/java/com/wcohen/ss/tokens/SimpleTokenizer.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/SimpleTokenizer.java
rename to src/main/java/com/wcohen/ss/tokens/SimpleTokenizer.java
diff --git a/src/com/wcohen/ss/tokens/TagLinkToken.java b/src/main/java/com/wcohen/ss/tokens/TagLinkToken.java
similarity index 100%
rename from src/com/wcohen/ss/tokens/TagLinkToken.java
rename to src/main/java/com/wcohen/ss/tokens/TagLinkToken.java

From 970f118266e6e5faa7bc64afbbd0826577053674 Mon Sep 17 00:00:00 2001
From: Nicolai Erbs <nico@erbs.eu>
Date: Tue, 19 Jan 2016 14:26:57 +0100
Subject: [PATCH 3/6] Added gitignore

---
 .gitignore | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ffc5df6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+/target/
+/.project
+/.classpath
+/.settings/

From 5904c46d39de8351cca813abbde28081a3a111a0 Mon Sep 17 00:00:00 2001
From: Nicolai Erbs <nico@erbs.eu>
Date: Tue, 19 Jan 2016 15:13:05 +0100
Subject: [PATCH 4/6] Updated om with license and scm information

---
 pom.xml | 39 ++++++++++++++++++++++++++++++++++++++-
 1 file changed, 38 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 7b98d72..6ff1bd2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,10 +1,34 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
   <modelVersion>4.0.0</modelVersion>
   <groupId>com.wcohen</groupId>
-  <artifactId>com.wcohen.ss</artifactId>
+  <artifactId>com.wcohen.secondstring</artifactId>
   <version>0.0.1-SNAPSHOT</version>
   <name>SecondString</name>
   <description>A bunch of fancy soft string matching routines, with some accompanying datasets</description>
+  <url>https://github.com/TeamCohen/secondstring</url>
+  <licenses>
+        <license>
+            <name>The University of Illinois/NCSA Open Source License (NCSA)</name>
+            <url>http://opensource.org/licenses/NCSA</url>
+            <distribution>repo</distribution>
+        </license>
+    </licenses>
+     <scm>
+        <connection>scm:git:git@github.com:TeamCohen/secondstring.git</connection>
+        <developerConnection>scm:git:git@github.com:TeamCohen/secondstring.git</developerConnection>
+        <url>git@github.com:TeamCohen/secondstring</url>
+    </scm>
+    <build>
+        <plugins>
+            <plugin>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <configuration>
+                    <source>1.5</source>
+                    <target>1.5</target>
+                </configuration>
+            </plugin>
+  </plugins>
+  </build>
   <dependencies>
   	<dependency>
   		<groupId>log4j</groupId>
@@ -12,4 +36,17 @@
   		<version>1.2.8</version>
   	</dependency>
   </dependencies>
+      <reporting>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jxr-plugin</artifactId>
+            </plugin>
+        </plugins>
+    </reporting>
+  
 </project>
\ No newline at end of file

From 2781ad7bc1444680ca10d0b84a8071470126fb37 Mon Sep 17 00:00:00 2001
From: Nicolai Erbs <nico@erbs.eu>
Date: Tue, 19 Jan 2016 15:29:53 +0100
Subject: [PATCH 5/6] Updated url for license

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 6ff1bd2..a5b5208 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,7 +9,7 @@
   <licenses>
         <license>
             <name>The University of Illinois/NCSA Open Source License (NCSA)</name>
-            <url>http://opensource.org/licenses/NCSA</url>
+            <url>http://www.opensource.org/licenses/UoI-NCSA.php</url>
             <distribution>repo</distribution>
         </license>
     </licenses>

From a10e278d417b814465728743bbb1e5af64e15511 Mon Sep 17 00:00:00 2001
From: Nicolai Erbs <nico@erbs.eu>
Date: Fri, 22 Jan 2016 11:30:55 +0100
Subject: [PATCH 6/6] Updated pom -Adding license to jar -Updating artifact
 name -Updating version number

---
 pom.xml | 251 ++++++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 200 insertions(+), 51 deletions(-)

diff --git a/pom.xml b/pom.xml
index a5b5208..b7697e4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,52 +1,201 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>com.wcohen</groupId>
-  <artifactId>com.wcohen.secondstring</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
-  <name>SecondString</name>
-  <description>A bunch of fancy soft string matching routines, with some accompanying datasets</description>
-  <url>https://github.com/TeamCohen/secondstring</url>
-  <licenses>
-        <license>
-            <name>The University of Illinois/NCSA Open Source License (NCSA)</name>
-            <url>http://www.opensource.org/licenses/UoI-NCSA.php</url>
-            <distribution>repo</distribution>
-        </license>
-    </licenses>
-     <scm>
-        <connection>scm:git:git@github.com:TeamCohen/secondstring.git</connection>
-        <developerConnection>scm:git:git@github.com:TeamCohen/secondstring.git</developerConnection>
-        <url>git@github.com:TeamCohen/secondstring</url>
-    </scm>
-    <build>
-        <plugins>
-            <plugin>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <configuration>
-                    <source>1.5</source>
-                    <target>1.5</target>
-                </configuration>
-            </plugin>
-  </plugins>
-  </build>
-  <dependencies>
-  	<dependency>
-  		<groupId>log4j</groupId>
-  		<artifactId>log4j</artifactId>
-  		<version>1.2.8</version>
-  	</dependency>
-  </dependencies>
-      <reporting>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-javadoc-plugin</artifactId>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jxr-plugin</artifactId>
-            </plugin>
-        </plugins>
-    </reporting>
-  
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>com.wcohen</groupId>
+	<artifactId>secondstring</artifactId>
+	<version>0.2</version>
+	<name>SecondString</name>
+	<description>A bunch of fancy soft string matching routines, with some accompanying datasets</description>
+	<url>https://github.com/TeamCohen/secondstring</url>
+	<licenses>
+		<license>
+			<name>The University of Illinois/NCSA Open Source License (NCSA)</name>
+			<url>http://www.opensource.org/licenses/UoI-NCSA.php</url>
+			<distribution>repo</distribution>
+		</license>
+	</licenses>
+	<scm>
+		<connection>scm:git:git@github.com:TeamCohen/secondstring.git</connection>
+		<developerConnection>scm:git:git@github.com:TeamCohen/secondstring.git</developerConnection>
+		<url>git@github.com:TeamCohen/secondstring</url>
+	</scm>
+	<developers>
+		<developer>
+			<name>William W. Cohen</name>
+			<url>http://wcohen.com/</url>
+		</developer>
+		<developer>
+			<name>Pradeep Ravikumar</name>
+			<url>http://www.cs.cmu.edu/~pradeepr</url>
+		</developer>
+		<developer>
+			<name>Stephen Fienberg</name>
+			<url>http://www.stat.cmu.edu/~fienberg</url>
+		</developer>
+		<developer>
+			<name>Kathryn Rivard</name>
+			<url>http://www.cs.cmu.edu/~krivard</url>
+		</developer>
+	</developers>
+	<dependencies>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+			<version>1.2.8</version>
+		</dependency>
+	</dependencies>
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-javadoc-plugin</artifactId>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jxr-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</reporting>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-gpg-plugin</artifactId>
+				<executions>
+					<execution>
+						<id>sign-artifacts</id>
+						<phase>verify</phase>
+						<goals>
+							<goal>sign</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-release-plugin</artifactId>
+				<version>2.5</version>
+				<configuration>
+					<autoVersionSubmodules>true</autoVersionSubmodules>
+					<useReleaseProfile>false</useReleaseProfile>
+					<releaseProfiles>release</releaseProfiles>
+					<goals>deploy</goals>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-source-plugin</artifactId>
+				<version>2.2.1</version>
+				<executions>
+					<execution>
+						<id>attach-sources</id>
+						<goals>
+							<goal>jar-no-fork</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-javadoc-plugin</artifactId>
+				<version>2.9.1</version>
+				<executions>
+					<execution>
+						<id>attach-javadocs</id>
+						<goals>
+							<goal>jar</goal>
+						</goals>
+						<configuration> <!-- add this to disable checking -->
+							<additionalparam>-Xdoclint:none</additionalparam>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+		</plugins>
+	</build>
+	<profiles>
+			<profile>
+			<!-- 
+			 - This profile takes care of copying the NOTICE, LICENSE, etc. files to the proper
+			 - locations.
+			 -->
+			<id>add-license</id>
+			<activation>
+				<file><exists>LICENSE.txt</exists></file>
+			</activation>
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.gmaven</groupId>
+						<artifactId>gmaven-plugin</artifactId>
+						<version>1.5</version>
+						<inherited>true</inherited>
+						<dependencies>
+						    <!-- 
+						      - Workaround for potential conflict between Groovy version used here
+						      - and in projects inheriting from this POM.
+						      -->
+							<dependency>
+								<groupId>org.codehaus.groovy</groupId>
+								<artifactId>groovy-all</artifactId>
+								<version>1.8.8</version>
+							</dependency>
+							<dependency>
+								<groupId>org.apache.ant</groupId>
+								<artifactId>ant</artifactId>
+								<version>1.7.0</version>
+							</dependency>
+						</dependencies>
+					</plugin>							
+					<!-- The DEPENDENCIES and NOTICE templates are read here -->
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-remote-resources-plugin</artifactId>
+						<inherited>true</inherited>
+						<executions>
+							<execution>
+								<id>process-remote-resources</id>
+								<phase>generate-resources</phase>
+								<goals>
+									<goal>process</goal>
+								</goals>
+								<configuration>
+									<resourceBundles>
+										<resourceBundle>de.tudarmstadt.ukp.dkpro.core:build-resources:1</resourceBundle>
+									</resourceBundles>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+					<plugin>
+						<groupId>org.apache.maven.plugins</groupId>
+						<artifactId>maven-resources-plugin</artifactId>
+						<inherited>true</inherited>
+						<executions>
+							<execution>
+								<id>copy-license</id>
+								<goals>
+									<goal>copy-resources</goal>
+								</goals>
+								<phase>generate-resources</phase>
+								<configuration>
+									<outputDirectory>${project.build.outputDirectory}/META-INF</outputDirectory>
+									<resources>
+										<resource>
+											<filtering>false</filtering>
+											<directory>${basedir}</directory>
+											<includes>
+												<include>README.txt</include>
+												<include>LICENSE.txt</include>
+											</includes>
+										</resource>
+									</resources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
 </project>
\ No newline at end of file