From 72e21f6e7a8417ea66be44277ee3fa19c3a0e0c0 Mon Sep 17 00:00:00 2001
From: Joel 'Aaron' Cohen <aaron@assonance.org>
Date: Wed, 19 Mar 2014 19:18:32 -0400
Subject: [PATCH] Minimal changes to compile against Weka 3.7.10

There is a weird junit dependency being pulled in that I haven't
figured out.
---
 project.clj                        | 11 ++++++++++-
 src/clj_ml/attribute_selection.clj |  3 ++-
 src/clj_ml/classifiers.clj         |  4 ++--
 src/clj_ml/data.clj                |  5 ++---
 test/clj_ml/data_test.clj          |  9 +++------
 test/clj_ml/filters_test.clj       |  2 +-
 6 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/project.clj b/project.clj
index 2962c75..9db893a 100644
--- a/project.clj
+++ b/project.clj
@@ -4,7 +4,16 @@
   :license {:name "MIT License"
             :url "http://opensource.org/licenses/MIT"}
   :url "https://github.com/joshuaeckroth/clj-ml"
-  :dependencies [[nz.ac.waikato.cms.weka/weka-stable "3.6.9"]
+  :dependencies [[nz.ac.waikato.cms.weka/weka-dev "3.7.10"]
+		 [nz.ac.waikato.cms.weka/chiSquaredAttributeEval "1.0.3"]
+		 [nz.ac.waikato.cms.weka/attributeSelectionSearchMethods "1.0.6"]
+		 [nz.ac.waikato.cms.weka/linearForwardSelection "1.0.1"]
+		 [nz.ac.waikato.cms.weka/rotationForest "1.0.3"]
+		 [nz.ac.waikato.cms.weka/paceRegression "1.0.2"]
+		 [nz.ac.waikato.cms.weka/SPegasos "1.0.2"]
+		 [nz.ac.waikato.cms.weka/LibSVM "1.0.5"]
+                 [org.clojars.remleduff/snowball "20051019-1"]
+		 [junit/junit "4.11"]
                  [tw.edu.ntu.csie/libsvm "3.1"]
                  [org.clojure/data.xml "0.0.7"]
                  [org.apache.lucene/lucene-analyzers-common "4.3.0"]]
diff --git a/src/clj_ml/attribute_selection.clj b/src/clj_ml/attribute_selection.clj
index e4b7219..b784516 100644
--- a/src/clj_ml/attribute_selection.clj
+++ b/src/clj_ml/attribute_selection.clj
@@ -9,7 +9,8 @@
             SymmetricalUncertAttributeEval ChiSquaredAttributeEval
             AttributeSelection CfsSubsetEval
             ;; search
-            GreedyStepwise BestFirst GeneticSearch Ranker RankSearch LinearForwardSelection]))
+            GreedyStepwise BestFirst Ranker RankSearch LinearForwardSelection]
+           [weka.classifiers.bayes.net.search.local GeneticSearch]))
 
 (defmulti  #^{:skip-wiki true}
   make-obj-options
diff --git a/src/clj_ml/classifiers.clj b/src/clj_ml/classifiers.clj
index bdd1b82..cf720c1 100644
--- a/src/clj_ml/classifiers.clj
+++ b/src/clj_ml/classifiers.clj
@@ -68,7 +68,7 @@
            (weka.classifiers.meta LogitBoost AdditiveRegression RotationForest)
            (weka.classifiers.bayes NaiveBayes NaiveBayesUpdateable)
            (weka.classifiers.functions MultilayerPerceptron SMO LinearRegression Logistic PaceRegression SPegasos LibSVM)
-           (weka.classifiers Classifier Evaluation)))
+           (weka.classifiers AbstractClassifier Classifier Evaluation)))
 
 
 ;; Setting up classifier options
@@ -544,7 +544,7 @@
 (defn classifier-copy
   "Performs a deep copy of the classifier"
   [^Classifier classifier]
-  (Classifier/makeCopy classifier))
+  (AbstractClassifier/makeCopy classifier))
 
 (defn classifier-copy-and-train
   "Performs a deep copy of the classifier, trains the copy, and returns it."
diff --git a/src/clj_ml/data.clj b/src/clj_ml/data.clj
index f701e66..fb852ea 100644
--- a/src/clj_ml/data.clj
+++ b/src/clj_ml/data.clj
@@ -16,7 +16,7 @@
   (:require [clojure.string :as str])
   (:require [clojure.set :as set])
   (:use [clojure.java.io :only [file]])
-  (:import (weka.core Instance Instances FastVector Attribute)
+  (:import (weka.core Instance DenseInstance Instances FastVector Attribute)
            (cljml ClojureInstances)))
 
 (declare dataset-seq)
@@ -134,8 +134,7 @@
   ([dataset vector]
      (make-instance dataset 1 vector))
   ([dataset weight vector]
-     (let [^Instance inst (new Instance
-                               (count vector))]
+     (let [^Instance inst (DenseInstance. (count vector))]
        (do (.setDataset inst dataset)
            (loop [vs vector
                   c 0]
diff --git a/test/clj_ml/data_test.clj b/test/clj_ml/data_test.clj
index d4ce413..7914def 100644
--- a/test/clj_ml/data_test.clj
+++ b/test/clj_ml/data_test.clj
@@ -7,8 +7,7 @@
                               [:a :b]
                               1)
         inst (make-instance dataset [1 2])]
-    (is (= (class inst)
-           weka.core.Instance))
+    (is (instance? weka.core.Instance inst))
     (is (= 2 (.numValues inst)))
     (is (= 1.0 (.value inst 0)))
     (is (= 2.0 (.value inst 1)))))
@@ -18,8 +17,7 @@
                               [:a {:b [:b1 :b2]}]
                               1)
         inst (make-instance dataset [1 :b1])]
-    (is (= (class inst)
-           weka.core.Instance))
+    (is (instance? weka.core.Instance inst))
     (is (= 2 (.numValues inst)))
     (is (= 1.0 (.value inst 0)))
     (is (= "b1" (.stringValue inst 1)))))
@@ -29,8 +27,7 @@
                               [:a :b]
                               1)
         inst (make-instance dataset [1 nil])]
-    (is (= (class inst)
-           weka.core.Instance))
+    (is (instance? weka.core.Instance inst))
     (is (= 2 (.numValues inst)))
     (is (= 1.0 (.value inst 0)))
     (is (Double/isNaN (.value inst 1)))))
diff --git a/test/clj_ml/filters_test.clj b/test/clj_ml/filters_test.clj
index 069e3d4..9bb2cdf 100644
--- a/test/clj_ml/filters_test.clj
+++ b/test/clj_ml/filters_test.clj
@@ -281,7 +281,7 @@
                                   (-> instance
                                       instance-to-vector
                                       (conj (- a-max (.value instance 0)))
-                                      (#(weka.core.Instance. 1 (into-array Double/TYPE %)))
+                                      (#(weka.core.DenseInstance. 1 (into-array Double/TYPE %)))
                                       add-instance))
                                 result))
         res (clj-batch ds