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src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java

Summary

Maintainability
F
1 wk
Test Coverage

File LDA.java has 728 lines of code (exceeds 250 allowed). Consider refactoring.
Open

package com.hongliangjie.fugue.topicmodeling.LDA;

import com.google.gson.Gson;
import com.hongliangjie.fugue.Message;
import com.hongliangjie.fugue.distributions.MultinomialDistribution;
Severity: Major
Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 day to fix

    Method optimize has a Cognitive Complexity of 37 (exceeds 5 allowed). Consider refactoring.
    Open

            @Override
        public void optimize() {
            double[] alpha = new double[modelPools.get(0).alpha.length];
            double alphaSum = modelPools.get(0).alphaSum;
            double[] beta = new double[modelPools.get(0).beta.length];
    Severity: Minor
    Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 5 hrs to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Method initTestModels has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring.
    Open

        public void initTestModels(){
        for (ModelCountainer m : modelPools){
            m.beta = new double[m.outsideBeta.size()];
            for (int v = 0; v < m.outsideBeta.size(); v++ ){
                // this is the default value
    Severity: Minor
    Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 3 hrs to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Method optimize has 69 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

            @Override
        public void optimize() {
            double[] alpha = new double[modelPools.get(0).alpha.length];
            double alphaSum = modelPools.get(0).alphaSum;
            double[] beta = new double[modelPools.get(0).beta.length];
    Severity: Major
    Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 2 hrs to fix

      Method sampleTestDoc has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.
      Open

              protected void sampleTestDoc(List<Document> docs, int maxIter, int docIndex) {
            // for each test document, half of the document is used to "fold-in" and the other half is used to compute "perplexity"
            for (int m = 0; m < modelPools.size(); m++) {
                docTopicAssignment = new ArrayList<Integer>();
                docTopicBuffer = new int[TOPIC_NUM];
      Severity: Minor
      Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 2 hrs to fix

      Cognitive Complexity

      Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

      A method's cognitive complexity is based on a few simple rules:

      • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
      • Code is considered more complex for each "break in the linear flow of the code"
      • Code is considered more complex when "flow breaking structures are nested"

      Further reading

      Method initTestModels has 50 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          public void initTestModels(){
        for (ModelCountainer m : modelPools){
            m.beta = new double[m.outsideBeta.size()];
            for (int v = 0; v < m.outsideBeta.size(); v++ ){
                // this is the default value
      Severity: Minor
      Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 2 hrs to fix

        Method sampleOverDocs has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
        Open

                public void sampleOverDocs(int modelID, List<Document> docs, int start, int end, int maxIter, int save){
            int overall_pos = 0;
            long overall_startTime = System.currentTimeMillis();
            for (CURRENT_ITER = 0; CURRENT_ITER < maxIter; CURRENT_ITER++) {
                LOGGER.info("Start to Iteration " + CURRENT_ITER);
        Severity: Minor
        Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

        Cognitive Complexity

        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

        A method's cognitive complexity is based on a few simple rules:

        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
        • Code is considered more complex for each "break in the linear flow of the code"
        • Code is considered more complex when "flow breaking structures are nested"

        Further reading

        Method sampleOverDocs has 43 lines of code (exceeds 25 allowed). Consider refactoring.
        Open

                public void sampleOverDocs(int modelID, List<Document> docs, int start, int end, int maxIter, int save){
            int overall_pos = 0;
            long overall_startTime = System.currentTimeMillis();
            for (CURRENT_ITER = 0; CURRENT_ITER < maxIter; CURRENT_ITER++) {
                LOGGER.info("Start to Iteration " + CURRENT_ITER);
        Severity: Minor
        Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

          Method initTrainModel has 43 lines of code (exceeds 25 allowed). Consider refactoring.
          Open

              protected void initTrainModel() {
        rebuildIndex();
        LOGGER.info("Start to initialize model.");
        LOGGER.info("Topic Num:" + TOPIC_NUM);
        LOGGER.info("ForwardIndex Size:" + wordsForwardIndex.size());
          Severity: Minor
          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

            Method sampleTestDoc has 38 lines of code (exceeds 25 allowed). Consider refactoring.
            Open

                    protected void sampleTestDoc(List<Document> docs, int maxIter, int docIndex) {
            // for each test document, half of the document is used to "fold-in" and the other half is used to compute "perplexity"
            for (int m = 0; m < modelPools.size(); m++) {
                docTopicAssignment = new ArrayList<Integer>();
                docTopicBuffer = new int[TOPIC_NUM];
            Severity: Minor
            Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

              Method loadModel has 32 lines of code (exceeds 25 allowed). Consider refactoring.
              Open

                  @SuppressWarnings("unchecked")
    public void loadModel() throws IOException {
        int multipleModels = Integer.parseInt(cmdArg.getParam("multipleModels").toString());
        String[] modelFileNames = null;
        LOGGER.info("Load Multiple Test Models:" + multipleModels);
              Severity: Minor
              Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

                Method setMessage has 30 lines of code (exceeds 25 allowed). Consider refactoring.
                Open

                    @Override
    @SuppressWarnings("unchecked")
    public void setMessage(Message m) {
        cmdArg = m;
        String randomGNRStr = cmdArg.getParam("random").toString();
                Severity: Minor
                Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

                  Method likelihood has 29 lines of code (exceeds 25 allowed). Consider refactoring.
                  Open

                      public double likelihood(List<int[]> wordTopicCounts, List<int[]> docTopicBuffers, double[] alpha, double[] beta, double alphaSum, double betaSum) {
        double result_1 = 0.0;
        double result_2 = 0.0;

        // topics side likelihood
                  Severity: Minor
                  Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 1 hr to fix

                    Method loadModel has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
                    Open

                        @SuppressWarnings("unchecked")
    public void loadModel() throws IOException {
        int multipleModels = Integer.parseInt(cmdArg.getParam("multipleModels").toString());
        String[] modelFileNames = null;
        LOGGER.info("Load Multiple Test Models:" + multipleModels);
                    Severity: Minor
                    Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 55 mins to fix

                    Cognitive Complexity

                    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                    A method's cognitive complexity is based on a few simple rules:

                    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                    • Code is considered more complex for each "break in the linear flow of the code"
                    • Code is considered more complex when "flow breaking structures are nested"

                    Further reading

                    Method sampleOverDocs has 6 arguments (exceeds 4 allowed). Consider refactoring.
                    Open

                            public void sampleOverDocs(int modelID, List<Document> docs, int start, int end, int maxIter, int save){
                    Severity: Minor
                    Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 45 mins to fix

                      Method likelihood has 6 arguments (exceeds 4 allowed). Consider refactoring.
                      Open

                          public double likelihood(List<int[]> wordTopicCounts, List<int[]> docTopicBuffers, double[] alpha, double[] beta, double alphaSum, double betaSum) {
                      Severity: Minor
                      Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 45 mins to fix

                        Method likelihood has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
                        Open

                            public double likelihood(List<int[]> wordTopicCounts, List<int[]> docTopicBuffers, double[] alpha, double[] beta, double alphaSum, double betaSum) {
        double result_1 = 0.0;
        double result_2 = 0.0;

        // topics side likelihood
                        Severity: Minor
                        Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 45 mins to fix

                        Cognitive Complexity

                        Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                        A method's cognitive complexity is based on a few simple rules:

                        • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                        • Code is considered more complex for each "break in the linear flow of the code"
                        • Code is considered more complex when "flow breaking structures are nested"

                        Further reading

                        Method sampleOverDocs has 6 arguments (exceeds 4 allowed). Consider refactoring.
                        Open

                                public void sampleOverDocs(int modelID, List<Document> docs, int start, int end, int maxIter, int save){
                        Severity: Minor
                        Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 45 mins to fix

                          Method getSampler has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
                          Open

                              protected Sampler getSampler(String samplerStr){
        Sampler s = null;
        if (samplerStr != null) {
            if ("normal".equals(samplerStr)) {
                s = new GibbsSampling();
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 35 mins to fix

                          Cognitive Complexity

                          Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                          A method's cognitive complexity is based on a few simple rules:

                          • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                          • Code is considered more complex for each "break in the linear flow of the code"
                          • Code is considered more complex when "flow breaking structures are nested"

                          Further reading

                          Method rebuildIndex has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                          Open

                              public void rebuildIndex(){
        /* build index */
        LOGGER.info("Start to build index.");
        wordsForwardIndex = new HashMap<String, Integer>();
        wordsForwardIndex.clear();
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 25 mins to fix

                          Cognitive Complexity

                          Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                          A method's cognitive complexity is based on a few simple rules:

                          • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                          • Code is considered more complex for each "break in the linear flow of the code"
                          • Code is considered more complex when "flow breaking structures are nested"

                          Further reading

                          Method initTrainModel has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                          Open

                              protected void initTrainModel() {
        rebuildIndex();
        LOGGER.info("Start to initialize model.");
        LOGGER.info("Topic Num:" + TOPIC_NUM);
        LOGGER.info("ForwardIndex Size:" + wordsForwardIndex.size());
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 25 mins to fix

                          Cognitive Complexity

                          Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                          A method's cognitive complexity is based on a few simple rules:

                          • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                          • Code is considered more complex for each "break in the linear flow of the code"
                          • Code is considered more complex when "flow breaking structures are nested"

                          Further reading

                          Method setMessage has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                          Open

                              @Override
    @SuppressWarnings("unchecked")
    public void setMessage(Message m) {
        cmdArg = m;
        String randomGNRStr = cmdArg.getParam("random").toString();
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java - About 25 mins to fix

                          Cognitive Complexity

                          Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

                          A method's cognitive complexity is based on a few simple rules:

                          • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
                          • Code is considered more complex for each "break in the linear flow of the code"
                          • Code is considered more complex when "flow breaking structures are nested"

                          Further reading

                          Similar blocks of code found in 2 locations. Consider refactoring.
                          Open

                              public void test(){
        int start = Integer.parseInt(cmdArg.getParam("start").toString());
        int end = Integer.parseInt(cmdArg.getParam("end").toString());
        if (start < 0)
            start = 0;
                          Severity: Major
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 668..676

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 81.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Similar blocks of code found in 2 locations. Consider refactoring.
                          Open

                              public void train(){
        int start = Integer.parseInt(cmdArg.getParam("start").toString());
        int end = Integer.parseInt(cmdArg.getParam("end").toString());
        if (start < 0)
            start = 0;
                          Severity: Major
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 753..761

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 81.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                              for(int i = 0; i < alpha.length; i++){
                        alphaNew[i] = randomGNR.nextDouble() * (alphaRight[i] - alphaLeft[i]) + alphaLeft[i];
                        alphaNewSum += alphaNew[i];
                    }
                          Severity: Major
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 284..287

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 74.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                              for(int i = 0; i < beta.length; i++){
                        betaNew[i] = randomGNR.nextDouble() * (betaRight[i] - betaLeft[i]) + betaLeft[i];
                        betaNewSum += betaNew[i];
                    }
                          Severity: Major
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 279..282

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 74.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                                  for(int i = 0; i < alpha.length; i++){
                            if(alphaNew[i] < alpha[i]){
                                alphaLeft[i] = alphaNew[i];
                            }
                            else{
                          Severity: Major
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 309..316

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 74.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                                  for(int i = 0; i < beta.length; i++){
                            if(betaNew[i] < beta[i]){
                                betaLeft[i] = betaNew[i];
                            }
                            else{
                          Severity: Major
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 301..308

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 74.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                          for (int i = 0; i < beta.length; i++){
                    betaLeft[i] = beta[i] - randomGNR.nextDouble() * _step;
                    betaRight[i] = betaLeft[i] + _step;
                }
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 264..267

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 68.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                          for (int i = 0; i < alpha.length; i++){
                    alphaLeft[i] = alpha[i] - randomGNR.nextDouble() * _step;
                    alphaRight[i] = alphaLeft[i] + _step;
                }
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 1 hr to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 269..272

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 68.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Similar blocks of code found in 2 locations. Consider refactoring.
                          Open

                              protected class GibbsLogSampling extends Sampler{
        public GibbsLogSampling(){
            dist = new MultinomialDistribution(TOPIC_NUM, mathLog, mathExp, "log");
            LOGGER.info("Gibbs Sampling: Log");
        }
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 55 mins to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 392..404

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 63.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Similar blocks of code found in 2 locations. Consider refactoring.
                          Open

                              protected class GibbsSampling extends Sampler{
        public GibbsSampling(){
            dist = new MultinomialDistribution(TOPIC_NUM, mathLog, mathExp, "normal");
            LOGGER.info("Gibbs Sampling: Normal");
        }
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 55 mins to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 406..418

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 63.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                  return likelihood(modelPools.get(modelID).wordTopicCounts, modelPools.get(modelID).docTopicBuffers, modelPools.get(modelID).alpha, modelPools.get(modelID).beta, modelPools.get(modelID).alphaSum, modelPools.get(modelID).betaSum);
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 40 mins to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 499..499

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 51.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

                          Identical blocks of code found in 2 locations. Consider refactoring.
                          Open

                                              double likelihood = likelihood(modelPools.get(modelID).wordTopicCounts, modelPools.get(modelID).docTopicBuffers, modelPools.get(modelID).alpha, modelPools.get(modelID).beta, modelPools.get(modelID).alphaSum, modelPools.get(modelID).betaSum);
                          Severity: Minor
                          Found in src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java and 1 other location - About 40 mins to fix
                          src/main/java/com/hongliangjie/fugue/topicmodeling/LDA/LDA.java on lines 332..332

                          Duplicated Code

                          Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

                          Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

                          When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

                          Tuning

                          This issue has a mass of 51.

                          We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

                          The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

                          If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

                          See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

                          Refactorings

                          Further Reading

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