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Method createOptions has 34 lines of code (exceeds 25 allowed). Consider refactoring.
Open

    protected static Options createOptions(){

        Options options = new Options();

        Option inputFileOption = Option.builder().longOpt("inputFile").desc("the input file").hasArg().argName("inputFile").build();
Severity: Minor
Found in src/main/java/com/hongliangjie/fugue/MainEntrance.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

        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

        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

        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

          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 < 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++){
                        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 < 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

          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

          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 3 locations. Consider refactoring.
          Open

                      for(i=0;i<8;i++) {
                xnum = xnum * x + p2[i];
                xden = xden * x + q2[i];
            }
          Severity: Major
          Found in src/main/java/com/hongliangjie/fugue/utils/LogGamma.java and 2 other locations - About 50 mins to fix
          src/main/java/com/hongliangjie/fugue/utils/LogGamma.java on lines 105..108
          src/main/java/com/hongliangjie/fugue/utils/LogGamma.java on lines 78..81

          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 60.

          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 3 locations. Consider refactoring.
          Open

                      for(i=0;i<8;i++) {
                xnum = xnum * x + p1[i];
                xden = xden * x + q1[i];
            }
          Severity: Major
          Found in src/main/java/com/hongliangjie/fugue/utils/LogGamma.java and 2 other locations - About 50 mins to fix
          src/main/java/com/hongliangjie/fugue/utils/LogGamma.java on lines 105..108
          src/main/java/com/hongliangjie/fugue/utils/LogGamma.java on lines 95..98

          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 60.

          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 3 locations. Consider refactoring.
          Open

                      for(i=0;i<8;i++) {
                xnum = xnum * x + p4[i];
                xden = xden * x + q4[i];
            }
          Severity: Major
          Found in src/main/java/com/hongliangjie/fugue/utils/LogGamma.java and 2 other locations - About 50 mins to fix
          src/main/java/com/hongliangjie/fugue/utils/LogGamma.java on lines 95..98
          src/main/java/com/hongliangjie/fugue/utils/LogGamma.java on lines 78..81

          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 60.

          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

          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 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
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