Package ru.autosome.commons.backgroundModel.mono

Examples of ru.autosome.commons.backgroundModel.mono.WordwiseBackground

29
30
31
32
33
34
35
  protected void extract_background(String str) {
    background = Background.fromString(str);
  }
  @Override
  protected void initialize_default_background() {
    background = new WordwiseBackground();
  }
View Full Code Here
22
23
24
25
26
27
28
  public PCM2PWM() {
    super();
  }

  protected BackgroundModel defaultBackground() {
    return new WordwiseBackground();
  }
View Full Code Here
30
31
32
33
34
35
36
37
38
39
40
    // But precalculation step should be done once
    Discretizer discretizer = new Discretizer(10000.0);
    // Wordwise background means that we calculate number of words instead of probabilities, this is a default mode
    // If one need to work with certain nucleotide background probabilities he should use:
    // BackgroundModel background = new Background(new double[]{pA, pC, pG, pT}); where {pA,... pT} are probabilities of respective nucleotides
    BackgroundModel background = new WordwiseBackground();
    // A actual pvalue will be less than requested. Not very important setting in this task
    BoundaryType pvalue_boundary = BoundaryType.LOWER;
    // Setting max_hash_size allows one to restrict memory exhausting during Pvalue calculation (using APE algorithm, not binary search)
    // Reasonable value is about 10 millions elements. But actually only specially constructed matrices can reach such high hash sizes.
    // So in standalone calculation we use null (not to check hash size) and in web version we use 1e7
View Full Code Here
28
29
30
31
32
33
34
35
    return Background.fromString(str);
  }

  @Override
  protected void initialize_default_background() {
    queryBackground = new WordwiseBackground();
    collectionBackground = new WordwiseBackground();
  }
View Full Code Here
27
28
29
30
31
32
33
    return "java ru.autosome.macroape.CollectDistanceMatrix";
  }

  @Override
  protected void initialize_default_background() {
    background = new WordwiseBackground();
  }
View Full Code Here
24
25
26
27
28
29
30
31
    return "java ru.autosome.macroape.EvalSimilarity";
  }

  @Override
  protected void initialize_default_background() {
    firstBackground = new WordwiseBackground();
    secondBackground = new WordwiseBackground();
  }
View Full Code Here
45
46
47
48
49
50
51
    return score(word.sequence, background);
  }

  @Override
  public double score(Sequence word) throws IllegalArgumentException {
    return score(word, new WordwiseBackground());
  }
View Full Code Here
20
21
22
23
24
25
26
27
28
29
30
      Discretizer discretizer = new Discretizer(100.0);

//      CountingPWM firstPWMCounting = new CountingPWM(firstPWM.discrete(discretizer), new WordwiseBackground(), null);
//      CountingPWM secondPWMCounting = new CountingPWM(secondPWM.discrete(discretizer), new WordwiseBackground(), null);

      BackgroundModel background = new WordwiseBackground();
//      BackgroundModel background = new Background(new double[]{0.25,0.25,0.25,0.25});

      CompareModels comparator = new CompareModels(firstPWM, secondPWM, background, background, discretizer, null, null);
      CompareModelsCountsGiven.SimilarityInfo similarityInfo = comparator.jaccard_by_weak_pvalue(0.0005);
      System.out.println("\n----------\n" + similarityInfo.similarity());
View Full Code Here
35
36
37
38
39
40
41
    return cache_calculator;
  }

  @Override
  protected void initialize_default_background() {
    background = new WordwiseBackground();
  }
View Full Code Here
23
24
25
26
27
28
29
  protected String DOC_run_string() {
    return "java ru.autosome.ape.FindThreshold";
  }
  @Override
  protected void initialize_default_background() {
    background = new WordwiseBackground();
  }
View Full Code Here
TOP

Related Classes of ru.autosome.commons.backgroundModel.mono.WordwiseBackground

  • ru.autosome.ape.example.FindPvalue
  • ru.autosome.ape.example.FindPvalueDinucleotide
  • ru.autosome.ape.example.FindThreshold
  • ru.autosome.ape.FindPvalue
  • ru.autosome.ape.FindThreshold
  • ru.autosome.ape.PrecalculateThresholdLists
  • ru.autosome.commons.converter.mono.PCM2PWM
  • ru.autosome.commons.motifModel.mono.PWM
  • ru.autosome.macroape.CollectDistanceMatrix
  • ru.autosome.macroape.EvalSimilarity
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.