Examples of loadMotif()

Examples of ru.autosome.commons.importer.DiPWMImporter.loadMotif()

107
108
109
110
111
112
113
114
115
116
117
      BackgroundModel queryBackgroundMononucleotide = Background.fromDiBackground(queryBackground);
      PWMImporter importer = new PWMImporter(queryBackgroundMononucleotide, dataModel, effectiveCount, queryTranspose);
      return DiPWM.fromPWM(importer.loadMotif(queryPMFilename));
    } else {
      DiPWMImporter importer = new DiPWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
      return importer.loadMotif(queryPMFilename);
    }
  }

  protected ru.autosome.macroape.calculation.di.ScanCollection calculator() {
    ru.autosome.macroape.calculation.di.ScanCollection calculator;
View Full Code Here

Examples of ru.autosome.commons.importer.DiPWMImporter.loadMotif()

77
78
79
80
81
82
83
84
85
86
87
      BackgroundModel firstBackgroundMononucleotide = Background.fromDiBackground(firstBackground);
      PWMImporter firstMotifImporter = new PWMImporter(firstBackgroundMononucleotide, dataModelFirst, effectiveCountFirst, transposeFirst);
      return DiPWM.fromPWM( firstMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter firstMotifImporter = new DiPWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
      return firstMotifImporter.loadMotif(filename);
    }
  }
  @Override
  protected DiPWM loadSecondPWM(String filename) {
    if (secondPWMFromMononucleotide) {
View Full Code Here

Examples of ru.autosome.commons.importer.DiPWMImporter.loadMotif()

88
89
90
91
92
93
94
95
96
97
98
      BackgroundModel secondBackgroundMononucleotide = Background.fromDiBackground(secondBackground);
      PWMImporter secondMotifImporter = new PWMImporter(secondBackgroundMononucleotide, dataModelSecond, effectiveCountSecond, transposeSecond);
      return DiPWM.fromPWM( secondMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter secondMotifImporter = new DiPWMImporter(secondBackground, dataModelSecond, effectiveCountSecond, transposeSecond);
      return secondMotifImporter.loadMotif(filename);
    }
  }

  private EvalSimilarity() {
    initialize_defaults();
View Full Code Here

Examples of ru.autosome.commons.importer.DiPWMImporter.loadMotif()

78
79
80
81
82
83
84
85
86
87
88
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, data_model, effective_count, transpose);
      return DiPWM.fromPWM( importer.loadMotif(filename) );
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, data_model, effective_count, transpose);
      return importer.loadMotif(filename);
    }
  }

  protected FindPvalue() {
    initialize_defaults();
View Full Code Here

Examples of ru.autosome.commons.importer.DiPWMImporter.loadMotif()

53
54
55
56
57
58
59
60
61
62
63
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, data_model, effective_count, transpose);
      return DiPWM.fromPWM( importer.loadMotif(filename) );
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, data_model, effective_count, transpose);
      return importer.loadMotif(filename);
    }
  }

  @Override
  protected void extract_background(String str) {
View Full Code Here

Examples of ru.autosome.commons.importer.DiPWMImporter.loadMotif()

48
49
50
51
52
53
54
55
56
57
58
      BackgroundModel backgroundMononucleotide = Background.fromDiBackground(background);
      PWMImporter importer = new PWMImporter(backgroundMononucleotide, data_model, effective_count, transpose);
      return DiPWM.fromPWM( importer.loadMotif(file) );
    } else {
      DiPWMImporter importer = new DiPWMImporter(background, data_model, effective_count, transpose);
      return importer.loadMotif(file);
    }
  }

  @Override
  protected String DOC_background_option() {
View Full Code Here

Examples of ru.autosome.commons.importer.PWMImporter.loadMotif()

104
105
106
107
108
109
110
111
112
113
114
  @Override
  protected DiPWM loadQueryMotif() {
    if (queryFromMononucleotide) {
      BackgroundModel queryBackgroundMononucleotide = Background.fromDiBackground(queryBackground);
      PWMImporter importer = new PWMImporter(queryBackgroundMononucleotide, dataModel, effectiveCount, queryTranspose);
      return DiPWM.fromPWM(importer.loadMotif(queryPMFilename));
    } else {
      DiPWMImporter importer = new DiPWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
      return importer.loadMotif(queryPMFilename);
    }
  }
View Full Code Here

Examples of ru.autosome.commons.importer.PWMImporter.loadMotif()

107
108
109
110
111
112
113
114
115
116
117
      BackgroundModel queryBackgroundMononucleotide = Background.fromDiBackground(queryBackground);
      PWMImporter importer = new PWMImporter(queryBackgroundMononucleotide, dataModel, effectiveCount, queryTranspose);
      return DiPWM.fromPWM(importer.loadMotif(queryPMFilename));
    } else {
      DiPWMImporter importer = new DiPWMImporter(queryBackground, dataModel, effectiveCount, queryTranspose);
      return importer.loadMotif(queryPMFilename);
    }
  }

  protected ru.autosome.macroape.calculation.di.ScanCollection calculator() {
    ru.autosome.macroape.calculation.di.ScanCollection calculator;
View Full Code Here

Examples of ru.autosome.commons.importer.PWMImporter.loadMotif()

74
75
76
77
78
79
80
81
82
83
84
  @Override
  protected DiPWM loadFirstPWM(String filename) {
    if (firstPWMFromMononucleotide) {
      BackgroundModel firstBackgroundMononucleotide = Background.fromDiBackground(firstBackground);
      PWMImporter firstMotifImporter = new PWMImporter(firstBackgroundMononucleotide, dataModelFirst, effectiveCountFirst, transposeFirst);
      return DiPWM.fromPWM( firstMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter firstMotifImporter = new DiPWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
      return firstMotifImporter.loadMotif(filename);
    }
  }
View Full Code Here

Examples of ru.autosome.commons.importer.PWMImporter.loadMotif()

77
78
79
80
81
82
83
84
85
86
87
      BackgroundModel firstBackgroundMononucleotide = Background.fromDiBackground(firstBackground);
      PWMImporter firstMotifImporter = new PWMImporter(firstBackgroundMononucleotide, dataModelFirst, effectiveCountFirst, transposeFirst);
      return DiPWM.fromPWM( firstMotifImporter.loadMotif(filename) );
    } else {
      DiPWMImporter firstMotifImporter = new DiPWMImporter(firstBackground, dataModelFirst, effectiveCountFirst, transposeFirst);
      return firstMotifImporter.loadMotif(filename);
    }
  }
  @Override
  protected DiPWM loadSecondPWM(String filename) {
    if (secondPWMFromMononucleotide) {
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. 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.