@Test public void testTransition3() { byte chr = 3; Variant v = new Variant(chr,13,"A","GC",null,dummyPhred); boolean b = v.isTransition(); Assert.assertEquals(false,b); }
public boolean isTransition() { if (! is_single_nucleotide_variant () ) return false; if (this.ref.equals("A") && this.alt.equals("G")) return true; else if (this.ref.equals("G") && this.alt.equals("A")) return true; if (this.ref.equals("C") && this.alt.equals("T")) return true; else if (this.ref.equals("T") && this.alt.equals("C")) return true; return false; }
Variant implements Comparable<Variant>, Constants { public boolean isTransition() { if (! is_single_nucleotide_variant () ) return false; if (this.ref.equals("A") && this.alt.equals("G")) return true; else if (this.ref.equals("G") && this.alt.equals("A")) return true; if (this.ref.equals("C") && this.alt.equals("T")) return true; else if (this.ref.equals("T") && this.alt.equals("C")) return true; return false; } }
Variant implements Comparable<Variant>, Constants { public boolean isTransition() { if (! is_single_nucleotide_variant () ) return false; if (this.ref.equals("A") && this.alt.equals("G")) return true; else if (this.ref.equals("G") && this.alt.equals("A")) return true; if (this.ref.equals("C") && this.alt.equals("T")) return true; else if (this.ref.equals("T") && this.alt.equals("C")) return true; return false; } Variant(byte c, int p, String r, String alternate, GenotypeCall gtype, float qual); }
Variant implements Comparable<Variant>, Constants { public boolean isTransition() { if (! is_single_nucleotide_variant () ) return false; if (this.ref.equals("A") && this.alt.equals("G")) return true; else if (this.ref.equals("G") && this.alt.equals("A")) return true; if (this.ref.equals("C") && this.alt.equals("T")) return true; else if (this.ref.equals("T") && this.alt.equals("C")) return true; return false; } Variant(byte c, int p, String r, String alternate, GenotypeCall gtype, float qual); void annotate(Chromosome c); void setChromosome(byte chr); void setPosition(int p); void setRef(String s); void setGenotype(GenotypeCall gtype); void setVar(String s); void setAnnotation(AnnotationList a); boolean affectsMultipleGenes(); int get_position(); String get_ref(); String get_alt(); String getGeneSymbol(); int getEntrezGeneID(); boolean is_missense_variant(); boolean isSynonymousVariant(); boolean isTransition(); boolean isTransversion(); boolean is_single_nucleotide_variant(); int get_chromosome(); byte getChromosomeAsByte(); String get_chromosome_as_string(); boolean is_X_chromosomal(); boolean is_Y_chromosomal(); boolean is_mitochondrial(); float getVariantPhredScore(); float getVariantGenotypeQualityIndividualN(int n); int getVariantReadDepth(); int getVariantReadDepthIndividualN(int n); boolean isHomozygousAlt(); boolean isHomozygousAltInIndividualN(int n); boolean isHeterozygous(); boolean isHeterozygousInIndividualN(int n); boolean isOffExomeTarget(); boolean isMissingInIndividualN(int n); GenotypeCall getGenotype(); Genotype getGenotypeInIndividualN(int n); String getGenotypeAsString(); ArrayList<String> getGenotypeList(); String get_position_as_string(); String get_chromosomal_variant(); String getAnnotation(); String getRepresentativeAnnotation(); ArrayList<String> getAnnotationList(); ArrayList<Annotation> getAnnotationObjectList(); ArrayList<String> getAnnotationListWithGeneSymbol(); ArrayList<String> getAnnotationListWithAnnotationClass(); ArrayList<String> getTranscriptAnnotations(); Annotation getMostPathogenicAnnotation(); String getVariantType(); VariantType getVariantTypeConstant(); String getChromosomalVariant(); String toString(); String get_variant_type_as_string(); int getDistanceFromExon(); @Override int compareTo(Variant other); }
Variant implements Comparable<Variant>, Constants { public boolean isTransition() { if (! is_single_nucleotide_variant () ) return false; if (this.ref.equals("A") && this.alt.equals("G")) return true; else if (this.ref.equals("G") && this.alt.equals("A")) return true; if (this.ref.equals("C") && this.alt.equals("T")) return true; else if (this.ref.equals("T") && this.alt.equals("C")) return true; return false; } Variant(byte c, int p, String r, String alternate, GenotypeCall gtype, float qual); void annotate(Chromosome c); void setChromosome(byte chr); void setPosition(int p); void setRef(String s); void setGenotype(GenotypeCall gtype); void setVar(String s); void setAnnotation(AnnotationList a); boolean affectsMultipleGenes(); int get_position(); String get_ref(); String get_alt(); String getGeneSymbol(); int getEntrezGeneID(); boolean is_missense_variant(); boolean isSynonymousVariant(); boolean isTransition(); boolean isTransversion(); boolean is_single_nucleotide_variant(); int get_chromosome(); byte getChromosomeAsByte(); String get_chromosome_as_string(); boolean is_X_chromosomal(); boolean is_Y_chromosomal(); boolean is_mitochondrial(); float getVariantPhredScore(); float getVariantGenotypeQualityIndividualN(int n); int getVariantReadDepth(); int getVariantReadDepthIndividualN(int n); boolean isHomozygousAlt(); boolean isHomozygousAltInIndividualN(int n); boolean isHeterozygous(); boolean isHeterozygousInIndividualN(int n); boolean isOffExomeTarget(); boolean isMissingInIndividualN(int n); GenotypeCall getGenotype(); Genotype getGenotypeInIndividualN(int n); String getGenotypeAsString(); ArrayList<String> getGenotypeList(); String get_position_as_string(); String get_chromosomal_variant(); String getAnnotation(); String getRepresentativeAnnotation(); ArrayList<String> getAnnotationList(); ArrayList<Annotation> getAnnotationObjectList(); ArrayList<String> getAnnotationListWithGeneSymbol(); ArrayList<String> getAnnotationListWithAnnotationClass(); ArrayList<String> getTranscriptAnnotations(); Annotation getMostPathogenicAnnotation(); String getVariantType(); VariantType getVariantTypeConstant(); String getChromosomalVariant(); String toString(); String get_variant_type_as_string(); int getDistanceFromExon(); @Override int compareTo(Variant other);  }