Module org.monarchinitiative.vmvt.core
Package org.monarchinitiative.vmvt.core

Class VmvtGenerator

java.lang.Object
org.monarchinitiative.vmvt.core.VmvtGenerator
public class VmvtGenerator extends Object
Public interface to VMVT: Variant-Motif Visualization Tool. For all functions listed here, there are two parameters: reference and alternate. In the case of the donor functions, these should be 9 nucleotide sequences (3:intron + 6: exon). In the case of the acceptor functions, these should be 27 nucleotide sequences (25:intron + 2 exon).
Author:
Peter N Robinson

  • Constructor Details

    • VmvtGenerator

      public VmvtGenerator()

    • VmvtGenerator

      public VmvtGenerator​(boolean framed)

  • Method Details

    • getDonorSequenceRuler

      public String getDonorSequenceRuler​(String reference, String alternate)

    • getDonorSequenceLogoRulerAndBarChart

      public String getDonorSequenceLogoRulerAndBarChart​(String ref, String alt)

    • getDonorSequenceRulerAndBarChartWithOffset

      public String getDonorSequenceRulerAndBarChartWithOffset​(String ref, String alt, int i)

    • getAcceptorSequenceRuler

      public String getAcceptorSequenceRuler​(String reference, String alternate)

    • getAcceptorSequenceRulerAndBarChartWithOffset

      public String getAcceptorSequenceRulerAndBarChartWithOffset​(String ref, String alt, int i)

    • getAcceptorSequenceLogoRulerAndBarChart

      public String getAcceptorSequenceLogoRulerAndBarChart​(String ref, String alt)

    • getDonorWalkerSvg

      public String getDonorWalkerSvg​(String reference)

    • getRefAltDonorWalkerSvg

      public String getRefAltDonorWalkerSvg​(String reference, String alternate)

    • getRefAltAcceptorWalkerSvg

      public String getRefAltAcceptorWalkerSvg​(String reference, String alternate)

    • getDonorLogoSvg

      public String getDonorLogoSvg()

    • getAcceptorLogoSvg

      public String getAcceptorLogoSvg()

    • getDonorTrekkerSvg

      public String getDonorTrekkerSvg​(String reference, String alternate)

    • getAcceptorTrekkerSvg

      public String getAcceptorTrekkerSvg​(String reference, String alternate)

    • getDonorDistributionSvg

      public String getDonorDistributionSvg​(String reference, String alternate)

    • getAcceptorDistributionSvg

      public String getAcceptorDistributionSvg​(String reference, String alternate)

    • getHexamerSvg

      public String getHexamerSvg​(String reference, String alternate)

    • getHeptamerSvg

      public String getHeptamerSvg​(String reference, String alternate)

    • getDelta

      public String getDelta​(String reference, String alternate)

    • getAcceptorTrekkerWithRi

      public String getAcceptorTrekkerWithRi​(String reference, String alternate)

    • getDonorTrekkerWithRi

      public String getDonorTrekkerWithRi​(String reference, String alternate)

    • getDonorIcBars

      public String getDonorIcBars​(String reference, String alternate)

    • getDonorIcBarsWithRi

      public String getDonorIcBarsWithRi​(String reference, String alternate)

    • getDonorIcBarsWithLogoAndRi

      public String getDonorIcBarsWithLogoAndRi​(String reference, String alternate)

    • getAcceptorIcBars

      public String getAcceptorIcBars​(String reference, String alternate)

    • getAcceptorIcBarsWithRi

      public String getAcceptorIcBarsWithRi​(String reference, String alternate)

    • getAcceptorIcBarsWithLogoAndRi

      public String getAcceptorIcBarsWithLogoAndRi​(String reference, String alternate)