Package org.snpeff.snpEffect.commandLine

Class SnpEffCmdPdb

java.lang.Object
org.snpeff.SnpEff
org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
All Implemented Interfaces:
CommandLine
public class SnpEffCmdPdb extends SnpEff
PDB distance analysis

References: http://biojava.org/wiki/BioJava:CookBook:PDB:read

Author:
pcingola

  • Field Details

  • Constructor Details

    • SnpEffCmdPdb

      public SnpEffCmdPdb()

  • Method Details

    • getDistanceResults

      public List<DistanceResult> getDistanceResults()

    • initialize

      public void initialize()
      Load all data

    • loadIdMapper

      public void loadIdMapper()

    • parseArgs

      public void parseArgs(String[] args)
      Parse command line arguments
      Specified by:
      parseArgs in interface CommandLine
      Overrides:
      parseArgs in class SnpEff

    • pdb

      public void pdb()
      PDB analysis

    • pdbAnalysis

      protected void pdbAnalysis()
      Check that protein sequences form PDB matches sequences from Genome Return an IdMapped of confirmed entries (i.e. AA sequence matches between transcript and PDB)

    • pdbAnalysis

      protected void pdbAnalysis(String pdbFileName)
      Analyze a PDB file

    • readPdbFile

      public org.biojava.nbio.structure.Structure readPdbFile(String pdbFileName)
      Read and parse PDB file

    • run

      public boolean run()
      Description copied from class: SnpEff
      Run according to command line options
      Specified by:
      run in interface CommandLine
      Overrides:
      run in class SnpEff

    • run

      public boolean run(boolean storeResults)

    • setDistanceThresholdNon

      public void setDistanceThresholdNon(double distanceThresholdNon)

    • usage

      public void usage(String message)
      Show 'usage;' message and exit with an error code '-1'
      Specified by:
      usage in interface CommandLine
      Overrides:
      usage in class SnpEff
      Parameters:
      message -